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-(function(a,d){a.ui=a.ui||{};if(a.ui.version){return}a.extend(a.ui,{version:"1.8.18",keyCode:{ALT:18,BACKSPACE:8,CAPS_LOCK:20,COMMA:188,COMMAND:91,COMMAND_LEFT:91,COMMAND_RIGHT:93,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,MENU:93,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38,WINDOWS:91}});a.fn.extend({propAttr:a.fn.prop||a.fn.attr,_focus:a.fn.focus,focus:function(e,f){return typeof e==="number"?this.each(function(){var g=this;setTimeout(function(){a(g).focus();if(f){f.call(g)}},e)}):this._focus.apply(this,arguments)},scrollParent:function(){var e;if((a.browser.msie&&(/(static|relative)/).test(this.css("position")))||(/absolute/).test(this.css("position"))){e=this.parents().filter(function(){return(/(relative|absolute|fixed)/).test(a.curCSS(this,"position",1))&&(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}else{e=this.parents().filter(function(){return(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}return(/fixed/).test(this.css("position"))||!e.length?a(document):e},zIndex:function(h){if(h!==d){return this.css("zIndex",h)}if(this.length){var f=a(this[0]),e,g;while(f.length&&f[0]!==document){e=f.css("position");if(e==="absolute"||e==="relative"||e==="fixed"){g=parseInt(f.css("zIndex"),10);if(!isNaN(g)&&g!==0){return g}}f=f.parent()}}return 0},disableSelection:function(){return this.bind((a.support.selectstart?"selectstart":"mousedown")+".ui-disableSelection",function(e){e.preventDefault()})},enableSelection:function(){return this.unbind(".ui-disableSelection")}});a.each(["Width","Height"],function(g,e){var f=e==="Width"?["Left","Right"]:["Top","Bottom"],h=e.toLowerCase(),k={innerWidth:a.fn.innerWidth,innerHeight:a.fn.innerHeight,outerWidth:a.fn.outerWidth,outerHeight:a.fn.outerHeight};function j(m,l,i,n){a.each(f,function(){l-=parseFloat(a.curCSS(m,"padding"+this,true))||0;if(i){l-=parseFloat(a.curCSS(m,"border"+this+"Width",true))||0}if(n){l-=parseFloat(a.curCSS(m,"margin"+this,true))||0}});return l}a.fn["inner"+e]=function(i){if(i===d){return k["inner"+e].call(this)}return this.each(function(){a(this).css(h,j(this,i)+"px")})};a.fn["outer"+e]=function(i,l){if(typeof i!=="number"){return k["outer"+e].call(this,i)}return this.each(function(){a(this).css(h,j(this,i,true,l)+"px")})}});function c(g,e){var j=g.nodeName.toLowerCase();if("area"===j){var i=g.parentNode,h=i.name,f;if(!g.href||!h||i.nodeName.toLowerCase()!=="map"){return false}f=a("img[usemap=#"+h+"]")[0];return !!f&&b(f)}return(/input|select|textarea|button|object/.test(j)?!g.disabled:"a"==j?g.href||e:e)&&b(g)}function b(e){return !a(e).parents().andSelf().filter(function(){return a.curCSS(this,"visibility")==="hidden"||a.expr.filters.hidden(this)}).length}a.extend(a.expr[":"],{data:function(g,f,e){return !!a.data(g,e[3])},focusable:function(e){return c(e,!isNaN(a.attr(e,"tabindex")))},tabbable:function(g){var e=a.attr(g,"tabindex"),f=isNaN(e);return(f||e>=0)&&c(g,!f)}});a(function(){var e=document.body,f=e.appendChild(f=document.createElement("div"));f.offsetHeight;a.extend(f.style,{minHeight:"100px",height:"auto",padding:0,borderWidth:0});a.support.minHeight=f.offsetHeight===100;a.support.selectstart="onselectstart" in f;e.removeChild(f).style.display="none"});a.extend(a.ui,{plugin:{add:function(f,g,j){var h=a.ui[f].prototype;for(var e in j){h.plugins[e]=h.plugins[e]||[];h.plugins[e].push([g,j[e]])}},call:function(e,g,f){var j=e.plugins[g];if(!j||!e.element[0].parentNode){return}for(var h=0;h0){return true}h[e]=1;g=(h[e]>0);h[e]=0;return g},isOverAxis:function(f,e,g){return(f>e)&&(f<(e+g))},isOver:function(j,f,i,h,e,g){return a.ui.isOverAxis(j,i,e)&&a.ui.isOverAxis(f,h,g)}})})(jQuery);/*!
- * jQuery UI Widget 1.8.18
- *
- * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
- * Dual licensed under the MIT or GPL Version 2 licenses.
- * http://jquery.org/license
- *
- * http://docs.jquery.com/UI/Widget
- */
-(function(b,d){if(b.cleanData){var c=b.cleanData;b.cleanData=function(f){for(var g=0,h;(h=f[g])!=null;g++){try{b(h).triggerHandler("remove")}catch(j){}}c(f)}}else{var a=b.fn.remove;b.fn.remove=function(e,f){return this.each(function(){if(!f){if(!e||b.filter(e,[this]).length){b("*",this).add([this]).each(function(){try{b(this).triggerHandler("remove")}catch(g){}})}}return a.call(b(this),e,f)})}}b.widget=function(f,h,e){var g=f.split(".")[0],j;f=f.split(".")[1];j=g+"-"+f;if(!e){e=h;h=b.Widget}b.expr[":"][j]=function(k){return !!b.data(k,f)};b[g]=b[g]||{};b[g][f]=function(k,l){if(arguments.length){this._createWidget(k,l)}};var i=new h();i.options=b.extend(true,{},i.options);b[g][f].prototype=b.extend(true,i,{namespace:g,widgetName:f,widgetEventPrefix:b[g][f].prototype.widgetEventPrefix||f,widgetBaseClass:j},e);b.widget.bridge(f,b[g][f])};b.widget.bridge=function(f,e){b.fn[f]=function(i){var g=typeof i==="string",h=Array.prototype.slice.call(arguments,1),j=this;i=!g&&h.length?b.extend.apply(null,[true,i].concat(h)):i;if(g&&i.charAt(0)==="_"){return j}if(g){this.each(function(){var k=b.data(this,f),l=k&&b.isFunction(k[i])?k[i].apply(k,h):k;if(l!==k&&l!==d){j=l;return false}})}else{this.each(function(){var k=b.data(this,f);if(k){k.option(i||{})._init()}else{b.data(this,f,new e(i,this))}})}return j}};b.Widget=function(e,f){if(arguments.length){this._createWidget(e,f)}};b.Widget.prototype={widgetName:"widget",widgetEventPrefix:"",options:{disabled:false},_createWidget:function(f,g){b.data(g,this.widgetName,this);this.element=b(g);this.options=b.extend(true,{},this.options,this._getCreateOptions(),f);var e=this;this.element.bind("remove."+this.widgetName,function(){e.destroy()});this._create();this._trigger("create");this._init()},_getCreateOptions:function(){return b.metadata&&b.metadata.get(this.element[0])[this.widgetName]},_create:function(){},_init:function(){},destroy:function(){this.element.unbind("."+this.widgetName).removeData(this.widgetName);this.widget().unbind("."+this.widgetName).removeAttr("aria-disabled").removeClass(this.widgetBaseClass+"-disabled ui-state-disabled")},widget:function(){return this.element},option:function(f,g){var e=f;if(arguments.length===0){return b.extend({},this.options)}if(typeof f==="string"){if(g===d){return this.options[f]}e={};e[f]=g}this._setOptions(e);return this},_setOptions:function(f){var e=this;b.each(f,function(g,h){e._setOption(g,h)});return this},_setOption:function(e,f){this.options[e]=f;if(e==="disabled"){this.widget()[f?"addClass":"removeClass"](this.widgetBaseClass+"-disabled ui-state-disabled").attr("aria-disabled",f)}return this},enable:function(){return this._setOption("disabled",false)},disable:function(){return this._setOption("disabled",true)},_trigger:function(e,f,g){var j,i,h=this.options[e];g=g||{};f=b.Event(f);f.type=(e===this.widgetEventPrefix?e:this.widgetEventPrefix+e).toLowerCase();f.target=this.element[0];i=f.originalEvent;if(i){for(j in i){if(!(j in f)){f[j]=i[j]}}}this.element.trigger(f,g);return !(b.isFunction(h)&&h.call(this.element[0],f,g)===false||f.isDefaultPrevented())}}})(jQuery);/*!
- * jQuery UI Mouse 1.8.18
- *
- * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
- * Dual licensed under the MIT or GPL Version 2 licenses.
- * http://jquery.org/license
- *
- * http://docs.jquery.com/UI/Mouse
- *
- * Depends:
- * jquery.ui.widget.js
- */
-(function(b,c){var a=false;b(document).mouseup(function(d){a=false});b.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var d=this;this.element.bind("mousedown."+this.widgetName,function(e){return d._mouseDown(e)}).bind("click."+this.widgetName,function(e){if(true===b.data(e.target,d.widgetName+".preventClickEvent")){b.removeData(e.target,d.widgetName+".preventClickEvent");e.stopImmediatePropagation();return false}});this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName)},_mouseDown:function(f){if(a){return}(this._mouseStarted&&this._mouseUp(f));this._mouseDownEvent=f;var e=this,g=(f.which==1),d=(typeof this.options.cancel=="string"&&f.target.nodeName?b(f.target).closest(this.options.cancel).length:false);if(!g||d||!this._mouseCapture(f)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){e.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(f)&&this._mouseDelayMet(f)){this._mouseStarted=(this._mouseStart(f)!==false);if(!this._mouseStarted){f.preventDefault();return true}}if(true===b.data(f.target,this.widgetName+".preventClickEvent")){b.removeData(f.target,this.widgetName+".preventClickEvent")}this._mouseMoveDelegate=function(h){return e._mouseMove(h)};this._mouseUpDelegate=function(h){return e._mouseUp(h)};b(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);f.preventDefault();a=true;return true},_mouseMove:function(d){if(b.browser.msie&&!(document.documentMode>=9)&&!d.button){return this._mouseUp(d)}if(this._mouseStarted){this._mouseDrag(d);return d.preventDefault()}if(this._mouseDistanceMet(d)&&this._mouseDelayMet(d)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,d)!==false);(this._mouseStarted?this._mouseDrag(d):this._mouseUp(d))}return !this._mouseStarted},_mouseUp:function(d){b(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;if(d.target==this._mouseDownEvent.target){b.data(d.target,this.widgetName+".preventClickEvent",true)}this._mouseStop(d)}return false},_mouseDistanceMet:function(d){return(Math.max(Math.abs(this._mouseDownEvent.pageX-d.pageX),Math.abs(this._mouseDownEvent.pageY-d.pageY))>=this.options.distance)},_mouseDelayMet:function(d){return this.mouseDelayMet},_mouseStart:function(d){},_mouseDrag:function(d){},_mouseStop:function(d){},_mouseCapture:function(d){return true}})})(jQuery);(function(c,d){c.widget("ui.resizable",c.ui.mouse,{widgetEventPrefix:"resize",options:{alsoResize:false,animate:false,animateDuration:"slow",animateEasing:"swing",aspectRatio:false,autoHide:false,containment:false,ghost:false,grid:false,handles:"e,s,se",helper:false,maxHeight:null,maxWidth:null,minHeight:10,minWidth:10,zIndex:1000},_create:function(){var f=this,k=this.options;this.element.addClass("ui-resizable");c.extend(this,{_aspectRatio:!!(k.aspectRatio),aspectRatio:k.aspectRatio,originalElement:this.element,_proportionallyResizeElements:[],_helper:k.helper||k.ghost||k.animate?k.helper||"ui-resizable-helper":null});if(this.element[0].nodeName.match(/canvas|textarea|input|select|button|img/i)){this.element.wrap(c('
').css({position:this.element.css("position"),width:this.element.outerWidth(),height:this.element.outerHeight(),top:this.element.css("top"),left:this.element.css("left")}));this.element=this.element.parent().data("resizable",this.element.data("resizable"));this.elementIsWrapper=true;this.element.css({marginLeft:this.originalElement.css("marginLeft"),marginTop:this.originalElement.css("marginTop"),marginRight:this.originalElement.css("marginRight"),marginBottom:this.originalElement.css("marginBottom")});this.originalElement.css({marginLeft:0,marginTop:0,marginRight:0,marginBottom:0});this.originalResizeStyle=this.originalElement.css("resize");this.originalElement.css("resize","none");this._proportionallyResizeElements.push(this.originalElement.css({position:"static",zoom:1,display:"block"}));this.originalElement.css({margin:this.originalElement.css("margin")});this._proportionallyResize()}this.handles=k.handles||(!c(".ui-resizable-handle",this.element).length?"e,s,se":{n:".ui-resizable-n",e:".ui-resizable-e",s:".ui-resizable-s",w:".ui-resizable-w",se:".ui-resizable-se",sw:".ui-resizable-sw",ne:".ui-resizable-ne",nw:".ui-resizable-nw"});if(this.handles.constructor==String){if(this.handles=="all"){this.handles="n,e,s,w,se,sw,ne,nw"}var l=this.handles.split(",");this.handles={};for(var g=0;g l.width),s=a(l.height)&&i.minHeight&&(i.minHeight>l.height);if(h){l.width=i.minWidth}if(s){l.height=i.minHeight}if(t){l.width=i.maxWidth}if(m){l.height=i.maxHeight}var f=this.originalPosition.left+this.originalSize.width,p=this.position.top+this.size.height;var k=/sw|nw|w/.test(q),e=/nw|ne|n/.test(q);if(h&&k){l.left=f-i.minWidth}if(t&&k){l.left=f-i.maxWidth}if(s&&e){l.top=p-i.minHeight}if(m&&e){l.top=p-i.maxHeight}var n=!l.width&&!l.height;if(n&&!l.left&&l.top){l.top=null}else{if(n&&!l.top&&l.left){l.left=null}}return l},_proportionallyResize:function(){var k=this.options;if(!this._proportionallyResizeElements.length){return}var g=this.helper||this.element;for(var f=0;f');var e=c.browser.msie&&c.browser.version<7,g=(e?1:0),h=(e?2:-1);this.helper.addClass(this._helper).css({width:this.element.outerWidth()+h,height:this.element.outerHeight()+h,position:"absolute",left:this.elementOffset.left-g+"px",top:this.elementOffset.top-g+"px",zIndex:++i.zIndex});this.helper.appendTo("body").disableSelection()}else{this.helper=this.element}},_change:{e:function(g,f,e){return{width:this.originalSize.width+f}},w:function(h,f,e){var j=this.options,g=this.originalSize,i=this.originalPosition;return{left:i.left+f,width:g.width-f}},n:function(h,f,e){var j=this.options,g=this.originalSize,i=this.originalPosition;return{top:i.top+e,height:g.height-e}},s:function(g,f,e){return{height:this.originalSize.height+e}},se:function(g,f,e){return c.extend(this._change.s.apply(this,arguments),this._change.e.apply(this,[g,f,e]))},sw:function(g,f,e){return c.extend(this._change.s.apply(this,arguments),this._change.w.apply(this,[g,f,e]))},ne:function(g,f,e){return c.extend(this._change.n.apply(this,arguments),this._change.e.apply(this,[g,f,e]))},nw:function(g,f,e){return c.extend(this._change.n.apply(this,arguments),this._change.w.apply(this,[g,f,e]))}},_propagate:function(f,e){c.ui.plugin.call(this,f,[e,this.ui()]);(f!="resize"&&this._trigger(f,e,this.ui()))},plugins:{},ui:function(){return{originalElement:this.originalElement,element:this.element,helper:this.helper,position:this.position,size:this.size,originalSize:this.originalSize,originalPosition:this.originalPosition}}});c.extend(c.ui.resizable,{version:"1.8.18"});c.ui.plugin.add("resizable","alsoResize",{start:function(f,g){var e=c(this).data("resizable"),i=e.options;var h=function(j){c(j).each(function(){var k=c(this);k.data("resizable-alsoresize",{width:parseInt(k.width(),10),height:parseInt(k.height(),10),left:parseInt(k.css("left"),10),top:parseInt(k.css("top"),10)})})};if(typeof(i.alsoResize)=="object"&&!i.alsoResize.parentNode){if(i.alsoResize.length){i.alsoResize=i.alsoResize[0];h(i.alsoResize)}else{c.each(i.alsoResize,function(j){h(j)})}}else{h(i.alsoResize)}},resize:function(g,i){var f=c(this).data("resizable"),j=f.options,h=f.originalSize,l=f.originalPosition;var k={height:(f.size.height-h.height)||0,width:(f.size.width-h.width)||0,top:(f.position.top-l.top)||0,left:(f.position.left-l.left)||0},e=function(m,n){c(m).each(function(){var q=c(this),r=c(this).data("resizable-alsoresize"),p={},o=n&&n.length?n:q.parents(i.originalElement[0]).length?["width","height"]:["width","height","top","left"];c.each(o,function(s,u){var t=(r[u]||0)+(k[u]||0);if(t&&t>=0){p[u]=t||null}});q.css(p)})};if(typeof(j.alsoResize)=="object"&&!j.alsoResize.nodeType){c.each(j.alsoResize,function(m,n){e(m,n)})}else{e(j.alsoResize)}},stop:function(e,f){c(this).removeData("resizable-alsoresize")}});c.ui.plugin.add("resizable","animate",{stop:function(i,n){var p=c(this).data("resizable"),j=p.options;var h=p._proportionallyResizeElements,e=h.length&&(/textarea/i).test(h[0].nodeName),f=e&&c.ui.hasScroll(h[0],"left")?0:p.sizeDiff.height,l=e?0:p.sizeDiff.width;var g={width:(p.size.width-l),height:(p.size.height-f)},k=(parseInt(p.element.css("left"),10)+(p.position.left-p.originalPosition.left))||null,m=(parseInt(p.element.css("top"),10)+(p.position.top-p.originalPosition.top))||null;p.element.animate(c.extend(g,m&&k?{top:m,left:k}:{}),{duration:j.animateDuration,easing:j.animateEasing,step:function(){var o={width:parseInt(p.element.css("width"),10),height:parseInt(p.element.css("height"),10),top:parseInt(p.element.css("top"),10),left:parseInt(p.element.css("left"),10)};if(h&&h.length){c(h[0]).css({width:o.width,height:o.height})}p._updateCache(o);p._propagate("resize",i)}})}});c.ui.plugin.add("resizable","containment",{start:function(f,r){var t=c(this).data("resizable"),j=t.options,l=t.element;var g=j.containment,k=(g instanceof c)?g.get(0):(/parent/.test(g))?l.parent().get(0):g;if(!k){return}t.containerElement=c(k);if(/document/.test(g)||g==document){t.containerOffset={left:0,top:0};t.containerPosition={left:0,top:0};t.parentData={element:c(document),left:0,top:0,width:c(document).width(),height:c(document).height()||document.body.parentNode.scrollHeight}}else{var n=c(k),i=[];c(["Top","Right","Left","Bottom"]).each(function(p,o){i[p]=b(n.css("padding"+o))});t.containerOffset=n.offset();t.containerPosition=n.position();t.containerSize={height:(n.innerHeight()-i[3]),width:(n.innerWidth()-i[1])};var q=t.containerOffset,e=t.containerSize.height,m=t.containerSize.width,h=(c.ui.hasScroll(k,"left")?k.scrollWidth:m),s=(c.ui.hasScroll(k)?k.scrollHeight:e);t.parentData={element:k,left:q.left,top:q.top,width:h,height:s}}},resize:function(g,q){var t=c(this).data("resizable"),i=t.options,f=t.containerSize,p=t.containerOffset,m=t.size,n=t.position,r=t._aspectRatio||g.shiftKey,e={top:0,left:0},h=t.containerElement;if(h[0]!=document&&(/static/).test(h.css("position"))){e=p}if(n.left<(t._helper?p.left:0)){t.size.width=t.size.width+(t._helper?(t.position.left-p.left):(t.position.left-e.left));if(r){t.size.height=t.size.width/i.aspectRatio}t.position.left=i.helper?p.left:0}if(n.top<(t._helper?p.top:0)){t.size.height=t.size.height+(t._helper?(t.position.top-p.top):t.position.top);if(r){t.size.width=t.size.height*i.aspectRatio}t.position.top=t._helper?p.top:0}t.offset.left=t.parentData.left+t.position.left;t.offset.top=t.parentData.top+t.position.top;var l=Math.abs((t._helper?t.offset.left-e.left:(t.offset.left-e.left))+t.sizeDiff.width),s=Math.abs((t._helper?t.offset.top-e.top:(t.offset.top-p.top))+t.sizeDiff.height);var k=t.containerElement.get(0)==t.element.parent().get(0),j=/relative|absolute/.test(t.containerElement.css("position"));if(k&&j){l-=t.parentData.left}if(l+t.size.width>=t.parentData.width){t.size.width=t.parentData.width-l;if(r){t.size.height=t.size.width/t.aspectRatio}}if(s+t.size.height>=t.parentData.height){t.size.height=t.parentData.height-s;if(r){t.size.width=t.size.height*t.aspectRatio}}},stop:function(f,n){var q=c(this).data("resizable"),g=q.options,l=q.position,m=q.containerOffset,e=q.containerPosition,i=q.containerElement;var j=c(q.helper),r=j.offset(),p=j.outerWidth()-q.sizeDiff.width,k=j.outerHeight()-q.sizeDiff.height;if(q._helper&&!g.animate&&(/relative/).test(i.css("position"))){c(this).css({left:r.left-e.left-m.left,width:p,height:k})}if(q._helper&&!g.animate&&(/static/).test(i.css("position"))){c(this).css({left:r.left-e.left-m.left,width:p,height:k})}}});c.ui.plugin.add("resizable","ghost",{start:function(g,h){var e=c(this).data("resizable"),i=e.options,f=e.size;e.ghost=e.originalElement.clone();e.ghost.css({opacity:0.25,display:"block",position:"relative",height:f.height,width:f.width,margin:0,left:0,top:0}).addClass("ui-resizable-ghost").addClass(typeof i.ghost=="string"?i.ghost:"");e.ghost.appendTo(e.helper)},resize:function(f,g){var e=c(this).data("resizable"),h=e.options;if(e.ghost){e.ghost.css({position:"relative",height:e.size.height,width:e.size.width})}},stop:function(f,g){var e=c(this).data("resizable"),h=e.options;if(e.ghost&&e.helper){e.helper.get(0).removeChild(e.ghost.get(0))}}});c.ui.plugin.add("resizable","grid",{resize:function(e,m){var p=c(this).data("resizable"),h=p.options,k=p.size,i=p.originalSize,j=p.originalPosition,n=p.axis,l=h._aspectRatio||e.shiftKey;h.grid=typeof h.grid=="number"?[h.grid,h.grid]:h.grid;var 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- * jQuery hashchange event - v1.3 - 7/21/2010
- * http://benalman.com/projects/jquery-hashchange-plugin/
- *
- * Copyright (c) 2010 "Cowboy" Ben Alman
- * Dual licensed under the MIT and GPL licenses.
- * http://benalman.com/about/license/
- */
-(function($,e,b){var c="hashchange",h=document,f,g=$.event.special,i=h.documentMode,d="on"+c in e&&(i===b||i>7);function a(j){j=j||location.href;return"#"+j.replace(/^[^#]*#?(.*)$/,"$1")}$.fn[c]=function(j){return j?this.bind(c,j):this.trigger(c)};$.fn[c].delay=50;g[c]=$.extend(g[c],{setup:function(){if(d){return false}$(f.start)},teardown:function(){if(d){return false}$(f.stop)}});f=(function(){var j={},p,m=a(),k=function(q){return q},l=k,o=k;j.start=function(){p||n()};j.stop=function(){p&&clearTimeout(p);p=b};function n(){var r=a(),q=o(m);if(r!==m){l(m=r,q);$(e).trigger(c)}else{if(q!==m){location.href=location.href.replace(/#.*/,"")+q}}p=setTimeout(n,$.fn[c].delay)}$.browser.msie&&!d&&(function(){var q,r;j.start=function(){if(!q){r=$.fn[c].src;r=r&&r+a();q=$('').hide().one("load",function(){r||l(a());n()}).attr("src",r||"javascript:0").insertAfter("body")[0].contentWindow;h.onpropertychange=function(){try{if(event.propertyName==="title"){q.document.title=h.title}}catch(s){}}}};j.stop=k;o=function(){return a(q.location.href)};l=function(v,s){var u=q.document,t=$.fn[c].domain;if(v!==s){u.title=h.title;u.open();t&&u.write('
-
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -91,9 +93,9 @@ $(document).ready(function(){initNavTree('mainpage_8dox.html','');});
diff --git a/doc/html/menu.js b/doc/html/menu.js
index 97db4c2..433c15b 100644
--- a/doc/html/menu.js
+++ b/doc/html/menu.js
@@ -1,3 +1,26 @@
+/*
+ @licstart The following is the entire license notice for the
+ JavaScript code in this file.
+
+ Copyright (C) 1997-2017 by Dimitri van Heesch
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend The above is the entire license notice
+ for the JavaScript code in this file
+ */
function initMenu(relPath,searchEnabled,serverSide,searchPage,search) {
function makeTree(data,relPath) {
var result='';
@@ -17,10 +40,11 @@ function initMenu(relPath,searchEnabled,serverSide,searchPage,search) {
$('#main-nav').children(':first').addClass('sm sm-dox').attr('id','main-menu');
if (searchEnabled) {
if (serverSide) {
- $('#main-menu').append('
');
+ $('#main-menu').append('
');
} else {
$('#main-menu').append('
');
}
}
$('#main-menu').smartmenus();
}
+/* @license-end */
diff --git a/doc/html/menudata.js b/doc/html/menudata.js
index c420af4..a850eaa 100644
--- a/doc/html/menudata.js
+++ b/doc/html/menudata.js
@@ -1,3 +1,25 @@
+/*
+@licstart The following is the entire license notice for the
+JavaScript code in this file.
+
+Copyright (C) 1997-2019 by Dimitri van Heesch
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of version 2 of the GNU General Public License as published by
+the Free Software Foundation
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+@licend The above is the entire license notice
+for the JavaScript code in this file
+*/
var menudata={children:[
{text:"Main Page",url:"index.html"},
{text:"Related Pages",url:"pages.html"},
diff --git a/doc/html/modules.html b/doc/html/modules.html
index fb95aa8..88d5994 100644
--- a/doc/html/modules.html
+++ b/doc/html/modules.html
@@ -1,9 +1,9 @@
-
+
-
+
PEARL Procedures: Packages
@@ -13,9 +13,6 @@
-
@@ -29,7 +26,7 @@
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -95,9 +97,9 @@ $(document).ready(function(){initNavTree('modules.html','');});
diff --git a/doc/html/namespace_pearl_anglescan_panel.html b/doc/html/namespace_pearl_anglescan_panel.html
index f001132..953174e 100644
--- a/doc/html/namespace_pearl_anglescan_panel.html
+++ b/doc/html/namespace_pearl_anglescan_panel.html
@@ -1,9 +1,9 @@
-
+
-
+
PEARL Procedures: PearlAnglescanPanel Namespace Reference
@@ -13,9 +13,6 @@
-
@@ -29,7 +26,7 @@
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_anglescan_panel.html',
interactive processing of angle scanned XPD data.
-More...
+
More...
PEARL Procedures: PearlAnglescanProcess Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_anglescan_process.html
processing and holographic mapping of angle scanned XPD data.
-More...
+
More...
processing and holographic mapping of angle scanned XPD data.
-
PearlAnglescanProcess is declared in pearl-anglescan-process.ipf .
+
PearlAnglescanProcess is declared in pearl-anglescan-process.ipf .
PEARL Procedures: PearlAreaDisplay Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,23 +89,24 @@ $(document).ready(function(){initNavTree('namespace_pearl_area_display.html','')
instant visualization of angle scan and manipulator position.
-More...
+
More...
instant visualization of angle scan and manipulator position.
-
scienta HDF5 import, display, and slicer how-to
- /// ad_display_brick(root:x03da_scienta_20130821_01560:data)
+scienta HDF5 import, display, and slicer how-to
/// ad_display_brick(root:x03da_scienta_20130821_01560:data)
/// ad_scale_scienta(root:x03da_scienta_20130821_01560:data)
/// ad_scale_extra(root:x03da_scienta_20130821_01560:data,root:x03da_scienta_20130821_01560:MonoEnergy,root:x03da_scienta_20130821_01560:data)
/// ad_display_brick(root:x03da_scienta_20130821_01560:data)
@@ -114,16 +117,17 @@ Miscellaneous
Licensed under the Apache License, Version 2.0 (the "License"); @n
you may not use this file except in compliance with the License. @n
You may obtain a copy of the License at
- http://www.apache.org/licenses/LICENSE-2.0 PearlAreaDisplay is declared in pearl-area-display.ipf .
+ http://www.apache.org/licenses/LICENSE-2.0
+ PearlAreaDisplay is declared in pearl-area-display.ipf .
PEARL Procedures: PearlAreaImport Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_area_import.html','');
HDF5 file import from EPICS area detectors.
-More...
+
More...
HDF5 file import from EPICS area detectors.
-
PearlAreaImport is declared in pearl-area-import.ipf .
+
PearlAreaImport is declared in pearl-area-import.ipf .
PEARL Procedures: PearlAreaProfiles Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,7 +89,7 @@ $(document).ready(function(){initNavTree('namespace_pearl_area_profiles.html',''
profile extraction for multi-dimensional datasets acquired from area detectors.
-More...
+
More...
profile extraction for multi-dimensional datasets acquired from area detectors.
PearlAnglescanTracker is declared in pearl-area-profiles.ipf .
@@ -97,9 +99,9 @@ $(document).ready(function(){initNavTree('namespace_pearl_area_profiles.html',''
diff --git a/doc/html/namespace_pearl_arpes.html b/doc/html/namespace_pearl_arpes.html
index 85553b6..4c2d4a3 100644
--- a/doc/html/namespace_pearl_arpes.html
+++ b/doc/html/namespace_pearl_arpes.html
@@ -1,9 +1,9 @@
-
+
-
+
PEARL Procedures: PearlArpes Namespace Reference
@@ -13,9 +13,6 @@
-
@@ -29,7 +26,7 @@
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_arpes.html','');});
data acquisition and analysis package for ARPES at PEARL.
-More...
+
More...
data acquisition and analysis package for ARPES at PEARL.
-
PearlArpes is declared in pearl-arpes.ipf .
+
PearlArpes is declared in pearl-arpes.ipf .
PEARL Procedures: PearlCompat Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_compat.html','');});
compatibility procedures for igor 8
-More...
+
More...
compatibility procedures for igor 8
-
PearlCompat is declared in pearl-compat.ipf .
+
PearlCompat is declared in pearl-compat.ipf .
PEARL Procedures: PearlDataExplorer Namespace Reference
-
-
-
-
-
-
- PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
-
- Igor procedures for the analysis of PEARL data
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
preview and import panel for PEARL data
-More...
-
-
preview and import panel for PEARL data
-
PearlDataExplorer is declared in pearl-data-explorer.ipf .
-
-
PEARL Procedures: PearlElog Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_elog.html','');});
interface for writing ELOG entries with Igor graphs as attachment.
-More...
+
More...
interface for writing ELOG entries with Igor graphs as attachment.
-
PearlElog is declared in pearl-elog.ipf .
+
PearlElog is declared in pearl-elog.ipf .
PEARL Procedures: PearlFitFuncs Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_fit_funcs.html','');})
various fit functions for photoelectron spectroscopy.
-More...
+
More...
various fit functions for photoelectron spectroscopy.
-
PearlFitFuncs is declared in pearl-fitfuncs.ipf .
+
PearlFitFuncs is declared in pearl-fitfuncs.ipf .
PEARL Procedures: PearlMatrixImport Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_matrix_import.html',''
data file import for omicron matrix (STM) files
-More...
+
More...
data file import for omicron matrix (STM) files
-
PearlMatrixImport is declared in pearl-matrix-import.ipf .
+
PearlMatrixImport is declared in pearl-matrix-import.ipf .
PEARL Procedures: PearlPShellImport Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_p_shell_import.html','
import data from PShell
-More...
+
More...
PEARL Procedures: PearlPmscoImport Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_pmsco_import.html','')
data import/export procedures for multiple scattering calculations.
-More...
+
More...
data import/export procedures for multiple scattering calculations.
-
PearlPmscoImport is declared in pearl-pmsco-import.ipf .
+
PearlPmscoImport is declared in pearl-pmsco-import.ipf .
PEARL Procedures: PearlScientaCountrate Namespace Reference
-
-
-
-
-
-
- PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
-
- Igor procedures for the analysis of PEARL data
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
count rate functions for Scienta detector images.
-More...
-
-
count rate functions for Scienta detector images.
-
PearlScientaCountrate is declared in pearl-scienta-countrate.ipf .
-
-
PEARL Procedures: PearlScientaPreprocess Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_scienta_preprocess.htm
preprocessing functions for Scienta detector images.
-More...
+
More...
PEARL Procedures: PearlVectorOperations Namespace Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -87,19 +89,19 @@ $(document).ready(function(){initNavTree('namespace_pearl_vector_operations.html
basic vector geometry operations.
-More...
+
More...
PEARL Procedures: Namespace List
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -94,15 +96,14 @@ $(document).ready(function(){initNavTree('namespaces.html','');});
N PearlAreaProfiles Profile extraction for multi-dimensional datasets acquired from area detectors N PearlArpes Data acquisition and analysis package for ARPES at PEARL N PearlCompat Compatibility procedures for igor 8
-
N PearlDataExplorer Preview and import panel for PEARL data
-
N PearlElog Interface for writing ELOG entries with Igor graphs as attachment
-
N PearlFitFuncs Various fit functions for photoelectron spectroscopy
-
N PearlMatrixImport Data file import for omicron matrix (STM) files
-
N PearlPmscoImport Data import/export procedures for multiple scattering calculations
-
N PearlPShellImport Import data from PShell
-
N PearlScientaCountrate Count rate functions for Scienta detector images
-
N PearlScientaPreprocess Preprocessing functions for Scienta detector images
-
N PearlVectorOperations Basic vector geometry operations
+
N PearlElog Interface for writing ELOG entries with Igor graphs as attachment
+
N PearlFitFuncs Various fit functions for photoelectron spectroscopy
+
N PearlMatrixImport Data file import for omicron matrix (STM) files
+
N PearlPmscoImport Data import/export procedures for multiple scattering calculations
+
N PearlPShellImport Import data from PShell
+
N PearlScientaLive Utility functions for operating the Scienta analyser
+
N PearlScientaPreprocess Preprocessing functions for Scienta detector images
+
N PearlVectorOperations Basic vector geometry operations PEARL Procedures: Angle-scan processing
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -80,7 +82,7 @@ $(document).ready(function(){initNavTree('pag_anglescan_processing.html','');});
-
@@ -348,7 +352,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); calculate the output using all enabled processing filters.
the diffractogram is calculated, to display the graph, call asp_display_output .
-Definition at line 620 of file pearl-anglescan-panel.ipf .
+Definition at line 623 of file pearl-anglescan-panel.ipf .
@@ -369,7 +373,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); close all graphs created by the angle scan panel
-Definition at line 728 of file pearl-anglescan-panel.ipf .
+Definition at line 731 of file pearl-anglescan-panel.ipf .
@@ -409,7 +413,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 273 of file pearl-anglescan-panel.ipf .
+Definition at line 276 of file pearl-anglescan-panel.ipf .
@@ -449,7 +453,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 666 of file pearl-anglescan-panel.ipf .
+Definition at line 669 of file pearl-anglescan-panel.ipf .
@@ -471,7 +475,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); display a graph window of the processed data.
if the window exists, it is updated and brought to the front of the window stack.
-Definition at line 249 of file pearl-anglescan-panel.ipf .
+Definition at line 252 of file pearl-anglescan-panel.ipf .
@@ -511,7 +515,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns name of the graph window Definition at line 768 of file pearl-anglescan-panel.ipf .
+Definition at line 771 of file pearl-anglescan-panel.ipf .
@@ -540,7 +544,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 204 of file pearl-anglescan-panel.ipf .
+Definition at line 207 of file pearl-anglescan-panel.ipf .
@@ -568,7 +572,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 816 of file pearl-anglescan-panel.ipf .
+Definition at line 819 of file pearl-anglescan-panel.ipf .
@@ -589,7 +593,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); save the output diffractogram to an igor text file
-Definition at line 801 of file pearl-anglescan-panel.ipf .
+Definition at line 804 of file pearl-anglescan-panel.ipf .
@@ -610,7 +614,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); create the angle scan processing panel
-Definition at line 900 of file pearl-anglescan-panel.ipf .
+Definition at line 903 of file pearl-anglescan-panel.ipf .
@@ -632,7 +636,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); update graphs with new color table or contrast
applies to the preview graph and the diffractogram.
-Definition at line 710 of file pearl-anglescan-panel.ipf .
+Definition at line 713 of file pearl-anglescan-panel.ipf .
@@ -660,7 +664,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 406 of file pearl-anglescan-panel.ipf .
+Definition at line 409 of file pearl-anglescan-panel.ipf .
@@ -1396,7 +1400,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 358 of file pearl-anglescan-panel.ipf .
+Definition at line 361 of file pearl-anglescan-panel.ipf .
@@ -1438,7 +1442,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 318 of file pearl-anglescan-panel.ipf .
+Definition at line 321 of file pearl-anglescan-panel.ipf .
@@ -1494,7 +1498,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 453 of file pearl-anglescan-panel.ipf .
+Definition at line 456 of file pearl-anglescan-panel.ipf .
@@ -1550,7 +1554,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 494 of file pearl-anglescan-panel.ipf .
+Definition at line 497 of file pearl-anglescan-panel.ipf .
@@ -1606,7 +1610,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 537 of file pearl-anglescan-panel.ipf .
+Definition at line 540 of file pearl-anglescan-panel.ipf .
@@ -1662,7 +1666,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 584 of file pearl-anglescan-panel.ipf .
+Definition at line 587 of file pearl-anglescan-panel.ipf .
@@ -1689,7 +1693,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); the preferences file is an Igor packed experiment file in a special preferences folder.
this function is called automatically when the procedure is first compiled, or whenever the user clicks the corresponding button.
-Definition at line 168 of file pearl-anglescan-panel.ipf .
+Definition at line 171 of file pearl-anglescan-panel.ipf .
@@ -1748,7 +1752,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); save persistent package data to the preferences file.
this function is called when the user clicks the corresponding button.
-Definition at line 142 of file pearl-anglescan-panel.ipf .
+Definition at line 145 of file pearl-anglescan-panel.ipf .
@@ -2110,7 +2114,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); update the popup menus to reflect the values of the global variables
-Definition at line 1210 of file pearl-anglescan-panel.ipf .
+Definition at line 1213 of file pearl-anglescan-panel.ipf .
@@ -2137,7 +2141,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); package name is used as data folder name
-Definition at line 45 of file pearl-anglescan-panel.ipf .
+Definition at line 48 of file pearl-anglescan-panel.ipf .
@@ -2163,7 +2167,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); data folder path
-Definition at line 47 of file pearl-anglescan-panel.ipf .
+Definition at line 50 of file pearl-anglescan-panel.ipf .
@@ -2173,9 +2177,9 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-anglescan-panel.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,96 +87,1569 @@ $(document).ready(function(){initNavTree('pearl-anglescan-panel_8ipf_source.html
pearl-anglescan-panel.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 3 #pragma IgorVersion = 6.2 4 #pragma ModuleName = PearlAnglescanPanel 5 #include "pearl-anglescan-process" 6 #include "pearl-pmsco-import" 47 static strconstant
package_path =
"root:packages:pearl_anglescan_panel:" 52 dfref savedf = GetDataFolderDFR()
57 if (nvar_exists(init_done))
68 variable /g init_done = 1
76 dfref savedf = getdatafolderdfr()
78 newdatafolder /o/s packages
79 newdatafolder /o/s $package_name
82 string /g graphname = "graph_anglescan_panel"
84 prefs_objects += "norm_alpha_enable;norm_alpha_mode;norm_alpha_smoothing;norm_phi_enable;norm_phi_mode;norm_phi_thetarange;"
85 prefs_objects += "norm_theta_enable;norm_theta_mode;norm_theta_domain;norm_theta_smoothing;norm_thetaphi_enable;norm_thetaphi_mode;norm_thetaphi_smoothing;"
86 prefs_objects += "output_folding;output_horizon;graph_mode;graph_projection;graph_colortable;graph_contrast;"
89 variable /g theta_offset = 0
90 variable /g tilt_offset = 0
91 variable /g phi_offset = 0
92 variable /g alpha_offset = 0
93 variable /g crop_enable = 0
94 variable /g crop_alpha = 25
95 variable /g crop_theta = 88
96 string /g crop_rows = ""
97 variable /g norm_alpha_enable = 0
98 variable /g norm_alpha_mode = 4
99 variable /g norm_alpha_smoothing = 0.25
100 variable /g norm_theta_enable = 0
101 variable /g norm_theta_mode = 4
102 variable /g norm_theta_domain = 0
103 variable /g norm_theta_smoothing = 0.25
104 variable /g norm_thetaphi_enable = 0
105 variable /g norm_thetaphi_mode = 4
106 variable /g norm_thetaphi_smoothing = 0.25
107 variable /g norm_phi_enable = 0
108 variable /g norm_phi_mode = 4
109 variable /g norm_phi_thetarange = 20
110 string /g output_name = "holo1"
111 variable /g output_folding = 1
112 variable /g output_horizon = 88
113 variable /g graph_mode = 1
115 string /g graph_colortable = "grays"
116 variable /g graph_contrast = 2
119 string /g source_path = ""
120 string /g export_folderpath = "root:"
121 variable /g export_format = 1
124 string /g panel_name = ""
125 string /g preview_graphname = ""
126 string /g dist_x_graphname = ""
127 string /g dist_y_graphname = ""
128 string /g output_graphname = ""
131 make /n=(10,10) /o raw_data, process_data
132 make /o dist_x, dist_x_smoo
133 make /o dist_y, dist_y_smoo
143 dfref saveDF = GetDataFolderDFR()
145 svar /sdfr=df prefs_objects
147 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
149 NewPath/O/C/Q tempPackagePrefsPath, fullPath
150 fullPath += ":preferences.pxp"
152 SetDataFolder root:packages
153 SetDataFolder $package_name
154 SaveData /O /Q /J=prefs_objects fullPath
156 KillPath/Z tempPackagePrefsPath
169 dfref saveDF = GetDataFolderDFR()
173 NewDataFolder /O/S packages
174 NewDataFolder /O/S $package_name
175 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
178 GetFileFolderInfo /Q /Z fullPath
180 fullPath += ":preferences.pxp"
181 GetFileFolderInfo /Q /Z fullPath
183 LoadData /O /R /Q fullPath
207 dfref saveDF = GetDataFolderDFR()
208 dfref datadf = GetWavesDataFolderDFR(raw_data)
209 dfref attrdf = datadf:attr
210 if (!DataFolderRefStatus(attrdf))
213 dfref parentdf = GetDataFolderDFR()
214 dfref attrdf = parentdf:attr
221 source_path = GetWavesDataFolder(raw_data, 2)
223 duplicate /o raw_data, raw, process_data
225 wave /sdfr=attrdf /z ManipulatorTheta
226 wave /sdfr=attrdf /z ManipulatorTilt
227 wave /sdfr=attrdf /z ManipulatorPhi
228 if (WaveExists(ManipulatorTheta) && WaveExists(ManipulatorTilt) && WaveExists(ManipulatorPhi))
229 duplicate /o attrdf:ManipulatorTheta, raw_theta, process_theta
230 duplicate /o attrdf:ManipulatorTilt, raw_tilt, process_tilt
231 duplicate /o attrdf:ManipulatorPhi, raw_phi, process_phi
233 DoAlert 0, "Can't find manipulator angle waves.\rCheck that the attr folder exists, or provide values in the following table."
234 make /n=(dimsize(raw_data, 1)) /o raw_theta, raw_tilt, raw_phi
235 make /n=(dimsize(raw_data, 1)) /o process_theta, process_tilt, process_phi
236 edit /k=1 raw_theta, raw_tilt, raw_phi
239 make /o /n=(dimsize(raw_data, 0)) dist_x, dist_x_smoo
240 make /o /n=(dimsize(raw_data, 1)) dist_y, dist_y_smoo
251 wave /sdfr=df process_data
252 svar /sdfr=df preview_graphname
254 if (strlen(preview_graphname) && (wintype(preview_graphname) == 1))
256 DoWindow /F $preview_graphname
261 nvar /sdfr=df graph_contrast
262 svar /sdfr=df graph_colortable
263 set_contrast (graph_contrast, graph_contrast, graphname=preview_graphname, colortable=graph_colortable)
274 variable xdist, ydist
279 wave /sdfr=df dist_x_smoo
280 wave /sdfr=df dist_y_smoo
281 svar /sdfr=df dist_x_graphname
282 svar /sdfr=df dist_y_graphname
285 if (strlen(dist_x_graphname) && (wintype(dist_x_graphname) == 1))
286 DoWindow /F $dist_x_graphname
288 display /k=1 /n=graph_asp_dist_x dist_x, dist_x_smoo
289 dist_x_graphname = s_name
290 ModifyGraph /w=$dist_x_graphname mode(dist_x)=2
291 ModifyGraph /w=$dist_x_graphname lsize(dist_x)=2
292 ModifyGraph /w=$dist_x_graphname rgb(dist_x)=(0,0,0)
297 if (strlen(dist_y_graphname) && (wintype(dist_y_graphname) == 1))
298 DoWindow /F $dist_y_graphname
300 display /k=1 /n=graph_asp_dist_y dist_y, dist_y_smoo
301 dist_y_graphname = s_name
302 ModifyGraph /w=$dist_y_graphname mode(dist_y)=2
303 ModifyGraph /w=$dist_y_graphname lsize(dist_y)=2
304 ModifyGraph /w=$dist_y_graphname rgb(dist_y)=(0,0,0)
323 wave /sdfr=df raw_theta
324 wave /sdfr=df raw_tilt
325 wave /sdfr=df raw_phi
326 nvar /sdfr=df theta_offset
327 nvar /sdfr=df tilt_offset
328 nvar /sdfr=df phi_offset
329 nvar /sdfr=df alpha_offset
331 duplicate /o raw, df:process_data
332 duplicate /o raw_theta, df:process_theta
333 duplicate /o raw_tilt, df:process_tilt
334 duplicate /o raw_phi, df:process_phi
336 wave /sdfr=df process_data
337 wave /sdfr=df process_theta
338 wave /sdfr=df process_tilt
339 wave /sdfr=df process_phi
341 process_theta = raw_theta - theta_offset
342 process_tilt = raw_tilt - tilt_offset
343 process_phi = raw_phi - phi_offset
344 setscale /p x dimoffset(raw, 0) - alpha_offset, dimdelta(raw, 0), waveunits(raw, 0), process_data
362 if (ParamIsDefault(force))
367 wave /sdfr=df process_data
368 wave /sdfr=df process_theta
369 wave /sdfr=df process_tilt
370 wave /sdfr=df process_phi
371 nvar /sdfr=df crop_enable
372 nvar /sdfr=df crop_alpha
373 nvar /sdfr=df crop_theta
374 svar /sdfr=df crop_rows
376 if (force || crop_enable)
378 if (crop_alpha > abs(dimdelta(process_data, 0)))
379 crop_strip (process_data, -crop_alpha, +crop_alpha)
382 if ((crop_theta >= 10) && (crop_theta < 90))
383 crop_strip_theta (process_data, -0.1, crop_theta + 0.1, process_theta, process_tilt, process_phi)
386 if (strlen(crop_rows) > 0)
387 delete_rows (crop_rows, process_data, process_theta, process_tilt, process_phi)
413 make /n=(numpnts(theta)) /i /free idx
415 variable nrows = ItemsInList(rows, ",")
419 for (irow = 0; irow < nrows; irow += 1)
420 srow = StringFromList(irow, rows, ",")
421 q1 = str2num(StringFromList(0, srow, "-"))
422 q2 = str2num(StringFromList(1, srow, "-"))
430 extract /free idx, idx, idx >= 0
431 variable nx = dimsize(data, 0)
432 variable ny = numpnts(idx)
436 redimension /n=(ny) theta, tilt, phi
437 duplicate /free data, data_copy
438 redimension /n=(nx,ny) data
439 data = data_copy[p][idx[q]]
457 if (ParamIsDefault(force))
461 dfref saveDF = GetDataFolderDFR()
463 wave /sdfr=df process_data
464 nvar /sdfr=df norm_alpha_enable
465 nvar /sdfr=df norm_alpha_mode
466 nvar /sdfr=df norm_alpha_smoothing
468 if (force || norm_alpha_enable)
469 dfref temp_df = newfreedatafolder()
470 setdatafolder temp_df
471 normalize_strip_x (process_data, smooth_method=norm_alpha_mode, smooth_factor=norm_alpha_smoothing, check=check)
475 duplicate /o check_dist, df:dist_x
476 duplicate /o check_smoo, df:dist_x_smoo
498 if (ParamIsDefault(force))
502 dfref saveDF = GetDataFolderDFR()
504 wave /sdfr=df process_data
505 wave /sdfr=df process_theta
506 wave /sdfr=df process_phi
507 nvar /sdfr=df norm_phi_enable
508 nvar /sdfr=df norm_phi_mode
509 nvar /sdfr=df norm_phi_thetarange
511 if (force || norm_phi_enable)
512 dfref temp_df = newfreedatafolder()
513 setdatafolder temp_df
514 normalize_strip_phi (process_data, process_theta, process_phi, theta_range=norm_phi_thetarange, check=check)
518 duplicate /o check_dist, df:dist_y
519 duplicate /o check_smoo, df:dist_y_smoo
541 if (ParamIsDefault(force))
545 dfref saveDF = GetDataFolderDFR()
547 wave /sdfr=df process_data
548 wave /sdfr=df process_theta
549 nvar /sdfr=df norm_theta_enable
550 nvar /sdfr=df norm_theta_mode
551 nvar /sdfr=df norm_theta_domain
552 nvar /sdfr=df norm_theta_smoothing
554 if (force || norm_theta_enable)
555 dfref temp_df = newfreedatafolder()
556 setdatafolder temp_df
557 if (norm_theta_domain==1)
558 normalize_strip_theta_scans (process_data, process_theta, smooth_method=norm_theta_mode, smooth_factor=norm_theta_smoothing, check=check)
560 normalize_strip_theta (process_data, process_theta, smooth_method=norm_theta_mode, smooth_factor=norm_theta_smoothing, check=check)
565 duplicate /o check_dist, df:dist_y
566 duplicate /o check_smoo, df:dist_y_smoo
588 if (ParamIsDefault(force))
592 dfref saveDF = GetDataFolderDFR()
594 wave /sdfr=df process_data
595 wave /sdfr=df process_theta
596 wave /sdfr=df process_phi
597 nvar /sdfr=df norm_thetaphi_enable
598 nvar /sdfr=df norm_thetaphi_mode
599 nvar /sdfr=df norm_thetaphi_smoothing
601 if (force || norm_thetaphi_enable)
602 dfref temp_df = newfreedatafolder()
603 setdatafolder temp_df
604 normalize_strip_thetaphi (process_data, process_theta, process_phi, smooth_method=norm_thetaphi_mode, smooth_factor=norm_thetaphi_smoothing, check=check)
608 duplicate /o check_dist, df:dist_y
609 duplicate /o check_smoo, df:dist_y_smoo
621 dfref saveDF = GetDataFolderDFR()
631 nvar folding=output_folding
632 nvar horizon=output_horizon
641 pizza_service_2 (process_data, output_name, process_theta, process_tilt, process_phi, folding=folding, nograph=1)
643 setdatafolder $output_name
647 values = pol <= horizon ? values : nan
671 svar /sdfr=pkg_df output_name
672 svar /sdfr=pkg_df output_graphname
673 nvar /sdfr=pkg_df graph_projection
674 nvar /sdfr=pkg_df graph_mode
675 svar /sdfr=pkg_df graph_colortable
676 nvar /sdfr=pkg_df graph_contrast
678 if (ParamIsDefault(data_df))
679 dfref data_df = pkg_df
681 if (ParamIsDefault(data_name))
682 data_name = output_name
685 dfref saveDF = GetDataFolderDFR()
686 setdatafolder data_df
692 string graphname = data_name
693 graphname =
display_hemi_scan (data_name, projection=graph_projection, graphtype=graph_mode, graphname=graphname)
694 if (ParamIsDefault(data_df))
695 output_graphname = graphname
699 if (strlen(graphname) && (wintype(graphname) == 1))
700 set_contrast (graph_contrast, graph_contrast, graphname=graphname, colortable=graph_colortable)
713 svar /sdfr=df preview_graphname
714 svar /sdfr=df output_graphname
715 svar /sdfr=df graph_colortable
716 nvar /sdfr=df graph_contrast
718 if (strlen(preview_graphname) && (wintype(preview_graphname) == 1))
719 set_contrast (graph_contrast, graph_contrast, graphname=preview_graphname, colortable=graph_colortable)
721 if (strlen(output_graphname) && (wintype(output_graphname) == 1))
722 set_contrast (graph_contrast, graph_contrast, graphname=output_graphname, colortable=graph_colortable)
731 svar /sdfr=df preview_graphname
732 svar /sdfr=df output_graphname
733 svar /sdfr=df dist_x_graphname
734 svar /sdfr=df dist_y_graphname
736 if (strlen(preview_graphname) && (wintype(preview_graphname) == 1))
737 killwindow $preview_graphname
739 if (strlen(output_graphname) && (wintype(output_graphname) == 1))
740 killwindow $output_graphname
742 if (strlen(dist_x_graphname) && (wintype(dist_x_graphname) == 1))
743 killwindow $dist_x_graphname
745 if (strlen(dist_y_graphname) && (wintype(dist_y_graphname) == 1))
746 killwindow $dist_y_graphname
749 preview_graphname = ""
750 output_graphname = ""
751 dist_x_graphname = ""
752 dist_y_graphname = ""
772 if (ParamIsDefault(do_graph))
777 svar /sdfr=df source_path
778 svar /sdfr=df output_name
779 svar /sdfr=df output_graphname
780 wave raw_data = $source_path
782 dfref saveDF = GetDataFolderDFR()
783 dfref raw_df = GetWavesDataFolderDFR(raw_data)
785 newdatafolder /o /s $dest_name
786 dfref dest_df = GetDataFolderDFR()
790 string graphname = ""
803 svar /sdfr=df output_name
805 dfref saveDF = GetDataFolderDFR()
820 svar /sdfr=df output_name
821 wave /sdfr=df process_data
823 dfref saveDF = GetDataFolderDFR()
826 string s_int = "values"
828 string s_polar = s_prefix + "pol"
829 string s_azim = s_prefix + "az"
831 pmsco_save_scan ("", "", num2str(ekin), s_polar, s_azim, "", s_int, "", sdfr=data_df)
847 asp_display_dist_check(0, 1)
854 asp_display_dist_check(0, 1)
861 asp_display_dist_check(0, 1)
873 do_norm_alpha(1, force=1)
880 do_norm_phi(1, force=1)
887 do_norm_theta(1, force=1)
894 do_norm_thetaphi(1, force=1)
902 svar /sdfr=df panel_name
904 if (strlen(panel_name) && (wintype(panel_name) == 7))
905 DoWindow /F $panel_name
909 NewPanel /K=1 /N=anglescan_panel /W=(200,50,480,874) as "angle scan processing"
912 GroupBox gb_source, title="data source"
914 Button b_source_select, help={
"select the source wave, e.g. ReducedData1. it must be in the scan or region data folder. the attr folder with the manipulator waves must be in the same folder or one level up." }
916 Button b_source_update, help={
"reload the process data from the previous source (link displayed below)" }
917 TitleBox tb_source_path, size={240,21}
918 TitleBox tb_source_path,variable= root:packages:pearl_anglescan_panel:source_path
920 GroupBox gb_offsets, title=
"offsets" 921 SetVariable sv_theta_offset, size={88,16},bodyWidth=60,title=
"theta" 922 SetVariable sv_theta_offset,value= root:packages:pearl_anglescan_panel:theta_offset
923 SetVariable sv_theta_offset, help={
"manipulator theta value that corresponds to normal emission." }
924 SetVariable sv_tilt_offset, size={74,16},bodyWidth=60,title=
"tilt" 925 SetVariable sv_tilt_offset,value= root:packages:pearl_anglescan_panel:tilt_offset
926 SetVariable sv_tilt_offset, help={
"manipulator tilt value that corresponds to normal emission." }
927 SetVariable sv_phi_offset, size={78,16},bodyWidth=60,title=
"phi" 928 SetVariable sv_phi_offset,value= root:packages:pearl_anglescan_panel:phi_offset
929 SetVariable sv_phi_offset, help={
"manipulator phi value that should map to the 3 o'clock angle." }
930 SetVariable sv_alpha_offset, size={90,16},bodyWidth=60,title=
"alpha" 931 SetVariable sv_alpha_offset,value= root:packages:pearl_anglescan_panel:alpha_offset
932 SetVariable sv_alpha_offset, help={
"alpha value that corresponds to normal emission (if the sample normal is properly aligned)." }
934 Button b_save_prefs, help={
"save settings as preferences." }
936 Button b_load_prefs, help={
"load settings from preferences." }
938 GroupBox gb_crop, title=
"crop and delete" 939 CheckBox cb_crop_enable, size={50,14}, title=
"enable" 940 CheckBox cb_crop_enable, help={
"crop at +/-alpha and +theta, delete arbitrary rows" }
941 CheckBox cb_crop_enable, variable= root:packages:pearl_anglescan_panel:crop_enable
942 SetVariable sv_crop_alpha, size={90,16},bodyWidth=60,title=
"alpha" 943 SetVariable sv_crop_alpha, limits={0,30,1},value= root:packages:pearl_anglescan_panel:crop_alpha
944 SetVariable sv_crop_alpha, help={
"alpha (detection angle) cropping angle (positive boundary), relative to normal emission" }
945 SetVariable sv_crop_theta, size={90,16},bodyWidth=60,title=
"theta" 946 SetVariable sv_crop_theta, limits={10,90,1},value= root:packages:pearl_anglescan_panel:crop_theta
947 SetVariable sv_crop_theta, help={
"theta (polar angle) upper limit, relative to normal emission" }
948 SetVariable sv_crop_rows, size={200,16},bodyWidth=160,title=
"rows" 949 SetVariable sv_crop_rows, limits={10,90,1},value= root:packages:pearl_anglescan_panel:crop_rows
950 SetVariable sv_crop_rows, help={
"rows to delete from the raw data. comma-separated point indices, hyphen for range." }
952 Button b_crop_preview, help={
"show a preview of the cropped dataset." }
954 GroupBox gb_norm_alpha, title=
"normalize alpha" 955 CheckBox cb_norm_alpha_enable, size={50,14}, title=
"enable" 956 CheckBox cb_norm_alpha_enable,variable= root:packages:pearl_anglescan_panel:norm_alpha_enable
957 CheckBox cb_norm_alpha_enable, help={
"enable normalization of the alpha distribution" }
959 PopupMenu pm_norm_alpha_mode, mode=5, popvalue=
"loess" , value= #
"\"none;binomial;boxcar;scienta;loess;\"" 960 PopupMenu pm_norm_alpha_mode, help={
"alpha normalization method. recommended: loess" }
961 SetVariable sv_norm_alpha_smoothing, size={112,16}, bodyWidth=60, title=
"smoothing" 962 SetVariable sv_norm_alpha_smoothing, limits={0,1,0.05}, value= root:packages:pearl_anglescan_panel:norm_alpha_smoothing
963 SetVariable sv_norm_alpha_smoothing, help={
"smoothing parameter (depends on the normalization method)." }
965 Button b_norm_alpha_check, help={
"show a graph of the normalization function" }
967 Button b_norm_alpha_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
969 GroupBox gb_norm_phi, title=
"normalize phi" 970 CheckBox cb_norm_phi_enable, size={50,14}, title=
"enable" 971 CheckBox cb_norm_phi_enable,variable= root:packages:pearl_anglescan_panel:norm_phi_enable
972 CheckBox cb_norm_phi_enable, help={
"enable normalization of the phi distribution to reduce the effect of wobble" }
973 SetVariable sv_norm_phi_range, size={118,16}, bodyWidth=60, title=
"theta range" 974 SetVariable sv_norm_phi_range, limits={0,90,1}, value= root:packages:pearl_anglescan_panel:norm_phi_thetarange
975 SetVariable sv_norm_phi_range, help={
"theta range (from normal) to factor into the normalization function" }
977 Button b_norm_phi_check, help={
"show a graph of the normalization function" }
979 Button b_norm_phi_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
981 GroupBox gb_norm_theta, title=
"normalize theta" 982 CheckBox cb_norm_theta_enable, size={50,14},title=
"enable" 983 CheckBox cb_norm_theta_enable, variable= root:packages:pearl_anglescan_panel:norm_theta_enable
984 CheckBox cb_norm_theta_enable, help={
"enable normalization of the theta distribution (integrated over phi)" }
986 PopupMenu pm_norm_theta_domain, mode=5, popvalue=
"loess" , value= #
"\"global;scans;\"" 987 PopupMenu pm_norm_theta_domain, help={
"smoothing domain: global or individual scans. use global unless there is a stronga or irregular phi variation." }
989 PopupMenu pm_norm_theta_mode,mode=5,popvalue=
"loess" ,value= #
"\"none;binomial;boxcar;polynomial;loess;\"" 990 PopupMenu pm_norm_theta_mode, help={
"theta normalization method. recommended: loess" }
991 SetVariable sv_norm_theta_smoothing, size={112,16}, bodyWidth=60, title=
"smoothing" 992 SetVariable sv_norm_theta_smoothing, limits={0,1,0.05}, value= root:packages:pearl_anglescan_panel:norm_theta_smoothing
993 SetVariable sv_norm_theta_smoothing, help={
"smoothing parameter (depends on the normalization method)." }
995 Button b_norm_theta_check, help={
"show a graph of the normalization function" }
997 Button b_norm_theta_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
999 GroupBox gb_norm_thetaphi, size={272,97},title=
"normalize (theta,phi)" 1000 CheckBox cb_norm_thetaphi_enable, size={50,14},title=
"enable" 1001 CheckBox cb_norm_thetaphi_enable, variable= root:packages:pearl_anglescan_panel:norm_thetaphi_enable
1002 CheckBox cb_norm_thetaphi_enable, help={
"enable normalization of the (theta, phi) distribution." }
1004 PopupMenu pm_norm_thetaphi_mode, mode=5, popvalue=
"loess" , value= #
"\"none;none;none;none;loess;\"" 1005 PopupMenu pm_norm_thetaphi_mode, help={
"theta normalization method. recommended: loess" }
1006 SetVariable sv_norm_thetaphi_smoothing, size={112,16}, bodyWidth=60, title=
"smoothing" 1007 SetVariable sv_norm_thetaphi_smoothing, limits={0,1,0.05}, value= root:packages:pearl_anglescan_panel:norm_thetaphi_smoothing
1008 SetVariable sv_norm_thetaphi_smoothing, help={
"smoothing parameter (depends on the normalization method)." }
1010 Button b_norm_thetaphi_check, help={
"show a graph of the normalization function" }
1012 Button b_norm_thetaphi_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
1014 GroupBox gb_output, title=
"output" 1015 SetVariable sv_output_folding, size={95,16}, bodyWidth=60, title=
"folding" 1016 SetVariable sv_output_folding, limits={1,20,1}, value= root:packages:pearl_anglescan_panel:output_folding
1017 SetVariable sv_output_folding, help={
"n-fold rotational average. 1=no averaging." }
1018 SetVariable sv_output_horizon, size={98,16}, bodyWidth=60, title=
"horizon" 1019 SetVariable sv_output_horizon, limits={1,90,1}, value= root:packages:pearl_anglescan_panel:output_horizon
1020 SetVariable sv_output_horizon, help={
"highest theta to display" }
1022 PopupMenu pm_graph_projection, mode=2, popvalue=
"stereographic" , value= #
"\"equidistant;stereographic;equal area;gnomonic;orthographic;\"" 1023 PopupMenu pm_graph_projection, help={
"projection (theta mapping) mode" }
1025 PopupMenu pm_graph_mode, mode=2, popvalue=
"dots" , value= #
"\"none;dots;none;image;\"" 1026 PopupMenu pm_graph_mode, help={
"graph type: dots = coloured dots on circles; image = interpolated matrix" }
1028 Button b_output_calc, help={
"execute data processing with the enabled filters and display the diffractogram." }
1030 Button b_output_duplicate, help={
"copy the result to an arbitrary data folder." }
1032 Button b_output_itx, help={
"save the result to an igor text file (itx)." }
1034 Button b_output_etpi, help={
"save the result to a pmsco angle scan file (etpi)." }
1036 GroupBox gb_graph, title=
"graph" 1038 PopupMenu pm_graph_colortable, mode=0, value= #
"\"*COLORTABLEPOPNONAMES*\"" 1039 PopupMenu pm_graph_colortable, help={
"color table to use in pseudocolor graphs." }
1040 SetVariable sv_graph_contrast, size={119,16}, bodyWidth=60, title=
"contrast (%)" 1041 SetVariable sv_graph_contrast, limits={0,25,1}, value= root:packages:pearl_anglescan_panel:graph_contrast
1042 SetVariable sv_graph_contrast, help={
"contrast value (percentile)." }
1044 Button b_graph_update, help={
"update the existing graph." }
1046 Button b_graph_png, help={
"save the graph in png format." }
1054 svar /sdfr=df panel_name
1056 variable gb_space = 2
1057 variable gb_internal_top = 16
1058 variable gb_internal_bot = 4
1059 variable line_space = 22
1077 GroupBox gb_source,pos={4,gb_top}
1078 gb_ht = gb_internal_top
1079 Button b_source_select,pos={17, gb_top + gb_ht + b_adj},size={50,20}
1080 Button b_source_update, pos={67, gb_top + gb_ht + b_adj},size={50,20}
1082 TitleBox tb_source_path,pos={18, gb_top + gb_ht + tb_adj},size={240,21}
1084 gb_ht += gb_internal_bot
1085 GroupBox gb_source, size={272,gb_ht}
1087 gb_top += gb_ht + gb_space
1088 GroupBox gb_offsets,pos={4,gb_top}
1089 gb_ht = gb_internal_top
1090 SetVariable sv_theta_offset,pos={46, gb_top + gb_ht + sv_adj},size={88,16}
1091 Button b_save_prefs,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1093 SetVariable sv_tilt_offset,pos={60, gb_top + gb_ht + sv_adj},size={74,16}
1094 Button b_load_prefs,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1096 SetVariable sv_phi_offset,pos={56, gb_top + gb_ht + sv_adj},size={78,16}
1098 SetVariable sv_alpha_offset,pos={44, gb_top + gb_ht + sv_adj},size={90,16}
1100 gb_ht += gb_internal_bot
1101 GroupBox gb_offsets, size={272,gb_ht}
1103 gb_top += gb_ht + gb_space
1104 GroupBox gb_crop,pos={4,gb_top}
1105 gb_ht = gb_internal_top
1106 CheckBox cb_crop_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
1108 SetVariable sv_crop_alpha, pos={44, gb_top + gb_ht + sv_adj}, size={90,16}
1109 Button b_crop_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1111 SetVariable sv_crop_theta, pos={44, gb_top + gb_ht + sv_adj}, size={90,16}
1113 SetVariable sv_crop_rows, pos={44, gb_top + gb_ht + sv_adj}, size={190,16}
1115 gb_ht += gb_internal_bot
1116 GroupBox gb_crop, size={272,gb_ht}
1118 gb_top += gb_ht + gb_space
1119 GroupBox gb_norm_alpha,pos={4,gb_top}
1120 gb_ht = gb_internal_top
1121 CheckBox cb_norm_alpha_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
1123 PopupMenu pm_norm_alpha_mode,pos={36, gb_top + gb_ht + pm_adj},size={138,21}
1124 Button b_norm_alpha_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1126 SetVariable sv_norm_alpha_smoothing,pos={22, gb_top + gb_ht + sv_adj},size={112,16}
1127 Button b_norm_alpha_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1129 gb_ht += gb_internal_bot
1130 GroupBox gb_norm_alpha, size={272,gb_ht}
1132 gb_top += gb_ht + gb_space
1133 GroupBox gb_norm_phi,pos={4,gb_top}
1134 gb_ht = gb_internal_top
1135 CheckBox cb_norm_phi_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
1136 Button b_norm_phi_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1138 SetVariable sv_norm_phi_range,pos={15, gb_top + gb_ht + sv_adj},size={118,16}
1139 Button b_norm_phi_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1141 gb_ht += gb_internal_bot
1142 GroupBox gb_norm_phi, size={272,gb_ht}
1144 gb_top += gb_ht + gb_space
1145 GroupBox gb_norm_theta,pos={4,gb_top}
1146 gb_ht = gb_internal_top
1147 CheckBox cb_norm_theta_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
1149 PopupMenu pm_norm_theta_domain, pos={35, gb_top + gb_ht + pm_adj}, size={138,21}
1150 Button b_norm_theta_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1152 PopupMenu pm_norm_theta_mode,pos={35, gb_top + gb_ht + pm_adj},size={138,21}
1153 Button b_norm_theta_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1155 SetVariable sv_norm_theta_smoothing,pos={21, gb_top + gb_ht + sv_adj},size={112,16}
1157 gb_ht += gb_internal_bot
1158 GroupBox gb_norm_theta, size={272,gb_ht}
1160 gb_top += gb_ht + gb_space
1161 GroupBox gb_norm_thetaphi,pos={4,gb_top}
1162 gb_ht = gb_internal_top
1163 CheckBox cb_norm_thetaphi_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
1165 PopupMenu pm_norm_thetaphi_mode,pos={35, gb_top + gb_ht + pm_adj},size={138,21}
1166 Button b_norm_thetaphi_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1168 SetVariable sv_norm_thetaphi_smoothing,pos={21, gb_top + gb_ht + sv_adj},size={112,16}
1169 Button b_norm_thetaphi_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1171 gb_ht += gb_internal_bot
1172 GroupBox gb_norm_thetaphi, size={272,gb_ht}
1174 gb_top += gb_ht + gb_space
1175 GroupBox gb_output,pos={4,gb_top}
1176 gb_ht = gb_internal_top
1177 SetVariable sv_output_folding,pos={38, gb_top + gb_ht + sv_adj},size={95,16}
1178 Button b_output_calc,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1180 SetVariable sv_output_horizon,pos={35, gb_top + gb_ht + sv_adj},size={98,16}
1181 Button b_output_duplicate,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1183 PopupMenu pm_graph_projection,pos={24, gb_top + gb_ht + pm_adj},size={149,21}
1184 Button b_output_itx,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1186 PopupMenu pm_graph_mode,pos={44, gb_top + gb_ht + pm_adj},size={129,21}
1187 Button b_output_etpi,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1189 gb_ht += gb_internal_bot
1190 GroupBox gb_output, size={272,gb_ht}
1192 gb_top += gb_ht + gb_space
1193 GroupBox gb_graph,pos={4,gb_top}
1194 gb_ht = gb_internal_top
1195 PopupMenu pm_graph_colortable,pos={21, gb_top + gb_ht + pm_adj},size={152,21}
1196 Button b_graph_update,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1198 SetVariable sv_graph_contrast,pos={14, gb_top + gb_ht + sv_adj},size={119,16}
1199 Button b_graph_png,pos={186, gb_top + gb_ht + b_adj},size={80,20}
1201 gb_ht += gb_internal_bot
1202 GroupBox gb_graph, size={272,gb_ht}
1204 gb_top += gb_ht + gb_space
1212 svar /sdfr=df panel_name
1213 if (wintype(panel_name) == 7)
1215 nvar /sdfr=df norm_alpha_mode
1216 m = norm_alpha_mode + 1
1217 PopupMenu pm_norm_alpha_mode win=$panel_name, mode=m
1218 nvar /sdfr=df norm_theta_domain
1219 m = norm_theta_domain + 1
1220 PopupMenu pm_norm_theta_domain win=$panel_name, mode=m
1221 nvar /sdfr=df norm_theta_mode
1222 m = norm_theta_mode + 1
1223 PopupMenu pm_norm_theta_mode win=$panel_name, mode=m
1224 nvar /sdfr=df norm_thetaphi_mode
1225 m = norm_thetaphi_mode + 1
1226 PopupMenu pm_norm_thetaphi_mode win=$panel_name, mode=m
1227 nvar /sdfr=df graph_mode
1229 PopupMenu pm_graph_mode win=$panel_name, mode=m
1230 nvar /sdfr=df graph_projection
1231 m = graph_projection + 1
1232 PopupMenu pm_graph_projection win=$panel_name, mode=m
1233 svar /sdfr=df graph_colortable
1234 m = 1 + WhichListItem(graph_colortable, CTabList())
1235 PopupMenu pm_graph_colortable win=$panel_name, mode=m
1240 STRUCT WMButtonAction &ba
1242 switch( ba.eventCode )
1254 STRUCT WMButtonAction &ba
1256 switch( ba.eventCode )
1268 STRUCT WMButtonAction &ba
1270 switch( ba.eventCode )
1272 dfref dfBefore = GetDataFolderDFR()
1273 Execute /q/z "CreateBrowser prompt=\"Select 2D holo scan wave\", showWaves=1, showVars=0, showStrs=0"
1274 dfref dfAfter = GetDataFolderDFR()
1275 SetDataFolder dfBefore
1277 SVAR list = S_BrowserList
1279 if ((flag != 0) && (ItemsInList(list) >= 1))
1280 string wname = StringFromList(0, list)
1294 STRUCT WMButtonAction &ba
1296 switch( ba.eventCode )
1298 dfref packdf = $package_path
1299 svar /sdfr=packdf source_path
1300 wave /z w = $source_path
1304 DoAlert 0, "can't find source data."
1315 STRUCT WMButtonAction &ba
1317 switch( ba.eventCode )
1329 STRUCT WMButtonAction &ba
1331 switch( ba.eventCode )
1343 STRUCT WMButtonAction &ba
1345 switch( ba.eventCode )
1357 STRUCT WMButtonAction &ba
1359 switch( ba.eventCode )
1371 STRUCT WMButtonAction &ba
1373 switch( ba.eventCode )
1385 STRUCT WMButtonAction &ba
1387 switch( ba.eventCode )
1399 STRUCT WMButtonAction &ba
1401 switch( ba.eventCode )
1413 STRUCT WMButtonAction &ba
1415 switch( ba.eventCode )
1427 STRUCT WMButtonAction &ba
1429 switch( ba.eventCode )
1441 STRUCT WMButtonAction &ba
1443 switch( ba.eventCode )
1456 STRUCT WMButtonAction &ba
1458 switch( ba.eventCode )
1461 variable do_graph = 1
1462 prompt dest_folder, "destination folder name (relative to data source)"
1463 prompt do_graph, "duplicate graph (yes = 1, no = 0)"
1464 doprompt "duplicate", dest_folder, do_graph
1477 STRUCT WMButtonAction &ba
1479 switch( ba.eventCode )
1482 wave /sdfr=df process_data
1484 ekin = NumberByKey("KineticEnergy", note(process_data), "=", "\r")
1485 prompt ekin, "kinetic energy"
1486 doprompt "save etpi", ekin
1499 STRUCT WMButtonAction &ba
1501 switch( ba.eventCode )
1513 STRUCT WMButtonAction &ba
1515 switch( ba.eventCode )
1527 STRUCT WMButtonAction &ba
1529 switch( ba.eventCode )
1532 svar /sdfr=df source_path
1533 svar /sdfr=df output_graphname
1534 if (WinType(output_graphname) == 1)
1535 SavePICT /WIN=$output_graphname /E=-5 /B=144 /TRAN=0
1546 STRUCT WMPopupAction &pa
1548 switch( pa.eventCode )
1551 nvar /sdfr=df norm_alpha_mode
1552 norm_alpha_mode = pa.popNum - 1
1562 STRUCT WMPopupAction &pa
1564 switch( pa.eventCode )
1567 nvar /sdfr=df norm_theta_domain
1568 norm_theta_domain = pa.popNum - 1
1578 STRUCT WMPopupAction &pa
1580 switch( pa.eventCode )
1583 nvar /sdfr=df norm_theta_mode
1584 norm_theta_mode = pa.popNum - 1
1594 STRUCT WMPopupAction &pa
1596 switch( pa.eventCode )
1599 nvar /sdfr=df norm_thetaphi_mode
1600 norm_thetaphi_mode = pa.popNum - 1
1610 STRUCT WMPopupAction &pa
1612 switch( pa.eventCode )
1615 nvar /sdfr=df graph_mode
1616 graph_mode = pa.popNum - 1
1626 STRUCT WMPopupAction &pa
1628 switch( pa.eventCode )
1631 nvar /sdfr=df graph_projection
1632 graph_projection = pa.popNum - 1
1642 STRUCT WMPopupAction &pa
1644 switch( pa.eventCode )
1647 svar /sdfr=df graph_colortable
1648 graph_colortable = StringFromList(pa.popNum - 1, CTabList())
static variable bp_norm_phi_preview(WMButtonAction *ba)
-
variable pizza_service_2(wave data, string nickname, wave m_theta, wave m_tilt, wave m_phi, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue)
create a pizza plot from a measured (energy-integrated) data strip
-
variable normalize_strip_theta(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average polar distribution.
-
static variable do_init_process(variable check)
initialize the process data with a copy of the raw data.
-
static variable preview_norm_alpha()
-
variable asp_calculate_output()
calculate the output using all enabled processing filters.
-
static variable check_norm_alpha()
-
variable asp_import_raw(wave raw_data)
import raw data
-
variable crop_strip(wave strip, variable xlo, variable xhi)
crop a strip at the sides.
-
variable ad_update_profiles(wave image)
update a profiles graph with new data.
-
static variable bp_save_prefs(WMButtonAction *ba)
-
static variable preview_crop()
-
variable asp_save_output_itx()
save the output diffractogram to an igor text file
-
string display_hemi_scan(string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue)
display a plot of a hemispherical angle scan.
-
static variable pmp_graph_colortable(WMPopupAction *pa)
-
static variable save_prefs()
save persistent package data to the preferences file.
-
static variable bp_graph_update(WMButtonAction *ba)
-
dfr find_hemi_data(string nickname, string *prefix, string *intwave)
finds the folder, prefix and name of holo waves given their nick name
-
static variable bp_norm_alpha_preview(WMButtonAction *ba)
-
static const string prefs_objects
semicolon-separated list of persistent variable, string, and wave names
-
static variable pmp_norm_alpha_mode(WMPopupAction *pa)
-
static variable init_package()
-
static variable preview_norm_theta()
-
static variable delete_rows(string rows, wave data, wave theta, wave tilt, wave phi)
delete individual rows from the data strip
-
static variable pmp_norm_theta_domain(WMPopupAction *pa)
-
static variable bp_source_update(WMButtonAction *ba)
-
static variable bp_norm_thetaphi_check(WMButtonAction *ba)
-
static variable bp_norm_theta_preview(WMButtonAction *ba)
-
static const string package_path
data folder path
-
static variable bp_crop_preview(WMButtonAction *ba)
-
variable crop_strip_theta(wave strip, variable theta_lo, variable theta_hi, wave theta, wave tilt, wave phi)
crop a strip in theta.
-
static variable do_norm_thetaphi(variable check, variable force=defaultValue)
theta,phi-normalize the process data.
-
static variable bp_load_prefs(WMButtonAction *ba)
-
static variable bp_output_etpi(WMButtonAction *ba)
-
variable asp_display_dist_check(variable xdist, variable ydist)
display a graph window of the distribution checks.
-
static variable bp_graph_png(WMButtonAction *ba)
-
static variable pmp_graph_mode(WMPopupAction *pa)
-
static variable preview_norm_phi()
-
string pmsco_save_scan(string pathname, string filename, string energy, string theta, string phi, string alpha, string intensity, string sigma, dfref sdfr=defaultValue)
save waves in a PMSCO scan data file.
-
static variable pmp_norm_theta_mode(WMPopupAction *pa)
-
variable interpolate_hemi_scan(string nickname, variable projection=defaultValue)
interpolate a hemispherical scan onto a rectangular grid
-
variable normalize_strip_theta_scans(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip piecewise by a smooth polar distribution.
-
static variable do_norm_phi(variable check, variable force=defaultValue)
phi-normalize the process data.
-
static variable bp_norm_thetaphi_preview(WMButtonAction *ba)
-
static variable do_norm_theta(variable check, variable force=defaultValue)
theta-normalize the process data.
-
static variable check_norm_phi()
-
variable asp_show_panel()
create the angle scan processing panel
-
static variable bp_output_calc(WMButtonAction *ba)
-
static variable arrange_controls()
-
static variable bp_norm_theta_check(WMButtonAction *ba)
-
variable save_hemi_scan(string nickname, string pathname, string filename)
save a hemispherical scan to an Igor text file
-
string asp_duplicate_output(string dest_name, variable do_graph=defaultValue)
copy the output data to a new folder
-
variable normalize_strip_phi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable theta_range=defaultValue, variable check=defaultValue)
divide the strip by a sine function in phi (wobble correction).
-
variable normalize_strip_thetaphi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by a smooth polar-azimuthal distribution.
-
const variable kProjStereo
-
static variable update_menus()
update the popup menus to reflect the values of the global variables
-
static variable bp_output_itx(WMButtonAction *ba)
-
variable asp_close_graphs()
close all graphs created by the angle scan panel
-
static variable do_norm_alpha(variable check, variable force=defaultValue)
alpha-normalize the process data.
-
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
-
static variable load_prefs()
load persistent package data from the preferences file.
-
static variable check_norm_theta()
-
variable set_contrast(variable pcmin, variable pcmax, string graphname=defaultValue, string colortable=defaultValue)
set the pseudocolor contrast by percentile.
-
variable asp_display_previews()
display a graph window of the processed data.
-
variable asp_save_output_etpi(variable ekin)
save the output diffractogram to a PMSCO ETPI file
-
static variable bp_output_duplicate(WMButtonAction *ba)
-
static variable bp_norm_alpha_check(WMButtonAction *ba)
-
static variable check_norm_thetaphi()
-
static variable bp_norm_phi_check(WMButtonAction *ba)
-
static variable bp_source_select(WMButtonAction *ba)
-
static variable AfterCompiledHook()
initialize package data once when the procedure is first loaded
-
variable duplicate_hemi_scan(string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue)
duplicate a hemispherical scan dataset.
-
static variable do_crop(variable check, variable force=defaultValue)
crop the process data.
-
static variable pmp_norm_thetaphi_mode(WMPopupAction *pa)
-
static variable preview_norm_thetaphi()
-
string asp_display_output(dfref data_df=defaultValue, string data_name=defaultValue)
display the output diffractogram
-
static const string package_name
package name is used as data folder name
-
variable asp_update_graph()
update graphs with new color table or contrast
-
interactive processing of angle scanned XPD data.
-
static variable pmp_graph_projection(WMPopupAction *pa)
-
variable normalize_strip_x(wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average X distribution.
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
+
4 #pragma IgorVersion = 6.2
+
5 #pragma ModuleName = PearlAnglescanPanel
+
6 #include "pearl-anglescan-process"
+
7 #include "pearl-pmsco-import"
+
8 #include "pearl-scienta-preprocess"
+
9 #include "pearl-area-display"
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50 static strconstant
package_path =
"root:packages:pearl_anglescan_panel:"
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55 dfref savedf = GetDataFolderDFR()
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60 if (nvar_exists(init_done))
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71 variable /g init_done = 1
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79 dfref savedf = getdatafolderdfr()
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81 newdatafolder /o/s packages
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82 newdatafolder /o/s $package_name
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+
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85 string /g graphname = "graph_anglescan_panel"
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87 prefs_objects += "norm_alpha_enable;norm_alpha_mode;norm_alpha_smoothing;norm_phi_enable;norm_phi_mode;norm_phi_thetarange;"
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88 prefs_objects += "norm_theta_enable;norm_theta_mode;norm_theta_domain;norm_theta_smoothing;norm_thetaphi_enable;norm_thetaphi_mode;norm_thetaphi_smoothing;"
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89 prefs_objects += "output_folding;output_horizon;graph_mode;graph_projection;graph_colortable;graph_contrast;"
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+
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92 variable /g theta_offset = 0
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93 variable /g tilt_offset = 0
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94 variable /g phi_offset = 0
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95 variable /g alpha_offset = 0
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96 variable /g crop_enable = 0
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97 variable /g crop_alpha = 25
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98 variable /g crop_theta = 88
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99 string /g crop_rows = ""
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100 variable /g norm_alpha_enable = 0
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101 variable /g norm_alpha_mode = 4
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102 variable /g norm_alpha_smoothing = 0.25
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103 variable /g norm_theta_enable = 0
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104 variable /g norm_theta_mode = 4
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105 variable /g norm_theta_domain = 0
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106 variable /g norm_theta_smoothing = 0.25
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107 variable /g norm_thetaphi_enable = 0
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108 variable /g norm_thetaphi_mode = 4
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109 variable /g norm_thetaphi_smoothing = 0.25
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110 variable /g norm_phi_enable = 0
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111 variable /g norm_phi_mode = 4
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112 variable /g norm_phi_thetarange = 20
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113 string /g output_name = "holo1"
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114 variable /g output_folding = 1
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115 variable /g output_horizon = 88
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116 variable /g graph_mode = 1
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118 string /g graph_colortable = "grays"
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119 variable /g graph_contrast = 2
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122 string /g source_path = ""
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123 string /g export_folderpath = "root:"
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124 variable /g export_format = 1
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127 string /g panel_name = ""
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128 string /g preview_graphname = ""
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129 string /g dist_x_graphname = ""
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130 string /g dist_y_graphname = ""
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131 string /g output_graphname = ""
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134 make /n=(10,10) /o raw_data, process_data
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135 make /o dist_x, dist_x_smoo
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136 make /o dist_y, dist_y_smoo
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146 dfref saveDF = GetDataFolderDFR()
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150 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
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152 NewPath/O/C/Q tempPackagePrefsPath, fullPath
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153 fullPath += ":preferences.pxp"
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155 SetDataFolder root:packages
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156 SetDataFolder $package_name
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159 KillPath/Z tempPackagePrefsPath
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172 dfref saveDF = GetDataFolderDFR()
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176 NewDataFolder /O/S packages
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177 NewDataFolder /O/S $package_name
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178 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
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181 GetFileFolderInfo /Q /Z fullPath
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183 fullPath += ":preferences.pxp"
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184 GetFileFolderInfo /Q /Z fullPath
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186 LoadData /O /R /Q fullPath
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210 dfref saveDF = GetDataFolderDFR()
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211 dfref datadf = GetWavesDataFolderDFR(raw_data)
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212 dfref attrdf = datadf:attr
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213 if (!DataFolderRefStatus(attrdf))
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216 dfref parentdf = GetDataFolderDFR()
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217 dfref attrdf = parentdf:attr
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224 source_path = GetWavesDataFolder(raw_data, 2)
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226 duplicate /o raw_data, raw, process_data
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228 wave /sdfr=attrdf /z ManipulatorTheta
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229 wave /sdfr=attrdf /z ManipulatorTilt
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230 wave /sdfr=attrdf /z ManipulatorPhi
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231 if (WaveExists(ManipulatorTheta) && WaveExists(ManipulatorTilt) && WaveExists(ManipulatorPhi))
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232 duplicate /o attrdf:ManipulatorTheta, raw_theta, process_theta
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233 duplicate /o attrdf:ManipulatorTilt, raw_tilt, process_tilt
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234 duplicate /o attrdf:ManipulatorPhi, raw_phi, process_phi
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236 DoAlert 0, "Can't find manipulator angle waves.\rCheck that the attr folder exists, or provide values in the following table."
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237 make /n=(dimsize(raw_data, 1)) /o raw_theta, raw_tilt, raw_phi
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238 make /n=(dimsize(raw_data, 1)) /o process_theta, process_tilt, process_phi
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239 edit /k=1 raw_theta, raw_tilt, raw_phi
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+
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242 make /o /n=(dimsize(raw_data, 0)) dist_x, dist_x_smoo
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243 make /o /n=(dimsize(raw_data, 1)) dist_y, dist_y_smoo
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254 wave /sdfr=df process_data
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255 svar /sdfr=df preview_graphname
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257 if (strlen(preview_graphname) && (wintype(preview_graphname) == 1))
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259 DoWindow /F $preview_graphname
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264 nvar /sdfr=df graph_contrast
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265 svar /sdfr=df graph_colortable
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266 set_contrast (graph_contrast, graph_contrast, graphname=preview_graphname, colortable=graph_colortable)
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277 variable xdist, ydist
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282 wave /sdfr=df dist_x_smoo
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283 wave /sdfr=df dist_y_smoo
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284 svar /sdfr=df dist_x_graphname
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285 svar /sdfr=df dist_y_graphname
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288 if (strlen(dist_x_graphname) && (wintype(dist_x_graphname) == 1))
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289 DoWindow /F $dist_x_graphname
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291 display /k=1 /n=graph_asp_dist_x dist_x, dist_x_smoo
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292 dist_x_graphname = s_name
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293 ModifyGraph /w=$dist_x_graphname mode(dist_x)=2
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294 ModifyGraph /w=$dist_x_graphname lsize(dist_x)=2
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295 ModifyGraph /w=$dist_x_graphname rgb(dist_x)=(0,0,0)
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300 if (strlen(dist_y_graphname) && (wintype(dist_y_graphname) == 1))
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301 DoWindow /F $dist_y_graphname
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303 display /k=1 /n=graph_asp_dist_y dist_y, dist_y_smoo
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304 dist_y_graphname = s_name
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305 ModifyGraph /w=$dist_y_graphname mode(dist_y)=2
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306 ModifyGraph /w=$dist_y_graphname lsize(dist_y)=2
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307 ModifyGraph /w=$dist_y_graphname rgb(dist_y)=(0,0,0)
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326 wave /sdfr=df raw_theta
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327 wave /sdfr=df raw_tilt
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328 wave /sdfr=df raw_phi
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329 nvar /sdfr=df theta_offset
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330 nvar /sdfr=df tilt_offset
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331 nvar /sdfr=df phi_offset
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332 nvar /sdfr=df alpha_offset
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334 duplicate /o raw, df:process_data
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335 duplicate /o raw_theta, df:process_theta
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336 duplicate /o raw_tilt, df:process_tilt
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337 duplicate /o raw_phi, df:process_phi
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339 wave /sdfr=df process_data
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340 wave /sdfr=df process_theta
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341 wave /sdfr=df process_tilt
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342 wave /sdfr=df process_phi
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344 process_theta = raw_theta - theta_offset
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345 process_tilt = raw_tilt - tilt_offset
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346 process_phi = raw_phi - phi_offset
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347 setscale /p x dimoffset(raw, 0) - alpha_offset, dimdelta(raw, 0), waveunits(raw, 0), process_data
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+
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+
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365 if (ParamIsDefault(force))
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370 wave /sdfr=df process_data
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371 wave /sdfr=df process_theta
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372 wave /sdfr=df process_tilt
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373 wave /sdfr=df process_phi
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374 nvar /sdfr=df crop_enable
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375 nvar /sdfr=df crop_alpha
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376 nvar /sdfr=df crop_theta
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377 svar /sdfr=df crop_rows
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379 if (force || crop_enable)
+
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381 if (crop_alpha > abs(dimdelta(process_data, 0)))
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382 crop_strip (process_data, -crop_alpha, +crop_alpha)
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385 if ((crop_theta >= 10) && (crop_theta < 90))
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386 crop_strip_theta (process_data, -0.1, crop_theta + 0.1, process_theta, process_tilt, process_phi)
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+
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389 if (strlen(crop_rows) > 0)
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390 delete_rows (crop_rows, process_data, process_theta, process_tilt, process_phi)
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416 make /n=(numpnts(theta)) /i /free idx
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418 variable nrows = ItemsInList(rows, ",")
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422 for (irow = 0; irow < nrows; irow += 1)
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423 srow = StringFromList(irow, rows, ",")
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424 q1 = str2num(StringFromList(0, srow, "-"))
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425 q2 = str2num(StringFromList(1, srow, "-"))
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433 extract /free idx, idx, idx >= 0
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434 variable nx = dimsize(data, 0)
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435 variable ny = numpnts(idx)
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436 theta[0,ny-1] = theta[idx]
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437 tilt[0,ny-1] = tilt[idx]
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438 phi[0,ny-1] = phi[idx]
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439 redimension /n=(ny) theta, tilt, phi
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440 duplicate /free data, data_copy
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441 redimension /n=(nx,ny) data
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442 data = data_copy[p][idx[q]]
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460 if (ParamIsDefault(force))
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+
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464 dfref saveDF = GetDataFolderDFR()
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466 wave /sdfr=df process_data
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467 nvar /sdfr=df norm_alpha_enable
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468 nvar /sdfr=df norm_alpha_mode
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469 nvar /sdfr=df norm_alpha_smoothing
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471 if (force || norm_alpha_enable)
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472 dfref temp_df = newfreedatafolder()
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473 setdatafolder temp_df
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474 normalize_strip_x (process_data, smooth_method=norm_alpha_mode, smooth_factor=norm_alpha_smoothing, check=check)
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+
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478 duplicate /o check_dist, df:dist_x
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479 duplicate /o check_smoo, df:dist_x_smoo
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501 if (ParamIsDefault(force))
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505 dfref saveDF = GetDataFolderDFR()
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507 wave /sdfr=df process_data
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508 wave /sdfr=df process_theta
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509 wave /sdfr=df process_phi
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510 nvar /sdfr=df norm_phi_enable
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511 nvar /sdfr=df norm_phi_mode
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512 nvar /sdfr=df norm_phi_thetarange
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514 if (force || norm_phi_enable)
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515 dfref temp_df = newfreedatafolder()
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516 setdatafolder temp_df
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517 normalize_strip_phi (process_data, process_theta, process_phi, theta_range=norm_phi_thetarange, check=check)
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+
+
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521 duplicate /o check_dist, df:dist_y
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522 duplicate /o check_smoo, df:dist_y_smoo
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+
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544 if (ParamIsDefault(force))
+
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+
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548 dfref saveDF = GetDataFolderDFR()
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550 wave /sdfr=df process_data
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551 wave /sdfr=df process_theta
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552 nvar /sdfr=df norm_theta_enable
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553 nvar /sdfr=df norm_theta_mode
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554 nvar /sdfr=df norm_theta_domain
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555 nvar /sdfr=df norm_theta_smoothing
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+
557 if (force || norm_theta_enable)
+
558 dfref temp_df = newfreedatafolder()
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559 setdatafolder temp_df
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560 if (norm_theta_domain==1)
+
561 normalize_strip_theta_scans (process_data, process_theta, smooth_method=norm_theta_mode, smooth_factor=norm_theta_smoothing, check=check)
+
+
563 normalize_strip_theta (process_data, process_theta, smooth_method=norm_theta_mode, smooth_factor=norm_theta_smoothing, check=check)
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568 duplicate /o check_dist, df:dist_y
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569 duplicate /o check_smoo, df:dist_y_smoo
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591 if (ParamIsDefault(force))
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595 dfref saveDF = GetDataFolderDFR()
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597 wave /sdfr=df process_data
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598 wave /sdfr=df process_theta
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599 wave /sdfr=df process_phi
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600 nvar /sdfr=df norm_thetaphi_enable
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601 nvar /sdfr=df norm_thetaphi_mode
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602 nvar /sdfr=df norm_thetaphi_smoothing
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+
604 if (force || norm_thetaphi_enable)
+
605 dfref temp_df = newfreedatafolder()
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606 setdatafolder temp_df
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607 normalize_strip_thetaphi (process_data, process_theta, process_phi, smooth_method=norm_thetaphi_mode, smooth_factor=norm_thetaphi_smoothing, check=check)
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+
+
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611 duplicate /o check_dist, df:dist_y
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612 duplicate /o check_smoo, df:dist_y_smoo
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+
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624 dfref saveDF = GetDataFolderDFR()
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634 nvar folding=output_folding
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635 nvar horizon=output_horizon
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644 pizza_service_2 (process_data, output_name, process_theta, process_tilt, process_phi, folding=folding, nograph=1)
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646 setdatafolder $output_name
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+
+
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650 values = pol <= horizon ? values : nan
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674 svar /sdfr=pkg_df output_name
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675 svar /sdfr=pkg_df output_graphname
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676 nvar /sdfr=pkg_df graph_projection
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677 nvar /sdfr=pkg_df graph_mode
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678 svar /sdfr=pkg_df graph_colortable
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679 nvar /sdfr=pkg_df graph_contrast
+
+
681 if (ParamIsDefault(data_df))
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682 dfref data_df = pkg_df
+
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684 if (ParamIsDefault(data_name))
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685 data_name = output_name
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+
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688 dfref saveDF = GetDataFolderDFR()
+
689 setdatafolder data_df
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695 string graphname = data_name
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696 graphname =
display_hemi_scan (data_name, projection=graph_projection, graphtype=graph_mode, graphname=graphname)
+
697 if (ParamIsDefault(data_df))
+
698 output_graphname = graphname
+
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702 if (strlen(graphname) && (wintype(graphname) == 1))
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703 set_contrast (graph_contrast, graph_contrast, graphname=graphname, colortable=graph_colortable)
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716 svar /sdfr=df preview_graphname
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717 svar /sdfr=df output_graphname
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718 svar /sdfr=df graph_colortable
+
719 nvar /sdfr=df graph_contrast
+
+
721 if (strlen(preview_graphname) && (wintype(preview_graphname) == 1))
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722 set_contrast (graph_contrast, graph_contrast, graphname=preview_graphname, colortable=graph_colortable)
+
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724 if (strlen(output_graphname) && (wintype(output_graphname) == 1))
+
725 set_contrast (graph_contrast, graph_contrast, graphname=output_graphname, colortable=graph_colortable)
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734 svar /sdfr=df preview_graphname
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735 svar /sdfr=df output_graphname
+
736 svar /sdfr=df dist_x_graphname
+
737 svar /sdfr=df dist_y_graphname
+
+
739 if (strlen(preview_graphname) && (wintype(preview_graphname) == 1))
+
740 killwindow $preview_graphname
+
+
742 if (strlen(output_graphname) && (wintype(output_graphname) == 1))
+
743 killwindow $output_graphname
+
+
745 if (strlen(dist_x_graphname) && (wintype(dist_x_graphname) == 1))
+
746 killwindow $dist_x_graphname
+
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748 if (strlen(dist_y_graphname) && (wintype(dist_y_graphname) == 1))
+
749 killwindow $dist_y_graphname
+
+
+
752 preview_graphname = ""
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753 output_graphname = ""
+
754 dist_x_graphname = ""
+
755 dist_y_graphname = ""
+
+
+
+
+
+
+
775 if (ParamIsDefault(do_graph))
+
+
+
+
+
780 svar /sdfr=df source_path
+
781 svar /sdfr=df output_name
+
782 svar /sdfr=df output_graphname
+
783 wave raw_data = $source_path
+
+
785 dfref saveDF = GetDataFolderDFR()
+
786 dfref raw_df = GetWavesDataFolderDFR(raw_data)
+
+
788 newdatafolder /o /s $dest_name
+
789 dfref dest_df = GetDataFolderDFR()
+
+
+
+
793 string graphname = ""
+
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806 svar /sdfr=df output_name
+
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808 dfref saveDF = GetDataFolderDFR()
+
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823 svar /sdfr=df output_name
+
824 wave /sdfr=df process_data
+
+
826 dfref saveDF = GetDataFolderDFR()
+
+
+
829 string s_int = "values"
+
+
831 string s_polar = s_prefix + "pol"
+
832 string s_azim = s_prefix + "az"
+
+
834 pmsco_save_scan ("", "", num2str(ekin), s_polar, s_azim, "", s_int, "", sdfr=data_df)
+
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905 svar /sdfr=df panel_name
+
+
907 if (strlen(panel_name) && (wintype(panel_name) == 7))
+
908 DoWindow /F $panel_name
+
+
+
+
912 NewPanel /K=1 /N=anglescan_panel /W=(200,50,480,874) as "angle scan processing"
+
+
+
915 GroupBox gb_source, title="data source"
+
+
917 Button b_source_select, help={
"select the source wave, e.g. ReducedData1. it must be in the scan or region data folder. the attr folder with the manipulator waves must be in the same folder or one level up." }
+
+
919 Button b_source_update, help={
"reload the process data from the previous source (link displayed below)" }
+
920 TitleBox tb_source_path, size={240,21}
+
921 TitleBox tb_source_path,variable= root:packages:pearl_anglescan_panel:source_path
+
+
923 GroupBox gb_offsets, title=
"offsets"
+
924 SetVariable sv_theta_offset, size={88,16},bodyWidth=60,title=
"theta"
+
925 SetVariable sv_theta_offset,value= root:packages:pearl_anglescan_panel:theta_offset
+
926 SetVariable sv_theta_offset, help={
"manipulator theta value that corresponds to normal emission." }
+
927 SetVariable sv_tilt_offset, size={74,16},bodyWidth=60,title=
"tilt"
+
928 SetVariable sv_tilt_offset,value= root:packages:pearl_anglescan_panel:tilt_offset
+
929 SetVariable sv_tilt_offset, help={
"manipulator tilt value that corresponds to normal emission." }
+
930 SetVariable sv_phi_offset, size={78,16},bodyWidth=60,title=
"phi"
+
931 SetVariable sv_phi_offset,value= root:packages:pearl_anglescan_panel:phi_offset
+
932 SetVariable sv_phi_offset, help={
"manipulator phi value that should map to the 3 o'clock angle." }
+
933 SetVariable sv_alpha_offset, size={90,16},bodyWidth=60,title=
"alpha"
+
934 SetVariable sv_alpha_offset,value= root:packages:pearl_anglescan_panel:alpha_offset
+
935 SetVariable sv_alpha_offset, help={
"alpha value that corresponds to normal emission (if the sample normal is properly aligned)." }
+
+
937 Button b_save_prefs, help={
"save settings as preferences." }
+
+
939 Button b_load_prefs, help={
"load settings from preferences." }
+
+
941 GroupBox gb_crop, title=
"crop and delete"
+
942 CheckBox cb_crop_enable, size={50,14}, title=
"enable"
+
943 CheckBox cb_crop_enable, help={
"crop at +/-alpha and +theta, delete arbitrary rows" }
+
944 CheckBox cb_crop_enable, variable= root:packages:pearl_anglescan_panel:crop_enable
+
945 SetVariable sv_crop_alpha, size={90,16},bodyWidth=60,title=
"alpha"
+
946 SetVariable sv_crop_alpha, limits={0,30,1},value= root:packages:pearl_anglescan_panel:crop_alpha
+
947 SetVariable sv_crop_alpha, help={
"alpha (detection angle) cropping angle (positive boundary), relative to normal emission" }
+
948 SetVariable sv_crop_theta, size={90,16},bodyWidth=60,title=
"theta"
+
949 SetVariable sv_crop_theta, limits={10,90,1},value= root:packages:pearl_anglescan_panel:crop_theta
+
950 SetVariable sv_crop_theta, help={
"theta (polar angle) upper limit, relative to normal emission" }
+
951 SetVariable sv_crop_rows, size={200,16},bodyWidth=160,title=
"rows"
+
952 SetVariable sv_crop_rows, limits={10,90,1},value= root:packages:pearl_anglescan_panel:crop_rows
+
953 SetVariable sv_crop_rows, help={
"rows to delete from the raw data. comma-separated point indices, hyphen for range." }
+
+
955 Button b_crop_preview, help={
"show a preview of the cropped dataset." }
+
+
957 GroupBox gb_norm_alpha, title=
"normalize alpha"
+
958 CheckBox cb_norm_alpha_enable, size={50,14}, title=
"enable"
+
959 CheckBox cb_norm_alpha_enable,variable= root:packages:pearl_anglescan_panel:norm_alpha_enable
+
960 CheckBox cb_norm_alpha_enable, help={
"enable normalization of the alpha distribution" }
+
+
962 PopupMenu pm_norm_alpha_mode, mode=5, popvalue=
"loess" , value= #
"\"none;binomial;boxcar;scienta;loess;\""
+
963 PopupMenu pm_norm_alpha_mode, help={
"alpha normalization method. recommended: loess" }
+
964 SetVariable sv_norm_alpha_smoothing, size={112,16}, bodyWidth=60, title=
"smoothing"
+
965 SetVariable sv_norm_alpha_smoothing, limits={0,1,0.05}, value= root:packages:pearl_anglescan_panel:norm_alpha_smoothing
+
966 SetVariable sv_norm_alpha_smoothing, help={
"smoothing parameter (depends on the normalization method)." }
+
+
968 Button b_norm_alpha_check, help={
"show a graph of the normalization function" }
+
+
970 Button b_norm_alpha_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
+
+
972 GroupBox gb_norm_phi, title=
"normalize phi"
+
973 CheckBox cb_norm_phi_enable, size={50,14}, title=
"enable"
+
974 CheckBox cb_norm_phi_enable,variable= root:packages:pearl_anglescan_panel:norm_phi_enable
+
975 CheckBox cb_norm_phi_enable, help={
"enable normalization of the phi distribution to reduce the effect of wobble" }
+
976 SetVariable sv_norm_phi_range, size={118,16}, bodyWidth=60, title=
"theta range"
+
977 SetVariable sv_norm_phi_range, limits={0,90,1}, value= root:packages:pearl_anglescan_panel:norm_phi_thetarange
+
978 SetVariable sv_norm_phi_range, help={
"theta range (from normal) to factor into the normalization function" }
+
+
980 Button b_norm_phi_check, help={
"show a graph of the normalization function" }
+
+
982 Button b_norm_phi_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
+
+
984 GroupBox gb_norm_theta, title=
"normalize theta"
+
985 CheckBox cb_norm_theta_enable, size={50,14},title=
"enable"
+
986 CheckBox cb_norm_theta_enable, variable= root:packages:pearl_anglescan_panel:norm_theta_enable
+
987 CheckBox cb_norm_theta_enable, help={
"enable normalization of the theta distribution (integrated over phi)" }
+
+
989 PopupMenu pm_norm_theta_domain, mode=5, popvalue=
"loess" , value= #
"\"global;scans;\""
+
990 PopupMenu pm_norm_theta_domain, help={
"smoothing domain: global or individual scans. use global unless there is a stronga or irregular phi variation." }
+
+
992 PopupMenu pm_norm_theta_mode,mode=5,popvalue=
"loess" ,value= #
"\"none;binomial;boxcar;polynomial;loess;\""
+
993 PopupMenu pm_norm_theta_mode, help={
"theta normalization method. recommended: loess" }
+
994 SetVariable sv_norm_theta_smoothing, size={112,16}, bodyWidth=60, title=
"smoothing"
+
995 SetVariable sv_norm_theta_smoothing, limits={0,1,0.05}, value= root:packages:pearl_anglescan_panel:norm_theta_smoothing
+
996 SetVariable sv_norm_theta_smoothing, help={
"smoothing parameter (depends on the normalization method)." }
+
+
998 Button b_norm_theta_check, help={
"show a graph of the normalization function" }
+
+
1000 Button b_norm_theta_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
+
+
1002 GroupBox gb_norm_thetaphi, size={272,97},title=
"normalize (theta,phi)"
+
1003 CheckBox cb_norm_thetaphi_enable, size={50,14},title=
"enable"
+
1004 CheckBox cb_norm_thetaphi_enable, variable= root:packages:pearl_anglescan_panel:norm_thetaphi_enable
+
1005 CheckBox cb_norm_thetaphi_enable, help={
"enable normalization of the (theta, phi) distribution." }
+
+
1007 PopupMenu pm_norm_thetaphi_mode, mode=5, popvalue=
"loess" , value= #
"\"none;none;none;none;loess;\""
+
1008 PopupMenu pm_norm_thetaphi_mode, help={
"theta normalization method. recommended: loess" }
+
1009 SetVariable sv_norm_thetaphi_smoothing, size={112,16}, bodyWidth=60, title=
"smoothing"
+
1010 SetVariable sv_norm_thetaphi_smoothing, limits={0,1,0.05}, value= root:packages:pearl_anglescan_panel:norm_thetaphi_smoothing
+
1011 SetVariable sv_norm_thetaphi_smoothing, help={
"smoothing parameter (depends on the normalization method)." }
+
+
1013 Button b_norm_thetaphi_check, help={
"show a graph of the normalization function" }
+
+
1015 Button b_norm_thetaphi_preview, help={
"show a preview of the normalized dataset (without other normalizations)." }
+
+
1017 GroupBox gb_output, title=
"output"
+
1018 SetVariable sv_output_folding, size={95,16}, bodyWidth=60, title=
"folding"
+
1019 SetVariable sv_output_folding, limits={1,20,1}, value= root:packages:pearl_anglescan_panel:output_folding
+
1020 SetVariable sv_output_folding, help={
"n-fold rotational average. 1=no averaging." }
+
1021 SetVariable sv_output_horizon, size={98,16}, bodyWidth=60, title=
"horizon"
+
1022 SetVariable sv_output_horizon, limits={1,90,1}, value= root:packages:pearl_anglescan_panel:output_horizon
+
1023 SetVariable sv_output_horizon, help={
"highest theta to display" }
+
+
1025 PopupMenu pm_graph_projection, mode=2, popvalue=
"stereographic" , value= #
"\"equidistant;stereographic;equal area;gnomonic;orthographic;\""
+
1026 PopupMenu pm_graph_projection, help={
"projection (theta mapping) mode" }
+
+
1028 PopupMenu pm_graph_mode, mode=2, popvalue=
"dots" , value= #
"\"none;dots;none;image;\""
+
1029 PopupMenu pm_graph_mode, help={
"graph type: dots = coloured dots on circles; image = interpolated matrix" }
+
+
1031 Button b_output_calc, help={
"execute data processing with the enabled filters and display the diffractogram." }
+
+
1033 Button b_output_duplicate, help={
"copy the result to an arbitrary data folder." }
+
+
1035 Button b_output_itx, help={
"save the result to an igor text file (itx)." }
+
+
1037 Button b_output_etpi, help={
"save the result to a pmsco angle scan file (etpi)." }
+
+
1039 GroupBox gb_graph, title=
"graph"
+
+
1041 PopupMenu pm_graph_colortable, mode=0, value= #
"\"*COLORTABLEPOPNONAMES*\""
+
1042 PopupMenu pm_graph_colortable, help={
"color table to use in pseudocolor graphs." }
+
1043 SetVariable sv_graph_contrast, size={119,16}, bodyWidth=60, title=
"contrast (%)"
+
1044 SetVariable sv_graph_contrast, limits={0,25,1}, value= root:packages:pearl_anglescan_panel:graph_contrast
+
1045 SetVariable sv_graph_contrast, help={
"contrast value (percentile)." }
+
+
1047 Button b_graph_update, help={
"update the existing graph." }
+
+
1049 Button b_graph_png, help={
"save the graph in png format." }
+
+
+
+
+
+
+
+
1057 svar /sdfr=df panel_name
+
+
1059 variable gb_space = 2
+
1060 variable gb_internal_top = 16
+
1061 variable gb_internal_bot = 4
+
1062 variable line_space = 22
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1080 GroupBox gb_source,pos={4,gb_top}
+
1081 gb_ht = gb_internal_top
+
1082 Button b_source_select,pos={17, gb_top + gb_ht + b_adj},size={50,20}
+
1083 Button b_source_update, pos={67, gb_top + gb_ht + b_adj},size={50,20}
+
+
1085 TitleBox tb_source_path,pos={18, gb_top + gb_ht + tb_adj},size={240,21}
+
+
1087 gb_ht += gb_internal_bot
+
1088 GroupBox gb_source, size={272,gb_ht}
+
+
1090 gb_top += gb_ht + gb_space
+
1091 GroupBox gb_offsets,pos={4,gb_top}
+
1092 gb_ht = gb_internal_top
+
1093 SetVariable sv_theta_offset,pos={46, gb_top + gb_ht + sv_adj},size={88,16}
+
1094 Button b_save_prefs,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1096 SetVariable sv_tilt_offset,pos={60, gb_top + gb_ht + sv_adj},size={74,16}
+
1097 Button b_load_prefs,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1099 SetVariable sv_phi_offset,pos={56, gb_top + gb_ht + sv_adj},size={78,16}
+
+
1101 SetVariable sv_alpha_offset,pos={44, gb_top + gb_ht + sv_adj},size={90,16}
+
+
1103 gb_ht += gb_internal_bot
+
1104 GroupBox gb_offsets, size={272,gb_ht}
+
+
1106 gb_top += gb_ht + gb_space
+
1107 GroupBox gb_crop,pos={4,gb_top}
+
1108 gb_ht = gb_internal_top
+
1109 CheckBox cb_crop_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
+
+
1111 SetVariable sv_crop_alpha, pos={44, gb_top + gb_ht + sv_adj}, size={90,16}
+
1112 Button b_crop_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1114 SetVariable sv_crop_theta, pos={44, gb_top + gb_ht + sv_adj}, size={90,16}
+
+
1116 SetVariable sv_crop_rows, pos={44, gb_top + gb_ht + sv_adj}, size={190,16}
+
+
1118 gb_ht += gb_internal_bot
+
1119 GroupBox gb_crop, size={272,gb_ht}
+
+
1121 gb_top += gb_ht + gb_space
+
1122 GroupBox gb_norm_alpha,pos={4,gb_top}
+
1123 gb_ht = gb_internal_top
+
1124 CheckBox cb_norm_alpha_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
+
+
1126 PopupMenu pm_norm_alpha_mode,pos={36, gb_top + gb_ht + pm_adj},size={138,21}
+
1127 Button b_norm_alpha_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1129 SetVariable sv_norm_alpha_smoothing,pos={22, gb_top + gb_ht + sv_adj},size={112,16}
+
1130 Button b_norm_alpha_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1132 gb_ht += gb_internal_bot
+
1133 GroupBox gb_norm_alpha, size={272,gb_ht}
+
+
1135 gb_top += gb_ht + gb_space
+
1136 GroupBox gb_norm_phi,pos={4,gb_top}
+
1137 gb_ht = gb_internal_top
+
1138 CheckBox cb_norm_phi_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
+
1139 Button b_norm_phi_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1141 SetVariable sv_norm_phi_range,pos={15, gb_top + gb_ht + sv_adj},size={118,16}
+
1142 Button b_norm_phi_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1144 gb_ht += gb_internal_bot
+
1145 GroupBox gb_norm_phi, size={272,gb_ht}
+
+
1147 gb_top += gb_ht + gb_space
+
1148 GroupBox gb_norm_theta,pos={4,gb_top}
+
1149 gb_ht = gb_internal_top
+
1150 CheckBox cb_norm_theta_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
+
+
1152 PopupMenu pm_norm_theta_domain, pos={35, gb_top + gb_ht + pm_adj}, size={138,21}
+
1153 Button b_norm_theta_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1155 PopupMenu pm_norm_theta_mode,pos={35, gb_top + gb_ht + pm_adj},size={138,21}
+
1156 Button b_norm_theta_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1158 SetVariable sv_norm_theta_smoothing,pos={21, gb_top + gb_ht + sv_adj},size={112,16}
+
+
1160 gb_ht += gb_internal_bot
+
1161 GroupBox gb_norm_theta, size={272,gb_ht}
+
+
1163 gb_top += gb_ht + gb_space
+
1164 GroupBox gb_norm_thetaphi,pos={4,gb_top}
+
1165 gb_ht = gb_internal_top
+
1166 CheckBox cb_norm_thetaphi_enable,pos={73, gb_top + gb_ht + cb_adj},size={50,14}
+
+
1168 PopupMenu pm_norm_thetaphi_mode,pos={35, gb_top + gb_ht + pm_adj},size={138,21}
+
1169 Button b_norm_thetaphi_check,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1171 SetVariable sv_norm_thetaphi_smoothing,pos={21, gb_top + gb_ht + sv_adj},size={112,16}
+
1172 Button b_norm_thetaphi_preview,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1174 gb_ht += gb_internal_bot
+
1175 GroupBox gb_norm_thetaphi, size={272,gb_ht}
+
+
1177 gb_top += gb_ht + gb_space
+
1178 GroupBox gb_output,pos={4,gb_top}
+
1179 gb_ht = gb_internal_top
+
1180 SetVariable sv_output_folding,pos={38, gb_top + gb_ht + sv_adj},size={95,16}
+
1181 Button b_output_calc,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1183 SetVariable sv_output_horizon,pos={35, gb_top + gb_ht + sv_adj},size={98,16}
+
1184 Button b_output_duplicate,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1186 PopupMenu pm_graph_projection,pos={24, gb_top + gb_ht + pm_adj},size={149,21}
+
1187 Button b_output_itx,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1189 PopupMenu pm_graph_mode,pos={44, gb_top + gb_ht + pm_adj},size={129,21}
+
1190 Button b_output_etpi,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1192 gb_ht += gb_internal_bot
+
1193 GroupBox gb_output, size={272,gb_ht}
+
+
1195 gb_top += gb_ht + gb_space
+
1196 GroupBox gb_graph,pos={4,gb_top}
+
1197 gb_ht = gb_internal_top
+
1198 PopupMenu pm_graph_colortable,pos={21, gb_top + gb_ht + pm_adj},size={152,21}
+
1199 Button b_graph_update,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1201 SetVariable sv_graph_contrast,pos={14, gb_top + gb_ht + sv_adj},size={119,16}
+
1202 Button b_graph_png,pos={186, gb_top + gb_ht + b_adj},size={80,20}
+
+
1204 gb_ht += gb_internal_bot
+
1205 GroupBox gb_graph, size={272,gb_ht}
+
+
1207 gb_top += gb_ht + gb_space
+
+
+
+
+
+
1215 svar /sdfr=df panel_name
+
1216 if (wintype(panel_name) == 7)
+
+
1218 nvar /sdfr=df norm_alpha_mode
+
1219 m = norm_alpha_mode + 1
+
1220 PopupMenu pm_norm_alpha_mode win=$panel_name, mode=m
+
1221 nvar /sdfr=df norm_theta_domain
+
1222 m = norm_theta_domain + 1
+
1223 PopupMenu pm_norm_theta_domain win=$panel_name, mode=m
+
1224 nvar /sdfr=df norm_theta_mode
+
1225 m = norm_theta_mode + 1
+
1226 PopupMenu pm_norm_theta_mode win=$panel_name, mode=m
+
1227 nvar /sdfr=df norm_thetaphi_mode
+
1228 m = norm_thetaphi_mode + 1
+
1229 PopupMenu pm_norm_thetaphi_mode win=$panel_name, mode=m
+
1230 nvar /sdfr=df graph_mode
+
+
1232 PopupMenu pm_graph_mode win=$panel_name, mode=m
+
1233 nvar /sdfr=df graph_projection
+
1234 m = graph_projection + 1
+
1235 PopupMenu pm_graph_projection win=$panel_name, mode=m
+
1236 svar /sdfr=df graph_colortable
+
1237 m = 1 + WhichListItem(graph_colortable, CTabList())
+
1238 PopupMenu pm_graph_colortable win=$panel_name, mode=m
+
+
+
+
+
1243 STRUCT WMButtonAction &ba
+
+
1245 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1257 STRUCT WMButtonAction &ba
+
+
1259 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1271 STRUCT WMButtonAction &ba
+
+
1273 switch( ba.eventCode )
+
+
1275 dfref dfBefore = GetDataFolderDFR()
+
1276 Execute /q/z "CreateBrowser prompt=\"Select 2D holo scan wave\", showWaves=1, showVars=0, showStrs=0"
+
1277 dfref dfAfter = GetDataFolderDFR()
+
1278 SetDataFolder dfBefore
+
+
1280 SVAR list = S_BrowserList
+
+
1282 if ((flag != 0) && (ItemsInList(list) >= 1))
+
1283 string wname = StringFromList(0, list)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1297 STRUCT WMButtonAction &ba
+
+
1299 switch( ba.eventCode )
+
+
1301 dfref packdf = $package_path
+
1302 svar /sdfr=packdf source_path
+
1303 wave /z w = $source_path
+
+
+
+
1307 DoAlert 0, "can't find source data."
+
+
+
+
+
+
+
+
+
+
+
1318 STRUCT WMButtonAction &ba
+
+
1320 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1332 STRUCT WMButtonAction &ba
+
+
1334 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1346 STRUCT WMButtonAction &ba
+
+
1348 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1360 STRUCT WMButtonAction &ba
+
+
1362 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1374 STRUCT WMButtonAction &ba
+
+
1376 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1388 STRUCT WMButtonAction &ba
+
+
1390 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1402 STRUCT WMButtonAction &ba
+
+
1404 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1416 STRUCT WMButtonAction &ba
+
+
1418 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1430 STRUCT WMButtonAction &ba
+
+
1432 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1444 STRUCT WMButtonAction &ba
+
+
1446 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
+
1459 STRUCT WMButtonAction &ba
+
+
1461 switch( ba.eventCode )
+
+
+
1464 variable do_graph = 1
+
1465 prompt dest_folder, "destination folder name (relative to data source)"
+
1466 prompt do_graph, "duplicate graph (yes = 1, no = 0)"
+
1467 doprompt "duplicate", dest_folder, do_graph
+
+
+
+
+
+
+
+
+
+
+
+
+
1480 STRUCT WMButtonAction &ba
+
+
1482 switch( ba.eventCode )
+
+
+
1485 wave /sdfr=df process_data
+
+
1487 ekin = NumberByKey("KineticEnergy", note(process_data), "=", "\r")
+
1488 prompt ekin, "kinetic energy"
+
1489 doprompt "save etpi", ekin
+
+
+
+
+
+
+
+
+
+
+
+
+
1502 STRUCT WMButtonAction &ba
+
+
1504 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1516 STRUCT WMButtonAction &ba
+
+
1518 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1530 STRUCT WMButtonAction &ba
+
+
1532 switch( ba.eventCode )
+
+
+
1535 svar /sdfr=df source_path
+
1536 svar /sdfr=df output_graphname
+
1537 if (WinType(output_graphname) == 1)
+
1538 SavePICT /WIN=$output_graphname /E=-5 /B=144 /TRAN=0
+
+
+
+
+
+
+
+
+
+
+
1549 STRUCT WMPopupAction &pa
+
+
1551 switch( pa.eventCode )
+
+
+
1554 nvar /sdfr=df norm_alpha_mode
+
1555 norm_alpha_mode = pa.popNum - 1
+
+
+
+
+
+
+
+
+
+
1565 STRUCT WMPopupAction &pa
+
+
1567 switch( pa.eventCode )
+
+
+
1570 nvar /sdfr=df norm_theta_domain
+
1571 norm_theta_domain = pa.popNum - 1
+
+
+
+
+
+
+
+
+
+
1581 STRUCT WMPopupAction &pa
+
+
1583 switch( pa.eventCode )
+
+
+
1586 nvar /sdfr=df norm_theta_mode
+
1587 norm_theta_mode = pa.popNum - 1
+
+
+
+
+
+
+
+
+
+
1597 STRUCT WMPopupAction &pa
+
+
1599 switch( pa.eventCode )
+
+
+
1602 nvar /sdfr=df norm_thetaphi_mode
+
1603 norm_thetaphi_mode = pa.popNum - 1
+
+
+
+
+
+
+
+
+
+
1613 STRUCT WMPopupAction &pa
+
+
1615 switch( pa.eventCode )
+
+
+
1618 nvar /sdfr=df graph_mode
+
1619 graph_mode = pa.popNum - 1
+
+
+
+
+
+
+
+
+
+
1629 STRUCT WMPopupAction &pa
+
+
1631 switch( pa.eventCode )
+
+
+
1634 nvar /sdfr=df graph_projection
+
1635 graph_projection = pa.popNum - 1
+
+
+
+
+
+
+
+
+
+
1645 STRUCT WMPopupAction &pa
+
+
1647 switch( pa.eventCode )
+
+
+
1650 svar /sdfr=df graph_colortable
+
1651 graph_colortable = StringFromList(pa.popNum - 1, CTabList())
+
+
+
+
+
+
+
+
static variable pmp_graph_colortable(WMPopupAction *pa)
static variable preview_norm_thetaphi()
variable asp_save_output_etpi(variable ekin)
save the output diffractogram to a PMSCO ETPI file
variable crop_strip(wave strip, variable xlo, variable xhi)
crop a strip at the sides.
static variable bp_norm_phi_preview(WMButtonAction *ba)
static variable bp_norm_thetaphi_preview(WMButtonAction *ba)
variable pizza_service_2(wave data, string nickname, wave m_theta, wave m_tilt, wave m_phi, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue)
create a pizza plot from a measured (energy-integrated) data strip
variable normalize_strip_theta(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average polar distribution.
variable normalize_strip_x(wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average X distribution.
variable asp_update_graph()
update graphs with new color table or contrast
static variable bp_load_prefs(WMButtonAction *ba)
static variable AfterCompiledHook()
initialize package data once when the procedure is first loaded
static variable check_norm_theta()
variable asp_import_raw(wave raw_data)
import raw data
static variable do_norm_alpha(variable check, variable force=defaultValue)
alpha-normalize the process data.
static variable do_crop(variable check, variable force=defaultValue)
crop the process data.
static variable bp_output_etpi(WMButtonAction *ba)
static variable bp_norm_alpha_preview(WMButtonAction *ba)
static const string package_path
data folder path
variable asp_show_panel()
create the angle scan processing panel
static variable do_init_process(variable check)
initialize the process data with a copy of the raw data.
static variable bp_norm_theta_preview(WMButtonAction *ba)
variable normalize_strip_theta_scans(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip piecewise by a smooth polar distribution.
variable crop_strip_theta(wave strip, variable theta_lo, variable theta_hi, wave theta, wave tilt, wave phi)
crop a strip in theta.
static variable pmp_norm_alpha_mode(WMPopupAction *pa)
variable asp_display_previews()
display a graph window of the processed data.
variable asp_display_dist_check(variable xdist, variable ydist)
display a graph window of the distribution checks.
variable ad_update_profiles(wave image)
update a profiles graph with new data.
static variable bp_norm_theta_check(WMButtonAction *ba)
dfr find_hemi_data(string nickname, string *prefix, string *intwave)
finds the folder, prefix and name of holo waves given their nick name
static variable check_norm_alpha()
string asp_duplicate_output(string dest_name, variable do_graph=defaultValue)
copy the output data to a new folder
static variable bp_output_itx(WMButtonAction *ba)
static variable pmp_graph_mode(WMPopupAction *pa)
static variable bp_norm_alpha_check(WMButtonAction *ba)
variable interpolate_hemi_scan(string nickname, variable projection=defaultValue)
interpolate a hemispherical scan onto a rectangular grid
static variable preview_norm_phi()
static variable pmp_norm_thetaphi_mode(WMPopupAction *pa)
static variable bp_save_prefs(WMButtonAction *ba)
static variable load_prefs()
load persistent package data from the preferences file.
static variable update_menus()
update the popup menus to reflect the values of the global variables
static variable bp_source_update(WMButtonAction *ba)
static variable do_norm_phi(variable check, variable force=defaultValue)
phi-normalize the process data.
static variable do_norm_theta(variable check, variable force=defaultValue)
theta-normalize the process data.
string pmsco_save_scan(string pathname, string filename, string energy, string theta, string phi, string alpha, string intensity, string sigma, dfref sdfr=defaultValue)
save waves in a PMSCO scan data file.
static variable pmp_norm_theta_mode(WMPopupAction *pa)
static const string prefs_objects
semicolon-separated list of persistent variable, string, and wave names
variable asp_close_graphs()
close all graphs created by the angle scan panel
static variable init_package()
static variable check_norm_thetaphi()
static variable delete_rows(string rows, wave data, wave theta, wave tilt, wave phi)
delete individual rows from the data strip
variable set_contrast(variable pcmin, variable pcmax, string graphname=defaultValue, string colortable=defaultValue, variable reversecolors=defaultValue, variable symmetric=defaultValue)
set the pseudocolor contrast by percentile.
static variable pmp_graph_projection(WMPopupAction *pa)
variable save_hemi_scan(string nickname, string pathname, string filename)
save a hemispherical scan to an Igor text file
static variable check_norm_phi()
const variable kProjStereo
variable normalize_strip_thetaphi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by a smooth polar-azimuthal distribution.
static variable preview_norm_alpha()
static variable arrange_controls()
static variable do_norm_thetaphi(variable check, variable force=defaultValue)
theta,phi-normalize the process data.
static variable pmp_norm_theta_domain(WMPopupAction *pa)
static variable bp_graph_update(WMButtonAction *ba)
static variable save_prefs()
save persistent package data to the preferences file.
static variable bp_output_calc(WMButtonAction *ba)
variable duplicate_hemi_scan(string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue)
duplicate a hemispherical scan dataset.
variable asp_calculate_output()
calculate the output using all enabled processing filters.
static variable bp_output_duplicate(WMButtonAction *ba)
variable normalize_strip_phi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable theta_range=defaultValue, variable check=defaultValue)
divide the strip by a sine function in phi (wobble correction).
static variable bp_norm_thetaphi_check(WMButtonAction *ba)
static variable bp_graph_png(WMButtonAction *ba)
variable asp_save_output_itx()
save the output diffractogram to an igor text file
static variable bp_norm_phi_check(WMButtonAction *ba)
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
static variable preview_norm_theta()
static variable preview_crop()
string asp_display_output(dfref data_df=defaultValue, string data_name=defaultValue)
display the output diffractogram
static const string package_name
package name is used as data folder name
static variable bp_crop_preview(WMButtonAction *ba)
static variable bp_source_select(WMButtonAction *ba)
string display_hemi_scan(string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue)
display a plot of a hemispherical angle scan.
interactive processing of angle scanned XPD data.
PEARL Procedures: pearl-anglescan-process.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -106,155 +108,164 @@ Namespaces
string strip_append (wave strip1, wave strip2) append an angle scan strip to another one More... variable strip_delete_frames (wave strip, variable qlo, variable qhi, wave theta, wave tilt, wave phi) delete a contiguous range of frames from a strip. More... delete a contiguous range of frames from a strip. More... variable normalize_strip_x (wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue) divide the strip by the average X distribution. More... divide the strip by the average X distribution. More... variable normalize_strip_phi (wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable theta_range=defaultValue, variable check=defaultValue) divide the strip by a sine function in phi (wobble correction). More... divide the strip by a sine function in phi (wobble correction). More... variable normalize_strip_theta (wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue) divide the strip by the average polar distribution. More... divide the strip by the average polar distribution. More... variable normalize_strip_thetaphi (wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue) divide the strip by a smooth polar-azimuthal distribution. More... divide the strip by a smooth polar-azimuthal distribution. More... variable normalize_strip_theta_scans (wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue) divide the strip piecewise by a smooth polar distribution. More... divide the strip piecewise by a smooth polar distribution. More... variable normalize_strip_2d (wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue) divide the strip by a two-dimensional normalization function. More... divide the strip by a two-dimensional normalization function. More... variable crop_strip (wave strip, variable xlo, variable xhi) crop a strip at the sides. More... crop a strip at the sides. More... variable crop_strip_theta (wave strip, variable theta_lo, variable theta_hi, wave theta, wave tilt, wave phi) crop a strip in theta. More... crop a strip in theta. More... variable pizza_service (wave data, string nickname, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue) create a pizza plot from a measured (energy-integrated) data strip More... create a pizza plot from a measured (energy-integrated) data strip More... variable pizza_service_2 (wave data, string nickname, wave m_theta, wave m_tilt, wave m_phi, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue) create a pizza plot from a measured (energy-integrated) data strip More... create a pizza plot from a measured (energy-integrated) data strip More... variable show_analyser_line (variable theta, variable tilt, variable phi, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable xpdplot=defaultValue) calculate and display the line seen by the analyser for a specific emission angle More... calculate and display the line seen by the analyser for a specific emission angle More... variable convert_angles_ttpd2polar (wave theta, wave tilt, wave phi, wave data, wave polar, wave azi) convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates. More... convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates. More... variable convert_angles_ttpa2polar (wave theta, wave tilt, wave phi, wave analyser, wave polar, wave azi) convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates. More... convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates. More... static variable line_average (wave source, wave dest) static variable calc_nth (variable Theta_st, variable Theta_in, variable th, variable Phi_ran, variable Phi_ref, string Holomode) calculate the number of phis for a given theta More... calculate the number of phis for a given theta More... static variable calc_phi_step (variable Theta_in, variable th, variable Theta_st, variable Phi_ran, variable Phi_ref, string Holomode) calculate delta-phi for a given theta More... calculate delta-phi for a given theta More... static variable Calc_The_step (variable th, variable Theta_st, string Holomode) calculate delta-theta for a given theta More... calculate delta-theta for a given theta More... static variable CalcN_Theta (string HoloMode, variable Theta_in, variable Theta_ran, variable Theta_st) calculate the number of thetas for a pattern More... calculate the number of thetas for a pattern More... variable make_hemi_grid (variable npol, string nickname, variable xpdplot=defaultValue) create a hemispherical, constant solid angle grid More... create a hemispherical, constant solid angle grid More... string get_hemi_nickname (wave w) finds the nick name given any hemi wave More... finds the nick name given any hemi wave More... string get_hemi_prefix (wave w) finds the prefix given any hemi wave More... finds the prefix given any hemi wave More... dfr find_hemi_data (string nickname, string *prefix, string *intwave) finds the folder, prefix and name of holo waves given their nick name More... finds the folder, prefix and name of holo waves given their nick name More... variable clear_hemi_grid (string nickname) clear a hemispherical scan grid More... clear a hemispherical scan grid More... variable duplicate_hemi_scan (string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue) duplicate a hemispherical scan dataset. More... duplicate a hemispherical scan dataset. More... variable rotate_hemi_scan (string nickname, variable angle) azimuthally rotate a hemispherical scan dataset. More... azimuthally rotate a hemispherical scan dataset. More... string prepare_hemi_scan_display (string nickname, variable projection=defaultValue) create waves for plotting a hemispherical angle scan. More... create waves for plotting a hemispherical angle scan. More... string display_hemi_scan (string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue) display a plot of a hemispherical angle scan. More... display a plot of a hemispherical angle scan. More... static string display_polar_graph (string graphname, variable angle_offset=defaultValue, variable do_ticks=defaultValue) displays an empty polar graph More... displays an empty polar graph More... static string draw_hemi_axes (string graphname, variable do_grids=defaultValue) draw polar and azimuthal grids in an existing polar graph. More... draw polar and azimuthal grids in an existing polar graph. More... variable draw_diffraction_cone (string graphname, string groupname, variable theta_axis, variable theta_inner, variable phi) draw the circle of a diffraction cone in a stereographic polar graph. More... draw the circle of a diffraction cone in a stereographic polar graph. More... string display_scanlines (string nickname, variable alpha_lo, variable alpha_hi, wave m_theta, wave m_tilt, wave m_phi, variable folding=defaultValue, variable projection=defaultValue) display a polar graph with lines indicating the angles covered by an angle scan. More... display a polar graph with lines indicating the angles covered by an angle scan. More... threadsafe variable calc_graph_radius (variable polar, variable projection=defaultValue) calculate the projected polar angle More... calculate the projected polar angle More... threadsafe variable calc_graph_polar (variable x, variable y, variable projection=defaultValue) calculate polar angle from Cartesian coordinate More... calculate polar angle from Cartesian coordinate More... threadsafe variable calc_graph_azi (variable x, variable y, variable projection=defaultValue, variable zeroAngle=defaultValue) calculate azimuthal angle from Cartesian coordinate More... calculate azimuthal angle from Cartesian coordinate More... static variable update_polar_info (string graphname) update the angles info based on cursors A and B of a given polar graph window More... update the angles info based on cursors A and B of a given polar graph window More... static variable polar_graph_hook (WMWinHookStruct *s) polar graph window hook More... polar graph window hook More... variable set_polar_graph_cursor (string nickname, string cursorname, variable polar_angle, variable azim_angle, string graphname=defaultValue) variable hemi_add_anglescan (string nickname, wave values, wave polar, wave azi, wave weights=defaultValue) add an arbitrary angle scan to a hemispherical scan grid. More... add arbitrary angle scan data to a hemispherical scan grid. More... static threadsafe dfr add_anglescan_worker (variable ith, wave values, wave weights, wave polar, wave azi, wave w_polar, wave w_azim, wave w_theta, wave w_index, wave w_dphi, wave w_nphis) thread worker for hemi_add_anglescan More... static threadsafe variable add_aziscan_core (wave values, wave weights, variable polar, wave azi, wave w_theta, wave w_azim, wave w_index, wave w_dphi, wave w_totals, wave w_weights) thread worker for hemi_add_anglescan and hemi_add_aziscan More... variable hemi_add_aziscan (string nickname, wave values, variable polar, wave azi, wave weights=defaultValue) add an azimuthal scan to a hemispherical scan grid. More... add azimuthal data to a hemispherical scan grid. More... variable interpolate_hemi_scan (string nickname, variable projection=defaultValue) interpolate a hemispherical scan onto a rectangular grid More... interpolate a hemispherical scan onto a rectangular grid More... variable quick_pizza_image (wave data, string nickname, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue) map angle scan data onto a rectangular grid in stereographic projection More... map angle scan data onto a rectangular grid in stereographic projection More... variable save_hemi_scan (string nickname, string pathname, string filename) save a hemispherical scan to an Igor text file More... save a hemispherical scan to an Igor text file More... variable load_hemi_scan (string nickname, string pathname, string filename) load a hemispherical scan from an Igor text file More... load a hemispherical scan from an Igor text file More... variable import_tpi_scan (string nickname, wave theta, wave phi, wave intensity, variable folding=defaultValue, variable npolar=defaultValue, variable nograph=defaultValue, variable xpdplot=defaultValue) import a hemispherical scan from theta-phi-intensity waves and display it More... import a hemispherical scan from theta-phi-intensity waves and display it More... variable trim_hemi_scan (string nickname, variable theta_max) trim a hemispherical scan at grazing angle More... trim a hemispherical scan at grazing angle More... wave hemi_polar_cut (string nickname, variable azim) extract a polar cut from a hemispherical scan. More... extract a polar cut from a hemispherical scan. More... wave hemi_azi_cut (string nickname, variable pol) extract an azimuthal cut from a hemispherical scan More... extract an azimuthal cut from a hemispherical scan More... static variable check_contrast (wave values, variable pcmin, variable pcmax, variable *vmin, variable *vmax) variable set_contrast (variable pcmin, variable pcmax, string graphname=defaultValue, string colortable=defaultValue) set the pseudocolor contrast by percentile. More... static variable check_contrast (wave values, variable pcmin, variable pcmax, variable *vmin, variable *vmax, variable sym) variable set_contrast (variable pcmin, variable pcmax, string graphname=defaultValue, string colortable=defaultValue, variable reversecolors=defaultValue, variable symmetric=defaultValue) set the pseudocolor contrast by percentile. More... variable AngleToK (wave inwave) k-space mapping of 2D angle-energy distribution (scienta image) More... k-space mapping of 2D angle-energy distribution (scienta image) More...
Definition at line 3332 of file pearl-anglescan-process.ipf .
+Definition at line 3562 of file pearl-anglescan-process.ipf .
@@ -392,7 +590,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Returns polar angle in degrees Definition at line 2393 of file pearl-anglescan-process.ipf .
+Definition at line 2467 of file pearl-anglescan-process.ipf .
@@ -429,7 +627,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
calculate polar angle from Cartesian coordinate
-
this is the reverse mapping to calc_graph_radius()
+
this is the reverse mapping to calc_graph_radius()
Parameters
x,y projected Cartesian coordinate Returns polar angle in degrees Definition at line 2340 of file pearl-anglescan-process.ipf .
+Definition at line 2414 of file pearl-anglescan-process.ipf .
@@ -493,7 +691,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Returns projected radius. the radius is scaled such that grazing emission maps to 2. Definition at line 2295 of file pearl-anglescan-process.ipf .
+Definition at line 2369 of file pearl-anglescan-process.ipf .
@@ -558,7 +756,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
calculate the number of phis for a given theta
adapted from XPDplot 8.03
-Definition at line 1149 of file pearl-anglescan-process.ipf .
+Definition at line 1223 of file pearl-anglescan-process.ipf .
@@ -623,7 +821,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
calculate delta-phi for a given theta
adapted from XPDplot 8.03
-Definition at line 1178 of file pearl-anglescan-process.ipf .
+Definition at line 1252 of file pearl-anglescan-process.ipf .
@@ -670,7 +868,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
calculate delta-theta for a given theta
adapted from XPDplot 8.03
-Definition at line 1222 of file pearl-anglescan-process.ipf .
+Definition at line 1296 of file pearl-anglescan-process.ipf .
@@ -723,12 +921,12 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
calculate the number of thetas for a pattern
adapted from XPDplot 8.03
-Definition at line 1253 of file pearl-anglescan-process.ipf .
+Definition at line 1327 of file pearl-anglescan-process.ipf .
-◆ ◆
@@ -764,7 +962,13 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
variable *
- vmax vmax ,
+ variable
+ sym
@@ -808,7 +1012,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 1532 of file pearl-anglescan-process.ipf .
+Definition at line 1606 of file pearl-anglescan-process.ipf .
@@ -877,7 +1081,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
for the output parameters polar and azi, you need to pass in existing numeric waves. dimension size does not matter, the waves are redimensioned by the function so that they have the same dimensions as the intensity data set. X dimension = analyser scale, Y dimension = manipulator scan.
-Definition at line 1088 of file pearl-anglescan-process.ipf .
+Definition at line 1162 of file pearl-anglescan-process.ipf .
@@ -932,9 +1136,9 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
@@ -982,7 +1186,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 673 of file pearl-anglescan-process.ipf .
+Definition at line 747 of file pearl-anglescan-process.ipf .
@@ -1050,7 +1254,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 705 of file pearl-anglescan-process.ipf .
+Definition at line 779 of file pearl-anglescan-process.ipf .
@@ -1120,7 +1324,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
graphtype type of graph
1 (pol, az) trace in Igor "New Polar" (default).
2 XPDplot (reserved, not implemented).
-3 matrix in Igor "New Polar". the matrix wave is a 2D wave with X and Y scaling corresponding to the selected projection. matrix waves can be created by interpolate_hemi_scan() . note: the pol and az waves are required as well.
+3 matrix in Igor "New Polar". the matrix wave is a 2D wave with X and Y scaling corresponding to the selected projection. matrix waves can be created by interpolate_hemi_scan() . note: the pol and az waves are required as well.
do_ticks select which ticks to draw. value must be the arithmetic OR of all selected items. default: 3
@@ -1141,7 +1345,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Returns the name of the graph window Definition at line 1784 of file pearl-anglescan-process.ipf .
+Definition at line 1858 of file pearl-anglescan-process.ipf .
@@ -1211,7 +1415,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Returns the name of the graph window. Version 1.7 interface change: the trace drawing code is moved to display_hemi_scan, so that this function can be reused by other graph types, e.g. display_scanlines. Definition at line 1929 of file pearl-anglescan-process.ipf .
+Definition at line 2003 of file pearl-anglescan-process.ipf .
@@ -1287,13 +1491,13 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
m_tilt manipulator tilt angles, 0 = normal emission. size = dimsize(data, 1) m_phi manipulator phi angles, 0 = azimuthal origin. size = dimsize(data, 1) folding rotational averaging, default = 1 projection mapping function from polar to cartesian coordinates. see calc_graph_radius() . projection mapping function from polar to cartesian coordinates. see calc_graph_radius() .
-
Definition at line 2180 of file pearl-anglescan-process.ipf .
+
Definition at line 2254 of file pearl-anglescan-process.ipf .
@@ -1355,7 +1559,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Warning EXPERIMENTAL! this function is under development. the interface and behaviour of this function may change significantly in future versions.
-
Definition at line 2116 of file pearl-anglescan-process.ipf .
+
Definition at line 2190 of file pearl-anglescan-process.ipf .
radial axes at 0 and 90 degree azimuth.
the objects are added to the ProgFront drawing layer and will appear in front of the data trace. in interactive drawing mode, you can select the active drawing layer by clicking the tree icon while holding the Alt key.
-the graph must have been created by display_polar_graph() . the function reads the projection mode from the window user data "projection".
+the graph must have been created by display_polar_graph() . the function reads the projection mode from the window user data "projection".
Parameters
graphname name of graph window. Warning EXPERIMENTAL! this function is under development. the interface and behaviour of this function may change significantly in future versions. Definition at line 2044 of file pearl-anglescan-process.ipf .
+Definition at line 2118 of file pearl-anglescan-process.ipf .
@@ -1457,7 +1661,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
duplicate a hemispherical scan dataset.
-
this function works only for hemi scans created by make_hemi_grid() (or compatible functions). the angle grid is recreated rather than copied point-by-point. the new dataset is independent from the original one.
+
this function works only for hemi scans created by make_hemi_grid() (or compatible functions). the angle grid is recreated rather than copied point-by-point. the new dataset is independent from the original one.
if the version of the source dataset is pre 1.6, it is converted to version 1.6.
Parameters
@@ -1473,7 +1677,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 1579 of file pearl-anglescan-process.ipf .
+Definition at line 1653 of file pearl-anglescan-process.ipf .
@@ -1526,7 +1730,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Returns reference of the data folder which contains the waves Definition at line 1498 of file pearl-anglescan-process.ipf .
+Definition at line 1572 of file pearl-anglescan-process.ipf .
@@ -1550,7 +1754,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
the nick name is either the name of a child folder in the current data folder (PEARL specification), or a prefix of the hemi wave names (XPDplot specification).
Returns the nick name Definition at line 1442 of file pearl-anglescan-process.ipf .
+Definition at line 1516 of file pearl-anglescan-process.ipf .
@@ -1574,7 +1778,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
the prefix is the part of the wave name before the first underscore. the prefix is used by XPDplot where it is identical to the nick name. the prefix is empty in the PEARL specification.
Returns the prefix Definition at line 1467 of file pearl-anglescan-process.ipf .
+Definition at line 1541 of file pearl-anglescan-process.ipf .
@@ -1622,10 +1826,23 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-
add an arbitrary angle scan to a hemispherical scan grid.
-
the hemi grid must have been created in the current data folder by the make_hemi_grid function. the function determines the bin size at the given polar angle, and adds all data points which fall into a bin. a point which lies exactly on the upper boundary falls into the next bin. this function does not clear previous values before adding new data. values are added to the _tot wave, weights to the _wt wave. the intensity (_i) wave is calculated as _tot / _wt.
+
add arbitrary angle scan data to a hemispherical scan grid.
+
the function fills the input data into bins defined by the hemi scan grid. it sums up the values and weights of the data points which fall into each bin, and adds the results to the totals and weights waves of the existing hemi grid. finally, it updates the values wave (values divided by weights).
+
the hemi grid must have been created in the current data folder by the make_hemi_grid() function. the function does not clear previous values before adding new data. values are added to the _tot wave, weights to the _wt wave. the intensity (_i/values) wave is calculated as _tot divided by _wt.
+
Parameters
+
+ nickname name prefix of holo waves. empty if waves are in current data folder. values counts/intensity values at the positions given in the polara nd azi waves. one- or two-dimensional. NaN values are ignored. polar polar angles (in degrees) of each data point. allowed range 0 <= theta <= 90. no specific ordering required. azi azimuthal angles (in degrees) of each data point. allowed range -360 <= phi < +360. no specific order required. weights weight or accumulation time of each point of values. weights must be positive. values with weight 0 are ignored. defaults to 1 if not specified.
+
+
+
the values, weights, polar and azi waves must have the same dimensions (one- or two-dimensional). no specific order is required, the function sorts (copies of) the arrays internally.
+
the actual binning is delegated to the thread-safe add_anglescan_worker() function under Igor's automatic multi-threading facility.
-
Definition at line 2538 of file pearl-anglescan-process.ipf .
+
Definition at line 2637 of file pearl-anglescan-process.ipf .
-
add an azimuthal scan to a hemispherical scan grid.
-
the hemi grid must have been created in the current data folder by the make_hemi_grid function. the function determines the bin size at the given polar angle, and calculates the mean values of the data points which fall into a bin. a point which lies exactly on the upper boundary falls into the next bin.
+
add azimuthal data to a hemispherical scan grid.
+
the hemi grid must have been created in the current data folder by the make_hemi_grid() function. the function determines the bin size at the given polar angle, sums up the values and weights of the data points which fall into each bin, and adds the results to the totals and weights waves of the existing hemi grid. finally, it updates the values wave (values divided by weights).
+
Parameters
+
+ nickname name prefix of holo waves. empty if waves are in current data folder. values counts/intensity values of the azimuthal scan at the positions given in the azi parameter. polar polar angle (in degrees) where to add the azi scan. azi angle positions of the azimuthal scan. acceptable range: >= -360 and < +360. no specific order required, the function sorts the array internally. weights weight or accumulation time of each point of values. defaults to 1 if not specified.
+
+
+
the actual binning is delegated to the thread-safe add_aziscan_core() function shared with hemi_add_anglescan() .
-
Definition at line 2608 of file pearl-anglescan-process.ipf .
+
Definition at line 2844 of file pearl-anglescan-process.ipf .
Returns reference of the created wave. the wave has the same name as the intensity wave of the dataset with the suffix "_azi" and the azimuthal angle rounded to integer. it is created in the same datafolder as the original data. Definition at line 3159 of file pearl-anglescan-process.ipf .
+Definition at line 3354 of file pearl-anglescan-process.ipf .
@@ -1760,7 +1988,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Returns reference of the created wave. the wave has the same name as the intensity wave of the dataset with the suffix "_azi" and the azimuthal angle rounded to integer. it is created in the same datafolder as the original data. Definition at line 3073 of file pearl-anglescan-process.ipf .
+Definition at line 3268 of file pearl-anglescan-process.ipf .
@@ -1854,7 +2082,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 2985 of file pearl-anglescan-process.ipf .
+Definition at line 3179 of file pearl-anglescan-process.ipf .
@@ -1888,7 +2116,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
the scan data must exist in the current data folder or in the sub-folder given by the nickname parameter.
the interpolated data is written to a new two-dimensional wave "matrix". the wave has a fixed size of 181 x 181 points optimized for 1-degree polar steps.
missing values (nan) are interpolated. this works well only if the missing values are reasonable sparse. the function also applies a gaussian filter to smooth the image. empty rings at high polar angles map are preserved.
-to display the result call display_hemi_scan() with graphtype=3.
+to display the result call display_hemi_scan() with graphtype=3.
Parameters
nickname name prefix of holo waves. may be empty. Definition at line 2726 of file pearl-anglescan-process.ipf .
+Definition at line 2920 of file pearl-anglescan-process.ipf .
@@ -1942,7 +2170,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
@@ -1981,7 +2209,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
load a hemispherical scan from an Igor text file
Todo: function not implemented Definition at line 2936 of file pearl-anglescan-process.ipf .
+Definition at line 3130 of file pearl-anglescan-process.ipf .
@@ -2033,7 +2261,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
Definition at line 1291 of file pearl-anglescan-process.ipf .
+Definition at line 1365 of file pearl-anglescan-process.ipf .
@@ -2106,7 +2334,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 613 of file pearl-anglescan-process.ipf .
+Definition at line 686 of file pearl-anglescan-process.ipf .
@@ -2186,7 +2414,7 @@ data imported with version 1.5 and earlier, must be offset by 180 deg in phi to
-Definition at line 283 of file pearl-anglescan-process.ipf .
+Definition at line 348 of file pearl-anglescan-process.ipf .
@@ -2275,7 +2503,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 366 of file pearl-anglescan-process.ipf .
+Definition at line 433 of file pearl-anglescan-process.ipf .
@@ -2332,7 +2560,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
divide the strip piecewise by a smooth polar distribution.
Warning experimental. this function is under development. Definition at line 523 of file pearl-anglescan-process.ipf .
+Definition at line 594 of file pearl-anglescan-process.ipf .
@@ -2426,7 +2654,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 464 of file pearl-anglescan-process.ipf .
+Definition at line 533 of file pearl-anglescan-process.ipf .
@@ -2498,7 +2726,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 187 of file pearl-anglescan-process.ipf .
+Definition at line 252 of file pearl-anglescan-process.ipf .
@@ -2571,7 +2799,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
create a pizza plot from a measured (energy-integrated) data strip
-
accepts angle-scan data as returned by adh5_load_reduced() , maps them onto a hemispherical scan grid, and displays a polar graph.
+
accepts angle-scan data as returned by adh5_load_reduced() , maps them onto a hemispherical scan grid, and displays a polar graph.
Parameters
data 2D intensity wave, see requirements above
@@ -2602,9 +2830,9 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-
Attention if you modify the structure of the data wave, e.g. delete some angles, this function cannot be used because the manipulator settings do not correspond to the original manipulator waves! instead, create your own manipulator waves and use pizza_service_2() .
+
Attention if you modify the structure of the data wave, e.g. delete some angles, this function cannot be used because the manipulator settings do not correspond to the original manipulator waves! instead, create your own manipulator waves and use pizza_service_2() .
-
Definition at line 769 of file pearl-anglescan-process.ipf .
+
Definition at line 843 of file pearl-anglescan-process.ipf .
@@ -2677,8 +2905,8 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
create a pizza plot from a measured (energy-integrated) data strip
-
accepts angle-scan data as returned by adh5_load_reduced() , maps them onto a hemispherical scan grid, and displays a polar graph.
-
the behaviour of this function is the same as pizza_service() except that the manipulator waves are specified explicitly.
+
accepts angle-scan data as returned by adh5_load_reduced() , maps them onto a hemispherical scan grid, and displays a polar graph.
+
the behaviour of this function is the same as pizza_service() except that the manipulator waves are specified explicitly.
Parameters
data 2D intensity wave, see requirements above
@@ -2710,7 +2938,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 862 of file pearl-anglescan-process.ipf .
+Definition at line 936 of file pearl-anglescan-process.ipf .
@@ -2741,7 +2969,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
polar graph window hook
this hook converts the cursor positions to polar coordinates and displays them in a text box on the graph. the text box is visible while the cursor info box is visible.
-Definition at line 2473 of file pearl-anglescan-process.ipf .
+Definition at line 2547 of file pearl-anglescan-process.ipf .
@@ -2788,7 +3016,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 1702 of file pearl-anglescan-process.ipf .
+Definition at line 1776 of file pearl-anglescan-process.ipf .
@@ -2865,7 +3093,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
Precondition manipulator angles as attributes in attr folder next to the data wave Warning EXPERIMENTAL Definition at line 2792 of file pearl-anglescan-process.ipf .
+Definition at line 2986 of file pearl-anglescan-process.ipf .
@@ -2896,7 +3124,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
azimuthally rotate a hemispherical scan dataset.
-
this function works only for hemi scans created by make_hemi_grid() (or compatible functions).
+
this function works only for hemi scans created by make_hemi_grid() (or compatible functions).
Parameters
nickname name prefix for waves. source data must be in current data folder. Definition at line 1654 of file pearl-anglescan-process.ipf .
+Definition at line 1728 of file pearl-anglescan-process.ipf .
@@ -2943,12 +3171,12 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
save a hemispherical scan to an Igor text file
-Definition at line 2903 of file pearl-anglescan-process.ipf .
+Definition at line 3097 of file pearl-anglescan-process.ipf .
-◆ ◆
@@ -2975,7 +3203,19 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
string
-
colortable = defaultValue
+
colortable = defaultValue,
+
+
+ variable
+ reversecolors = defaultValue,
+
+ variable
+ symmetric = defaultValue
pcmax percentile above the maximum color (0-100). graphname name of graph. default: top graph. colortable name of new colortable. default: keep current table.
+
reversecolors reverse colors of new colorable. takes effect only if colortable argument is defined.
+0 (default) normal colors,
+1 reverse color table
+
+
+
symmetric make scale symmetric about zero (for modulation functions, e.g.).
+0 (default) do not enforce symmetry.
+1 try symmetric scale if "reasonable".
+
+
-
Definition at line 3247 of file pearl-anglescan-process.ipf .
+
Definition at line 3463 of file pearl-anglescan-process.ipf .
@@ -3047,7 +3297,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3145,7 +3395,50 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 979 of file pearl-anglescan-process.ipf .
+Definition at line 1053 of file pearl-anglescan-process.ipf .
+
+
+
+◆
+
+
+
+ string strip_append
+ (
+ wave
+ strip1 ,
+
+ wave
+ strip2
+
+ )
+
+
+
+
+
append an angle scan strip to another one
+
concatenate two angle scan strips including matching attribute waves and replace the first strip with the resulting waves. this is useful if a scan was interrupted and continues in a second data file.
+
all accompanying 1D waves which have a matching length and exist in both source and destination folders are concatenated and stored in the destination. 'accompanying waves' are those in the same folder as the 2D strip wave and those in the :attr sub-folder.
+
Attention this function modifies all matching waves in the data and attr folders of strip1! consider a backup before calling the function, or work on a copy of the original data (cf. Igor's DuplicateDataFolder operation)!
+
Parameters
+
+ [in,out] strip1 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan. this is the first source wave and destination wave. [in] strip2 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan. this is the second source wave.
+
+
+
Returns (string) semicolon-separated list of modified wave names (without folder path).
+
+
Definition at line 106 of file pearl-anglescan-process.ipf .
Definition at line 105 of file pearl-anglescan-process.ipf .
+Definition at line 170 of file pearl-anglescan-process.ipf .
@@ -3253,7 +3546,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 3034 of file pearl-anglescan-process.ipf .
+Definition at line 3229 of file pearl-anglescan-process.ipf .
@@ -3291,7 +3584,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
-Definition at line 2438 of file pearl-anglescan-process.ipf .
+Definition at line 2512 of file pearl-anglescan-process.ipf .
@@ -3308,7 +3601,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3324,7 +3617,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3340,7 +3633,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3356,7 +3649,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3380,7 +3673,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3404,7 +3697,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3428,7 +3721,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3452,7 +3745,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3476,7 +3769,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3492,7 +3785,7 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
@@ -3502,9 +3795,9 @@ caution: binomial and boxcar smoothing are not aware of theta. this may give unp
diff --git a/doc/html/pearl-anglescan-process_8ipf.js b/doc/html/pearl-anglescan-process_8ipf.js
index 8a4dea7..71dd876 100644
--- a/doc/html/pearl-anglescan-process_8ipf.js
+++ b/doc/html/pearl-anglescan-process_8ipf.js
@@ -1,5 +1,7 @@
var pearl_anglescan_process_8ipf =
[
+ [ "add_anglescan_worker", "pearl-anglescan-process_8ipf.html#a8c83a187e371783dea62c9f2bc97c52c", null ],
+ [ "add_aziscan_core", "pearl-anglescan-process_8ipf.html#a8eabc7feca73f9e0db2109a78ee382cb", null ],
[ "AngleToK", "pearl-anglescan-process_8ipf.html#acf6fddb73624fe2d21429e38c4994088", null ],
[ "calc_graph_azi", "pearl-anglescan-process_8ipf.html#a4fc744e24e3e9c5efb17f14ab622bcae", null ],
[ "calc_graph_polar", "pearl-anglescan-process_8ipf.html#ae2b036a06ffac8d2bb292a65401f8a9a", null ],
@@ -8,7 +10,7 @@ var pearl_anglescan_process_8ipf =
[ "calc_phi_step", "pearl-anglescan-process_8ipf.html#a999a9cd7d00d3e1ec8e768228a664ad1", null ],
[ "Calc_The_step", "pearl-anglescan-process_8ipf.html#a1fb6aa7870dfbf0ed92660b7aae579e0", null ],
[ "CalcN_Theta", "pearl-anglescan-process_8ipf.html#ac0def1ded61f9cd758df0c99f4ff9470", null ],
- [ "check_contrast", "pearl-anglescan-process_8ipf.html#a2e1ed05781f9eb4be5e77695ef049962", null ],
+ [ "check_contrast", "pearl-anglescan-process_8ipf.html#a67d53a1c362d7e5bbeccf1c9c12ae0c2", null ],
[ "clear_hemi_grid", "pearl-anglescan-process_8ipf.html#a3ec6935a5903d0974c93a2072d743013", null ],
[ "convert_angles_ttpa2polar", "pearl-anglescan-process_8ipf.html#a3cc7eddf5c6b0658260cfb32dd2c026d", null ],
[ "convert_angles_ttpd2polar", "pearl-anglescan-process_8ipf.html#a2b38c6c9b6e60593ba69d3773b6bc779", null ],
@@ -45,9 +47,10 @@ var pearl_anglescan_process_8ipf =
[ "quick_pizza_image", "pearl-anglescan-process_8ipf.html#a0b9e2b025e1d55d2a064edccf6c1c3e3", null ],
[ "rotate_hemi_scan", "pearl-anglescan-process_8ipf.html#a5162488b366e217195d8f8bd7cdde0ce", null ],
[ "save_hemi_scan", "pearl-anglescan-process_8ipf.html#a48cbd596656bc6d849c53afb4c58b90d", null ],
- [ "set_contrast", "pearl-anglescan-process_8ipf.html#a666dab03bb2e97ffef81cea450184d42", null ],
+ [ "set_contrast", "pearl-anglescan-process_8ipf.html#af9874b5c1ce1d216741c7880a5fdcfcc", null ],
[ "set_polar_graph_cursor", "pearl-anglescan-process_8ipf.html#a70b0e243bcbd549e2b1da74aab605629", null ],
[ "show_analyser_line", "pearl-anglescan-process_8ipf.html#a01bac9e7d4ba743c3c34177a05070466", null ],
+ [ "strip_append", "pearl-anglescan-process_8ipf.html#ab97a936bc0fa6137b6d0b43cb61d39a1", null ],
[ "strip_delete_frames", "pearl-anglescan-process_8ipf.html#a13e0d37ae23f68cdc5da3d84cb4beed8", null ],
[ "trim_hemi_scan", "pearl-anglescan-process_8ipf.html#a5dc0cc7db9d3d7a6b3fa3f1b04d84a5e", null ],
[ "update_polar_info", "pearl-anglescan-process_8ipf.html#a1baaa3ffd9495ed427b43cbfe6e1edf8", null ],
diff --git a/doc/html/pearl-anglescan-process_8ipf_source.html b/doc/html/pearl-anglescan-process_8ipf_source.html
index 01e7a39..9276d42 100644
--- a/doc/html/pearl-anglescan-process_8ipf_source.html
+++ b/doc/html/pearl-anglescan-process_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-anglescan-process.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,85 +87,2690 @@ $(document).ready(function(){initNavTree('pearl-anglescan-process_8ipf_source.ht
pearl-anglescan-process.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 3 #pragma IgorVersion = 6.2 4 #pragma ModuleName = PearlAnglescanProcess 5 #include "pearl-vector-operations" 6 #include "pearl-polar-coordinates" 7 #include <New Polar Graphs> 118 variable snx = dimsize(strip, 0)
119 variable sny = dimsize(strip, 1)
121 variable sq1hi = max(qlo-1, 0)
122 variable sq2lo = min(qhi+1, sny - 1)
123 variable sq2hi = dimsize(strip, 1) - 1
127 variable dny = sny - (sq2lo - sq1hi + 1)
129 variable dq1hi = sq1hi
130 variable dq2lo = dq1hi + 1
131 variable dq2hi = dny - 1
132 variable q1ofs = sq1lo - dq1lo
133 variable q2ofs = sq2lo - dq2lo
135 duplicate /free strip, strip_copy
136 redimension /n=(dnx,dny) strip
137 strip[][dq1lo,dq1hi] = strip_copy[p][q + q1ofs]
138 strip[][dq2lo,dq2hi] = strip_copy[p][q + q2ofs]
140 duplicate /free theta, theta_copy
141 redimension /n=(dny) theta
142 theta[dq1lo,dq1hi] = theta_copy[p + q1ofs]
143 theta[dq2lo,dq2hi] = theta_copy[p + q2ofs]
145 duplicate /free tilt, tilt_copy
146 redimension /n=(dny) tilt
147 tilt[dq1lo,dq1hi] = tilt_copy[p + q1ofs]
148 tilt[dq2lo,dq2hi] = tilt_copy[p + q2ofs]
150 duplicate /free phi, phi_copy
151 redimension /n=(dny) phi
152 phi[dq1lo,dq1hi] = phi_copy[p + q1ofs]
153 phi[dq2lo,dq2hi] = phi_copy[p + q2ofs]
189 variable smooth_method
190 variable smooth_factor
193 if (ParamIsDefault(smooth_method))
196 if (ParamIsDefault(smooth_factor))
197 switch(smooth_method)
205 if (ParamIsDefault(check))
213 extract /free /indx raw_dist, clean_index, numtype(raw_dist) == 0
214 duplicate /free raw_dist, dist, dist_x
215 redimension /n=(numpnts(clean_index)) dist, dist_x
216 dist = raw_dist[clean_index[p]]
217 dist_x = pnt2x(raw_dist, clean_index[p])
218 variable div = mean(dist)
222 duplicate /o raw_dist, check_dist
223 check_dist = numtype(raw_dist) == 0 ? interp(x, dist_x, dist) : nan
227 switch(smooth_method)
229 Smooth /B /E=3 smooth_factor, dist
232 Smooth /E=3 smooth_factor, dist
235 make /n=1 /d /free fit_params
236 fit_scienta_ang_transm(raw_dist, fit_params)
237 duplicate /free raw_dist, dist, dist_x
239 dist = scienta_ang_transm(fit_params, x)
242 loess /smth=(smooth_factor) srcWave=dist, factors={dist_x}
247 duplicate /o raw_dist, check_smoo
248 check_smoo = interp(x, dist_x, dist)
253 strip /= interp(x, dist_x, dist)
287 variable theta_offset
291 if (ParamIsDefault(check))
294 if (ParamIsDefault(theta_offset))
297 if (ParamIsDefault(theta_range))
305 duplicate /free dist, dist_smoo
306 duplicate /free theta, theta_int
307 theta_int = theta - theta_offset
308 duplicate /free phi, phi_int
309 setscale /p x phi_int[0], phi_int[1] - phi_int[0], waveunits(phi, -1), dist, dist_smoo
311 extract /free /indx dist, red_idx, theta_int < theta_range
312 duplicate /free red_idx, red_dist, red_phi
313 red_dist = dist[red_idx]
314 red_phi = phi_int[red_idx]
316 variable wavg = mean(red_dist)
317 make /n=4 /d /free coef
318 coef[0] = {wavg, wavg/100, pi/180, 0}
319 CurveFit /q /h=
"0010" /g /w=2 sin, kwcWave=coef, red_dist /x=red_phi
320 dist_smoo = coef[0] + coef[1] * sin(coef[2] * phi_int[p] + coef[3])
324 strip = strip / dist_smoo[q] * coef[0]
329 duplicate /o dist, check_dist
330 duplicate /o dist_smoo, check_smoo
331 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
369 variable theta_offset
370 variable smooth_method
371 variable smooth_factor
374 if (ParamIsDefault(check))
377 if (ParamIsDefault(theta_offset))
380 if (ParamIsDefault(smooth_method))
383 if (ParamIsDefault(smooth_factor))
391 duplicate /free dist, dist_smoo
392 duplicate /free theta, theta_int
393 theta_int = theta - theta_offset
394 setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
395 variable nx = dimsize(strip, 0)
398 switch(smooth_method)
400 Smooth /B /E=3 smooth_factor, dist_smoo
403 Smooth /E=3 smooth_factor, dist_smoo
406 loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={theta_int}
409 for (ix = 0; ix < nx; ix += 1)
411 if (smooth_factor > 1)
412 CurveFit /nthr=0 /q /w=2 poly smooth_factor+1, dist /x=theta_int /d=dist_smoo
414 CurveFit /nthr=0 /q /w=2 line, dist /x=theta_int /d=dist_smoo
416 strip[ix,ix][] /= dist_smoo[q]
424 strip /= dist_smoo[q]
429 duplicate /o dist, check_dist
430 duplicate /o dist_smoo, check_smoo
431 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
468 variable theta_offset
469 variable smooth_method
470 variable smooth_factor
473 if (ParamIsDefault(check))
476 if (ParamIsDefault(theta_offset))
479 if (ParamIsDefault(smooth_method))
482 if (ParamIsDefault(smooth_factor))
490 duplicate /free dist, dist_smoo
491 duplicate /free theta, theta_int
492 theta_int = theta - theta_offset
493 setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
494 variable nx = dimsize(strip, 0)
497 switch(smooth_method)
499 loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={theta_int, phi}
502 abort
"smooth method not supported" 507 strip /= dist_smoo[q]
512 duplicate /o dist, check_dist
513 duplicate /o dist_smoo, check_smoo
514 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
526 variable theta_offset
527 variable smooth_method
528 variable smooth_factor
531 if (ParamIsDefault(check))
534 if (ParamIsDefault(theta_offset))
537 if (ParamIsDefault(smooth_method))
540 if (ParamIsDefault(smooth_factor))
548 duplicate /free dist, dist_smoo
549 duplicate /free theta, theta_int
550 theta_int = theta - theta_offset
551 setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
554 duplicate /free theta_int, d1_theta, d2_theta
555 Differentiate /METH=2 theta_int /D=d1_theta
556 Differentiate /METH=2 d1_theta /D=d2_theta
557 d2_theta = abs(d2_theta)
559 FindLevels /edge=1 /p /q /d=w_levels d2_theta, 0.1
561 abort "unrecognized scanning scheme"
563 w_levels = ceil(w_levels)
564 InsertPoints 0, 1, w_levels
566 InsertPoints numpnts(w_levels), 1, w_levels
567 w_levels[numpnts(w_levels)-1] = numpnts(theta_int)
569 variable n_scans = numpnts(w_levels) - 1
572 for (i_scan = 0; i_scan < n_scans; i_scan += 1)
573 p1 = w_levels[i_scan]
574 p2 = w_levels[i_scan+1] - 1
575 duplicate /free /r=[p1, p2] dist, dist_piece, smooth_piece
576 duplicate /free /r=[p1, p2] theta_int, theta_piece
577 switch(smooth_method)
579 loess /dest=smooth_piece /smth=(smooth_factor) srcWave=dist_piece, factors={theta_piece}
582 abort
"smooth method not supported" 584 dist_smoo[p1, p2] = smooth_piece[p - p1]
589 strip /= dist_smoo[q]
594 duplicate /o dist, check_dist
595 duplicate /o dist_smoo, check_smoo
596 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
616 variable theta_offset
617 variable smooth_method
618 variable smooth_factor
621 if (ParamIsDefault(check))
624 if (ParamIsDefault(theta_offset))
627 if (ParamIsDefault(smooth_method))
630 if (ParamIsDefault(smooth_factor))
634 variable nx = dimsize(strip, 0)
635 variable ny = dimsize(strip, 1)
637 duplicate /free strip, dist, alpha_int, theta_int
638 theta_int = theta[q] - theta_offset
639 alpha_int = dimoffset(strip, 0) + p * dimdelta(strip, 0)
640 redimension /n=(nx * ny) dist, alpha_int, theta_int
642 switch(smooth_method)
644 loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={alpha_int, theta_int}
645 redimension /n=(nx, ny) dist_smoo
648 Abort
"undefined smooth method" 660 duplicate /o dist_smoo, check_smoo
678 variable plo = round((xlo - dimoffset(strip, 0)) / dimdelta(strip, 0))
679 variable phi = round((xhi - dimoffset(strip, 0)) / dimdelta(strip, 0))
680 xlo = plo * dimdelta(strip, 0) + dimoffset(strip, 0)
681 xhi = phi * dimdelta(strip, 0) + dimoffset(strip, 0)
682 variable nx = phi - plo + 1
683 variable ny = dimsize(strip, 1)
685 duplicate /free strip, strip_copy
686 redimension /n=(nx,ny) strip
687 strip = strip_copy[p + plo][q]
688 setscale /i x xlo, xhi, waveunits(strip, 0), strip
713 extract /indx /free theta, idx, (theta >= theta_lo) && (theta <= theta_hi)
714 variable nx = dimsize(strip, 0)
715 variable ny = numpnts(idx)
717 theta[0, ny-1] = theta[idx]
718 tilt[0, ny-1] = tilt[idx]
719 phi[0, ny-1] = phi[idx]
720 redimension /n=(ny) theta, tilt, phi
722 duplicate /free strip, strip_copy
723 redimension /n=(nx,ny) strip
724 strip = strip_copy[p][idx[q]]
769 function
pizza_service (data, nickname, theta_offset, tilt_offset, phi_offset, [npolar, nograph, folding, xpdplot])
772 variable theta_offset
780 if (ParamIsDefault(npolar))
783 if (ParamIsDefault(nograph))
786 if (ParamIsDefault(folding))
789 if (ParamIsDefault(xpdplot))
794 dfref saveDF = GetDataFolderDFR()
795 dfref dataDF = GetWavesDataFolderDFR(data)
797 if (DataFolderExists(":attr"))
800 dfref attrDF = GetDataFolderDFR()
802 wave /sdfr=attrDF ManipulatorTheta
803 wave /sdfr=attrDF ManipulatorTilt
804 wave /sdfr=attrDF ManipulatorPhi
806 if ((dimsize(ManipulatorTheta, 0) != dimsize(data, 1)) || (dimsize(ManipulatorTilt, 0) != dimsize(data, 1)) || (dimsize(ManipulatorPhi, 0) != dimsize(data, 1)))
807 Abort "Warning: The dimension size of the manipulator waves does not match the Y dimension of the data wave!\rIf you restructured the data wave, please use
pizza_service_2 with properly scaled manipulator waves."
810 duplicate /free ManipulatorTheta, m_theta
811 duplicate /free ManipulatorTilt, m_tilt
812 duplicate /free ManipulatorPhi, m_phi
814 m_theta -= theta_offset
815 m_tilt -= tilt_offset
818 pizza_service_2 (data, nickname, m_theta, m_tilt, m_phi, npolar=npolar, nograph=nograph, folding=folding, xpdplot=xpdplot)
862 function
pizza_service_2 (data, nickname, m_theta, m_tilt, m_phi, [npolar, nograph, folding, xpdplot])
873 if (ParamIsDefault(npolar))
876 if (ParamIsDefault(nograph))
879 if (ParamIsDefault(folding))
882 if (ParamIsDefault(xpdplot))
886 if ((dimsize(m_theta, 0) != dimsize(data, 1)) || (dimsize(m_tilt, 0) != dimsize(data, 1)) || (dimsize(m_phi, 0) != dimsize(data, 1)))
887 Abort "Warning: The dimension size of the manipulator waves does not match the Y dimension of the data wave!"
890 string graphname = "graph_" + nickname
891 string outprefix = nickname
894 dfref saveDF = GetDataFolderDFR()
895 dfref dataDF = GetWavesDataFolderDFR(data)
903 newdatafolder /s/o $nickname
906 dfref destDF = GetDataFolderDFR()
910 variable /g pol_perf_secs
911 timerRefNum = startMSTimer
913 duplicate /free m_tilt, corr_tilt
914 duplicate /free m_phi, corr_phi
918 make /n=1/d/free d_polar, d_azi
924 for (ifold = 0; ifold < folding; ifold += 1)
925 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
927 d_azi += 360 / folding
931 if (strlen(outprefix))
932 string s_prefix = outprefix + "_"
933 string s_int = s_prefix + "i"
947 if (timerRefNum >= 0)
948 pol_perf_secs = stopMSTimer(timerRefNum) / 1e6
979 function
show_analyser_line (theta, tilt, phi, theta_offset, tilt_offset, phi_offset, [npolar, nograph, xpdplot])
983 variable theta_offset
990 string nickname = "analyser"
992 if (ParamIsDefault(npolar))
995 if (ParamIsDefault(nograph))
998 if (ParamIsDefault(xpdplot))
1001 string graphname = "graph_" + nickname
1002 string outprefix = nickname
1005 dfref saveDF = GetDataFolderDFR()
1006 dfref dataDF = saveDF
1009 outprefix = nickname
1011 setdatafolder dataDF
1012 newdatafolder /s/o $nickname
1015 dfref destDF = GetDataFolderDFR()
1017 make /n=1 /free m_theta
1018 make /n=1 /free m_tilt
1019 make /n=1 /free m_phi
1020 m_theta = theta - theta_offset
1021 m_tilt = tilt - tilt_offset
1023 m_phi = phi - phi_offset
1026 make /n=60 /free data
1027 setscale /i x -30, 30, data
1029 make /n=1/d/free d_polar, d_azi
1033 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
1041 setdatafolder saveDF
1050 wave theta, tilt, phi
1055 make /n=(dimsize(data, 0)) /d /free ana
1056 setscale /p x dimoffset(data, 0), dimdelta(data, 0), waveunits(data, 0), ana
1095 variable nn = numpnts(theta)
1096 variable na = numpnts(analyser)
1097 redimension /n=(na, nn) polar, azi
1104 make /n=(3,na) /d /free w_orig_polar, w_orig_cart, w_rot_cart, w_rot_polar
1105 w_orig_polar[0][] = radius
1106 w_orig_polar[1][] = analyser[q]
1107 w_orig_polar[2][] = 0
1113 for (ii = 0; ii < nn; ii += 1)
1119 w_rot_cart = w_orig_cart
1126 polar[][ii] = w_rot_polar[1][p]
1127 azi[][ii] = w_rot_polar[2][p]
1137 variable nn = dimsize(source, 1)
1138 make /n=(dimsize(source, 0))/d/free line
1139 for (ii = 0; ii < nn; ii += 1)
1140 line = source[p][ii]
1142 dest[][ii] = line[p] / v_max
1149 static function
calc_nth (Theta_st, Theta_in, th, Phi_ran, Phi_ref, Holomode)
1150 Variable Theta_st, Theta_in, th, Phi_ran, Phi_ref
1153 Variable deg2rad=0.01745329
1155 if ( cmpstr(Holomode, "Stereographic") == 0)
1156 The_step =trunc( Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st )
1158 The_step =trunc( Phi_ran*sin(th*pi/180)*Phi_ref/Theta_st )
1161 if (cmpstr(Holomode, "Parallel") == 0)
1162 The_step=trunc( Phi_ran*tan(th*deg2rad)*Phi_ref/Theta_st )
1164 if ( cmpstr(Holomode, "h") == 0)
1165 The_step=trunc( th/Theta_in*Phi_ran/Theta_st )
1178 static function
calc_phi_step (Theta_in, th, Theta_st, Phi_ran, Phi_ref, Holomode)
1179 Variable Theta_in, th, Theta_st, Phi_ran, Phi_ref
1183 Variable deg2rad=0.01745329
1185 if ( cmpstr(Holomode, "Stereographic") == 0 )
1186 if ((th < 0.5) || (trunc(Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st) == 0))
1189 Phi_st=Phi_ran/(trunc(Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st))
1196 if ( cmpstr(Holomode, "Parallel") == 0 )
1197 if((th < 0.5) || (trunc(Phi_ran*tan(th*deg2rad)*Phi_ref/Theta_st) == 0))
1200 Phi_st=Phi_ran/(trunc(Phi_ran*tan(th*deg2rad)*Phi_ref/Theta_st))
1204 if ( cmpstr(Holomode, "h") == 0 )
1205 if((th < 0.5) || (trunc(Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st) == 0))
1208 Phi_st=Phi_ran/trunc(th/Theta_in*Phi_ran/Theta_st)
1224 Variable th, Theta_st
1226 Variable deg2rad=0.01745329, dt_loc,The_step
1228 if ( (cmpstr(Holomode, "Stereographic")) ==0 )
1232 if ( (cmpstr(Holomode, "h")) ==0 )
1236 if ( cmpstr(Holomode, "Parallel") == 0 )
1238 dt_loc = Theta_st/cos(th*deg2rad)
1255 Variable Theta_in,Theta_ran,Theta_st
1256 Variable n_theta, aux, aux1,ii
1259 aux1= Theta_in - Theta_ran
1263 if(aux<=Theta_in-Theta_ran)
1264 aux=Theta_in-Theta_ran
1267 while((aux>aux1)%&(Theta_in-aux<=Theta_ran))
1296 if (ParamIsDefault(xpdplot))
1300 string HoloMode = "h"
1301 variable Theta_in = 90
1302 variable Theta_ran = 90
1303 variable Theta_st = 90 / (npol - 1)
1304 variable Phi_ran = 360
1305 variable Phi_ref = 1
1308 variable n_theta =
CalcN_Theta (HoloMode, Theta_in, Theta_ran, Theta_st)
1311 if (strlen(nickname))
1312 string s_prefix = nickname + "_"
1313 string s_int = s_prefix + "i"
1318 string s_polar = s_prefix + "pol"
1319 string s_azim = s_prefix + "az"
1321 string s_index = s_prefix + "index"
1322 string s_theta = s_prefix + "th"
1323 string s_dphi = s_prefix + "dphi"
1324 string s_nphis = s_prefix + "nphis"
1326 string s_HoloData = s_prefix + "data"
1327 string s_HoloInfo = s_prefix + "info"
1330 string s_tot = s_prefix + "tot"
1331 string s_weight = s_prefix + "wt"
1333 make /O/D/n=(n_theta) $s_index /wave=index
1334 make /O/D/n=(n_theta) $s_theta /wave=theta
1335 make /O/D/n=(n_theta) $s_dphi /wave=dphi
1336 make /O/D/n=(n_theta) $s_nphis /wave=nphis
1340 dphi[0] =
calc_phi_step (Theta_in, Theta_in, aux, Phi_ran, Phi_ref, HoloMode)
1342 nphis[0] =
calc_nth (aux, Theta_in, Theta_in, Phi_ran, Phi_ref, HoloMode)
1348 Theta[ii] = Theta[ii-1] - aux
1349 if(Theta[ii] <= Theta_in-Theta_ran)
1350 Theta[ii] = Theta_in-Theta_ran
1353 dphi[ii] =
calc_phi_step (Theta_in, Theta[ii], aux, Phi_ran, Phi_ref, HoloMode)
1354 nphis[ii] =
calc_nth (aux, Theta_in, Theta[ii], Phi_ran, Phi_ref, HoloMode)
1355 Index[ii] = Index[ii-1] + nphis[ii]
1359 if (Index[n_theta-1]==Index[n_theta-2])
1360 Index[n_theta-1]=Index[n_theta-2]+1
1364 variable NumPoints = sum(nphis, 0, numpnts(nphis))
1367 make /O/D/N=(NumPoints) $s_polar /wave=polar, $s_azim /wave=azim
1371 variable StartIndex = 0
1375 Polar[StartIndex, EndIndex-1]=Theta[ii]
1376 Azim[StartIndex, EndIndex-1]= mod(Phi_ran+(x-StartIndex)*dphi[ii]+Phi_in,Phi_ran)
1378 StartIndex = EndIndex
1381 duplicate /o azim, $s_int /wave=values
1382 duplicate /o azim, $s_tot /wave=totals
1383 duplicate /o azim, $s_weight /wave=weights
1390 string s_FileName = ""
1391 string s_Comment = "created by pearl-anglescan-process.ipf"
1392 string s_HoloMode = "Stereographic"
1393 variable /g gb_SpectraFile = 0
1395 Make/O/D/n=22 $s_HoloData /wave=HoloData
1398 HoloData[6] = NumPoints
1399 HoloData[7] = Theta_in
1400 HoloData[8] = Theta_ran
1401 HoloData[9] = Theta_st
1402 HoloData[11] = Phi_in
1403 HoloData[12] = Phi_ran
1404 HoloData[13] = Theta_st
1405 HoloData[15] = Phi_ref
1406 HoloData[16] = Phi_ran
1409 Make/O/T/n=22 $s_HoloInfo /wave=HoloInfo
1410 HoloInfo[0] = s_FileName
1411 HoloInfo[1] = s_Comment
1412 HoloInfo[10] = s_HoloMode
1416 if (WinType(NickName) == 5)
1417 Notebook $NickName selection={startOfFile, endOfFile}
1418 Notebook $NickName text=
"" 1420 NewNotebook /F=0 /K=1 /N=$NickName /W=(5,40,341,260)
1421 Notebook $NickName defaultTab=140
1422 Notebook $NickName statusWidth=300
1423 Notebook $NickName backRGB=(56797,56797,56797)
1424 Notebook $NickName pageMargins={80,80,80,80}
1425 Notebook $NickName fSize=10
1426 Notebook $NickName fStyle=0,textRGB=(65535,0,26214)
1427 Notebook $NickName textRGB=(65535,0,26214)
1429 Notebook $NickName text =
"File:\t" + s_FileName +
"\r" 1430 Notebook $NickName text =
"*** " + s_Comment +
" ***\r\r" 1431 Notebook $NickName text =
"Angle-Mode:\t" + s_HoloMode +
"\r" 1432 Notebook $NickName text =
"XPDplot Nickname:\t" + NickName +
"\r" 1446 string wname = nameofwave(w)
1452 string s_wave_df = GetWavesDataFolder(w, 1)
1453 dfref parent_df = $(s_wave_df + "::")
1454 nickname = GetDataFolder(0, parent_df)
1470 string wname = nameofwave(w)
1472 if (ItemsInList(wname, "_") >= 2)
1473 prefix = StringFromList(0, wname, "_")
1506 if (strlen(nickname))
1507 if (DataFolderExists(nickname))
1510 datadf = getdatafolderdfr()
1511 prefix = nickname + "_"
1512 intwave = prefix + "i"
1513 if (exists(intwave) != 1)
1518 datadf = getdatafolderdfr()
1540 string s_totals = s_prefix + "tot"
1541 string s_weights = s_prefix + "wt"
1543 wave /sdfr=datadf /z w_values = $s_int
1544 wave /sdfr=datadf /z w_totals = $s_totals
1545 wave /sdfr=datadf /z w_weights = $s_weights
1547 if (waveexists(w_totals))
1550 if (waveexists(w_weights))
1553 if (waveexists(w_values))
1580 string source_nickname
1582 string dest_nickname
1585 if (ParamIsDefault(xpdplot))
1589 dfref savedf = getdatafolderdfr()
1592 string s_prefix = ""
1593 string s_int = "values"
1594 dfref source_df =
find_hemi_data (source_nickname, s_prefix, s_int)
1595 string s_polar = s_prefix + "pol"
1596 string s_azim = s_prefix + "az"
1597 string s_theta = s_prefix + "th"
1598 string s_tot = s_prefix + "tot"
1599 string s_weight = s_prefix + "wt"
1600 string s_matrix = s_prefix + "matrix"
1602 wave /sdfr=source_df theta1 = $s_theta
1603 wave /sdfr=source_df polar1 = $s_polar
1604 wave /sdfr=source_df azim1 = $s_azim
1605 wave /sdfr=source_df tot1 = $s_tot
1606 wave /sdfr=source_df weight1 = $s_weight
1607 wave /sdfr=source_df values1 = $s_int
1608 wave /sdfr=source_df /z matrix1 = $s_matrix
1610 variable npol = numpnts(theta1)
1612 setdatafolder dest_folder
1617 s_polar = s_prefix + "pol"
1618 s_azim = s_prefix + "az"
1619 s_theta = s_prefix + "th"
1620 s_tot = s_prefix + "tot"
1621 s_weight = s_prefix + "wt"
1622 s_matrix = s_prefix + "matrix"
1624 wave /sdfr=dest_df theta2 = $s_theta
1625 wave /sdfr=dest_df polar2 = $s_polar
1626 wave /sdfr=dest_df azim2 = $s_azim
1627 wave /sdfr=dest_df tot2 = $s_tot
1628 wave /sdfr=dest_df weight2 = $s_weight
1629 wave /sdfr=dest_df values2 = $s_int
1634 if (waveexists(matrix1))
1635 setdatafolder dest_df
1636 duplicate /o matrix1, $s_matrix
1639 if (!(NumberByKey("
version ", note(azim1), "=", "\r") >= 1.6))
1641 azim2 = azim2 >= 360 ? azim2 - 360 : azim2
1644 setdatafolder saveDF
1658 dfref savedf = getdatafolderdfr()
1660 string s_prefix = ""
1661 string s_int = "values"
1664 string s_polar = s_prefix + "pol"
1665 string s_azim = s_prefix + "az"
1666 string s_tot = s_prefix + "tot"
1667 string s_weight = s_prefix + "wt"
1669 wave /sdfr=df polar = $s_polar
1670 wave /sdfr=df azim = $s_azim
1671 wave /sdfr=df tot = $s_tot
1672 wave /sdfr=df weight = $s_weight
1673 wave /sdfr=df values = $s_int
1676 azim = azim < 0 ? azim + 360 : azim
1677 azim = azim >= 360 ? azim - 360 : azim
1679 duplicate /free polar, neg_polar
1681 sort {neg_polar, azim}, polar, azim, tot, weight, values
1683 setdatafolder saveDF
1706 dfref savedf = getdatafolderdfr()
1708 if (ParamIsDefault(projection))
1713 string s_prefix = ""
1714 string s_int = "values"
1717 string s_polar = s_prefix + "pol"
1718 string s_azim = s_prefix + "az"
1720 wave /sdfr=df /z values = $s_int
1721 wave /sdfr=df /z azim = $s_azim
1722 wave /sdfr=df /z polar = $s_polar
1725 string s_ster_rad = s_prefix + "ster_rad"
1726 duplicate /o polar, $s_ster_rad /wave=ster_rad
1729 string s_ster_x = s_prefix + "ster_x"
1730 string s_ster_y = s_prefix + "ster_y"
1731 duplicate /o azim, $s_ster_x /wave=ster_x, $s_ster_y /wave=ster_y
1732 ster_x = ster_rad * cos(azim * pi / 180)
1733 ster_y = ster_rad * sin(azim * pi / 180)
1735 setdatafolder savedf
1792 dfref savedf = getdatafolderdfr()
1794 if (ParamIsDefault(projection))
1797 if (ParamIsDefault(graphtype))
1800 if (ParamIsDefault(do_ticks))
1803 if (ParamIsDefault(do_grids))
1806 if (ParamIsDefault(graphname))
1807 if (strlen(nickname) > 0)
1808 graphname = nickname
1810 graphname = GetDataFolder(0)
1817 string s_prefix = ""
1818 string s_int = "values"
1821 string s_polar = s_prefix + "pol"
1822 string s_azim = s_prefix + "az"
1823 string s_matrix = s_prefix + "matrix"
1824 string s_ster_rad = s_prefix + "ster_rad"
1826 wave /sdfr=df /z values = $s_int
1827 wave /sdfr=df /z azim = $s_azim
1828 wave /sdfr=df /z polar = $s_polar
1829 wave /sdfr=df /z ster_rad = $s_ster_rad
1830 wave /sdfr=df /z matrix = $s_matrix
1833 variable azim_offset = 0
1834 if (!(NumberByKey("
version ", note(azim), "=", "\r") >= 1.6))
1835 DoAlert /T="display hemi scan" 0, "your dataset doesn't include the version 1.6 flag. if it was created with an earlier version that might be okay. please check that the orientation is correct!"
1842 if (str2num(GetUserData(graphname, "", "graphtype")) == graphtype)
1847 killwindow $graphname
1855 s_trace = WMPolarAppendTrace(graphname, ster_rad, azim, 360)
1856 ModifyGraph /W=$graphname mode($s_trace)=2, lsize($s_trace)=2
1857 ModifyGraph /W=$graphname zColor($s_trace)={values,*,*,BlueGreenOrange,0}
1859 ColorScale /W=$graphname /C /N=text0 /E=2 /F=0 /B=1 /A=RB /X=0.00 /Y=0.00 trace=polarY0
1860 ColorScale /W=$graphname /C /N=text0 side=2, width=5, heightPct=40, frame=0.50, lblMargin=0
1861 ColorScale /W=$graphname /C /N=text0 nticks=2, minor=1, tickLen=4.00, tickThick=0.50
1863 SetWindow $graphname, userdata(projection)=num2str(projection)
1864 SetWindow $graphname, userdata(graphtype)=num2str(graphtype)
1870 s_trace = WMPolarAppendTrace(graphname, ster_rad, azim, 360)
1871 ModifyGraph /W=$graphname mode($s_trace)=0, lsize($s_trace)=0
1872 AppendImage /L=VertCrossing /B=HorizCrossing matrix
1874 ColorScale /W=$graphname /C /N=text0 /E=2 /F=0 /B=1 /A=RB /X=0.00 /Y=0.00 image=$s_matrix
1875 ColorScale /W=$graphname /C /N=text0 side=2, width=5, heightPct=40, frame=0.50, lblMargin=0
1876 ColorScale /W=$graphname /C /N=text0 nticks=2, minor=1, tickLen=4.00, tickThick=0.50
1878 SetWindow $graphname, userdata(projection)=num2str(projection)
1879 SetWindow $graphname, userdata(graphtype)=num2str(graphtype)
1884 setdatafolder savedf
1932 variable angle_offset
1935 dfref savedf = GetDataFolderDFR()
1937 if (ParamIsDefault(angle_offset))
1940 if (ParamIsDefault(do_ticks))
1944 if ((strlen(graphname) == 0) || (wintype(graphname) == 0))
1945 Display /k=1 /W=(10,45,360,345)
1946 DoWindow /C $graphname
1947 graphname = WMNewPolarGraph("", graphname)
1948 WMPolarGraphSetVar(graphname, "zeroAngleWhere", angle_offset)
1950 WMPolarGraphSetVar(graphname, "angleAxisThick", 0.5)
1951 WMPolarGraphSetStr(graphname, "doMajorAngleTicks", "manual")
1952 WMPolarGraphSetVar(graphname, "majorAngleInc", 30)
1953 WMPolarGraphSetVar(graphname, "minorAngleTicks", 2)
1954 WMPolarGraphSetStr(graphname, "angleTicksLocation", "Outside")
1955 WMPolarGraphSetVar(graphname, "doAngleTickLabelSubRange", 1)
1956 WMPolarGraphSetVar(graphname, "angleTickLabelRangeStart", 0)
1957 WMPolarGraphSetVar(graphname, "angleTickLabelRangeExtent", 90)
1958 WMPolarGraphSetStr(graphname, "angleTickLabelNotation", "%g°")
1960 WMPolarGraphSetVar(graphname, "doPolarGrids", 0)
1961 WMPolarGraphSetVar(graphname, "doRadiusTickLabels", 0)
1962 WMPolarGraphSetStr(graphname, "radiusAxesWhere", " Off")
1963 WMPolarGraphSetStr(graphname, "radiusTicksLocation", "Off")
1965 WMPolarGraphSetVar(graphname, "majorTickLength", 2)
1966 WMPolarGraphSetVar(graphname, "majorTickThick", 0.5)
1967 WMPolarGraphSetVar(graphname, "minorTickLength", 1)
1968 WMPolarGraphSetVar(graphname, "minorTickThick", 0.5)
1969 WMPolarGraphSetVar(graphname, "tickLabelOpaque", 0)
1970 WMPolarGraphSetVar(graphname, "tickLabelFontSize", 7)
1974 WMPolarGraphSetStr(graphname, "angleTicksLocation", "Outside")
1976 WMPolarGraphSetStr(graphname, "angleTicksLocation", "Off")
1979 WMPolarGraphSetVar(graphname, "doMinorAngleTicks", 1)
1981 WMPolarGraphSetVar(graphname, "doMinorAngleTicks", 0)
1984 DoWindow /T $graphname, graphname
1987 string graphdf = "root:packages:WMPolarGraphs:" + graphname
1988 setdatafolder graphdf
1990 variable /g csrA_theta
1991 variable /g csrA_phi
1992 variable /g csrB_theta
1993 variable /g csrB_phi
1997 tb = tb + " \
"A = (%.1f, %.1f)\"," 1998 tb = tb + graphdf +
":csrA_theta," 1999 tb = tb + graphdf +
":csrA_phi" 2001 TextBox /W=$graphname /A=LT /B=1 /E=2 /F=0 /N=tb_angles /X=1 /Y=1 /V=0 tb
2003 tb = tb +
"\"B = (%.1f, %.1f)\"," 2004 tb = tb + graphdf +
":csrB_theta," 2005 tb = tb + graphdf +
":csrB_phi" 2007 AppendText /W=$graphname /N=tb_angles tb
2012 DoWindow /F $graphname
2015 setdatafolder savedf
2048 if (ParamIsDefault(do_grids))
2052 dfref savedf = GetDataFolderDFR()
2054 string sproj = GetUserData(graphname, "", "projection")
2055 variable projection = str2num("0" + sproj)
2057 SetDrawLayer /W=$graphname ProgFront
2060 SetDrawEnv /W=$graphname xcoord=HorizCrossing, ycoord=VertCrossing
2061 SetDrawEnv /W=$graphname linethick= 0.5
2062 SetDrawEnv /W=$graphname dash=2
2063 SetDrawEnv /W=$graphname fillpat=0
2064 SetDrawEnv /W=$graphname fname="default", fsize=7
2065 SetDrawEnv /W=$graphname textxjust=1, textyjust=1
2067 SetDrawEnv /W=$graphname save
2070 DrawLine /W=$graphname 0, -2, 0, 2
2071 DrawLine /W=$graphname -2, 0, 2, 0
2077 DrawOval /W=$graphname -radi, radi, radi, -radi
2078 radi = calc_graph_radius(30, projection=projection)
2079 DrawOval /W=$graphname -radi, radi, radi, -radi
2080 radi = calc_graph_radius(60, projection=projection)
2081 DrawOval /W=$graphname -radi, radi, radi, -radi
2083 SetDrawEnv /W=$graphname textxjust= 1,textyjust= 2
2084 SetDrawEnv /W=$graphname save
2085 radi = calc_graph_radius(30, projection=projection)
2086 DrawText /W=$graphname radi, -0.1, "30°"
2087 radi = calc_graph_radius(60, projection=projection)
2088 DrawText /W=$graphname radi, -0.1, "60°"
2091 setdatafolder savedf
2121 variable theta_inner
2124 variable r_axis = calc_graph_radius(theta_axis)
2125 variable r_inner = calc_graph_radius(theta_inner)
2126 variable r_outer = calc_graph_radius(2 * theta_axis - theta_inner)
2129 SetDrawLayer UserFront
2130 DrawAction getgroup=$groupname, delete
2131 SetDrawEnv gstart, gname=$groupname
2132 variable xc, yc, xr, yr
2135 variable r_center = (r_outer + r_inner) / 2
2136 variable r_radius = (r_outer - r_inner) / 2
2137 xc = r_center * cos(phi * pi / 180)
2138 yc = r_center * sin(phi * pi / 180)
2141 SetDrawEnv xcoord=HorizCrossing, ycoord=VertCrossing
2142 SetDrawEnv dash=11, fillpat=0
2143 DrawOval xc - xr, yc - yr, xc + xr, yc + yr
2146 xc = r_axis * cos(phi * pi / 180)
2147 yc = r_axis * sin(phi * pi / 180)
2148 r_radius = calc_graph_radius(2)
2151 SetDrawEnv xcoord=HorizCrossing, ycoord=VertCrossing
2152 SetDrawEnv fillfgc=(0,0,0)
2153 DrawOval xc - xr, yc - yr, xc + xr, yc + yr
2180 function /s
display_scanlines (nickname, alpha_lo, alpha_hi, m_theta, m_tilt, m_phi, [folding, projection])
2190 if (ParamIsDefault(folding))
2193 if (ParamIsDefault(projection))
2198 dfref saveDF = GetDataFolderDFR()
2199 newdatafolder /s/o $nickname
2200 string graphname = "graph_" + nickname
2202 duplicate /free m_tilt, loc_m_tilt
2203 loc_m_tilt = -m_tilt
2205 make /n=1 /d /free d_polar, d_azi
2206 variable n_alpha = round(alpha_hi - alpha_lo) + 1
2207 make /n=(n_alpha) /d /free analyser
2208 setscale /i x alpha_lo, alpha_hi, "°", analyser
2212 duplicate /free d_polar, d_radius
2213 d_radius = calc_graph_radius(d_polar, projection=projection)
2217 SetWindow $graphname, userdata(projection)=num2str(projection)
2221 variable nang = numpnts(m_theta)
2225 for (ifold = 0; ifold < folding; ifold += 1)
2226 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
2227 for (iang = 0; iang < nang; iang += 1)
2228 sprintf s_rad, "rad_%d_%d", ifold, iang
2229 duplicate /o analyser, $s_rad
2231 w_rad = d_radius[p][iang]
2233 sprintf s_azi, "azi_%d_%d", ifold, iang
2234 duplicate /o analyser, $s_azi
2236 w_azi = d_azi[p][iang]
2238 if (numtype(sum(w_rad)) == 0)
2239 s_trace = WMPolarAppendTrace(graphname, w_rad, w_azi, 360)
2240 ModifyGraph /w=$graphname mode($s_trace)=0, lsize($s_trace)=0.5
2243 d_azi += 360 / folding
2248 setdatafolder saveDF
2295 threadsafe function calc_graph_radius(polar, [projection])
2299 if (ParamIsDefault(projection))
2312 radius = polar < 90 ?
kProjScaleGnom * tan(polar * pi / 180) : inf
2345 if (ParamIsDefault(projection))
2352 radius = sqrt(x^2 + y^2)
2399 if (ParamIsDefault(projection))
2402 if (ParamIsDefault(zeroAngle))
2408 azi = atan(y / x) * 180 / pi
2410 azi = atan(y / x) * 180 / pi + 180
2420 if (numtype(azi) != 0)
2441 dfref savedf = GetDataFolderDFR()
2443 string graphdf = "root:packages:WMPolarGraphs:" + graphname
2444 setdatafolder graphdf
2451 string sproj = GetUserData(graphname, "", "projection")
2452 variable projection = str2num("0" + sproj)
2455 variable x = hcsr(A, graphname)
2456 variable y = vcsr(A, graphname)
2458 csrA_phi =
calc_graph_azi (x, y, projection=projection, zeroAngle=zeroAngleWhere)
2460 x = hcsr(B, graphname)
2461 y = vcsr(B, graphname)
2463 csrB_phi =
calc_graph_azi (x, y, projection=projection, zeroAngle=zeroAngleWhere)
2465 setdatafolder savedf
2474 STRUCT WMWinHookStruct &s
2476 Variable hookResult = 0
2483 TextBox /W=$s.winname /N=tb_angles /C /V=1
2486 TextBox /W=$s.winname /N=tb_angles /C /V=0
2496 variable polar_angle
2500 if (ParamIsDefault(graphname))
2501 if (strlen(nickname) > 0)
2502 graphname = nickname
2504 graphname = GetDataFolder(0)
2508 string s_prefix = ""
2509 string s_int = "values"
2512 string s_polar = s_prefix + "pol"
2513 string s_azim = s_prefix + "az"
2514 wave /sdfr=df /z azim = $s_azim
2515 wave /sdfr=df /z polar = $s_polar
2517 FindLevel /P /Q polar, polar_angle
2519 variable polar_level = floor(v_levelx)
2520 FindLevel /P /Q /R=[polar_level] azim, azim_angle
2522 variable azim_level = round(v_levelx)
2523 string tracename = "polarY0"
2524 Cursor /W=$graphname /P $cursorname $traceName azim_level
2550 if (ParamIsDefault(weights))
2551 duplicate /free values, weights
2556 string s_prefix = ""
2557 string s_int = "values"
2560 string s_polar = s_prefix + "pol"
2561 string s_azim = s_prefix + "az"
2562 string s_theta = s_prefix + "th"
2564 wave /sdfr=df /z w_values = $s_int
2565 wave /sdfr=df /z w_azim = $s_azim
2566 wave /sdfr=df /z w_polar = $s_polar
2567 wave /sdfr=df /z w_theta = $s_theta
2568 if (!waveexists(w_values) || !waveexists(w_azim) || !waveexists(w_polar))
2569 abort "Missing hemispherical scan grid. Please call
make_hemi_grid () first."
2573 duplicate /free values, values_copy
2574 duplicate /free polar, polar_copy
2575 duplicate /free azi, azi_copy
2576 duplicate /free weights, weights_copy
2577 variable nn = dimsize(values, 0) * max(dimsize(values, 1), 1)
2578 redimension /n=(nn) values_copy, polar_copy, azi_copy, weights_copy
2579 sort /r polar_copy, polar_copy, azi_copy, values_copy, weights_copy
2582 variable pol_st = abs(w_theta[1] - w_theta[0])
2585 duplicate /free azi_copy, azi_slice
2586 duplicate /free values_copy, values_slice
2587 duplicate /free weights_copy, weights_slice
2588 for (pol = 90; pol >= 0; pol -= pol_st)
2589 pol1 = pol - pol_st / 2
2590 pol2 = pol + pol_st / 2
2591 extract /free /indx polar_copy, sel, (pol1 < polar_copy) && (polar_copy <= pol2)
2592 if (numpnts(sel) > 0)
2593 redimension /n=(numpnts(sel)) azi_slice, values_slice, weights_slice
2594 azi_slice = azi_copy[sel]
2595 values_slice = values_copy[sel]
2596 weights_slice = weights_copy[sel]
2597 hemi_add_aziscan (nickname, values_slice, pol, azi_slice, weights=weights_slice)
2618 if (ParamIsDefault(weights))
2619 duplicate /free values, weights
2624 string s_prefix = ""
2625 string s_int = "values"
2628 string s_totals = s_prefix + "tot"
2629 string s_weights = s_prefix + "wt"
2630 string s_polar = s_prefix + "pol"
2631 string s_azim = s_prefix + "az"
2632 string s_index = s_prefix + "index"
2633 string s_theta = s_prefix + "th"
2634 string s_dphi = s_prefix + "dphi"
2635 string s_nphis = s_prefix + "nphis"
2637 wave /sdfr=df w_polar = $s_polar
2638 wave /sdfr=df w_azim = $s_azim
2639 wave /sdfr=df w_values = $s_int
2640 wave /sdfr=df w_totals = $s_totals
2641 wave /sdfr=df w_weights = $s_weights
2642 wave /sdfr=df w_index = $s_index
2643 wave /sdfr=df w_theta = $s_theta
2644 wave /sdfr=df w_dphi = $s_dphi
2645 wave /sdfr=df w_nphis = $s_nphis
2650 variable ipol = BinarySearch(w_theta, polar)
2652 abort "assertion failed in
hemi_add_aziscan (): polar angle not found in grid."
2657 d1 = w_index[ipol - 1]
2661 d2 = w_index[ipol] - 1
2662 variable nd = d2 - d1 + 1
2663 variable dphi = w_dphi[ipol]
2668 azi = azi < 0 ? azi + 360 : azi
2669 azi = azi >= 360 - dphi/2 ? azi - 360 : azi
2670 duplicate /free values, sel_values
2671 duplicate /free weights, sel_weights
2675 variable v1, v2, w1, w2
2676 for (
id = 0;
id < nd;
id += 1)
2677 az1 = (
id - 0.5) * dphi
2678 az2 = (
id + 0.5) * dphi
2679 extract /free /indx azi, sel, (az1 <= azi) && (azi < az2)
2680 if (numpnts(sel) > 0)
2681 redimension /n=(numpnts(sel)) sel_values, sel_weights
2682 sel_values = values[sel]
2683 sel_weights = weights[sel]
2684 v1 = w_totals[d1 +
id ]
2685 w1 = w_weights[d1 +
id ]
2686 if ((numtype(v1) == 2) || (w1 <= 0))
2690 v2 = sum(sel_values)
2691 w2 = sum(sel_weights)
2692 w_totals[d1 +
id ] = v1 + v2
2693 w_weights[d1 +
id ] = w1 + w2
2696 w_values[d1, d1 + nd - 1] = w_totals[p] / w_weights[p]
2730 dfref savedf = GetDataFolderDFR()
2732 if (ParamIsDefault(projection))
2736 string s_prefix = ""
2737 string s_int = "values"
2741 string s_polar = s_prefix + "pol"
2742 string s_azim = s_prefix + "az"
2743 string s_matrix = s_prefix + "matrix"
2744 string s_ster_rad = s_prefix + "ster_rad"
2745 string s_ster_x = s_prefix + "ster_x"
2746 string s_ster_y = s_prefix + "ster_y"
2748 wave /sdfr=df /z values = $s_int
2749 wave /sdfr=df /z azim = $s_azim
2750 wave /sdfr=df /z polar = $s_polar
2751 wave /sdfr=df /z ster_rad = $s_ster_rad
2752 wave /sdfr=df /z ster_x = $s_ster_x
2753 wave /sdfr=df /z ster_y = $s_ster_y
2755 variable min_ster_x = wavemin(ster_x)
2756 variable max_ster_x = wavemax(ster_x)
2757 variable x0 = min_ster_x
2759 variable dx = (max_ster_x - min_ster_x) / (xn - 1)
2760 make /n=(numpnts(ster_x), 3) /free triplet
2761 triplet[][0] = ster_x[p]
2762 triplet[][1] = ster_y[p]
2763 triplet[][2] = values[p]
2767 make /n=(size, size) /d /o $(s_prefix + "matrix") /wave=matrix
2768 make /n=(size, size) /free mnorm
2769 ImageFromXYZ /as {ster_x, ster_y, values}, matrix, mnorm
2771 matrixfilter NanZapMedian, matrix
2772 matrixfilter gauss, matrix
2774 duplicate /free values, ster_finite
2775 ster_finite = (numtype(values) == 0) * (ster_x^2 + ster_y^2)
2776 variable ster_max = wavemax(ster_finite)
2777 matrix = (x^2 + y^2) <= ster_max ? matrix : nan
2779 setdatafolder savedf
2792 function quick_pizza_image (data, nickname, theta_offset, tilt_offset, phi_offset, [npolar, nograph, folding])
2797 variable theta_offset
2798 variable tilt_offset
2806 if (ParamIsDefault(npolar))
2809 if (ParamIsDefault(nograph))
2812 if (ParamIsDefault(folding))
2815 string graphname =
"graph_" + nickname
2816 string s_prefix =
"" 2819 dfref saveDF = GetDataFolderDFR()
2820 dfref dataDF = GetWavesDataFolderDFR(data)
2821 setdatafolder dataDF
2822 if (DataFolderExists(
":attr" ))
2825 dfref attrDF = GetDataFolderDFR()
2826 setdatafolder dataDF
2827 newdatafolder /s/o $nickname
2828 dfref destDF = GetDataFolderDFR()
2831 variable timerRefNum
2832 variable /g xyz_perf_secs
2833 timerRefNum = startMSTimer
2835 wave /sdfr=attrDF ManipulatorTheta
2836 wave /sdfr=attrDF ManipulatorTilt
2837 wave /sdfr=attrDF ManipulatorPhi
2838 duplicate /free ManipulatorTheta, m_theta
2839 duplicate /free ManipulatorTilt, m_tilt
2840 duplicate /free ManipulatorPhi, m_phi
2841 m_theta -= theta_offset
2842 m_tilt -= tilt_offset
2847 make /n=1/d/free d_polar, d_azi
2850 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
2852 duplicate /free data, values
2853 variable nn = dimsize(values, 0) * max(dimsize(values, 1), 1)
2854 redimension /n=(nn) values, d_polar, d_azi
2855 duplicate /o d_polar, ster_rad, ster_x, ster_y
2857 variable projection = 1
2860 ster_rad = 2 * tan(d_polar / 2 * pi / 180)
2863 ster_rad = 2 * cos((180 - d_polar) / 2 * pi / 180)
2866 string s_ster_x = s_prefix + "ster_x"
2867 string s_ster_y = s_prefix + "ster_y"
2870 make /n=(nn, nn) /d /o matrix
2871 make /n=(nn, nn) /free mnorm
2872 setscale /i x -2, +2, matrix, mnorm
2873 setscale /i y -2, +2, matrix, mnorm
2878 for (ifold = 0; ifold < folding; ifold += 1)
2879 ster_x = ster_rad * cos(d_azi * pi / 180)
2880 ster_y = ster_rad * sin(d_azi * pi / 180)
2881 ImageFromXYZ {ster_x, ster_y, values}, matrix, mnorm
2882 d_azi = d_azi >= 180 ? d_azi + 360 / folding - 180 : d_azi + 360 / folding
2886 matrixfilter /n=5 NanZapMedian matrix
2887 matrixfilter /n=3 gauss matrix
2892 modifygraph width={Plan,1,bottom,left}
2895 if (timerRefNum >= 0)
2896 xyz_perf_secs = stopMSTimer(timerRefNum) / 1e6
2899 setdatafolder saveDF
2908 dfref savedf = getdatafolderdfr()
2911 string s_prefix = ""
2912 string s_int = "values"
2915 string s_polar = s_prefix + "pol"
2916 string s_azim = s_prefix + "az"
2917 string s_theta = s_prefix + "th"
2918 string s_tot = s_prefix + "tot"
2919 string s_weight = s_prefix + "wt"
2921 wave /sdfr=df theta1 = $s_theta
2922 wave /sdfr=df polar1 = $s_polar
2923 wave /sdfr=df azim1 = $s_azim
2924 wave /sdfr=df tot1 = $s_tot
2925 wave /sdfr=df weight1 = $s_weight
2926 wave /sdfr=df values1 = $s_int
2928 save /m="\r\n" /o /p=$pathname /t theta1, polar1, azim1, tot1, weight1, values1 as filename
2930 setdatafolder saveDF
2941 dfref savedf = getdatafolderdfr()
2950 setdatafolder saveDF
2985 function
import_tpi_scan (nickname, theta, phi, intensity, [folding, npolar, nograph, xpdplot])
2996 if (ParamIsDefault(npolar))
2999 if (ParamIsDefault(nograph))
3002 if (ParamIsDefault(folding))
3005 if (ParamIsDefault(xpdplot))
3012 duplicate /free phi, fold_phi
3013 for (ifold = 0; ifold < folding; ifold += 1)
3015 fold_phi = fold_phi >= 180 ? fold_phi + 360 / folding - fold_phi : fold_phi + 360 / folding
3038 string s_prefix = ""
3039 string s_int = "values"
3042 string s_totals = s_prefix + "tot"
3043 string s_weights = s_prefix + "wt"
3044 string s_polar = s_prefix + "pol"
3046 wave /sdfr=df w_polar = $s_polar
3047 wave /sdfr=df w_values = $s_int
3048 wave /sdfr=df w_totals = $s_totals
3049 wave /sdfr=df w_weights = $s_weights
3051 w_values = w_polar <= theta_max ? w_totals / w_weights : nan
3077 dfref savedf = getdatafolderdfr()
3078 string s_prefix = ""
3079 string s_int = "values"
3082 string s_totals = s_prefix + "tot"
3083 string s_weights = s_prefix + "wt"
3084 string s_polar = s_prefix + "pol"
3085 string s_azim = s_prefix + "az"
3086 string s_index = s_prefix + "index"
3087 string s_theta = s_prefix + "th"
3088 string s_dphi = s_prefix + "dphi"
3089 string s_nphis = s_prefix + "nphis"
3091 sprintf s_cut, "%s_azi%03u", s_int, round(azim)
3093 wave /sdfr=df w_polar = $s_polar
3094 wave /sdfr=df w_azim = $s_azim
3095 wave /sdfr=df w_values = $s_int
3096 wave /sdfr=df w_totals = $s_totals
3097 wave /sdfr=df w_weights = $s_weights
3098 wave /sdfr=df w_index = $s_index
3099 wave /sdfr=df w_theta = $s_theta
3100 wave /sdfr=df w_dphi = $s_dphi
3101 wave /sdfr=df w_nphis = $s_nphis
3103 variable npol = numpnts(w_theta)
3105 variable pol_st = abs(w_theta[1] - w_theta[0])
3111 make /n=(npol) /o $s_cut
3113 setscale /i x w_theta[0], w_theta[numpnts(w_theta)-1], "deg", w_cut
3114 make /n=1 /free azi_slice
3115 make /n=1 /free values_slice
3117 for (ipol = 0; ipol < npol; ipol += 1)
3119 pol1 = pol - pol_st / 2
3120 pol2 = pol + pol_st / 2
3121 extract /free /indx w_polar, sel, (pol1 < w_polar) && (w_polar <= pol2)
3124 redimension /n=(nsel+2) azi_slice, values_slice
3125 azi_slice[1, nsel] = w_azim[sel[p-1]]
3126 azi_slice[0] = azi_slice[nsel] - 360
3127 azi_slice[nsel+1] = azi_slice[1] + 360
3128 values_slice[1, nsel] = w_values[sel[p-1]]
3129 values_slice[0] = values_slice[nsel]
3130 values_slice[nsel+1] = values_slice[1]
3131 w_cut[ipol] = interp(azim, azi_slice, values_slice)
3137 setdatafolder savedf
3163 dfref savedf = getdatafolderdfr()
3164 string s_prefix = ""
3165 string s_int = "values"
3168 string s_totals = s_prefix + "tot"
3169 string s_weights = s_prefix + "wt"
3170 string s_polar = s_prefix + "pol"
3171 string s_azim = s_prefix + "az"
3172 string s_index = s_prefix + "index"
3173 string s_theta = s_prefix + "th"
3174 string s_dphi = s_prefix + "dphi"
3175 string s_nphis = s_prefix + "nphis"
3177 sprintf s_cut, "%s_pol%03u", s_int, round(pol)
3179 wave /sdfr=df w_polar = $s_polar
3180 wave /sdfr=df w_azim = $s_azim
3181 wave /sdfr=df w_values = $s_int
3182 wave /sdfr=df w_totals = $s_totals
3183 wave /sdfr=df w_weights = $s_weights
3184 wave /sdfr=df w_index = $s_index
3185 wave /sdfr=df w_theta = $s_theta
3186 wave /sdfr=df w_dphi = $s_dphi
3187 wave /sdfr=df w_nphis = $s_nphis
3189 variable pol_st = abs(w_theta[1] - w_theta[0])
3193 pol1 = pol - pol_st / 2
3194 pol2 = pol + pol_st / 2
3195 extract /free /indx w_polar, sel, (pol1 < w_polar) && (w_polar <= pol2)
3199 make /n=(nsel) /o $s_cut
3201 w_cut = w_values[sel]
3202 setscale /i x w_azim[sel[0]], w_azim[sel[nsel-1]], "°", w_cut
3203 setdatafolder savedf
3206 setdatafolder savedf
3209 setdatafolder savedf
3219 dfref save_df = GetDataFolderDFR()
3220 dfref dfr = NewFreeDataFolder()
3222 StatsQuantiles /inan /iw /q /z values
3223 wave index = w_quantilesindex
3224 variable imin = round(numpnts(index) * pcmin / 100)
3225 variable imax = round(numpnts(index) * (100 - pcmax) / 100)
3226 vmin = values[index[imin]]
3227 vmax = values[index[imax]]
3228 setdatafolder save_df
3253 if (ParamIsDefault(graphname))
3256 if (ParamIsDefault(colortable))
3260 dfref save_df = GetDataFolderDFR()
3272 string traces = TraceNameList(graphname, ";", 1+4)
3273 n = ItemsInList(traces, ";")
3274 for (i = 0; i < n; i += 1)
3275 objname = StringFromList(i, traces, ";")
3276 info = TraceInfo(graphname, objname, 0)
3277 if (strlen(info) > 0)
3278 info = StringByKey("RECREATION", info, ":", ";")
3279 info = StringByKey("zColor(x)", info, "=", ";")
3280 if (strlen(info) > 2)
3281 info = info[1,strlen(info)-2]
3282 wname = StringFromList(0, info, ",")
3284 ctab = StringFromList(3, info, ",")
3285 rev = str2num("0" + StringFromList(4, info, ","))
3286 if (strlen(colortable) > 0)
3290 ModifyGraph /w=$graphname zColor($objname)={w, vmin, vmax, $ctab, rev}
3295 string images = ImageNameList(graphname,
";" )
3296 n = ItemsInList(images,
";" )
3297 for (i = 0; i < n; i += 1)
3298 objname = StringFromList(i, images,
";" )
3299 wave w = ImageNameToWaveRef(graphname, objname)
3300 info = ImageInfo(graphname, objname, 0)
3301 if (strlen(info) > 0)
3302 info = StringByKey(
"RECREATION" , info,
":" ,
";" )
3303 info = StringByKey(
"ctab" , info,
"=" ,
";" )
3304 if (strlen(info) > 2)
3305 info = info[1,strlen(info)-2]
3306 ctab = StringFromList(2, info,
"," )
3307 rev = str2num(
"0" + StringFromList(3, info,
"," ))
3308 if (strlen(colortable) > 0)
3312 ModifyImage /w=$graphname $objname ctab={vmin, vmax, $ctab, rev}
3317 setdatafolder save_df
3334 String newname = NameofWave(inwave)+
"_k" 3335 Duplicate/O inwave, $newname
3336 Wave outwave = $newname
3337 Variable rows,columns,xdelta,xoffset,ydelta,yoffset,kmin,kmax,Emax
3339 rows = DimSize(inwave,0)
3340 columns = DimSize(inwave,1)
3341 xdelta = DimDelta(inwave,0)
3342 xoffset = DimOffset(inwave,0)
3343 ydelta = DimDelta(inwave,1)
3344 yoffset = DimOffset(inwave,1)
3345 Emax= xoffset + xdelta*(rows-1)
3346 kmin = 0.5123*sqrt(Emax)*sin(pi/180*(yoffset))
3347 kmax = 0.5123*sqrt(Emax)*sin(pi/180*(yoffset+(columns-1)*ydelta))
3348 SetScale/I y kmin,kmax,"Ang^-1", outwave
3350 outwave = interp2D(inwave, x, 180/pi*asin(y/ (0.5123*sqrt(x))))
3351 outwave = (NumType(outwave)==2) ? 0 : outwave
wave hemi_polar_cut(string nickname, variable azim)
extract a polar cut from a hemispherical scan.
-
variable trim_hemi_scan(string nickname, variable theta_max)
trim a hemispherical scan at grazing angle
-
string prepare_hemi_scan_display(string nickname, variable projection=defaultValue)
create waves for plotting a hemispherical angle scan.
-
variable pizza_service_2(wave data, string nickname, wave m_theta, wave m_tilt, wave m_phi, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue)
create a pizza plot from a measured (energy-integrated) data strip
-
variable AngleToK(wave inwave)
k-space mapping of 2D angle-energy distribution (scienta image)
-
static const variable kProjScaleOrtho
-
variable polar2cart_wave(wave in, wave out)
-
variable normalize_strip_theta(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average polar distribution.
-
variable normalize_strip_2d(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by a two-dimensional normalization function.
-
variable crop_strip(wave strip, variable xlo, variable xhi)
crop a strip at the sides.
-
-
threadsafe wave ad_profile_y(wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along Y dimension, new destination wave.
-
variable make_hemi_grid(variable npol, string nickname, variable xpdplot=defaultValue)
create a hemispherical, constant solid angle grid
-
variable hemi_add_anglescan(string nickname, wave values, wave polar, wave azi, wave weights=defaultValue)
add an arbitrary angle scan to a hemispherical scan grid.
-
string get_hemi_nickname(wave w)
finds the nick name given any hemi wave
-
string get_hemi_prefix(wave w)
finds the prefix given any hemi wave
-
string display_hemi_scan(string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue)
display a plot of a hemispherical angle scan.
-
static variable CalcN_Theta(string HoloMode, variable Theta_in, variable Theta_ran, variable Theta_st)
calculate the number of thetas for a pattern
-
dfr find_hemi_data(string nickname, string *prefix, string *intwave)
finds the folder, prefix and name of holo waves given their nick name
-
variable convert_angles_ttpd2polar(wave theta, wave tilt, wave phi, wave data, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
-
variable clear_hemi_grid(string nickname)
clear a hemispherical scan grid
-
static const variable kProjScaleDist
-
threadsafe variable calc_graph_polar(variable x, variable y, variable projection=defaultValue)
calculate polar angle from Cartesian coordinate
-
static variable check_contrast(wave values, variable pcmin, variable pcmax, variable *vmin, variable *vmax)
-
static variable Calc_The_step(variable th, variable Theta_st, string Holomode)
calculate delta-theta for a given theta
-
-
static variable line_average(wave source, wave dest)
-
threadsafe variable calc_graph_radius(variable polar, variable projection=defaultValue)
calculate the projected polar angle
-
variable pizza_service(wave data, string nickname, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue)
create a pizza plot from a measured (energy-integrated) data strip
-
variable rotate_x_wave(wave inout, variable angle)
rotate a wave of 3-vectors about the x axis.
-
variable cart2polar_wave(wave in, wave out)
-
variable crop_strip_theta(wave strip, variable theta_lo, variable theta_hi, wave theta, wave tilt, wave phi)
crop a strip in theta.
-
-
string display_scanlines(string nickname, variable alpha_lo, variable alpha_hi, wave m_theta, wave m_tilt, wave m_phi, variable folding=defaultValue, variable projection=defaultValue)
display a polar graph with lines indicating the angles covered by an angle scan.
-
wave hemi_azi_cut(string nickname, variable pol)
extract an azimuthal cut from a hemispherical scan
-
variable draw_diffraction_cone(string graphname, string groupname, variable theta_axis, variable theta_inner, variable phi)
draw the circle of a diffraction cone in a stereographic polar graph.
-
variable interpolate_hemi_scan(string nickname, variable projection=defaultValue)
interpolate a hemispherical scan onto a rectangular grid
-
variable normalize_strip_theta_scans(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip piecewise by a smooth polar distribution.
-
variable hemi_add_aziscan(string nickname, wave values, variable polar, wave azi, wave weights=defaultValue)
add an azimuthal scan to a hemispherical scan grid.
-
static const variable kProjScaleGnom
-
variable rotate_y_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the y axis
-
variable rotate_hemi_scan(string nickname, variable angle)
azimuthally rotate a hemispherical scan dataset.
-
static const variable kProjScaleStereo
-
processing and holographic mapping of angle scanned XPD data.
-
static string display_polar_graph(string graphname, variable angle_offset=defaultValue, variable do_ticks=defaultValue)
displays an empty polar graph
-
const variable kProjOrtho
-
variable save_hemi_scan(string nickname, string pathname, string filename)
save a hemispherical scan to an Igor text file
-
variable normalize_strip_phi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable theta_range=defaultValue, variable check=defaultValue)
divide the strip by a sine function in phi (wobble correction).
-
variable normalize_strip_thetaphi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by a smooth polar-azimuthal distribution.
-
const variable kProjStereo
-
variable quick_pizza_image(wave data, string nickname, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue)
map angle scan data onto a rectangular grid in stereographic projection
-
static variable polar_graph_hook(WMWinHookStruct *s)
polar graph window hook
-
-
threadsafe variable calc_graph_azi(variable x, variable y, variable projection=defaultValue, variable zeroAngle=defaultValue)
calculate azimuthal angle from Cartesian coordinate
-
variable set_contrast(variable pcmin, variable pcmax, string graphname=defaultValue, string colortable=defaultValue)
set the pseudocolor contrast by percentile.
-
variable strip_delete_frames(wave strip, variable qlo, variable qhi, wave theta, wave tilt, wave phi)
delete a contiguous range of frames from a strip.
-
variable rotate_z_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the z axis
-
static variable calc_nth(variable Theta_st, variable Theta_in, variable th, variable Phi_ran, variable Phi_ref, string Holomode)
calculate the number of phis for a given theta
-
static const variable kProjScaleArea
-
variable show_analyser_line(variable theta, variable tilt, variable phi, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable xpdplot=defaultValue)
calculate and display the line seen by the analyser for a specific emission angle ...
-
variable convert_angles_ttpa2polar(wave theta, wave tilt, wave phi, wave analyser, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
-
static string draw_hemi_axes(string graphname, variable do_grids=defaultValue)
draw polar and azimuthal grids in an existing polar graph.
-
variable duplicate_hemi_scan(string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue)
duplicate a hemispherical scan dataset.
-
variable set_polar_graph_cursor(string nickname, string cursorname, variable polar_angle, variable azim_angle, string graphname=defaultValue)
-
static variable update_polar_info(string graphname)
update the angles info based on cursors A and B of a given polar graph window
-
variable import_tpi_scan(string nickname, wave theta, wave phi, wave intensity, variable folding=defaultValue, variable npolar=defaultValue, variable nograph=defaultValue, variable xpdplot=defaultValue)
import a hemispherical scan from theta-phi-intensity waves and display it
-
variable load_hemi_scan(string nickname, string pathname, string filename)
load a hemispherical scan from an Igor text file
-
threadsafe wave ad_profile_x(wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, new destination wave.
-
static variable calc_phi_step(variable Theta_in, variable th, variable Theta_st, variable Phi_ran, variable Phi_ref, string Holomode)
calculate delta-phi for a given theta
-
variable normalize_strip_x(wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average X distribution.
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
+
4 #pragma IgorVersion = 6.2
+
5 #pragma ModuleName = PearlAnglescanProcess
+
6 #include "pearl-vector-operations"
+
7 #include "pearl-polar-coordinates"
+
8 #include <New Polar Graphs>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
110 dfref df1 = GetWavesDataFolderDFR(strip1)
+
111 dfref df2 = GetWavesDataFolderDFR(strip2)
+
112 variable ny1 = dimsize(strip1, 1)
+
113 variable ny2 = dimsize(strip2, 1)
+
+
115 concatenate /np=1 {strip2}, strip1
+
116 string modified = AddListItem(NameOfWave(strip1),
"" )
+
+
+
+
+
+
122 wave /z w1 = WaveRefIndexedDFR(df1, iw)
+
+
+
+
+
127 wave /z w2 = df2:$(NameOfWave(w1))
+
128 if (WaveExists(w1) && WaveExists(w2))
+
129 if ((DimSize(w1, 0) == ny1) && (DimSize(w1, 1) == 0) && (DimSize(w2, 0) == ny2) && (DimSize(w2, 1) == 0))
+
130 concatenate /np=0 {w2}, w1
+
131 modified = AddListItem(NameOfWave(w1), modified,
"" , Inf)
+
+
+
+
+
+
+
+
139 if ((DataFolderRefStatus(df1) != 1) || (DataFolderRefStatus(df2) != 1))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
183 variable snx = dimsize(strip, 0)
+
184 variable sny = dimsize(strip, 1)
+
+
186 variable sq1hi = max(qlo-1, 0)
+
187 variable sq2lo = min(qhi+1, sny - 1)
+
188 variable sq2hi = dimsize(strip, 1) - 1
+
+
+
+
192 variable dny = sny - (sq2lo - sq1hi + 1)
+
+
194 variable dq1hi = sq1hi
+
195 variable dq2lo = dq1hi + 1
+
196 variable dq2hi = dny - 1
+
197 variable q1ofs = sq1lo - dq1lo
+
198 variable q2ofs = sq2lo - dq2lo
+
+
200 duplicate /free strip, strip_copy
+
201 redimension /n=(dnx,dny) strip
+
202 strip[][dq1lo,dq1hi] = strip_copy[p][q + q1ofs]
+
203 strip[][dq2lo,dq2hi] = strip_copy[p][q + q2ofs]
+
+
205 duplicate /free theta, theta_copy
+
206 redimension /n=(dny) theta
+
207 theta[dq1lo,dq1hi] = theta_copy[p + q1ofs]
+
208 theta[dq2lo,dq2hi] = theta_copy[p + q2ofs]
+
+
210 duplicate /free tilt, tilt_copy
+
211 redimension /n=(dny) tilt
+
212 tilt[dq1lo,dq1hi] = tilt_copy[p + q1ofs]
+
213 tilt[dq2lo,dq2hi] = tilt_copy[p + q2ofs]
+
+
215 duplicate /free phi, phi_copy
+
216 redimension /n=(dny) phi
+
217 phi[dq1lo,dq1hi] = phi_copy[p + q1ofs]
+
218 phi[dq2lo,dq2hi] = phi_copy[p + q2ofs]
+
+
+
+
+
+
+
254 variable smooth_method
+
255 variable smooth_factor
+
+
+
258 if (ParamIsDefault(smooth_method))
+
+
+
261 if (ParamIsDefault(smooth_factor))
+
262 switch(smooth_method)
+
+
+
+
+
+
+
+
270 if (ParamIsDefault(check))
+
+
+
+
+
+
+
+
278 extract /free /indx raw_dist, clean_index, numtype(raw_dist) == 0
+
279 duplicate /free raw_dist, dist, dist_x
+
280 redimension /n=(numpnts(clean_index)) dist, dist_x
+
281 dist = raw_dist[clean_index[p]]
+
282 dist_x = pnt2x(raw_dist, clean_index[p])
+
283 variable div = mean(dist)
+
+
+
+
287 duplicate /o raw_dist, check_dist
+
288 check_dist = numtype(raw_dist) == 0 ? interp(x, dist_x, dist) : nan
+
+
+
+
292 switch(smooth_method)
+
+
294 Smooth /B /E=3 smooth_factor, dist
+
+
+
297 Smooth /E=3 smooth_factor, dist
+
+
+
300 make /n=1 /d /free fit_params
+
301 fit_scienta_ang_transm(raw_dist, fit_params)
+
302 duplicate /free raw_dist, dist, dist_x
+
+
304 dist = scienta_ang_transm(fit_params, x)
+
+
+
307 loess /smth=(smooth_factor) srcWave=dist, factors={dist_x}
+
+
+
+
+
312 duplicate /o raw_dist, check_smoo
+
313 check_smoo = interp(x, dist_x, dist)
+
+
+
+
+
318 strip /= interp(x, dist_x, dist)
+
+
+
+
+
+
+
+
352 variable theta_offset
+
+
+
+
356 if (ParamIsDefault(check))
+
+
+
359 if (ParamIsDefault(theta_offset))
+
+
+
362 if (ParamIsDefault(theta_range))
+
+
+
+
+
367 duplicate /free strip, strip_copy
+
368 MatrixFilter NanZapMedian strip_copy
+
+
+
+
372 duplicate /free dist, dist_smoo
+
373 duplicate /free theta, theta_int
+
374 theta_int = theta - theta_offset
+
375 duplicate /free phi, phi_int
+
376 setscale /p x phi_int[0], phi_int[1] - phi_int[0], waveunits(phi, -1), dist, dist_smoo
+
+
378 extract /free /indx dist, red_idx, theta_int < theta_range
+
379 duplicate /free red_idx, red_dist, red_phi
+
380 red_dist = dist[red_idx]
+
381 red_phi = phi_int[red_idx]
+
+
383 variable wavg = mean(red_dist)
+
384 make /n=4 /d /free coef
+
385 coef[0] = {wavg, wavg/100, pi/180, 0}
+
386 CurveFit /q /h=
"0010" /g /w=2 sin, kwcWave=coef, red_dist /x=red_phi
+
387 dist_smoo = coef[0] + coef[1] * sin(coef[2] * phi_int[p] + coef[3])
+
+
+
+
391 strip = strip / dist_smoo[q] * coef[0]
+
+
+
+
+
396 duplicate /o dist, check_dist
+
397 duplicate /o dist_smoo, check_smoo
+
398 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
+
+
+
+
+
+
+
436 variable theta_offset
+
437 variable smooth_method
+
438 variable smooth_factor
+
+
+
441 if (ParamIsDefault(check))
+
+
+
444 if (ParamIsDefault(theta_offset))
+
+
+
447 if (ParamIsDefault(smooth_method))
+
+
+
450 if (ParamIsDefault(smooth_factor))
+
+
+
+
+
455 duplicate /free strip, strip_copy
+
456 MatrixFilter NanZapMedian strip_copy
+
+
+
+
460 duplicate /free dist, dist_smoo
+
461 duplicate /free theta, theta_int
+
462 theta_int = theta - theta_offset
+
463 setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
+
464 variable nx = dimsize(strip, 0)
+
+
+
467 switch(smooth_method)
+
+
469 Smooth /B /E=3 smooth_factor, dist_smoo
+
+
+
472 Smooth /E=3 smooth_factor, dist_smoo
+
+
+
475 loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={theta_int}
+
+
+
478 for (ix = 0; ix < nx; ix += 1)
+
+
480 if (smooth_factor > 1)
+
481 CurveFit /nthr=0 /q /w=2 poly smooth_factor+1, dist /x=theta_int /d=dist_smoo
+
+
483 CurveFit /nthr=0 /q /w=2 line, dist /x=theta_int /d=dist_smoo
+
+
485 strip[ix,ix][] /= dist_smoo[q]
+
+
+
+
+
+
+
+
493 strip /= dist_smoo[q]
+
+
+
+
+
498 duplicate /o dist, check_dist
+
499 duplicate /o dist_smoo, check_smoo
+
500 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
+
+
+
+
+
+
+
+
537 variable theta_offset
+
538 variable smooth_method
+
539 variable smooth_factor
+
+
+
542 if (ParamIsDefault(check))
+
+
+
545 if (ParamIsDefault(theta_offset))
+
+
+
548 if (ParamIsDefault(smooth_method))
+
+
+
551 if (ParamIsDefault(smooth_factor))
+
+
+
+
+
556 duplicate /free strip, strip_copy
+
557 MatrixFilter NanZapMedian strip_copy
+
+
+
+
561 duplicate /free dist, dist_smoo
+
562 duplicate /free theta, theta_int
+
563 theta_int = theta - theta_offset
+
564 setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
+
565 variable nx = dimsize(strip, 0)
+
+
+
568 switch(smooth_method)
+
+
570 loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={theta_int, phi}
+
+
+
573 abort
"smooth method not supported"
+
+
+
+
+
578 strip /= dist_smoo[q]
+
+
+
+
+
583 duplicate /o dist, check_dist
+
584 duplicate /o dist_smoo, check_smoo
+
585 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
+
+
+
+
+
+
+
597 variable theta_offset
+
598 variable smooth_method
+
599 variable smooth_factor
+
+
+
602 if (ParamIsDefault(check))
+
+
+
605 if (ParamIsDefault(theta_offset))
+
+
+
608 if (ParamIsDefault(smooth_method))
+
+
+
611 if (ParamIsDefault(smooth_factor))
+
+
+
+
+
616 duplicate /free strip, strip_copy
+
617 MatrixFilter NanZapMedian strip_copy
+
+
+
+
621 duplicate /free dist, dist_smoo
+
622 duplicate /free theta, theta_int
+
623 theta_int = theta - theta_offset
+
624 setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
+
+
+
627 duplicate /free theta_int, d1_theta, d2_theta
+
628 Differentiate /METH=2 theta_int /D=d1_theta
+
629 Differentiate /METH=2 d1_theta /D=d2_theta
+
630 d2_theta = abs(d2_theta)
+
+
632 FindLevels /edge=1 /p /q /d=w_levels d2_theta, 0.1
+
+
634 abort "unrecognized scanning scheme"
+
+
636 w_levels = ceil(w_levels)
+
637 InsertPoints 0, 1, w_levels
+
+
639 InsertPoints numpnts(w_levels), 1, w_levels
+
640 w_levels[numpnts(w_levels)-1] = numpnts(theta_int)
+
+
642 variable n_scans = numpnts(w_levels) - 1
+
+
+
645 for (i_scan = 0; i_scan < n_scans; i_scan += 1)
+
646 p1 = w_levels[i_scan]
+
647 p2 = w_levels[i_scan+1] - 1
+
648 duplicate /free /r=[p1, p2] dist, dist_piece, smooth_piece
+
649 duplicate /free /r=[p1, p2] theta_int, theta_piece
+
650 switch(smooth_method)
+
+
652 loess /dest=smooth_piece /smth=(smooth_factor) srcWave=dist_piece, factors={theta_piece}
+
+
+
655 abort
"smooth method not supported"
+
+
657 dist_smoo[p1, p2] = smooth_piece[p - p1]
+
+
+
+
+
662 strip /= dist_smoo[q]
+
+
+
+
+
667 duplicate /o dist, check_dist
+
668 duplicate /o dist_smoo, check_smoo
+
669 setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
+
+
+
+
+
+
+
689 variable theta_offset
+
690 variable smooth_method
+
691 variable smooth_factor
+
+
+
694 if (ParamIsDefault(check))
+
+
+
697 if (ParamIsDefault(theta_offset))
+
+
+
700 if (ParamIsDefault(smooth_method))
+
+
+
703 if (ParamIsDefault(smooth_factor))
+
+
+
+
707 variable nx = dimsize(strip, 0)
+
708 variable ny = dimsize(strip, 1)
+
+
710 duplicate /free strip, dist, alpha_int, theta_int
+
711 MatrixFilter NanZapMedian dist
+
712 theta_int = theta[q] - theta_offset
+
713 alpha_int = dimoffset(strip, 0) + p * dimdelta(strip, 0)
+
714 redimension /n=(nx * ny) dist, alpha_int, theta_int
+
+
716 switch(smooth_method)
+
+
718 loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={alpha_int, theta_int}
+
719 redimension /n=(nx, ny) dist_smoo
+
+
+
722 Abort
"undefined smooth method"
+
+
+
+
+
+
+
+
+
+
+
+
734 duplicate /o dist_smoo, check_smoo
+
+
+
+
+
+
+
+
+
752 variable plo = round((xlo - dimoffset(strip, 0)) / dimdelta(strip, 0))
+
753 variable phi = round((xhi - dimoffset(strip, 0)) / dimdelta(strip, 0))
+
754 xlo = plo * dimdelta(strip, 0) + dimoffset(strip, 0)
+
755 xhi = phi * dimdelta(strip, 0) + dimoffset(strip, 0)
+
756 variable nx = phi - plo + 1
+
757 variable ny = dimsize(strip, 1)
+
+
759 duplicate /free strip, strip_copy
+
760 redimension /n=(nx,ny) strip
+
761 strip = strip_copy[p + plo][q]
+
762 setscale /i x xlo, xhi, waveunits(strip, 0), strip
+
+
+
+
+
+
+
+
+
+
+
787 extract /indx /free theta, idx, (theta >= theta_lo) && (theta <= theta_hi)
+
788 variable nx = dimsize(strip, 0)
+
789 variable ny = numpnts(idx)
+
+
791 theta[0, ny-1] = theta[idx]
+
792 tilt[0, ny-1] = tilt[idx]
+
793 phi[0, ny-1] = phi[idx]
+
794 redimension /n=(ny) theta, tilt, phi
+
+
796 duplicate /free strip, strip_copy
+
797 redimension /n=(nx,ny) strip
+
798 strip = strip_copy[p][idx[q]]
+
+
+
843 function
pizza_service (data, nickname, theta_offset, tilt_offset, phi_offset, [npolar, nograph, folding, xpdplot])
+
+
+
846 variable theta_offset
+
+
+
+
+
+
+
+
854 if (ParamIsDefault(npolar))
+
+
+
857 if (ParamIsDefault(nograph))
+
+
+
860 if (ParamIsDefault(folding))
+
+
+
863 if (ParamIsDefault(xpdplot))
+
+
+
+
+
868 dfref saveDF = GetDataFolderDFR()
+
869 dfref dataDF = GetWavesDataFolderDFR(data)
+
+
871 if (DataFolderExists(":attr"))
+
+
+
874 dfref attrDF = GetDataFolderDFR()
+
+
876 wave /sdfr=attrDF ManipulatorTheta
+
877 wave /sdfr=attrDF ManipulatorTilt
+
878 wave /sdfr=attrDF ManipulatorPhi
+
+
880 if ((dimsize(ManipulatorTheta, 0) != dimsize(data, 1)) || (dimsize(ManipulatorTilt, 0) != dimsize(data, 1)) || (dimsize(ManipulatorPhi, 0) != dimsize(data, 1)))
+
881 Abort "Warning: The dimension size of the manipulator waves does not match the Y dimension of the data wave!\rIf you restructured the data wave, please use
pizza_service_2 with properly scaled manipulator waves."
+
+
+
884 duplicate /free ManipulatorTheta, m_theta
+
885 duplicate /free ManipulatorTilt, m_tilt
+
886 duplicate /free ManipulatorPhi, m_phi
+
+
888 m_theta -= theta_offset
+
889 m_tilt -= tilt_offset
+
+
+
892 pizza_service_2 (data, nickname, m_theta, m_tilt, m_phi, npolar=npolar, nograph=nograph, folding=folding, xpdplot=xpdplot)
+
+
+
+
+
936 function
pizza_service_2 (data, nickname, m_theta, m_tilt, m_phi, [npolar, nograph, folding, xpdplot])
+
+
+
+
+
+
+
+
+
+
+
947 if (ParamIsDefault(npolar))
+
+
+
950 if (ParamIsDefault(nograph))
+
+
+
953 if (ParamIsDefault(folding))
+
+
+
956 if (ParamIsDefault(xpdplot))
+
+
+
+
960 if ((dimsize(m_theta, 0) != dimsize(data, 1)) || (dimsize(m_tilt, 0) != dimsize(data, 1)) || (dimsize(m_phi, 0) != dimsize(data, 1)))
+
961 Abort "Warning: The dimension size of the manipulator waves does not match the Y dimension of the data wave!"
+
+
+
964 string graphname = "graph_" + nickname
+
965 string outprefix = nickname
+
+
+
968 dfref saveDF = GetDataFolderDFR()
+
969 dfref dataDF = GetWavesDataFolderDFR(data)
+
+
+
+
+
+
+
+
977 newdatafolder /s/o $nickname
+
+
+
980 dfref destDF = GetDataFolderDFR()
+
+
+
+
984 variable /g pol_perf_secs
+
985 timerRefNum = startMSTimer
+
+
987 duplicate /free m_tilt, corr_tilt
+
988 duplicate /free m_phi, corr_phi
+
+
+
+
992 make /n=1/d/free d_polar, d_azi
+
+
+
+
+
+
998 for (ifold = 0; ifold < folding; ifold += 1)
+
999 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
+
+
1001 d_azi += 360 / folding
+
+
+
+
1005 if (strlen(outprefix))
+
1006 string s_prefix = outprefix + "_"
+
1007 string s_int = s_prefix + "i"
+
+
+
+
+
+
1013 wave values = $s_int
+
+
+
+
+
+
+
+
1021 if (timerRefNum >= 0)
+
1022 pol_perf_secs = stopMSTimer(timerRefNum) / 1e6
+
+
+
1025 setdatafolder saveDF
+
+
+
1053 function
show_analyser_line (theta, tilt, phi, theta_offset, tilt_offset, phi_offset, [npolar, nograph, xpdplot])
+
+
+
+
1057 variable theta_offset
+
1058 variable tilt_offset
+
+
+
+
+
+
1064 string nickname = "analyser"
+
+
1066 if (ParamIsDefault(npolar))
+
+
+
1069 if (ParamIsDefault(nograph))
+
+
+
1072 if (ParamIsDefault(xpdplot))
+
+
+
1075 string graphname = "graph_" + nickname
+
1076 string outprefix = nickname
+
+
+
1079 dfref saveDF = GetDataFolderDFR()
+
1080 dfref dataDF = saveDF
+
+
+
1083 outprefix = nickname
+
+
1085 setdatafolder dataDF
+
1086 newdatafolder /s/o $nickname
+
+
+
1089 dfref destDF = GetDataFolderDFR()
+
+
1091 make /n=1 /free m_theta
+
1092 make /n=1 /free m_tilt
+
1093 make /n=1 /free m_phi
+
1094 m_theta = theta - theta_offset
+
1095 m_tilt = tilt - tilt_offset
+
+
1097 m_phi = phi - phi_offset
+
+
+
1100 make /n=60 /free data
+
1101 setscale /i x -30, 30, data
+
+
1103 make /n=1/d/free d_polar, d_azi
+
+
+
+
1107 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
+
+
+
+
+
+
+
+
1115 setdatafolder saveDF
+
+
+
+
+
1124 wave theta, tilt, phi
+
+
+
+
+
1129 make /n=(dimsize(data, 0)) /d /free ana
+
1130 setscale /p x dimoffset(data, 0), dimdelta(data, 0), waveunits(data, 0), ana
+
+
+
+
+
+
+
+
+
+
+
+
1169 variable nn = numpnts(theta)
+
1170 variable na = numpnts(analyser)
+
1171 redimension /n=(na, nn) polar, azi
+
+
+
+
+
+
+
1178 make /n=(3,na) /d /free w_orig_polar, w_orig_cart, w_rot_cart, w_rot_polar
+
1179 w_orig_polar[0][] = radius
+
1180 w_orig_polar[1][] = analyser[q]
+
1181 w_orig_polar[2][] = 0
+
+
+
+
+
+
1187 for (ii = 0; ii < nn; ii += 1)
+
+
+
+
+
+
1193 w_rot_cart = w_orig_cart
+
+
+
+
+
+
+
1200 polar[][ii] = w_rot_polar[1][p]
+
1201 azi[][ii] = w_rot_polar[2][p]
+
+
+
+
+
+
+
+
+
+
1211 variable nn = dimsize(source, 1)
+
1212 make /n=(dimsize(source, 0))/d/free line
+
1213 for (ii = 0; ii < nn; ii += 1)
+
1214 line = source[p][ii]
+
+
1216 dest[][ii] = line[p] / v_max
+
+
+
+
1223 static function
calc_nth (Theta_st, Theta_in, th, Phi_ran, Phi_ref, Holomode)
+
1224 Variable Theta_st, Theta_in, th, Phi_ran, Phi_ref
+
+
+
1227 Variable deg2rad=0.01745329
+
+
1229 if ( cmpstr(Holomode, "Stereographic") == 0)
+
1230 The_step =trunc( Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st )
+
+
1232 The_step =trunc( Phi_ran*sin(th*pi/180)*Phi_ref/Theta_st )
+
+
+
1235 if (cmpstr(Holomode, "Parallel") == 0)
+
1236 The_step=trunc( Phi_ran*tan(th*deg2rad)*Phi_ref/Theta_st )
+
+
1238 if ( cmpstr(Holomode, "h") == 0)
+
1239 The_step=trunc( th/Theta_in*Phi_ran/Theta_st )
+
+
+
+
+
+
+
+
+
+
1252 static function
calc_phi_step (Theta_in, th, Theta_st, Phi_ran, Phi_ref, Holomode)
+
1253 Variable Theta_in, th, Theta_st, Phi_ran, Phi_ref
+
+
+
+
1257 Variable deg2rad=0.01745329
+
+
1259 if ( cmpstr(Holomode, "Stereographic") == 0 )
+
1260 if ((th < 0.5) || (trunc(Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st) == 0))
+
+
+
1263 Phi_st=Phi_ran/(trunc(Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st))
+
+
+
+
+
+
+
1270 if ( cmpstr(Holomode, "Parallel") == 0 )
+
1271 if((th < 0.5) || (trunc(Phi_ran*tan(th*deg2rad)*Phi_ref/Theta_st) == 0))
+
+
+
1274 Phi_st=Phi_ran/(trunc(Phi_ran*tan(th*deg2rad)*Phi_ref/Theta_st))
+
+
+
+
1278 if ( cmpstr(Holomode, "h") == 0 )
+
1279 if((th < 0.5) || (trunc(Phi_ran*sin(th*deg2rad)*Phi_ref/Theta_st) == 0))
+
+
+
1282 Phi_st=Phi_ran/trunc(th/Theta_in*Phi_ran/Theta_st)
+
+
+
+
+
+
+
+
+
+
+
+
+
1298 Variable th, Theta_st
+
+
1300 Variable deg2rad=0.01745329, dt_loc,The_step
+
+
1302 if ( (cmpstr(Holomode, "Stereographic")) ==0 )
+
+
+
+
1306 if ( (cmpstr(Holomode, "h")) ==0 )
+
+
+
+
1310 if ( cmpstr(Holomode, "Parallel") == 0 )
+
+
1312 dt_loc = Theta_st/cos(th*deg2rad)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1329 Variable Theta_in,Theta_ran,Theta_st
+
1330 Variable n_theta, aux, aux1,ii
+
+
+
1333 aux1= Theta_in - Theta_ran
+
+
+
+
1337 if(aux<=Theta_in-Theta_ran)
+
1338 aux=Theta_in-Theta_ran
+
+
+
1341 while((aux>aux1)%&(Theta_in-aux<=Theta_ran))
+
+
+
+
+
+
+
+
+
+
1370 if (ParamIsDefault(xpdplot))
+
+
+
+
1374 string HoloMode = "h"
+
1375 variable Theta_in = 90
+
1376 variable Theta_ran = 90
+
1377 variable Theta_st = 90 / (npol - 1)
+
1378 variable Phi_ran = 360
+
1379 variable Phi_ref = 1
+
+
+
1382 variable n_theta =
CalcN_Theta (HoloMode, Theta_in, Theta_ran, Theta_st)
+
+
+
1385 if (strlen(nickname))
+
1386 string s_prefix = nickname + "_"
+
1387 string s_int = s_prefix + "i"
+
+
+
+
+
1392 string s_polar = s_prefix + "pol"
+
1393 string s_azim = s_prefix + "az"
+
+
1395 string s_index = s_prefix + "index"
+
1396 string s_theta = s_prefix + "th"
+
1397 string s_dphi = s_prefix + "dphi"
+
1398 string s_nphis = s_prefix + "nphis"
+
+
1400 string s_HoloData = s_prefix + "data"
+
1401 string s_HoloInfo = s_prefix + "info"
+
+
+
1404 string s_tot = s_prefix + "tot"
+
1405 string s_weight = s_prefix + "wt"
+
+
1407 make /O/D/n=(n_theta) $s_index /wave=index
+
1408 make /O/D/n=(n_theta) $s_theta /wave=theta
+
1409 make /O/D/n=(n_theta) $s_dphi /wave=dphi
+
1410 make /O/D/n=(n_theta) $s_nphis /wave=nphis
+
+
+
+
1414 dphi[0] =
calc_phi_step (Theta_in, Theta_in, aux, Phi_ran, Phi_ref, HoloMode)
+
+
1416 nphis[0] =
calc_nth (aux, Theta_in, Theta_in, Phi_ran, Phi_ref, HoloMode)
+
+
+
+
+
+
1422 Theta[ii] = Theta[ii-1] - aux
+
1423 if(Theta[ii] <= Theta_in-Theta_ran)
+
1424 Theta[ii] = Theta_in-Theta_ran
+
+
+
1427 dphi[ii] =
calc_phi_step (Theta_in, Theta[ii], aux, Phi_ran, Phi_ref, HoloMode)
+
1428 nphis[ii] =
calc_nth (aux, Theta_in, Theta[ii], Phi_ran, Phi_ref, HoloMode)
+
1429 Index[ii] = Index[ii-1] + nphis[ii]
+
+
+
+
1433 if (Index[n_theta-1]==Index[n_theta-2])
+
1434 Index[n_theta-1]=Index[n_theta-2]+1
+
+
+
+
1438 variable NumPoints = sum(nphis, 0, numpnts(nphis))
+
+
+
1441 make /O/D/N=(NumPoints) $s_polar /wave=polar, $s_azim /wave=azim
+
+
+
+
1445 variable StartIndex = 0
+
+
+
+
1449 Polar[StartIndex, EndIndex-1]=Theta[ii]
+
1450 Azim[StartIndex, EndIndex-1]= mod(Phi_ran+(x-StartIndex)*dphi[ii]+Phi_in,Phi_ran)
+
+
1452 StartIndex = EndIndex
+
+
+
1455 duplicate /o azim, $s_int /wave=values
+
1456 duplicate /o azim, $s_tot /wave=totals
+
1457 duplicate /o azim, $s_weight /wave=weights
+
+
+
+
+
+
+
1464 string s_FileName = ""
+
1465 string s_Comment = "created by pearl-anglescan-process.ipf"
+
1466 string s_HoloMode = "Stereographic"
+
1467 variable /g gb_SpectraFile = 0
+
+
1469 Make/O/D/n=22 $s_HoloData /wave=HoloData
+
+
+
1472 HoloData[6] = NumPoints
+
1473 HoloData[7] = Theta_in
+
1474 HoloData[8] = Theta_ran
+
1475 HoloData[9] = Theta_st
+
1476 HoloData[11] = Phi_in
+
1477 HoloData[12] = Phi_ran
+
1478 HoloData[13] = Theta_st
+
1479 HoloData[15] = Phi_ref
+
1480 HoloData[16] = Phi_ran
+
+
+
1483 Make/O/T/n=22 $s_HoloInfo /wave=HoloInfo
+
1484 HoloInfo[0] = s_FileName
+
1485 HoloInfo[1] = s_Comment
+
1486 HoloInfo[10] = s_HoloMode
+
+
+
+
1490 if (WinType(NickName) == 5)
+
1491 Notebook $NickName selection={startOfFile, endOfFile}
+
1492 Notebook $NickName text=
""
+
+
1494 NewNotebook /F=0 /K=1 /N=$NickName /W=(5,40,341,260)
+
1495 Notebook $NickName defaultTab=140
+
1496 Notebook $NickName statusWidth=300
+
1497 Notebook $NickName backRGB=(56797,56797,56797)
+
1498 Notebook $NickName pageMargins={80,80,80,80}
+
1499 Notebook $NickName fSize=10
+
1500 Notebook $NickName fStyle=0,textRGB=(65535,0,26214)
+
1501 Notebook $NickName textRGB=(65535,0,26214)
+
+
1503 Notebook $NickName text =
"File:\t" + s_FileName +
"\r"
+
1504 Notebook $NickName text =
"*** " + s_Comment +
" ***\r\r"
+
1505 Notebook $NickName text =
"Angle-Mode:\t" + s_HoloMode +
"\r"
+
1506 Notebook $NickName text =
"XPDplot Nickname:\t" + NickName +
"\r"
+
+
+
+
+
+
+
+
1520 string wname = nameofwave(w)
+
+
+
+
+
+
1526 string s_wave_df = GetWavesDataFolder(w, 1)
+
1527 dfref parent_df = $(s_wave_df + "::")
+
1528 nickname = GetDataFolder(0, parent_df)
+
+
+
+
+
+
+
+
+
1544 string wname = nameofwave(w)
+
+
1546 if (ItemsInList(wname, "_") >= 2)
+
1547 prefix = StringFromList(0, wname, "_")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1580 if (strlen(nickname))
+
1581 if (DataFolderExists(nickname))
+
+
+
1584 datadf = getdatafolderdfr()
+
1585 prefix = nickname + "_"
+
1586 intwave = prefix + "i"
+
1587 if (exists(intwave) != 1)
+
+
+
+
+
1592 datadf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1614 string s_totals = s_prefix + "tot"
+
1615 string s_weights = s_prefix + "wt"
+
+
1617 wave /sdfr=datadf /z w_values = $s_int
+
1618 wave /sdfr=datadf /z w_totals = $s_totals
+
1619 wave /sdfr=datadf /z w_weights = $s_weights
+
+
1621 if (waveexists(w_totals))
+
+
+
1624 if (waveexists(w_weights))
+
+
+
1627 if (waveexists(w_values))
+
+
+
+
+
+
1654 string source_nickname
+
+
1656 string dest_nickname
+
+
+
1659 if (ParamIsDefault(xpdplot))
+
+
+
+
1663 dfref savedf = getdatafolderdfr()
+
+
+
1666 string s_prefix = ""
+
1667 string s_int = "values"
+
1668 dfref source_df =
find_hemi_data (source_nickname, s_prefix, s_int)
+
1669 string s_polar = s_prefix + "pol"
+
1670 string s_azim = s_prefix + "az"
+
1671 string s_theta = s_prefix + "th"
+
1672 string s_tot = s_prefix + "tot"
+
1673 string s_weight = s_prefix + "wt"
+
1674 string s_matrix = s_prefix + "matrix"
+
+
1676 wave /sdfr=source_df theta1 = $s_theta
+
1677 wave /sdfr=source_df polar1 = $s_polar
+
1678 wave /sdfr=source_df azim1 = $s_azim
+
1679 wave /sdfr=source_df tot1 = $s_tot
+
1680 wave /sdfr=source_df weight1 = $s_weight
+
1681 wave /sdfr=source_df values1 = $s_int
+
1682 wave /sdfr=source_df /z matrix1 = $s_matrix
+
+
1684 variable npol = numpnts(theta1)
+
+
1686 setdatafolder dest_folder
+
+
+
+
+
1691 s_polar = s_prefix + "pol"
+
1692 s_azim = s_prefix + "az"
+
1693 s_theta = s_prefix + "th"
+
1694 s_tot = s_prefix + "tot"
+
1695 s_weight = s_prefix + "wt"
+
1696 s_matrix = s_prefix + "matrix"
+
+
1698 wave /sdfr=dest_df theta2 = $s_theta
+
1699 wave /sdfr=dest_df polar2 = $s_polar
+
1700 wave /sdfr=dest_df azim2 = $s_azim
+
1701 wave /sdfr=dest_df tot2 = $s_tot
+
1702 wave /sdfr=dest_df weight2 = $s_weight
+
1703 wave /sdfr=dest_df values2 = $s_int
+
+
+
+
+
1708 if (waveexists(matrix1))
+
1709 setdatafolder dest_df
+
1710 duplicate /o matrix1, $s_matrix
+
+
+
1713 if (!(NumberByKey("
version ", note(azim1), "=", "\r") >= 1.6))
+
+
1715 azim2 = azim2 >= 360 ? azim2 - 360 : azim2
+
+
+
1718 setdatafolder saveDF
+
+
+
+
+
+
+
1732 dfref savedf = getdatafolderdfr()
+
+
1734 string s_prefix = ""
+
1735 string s_int = "values"
+
+
+
1738 string s_polar = s_prefix + "pol"
+
1739 string s_azim = s_prefix + "az"
+
1740 string s_tot = s_prefix + "tot"
+
1741 string s_weight = s_prefix + "wt"
+
+
1743 wave /sdfr=df polar = $s_polar
+
1744 wave /sdfr=df azim = $s_azim
+
1745 wave /sdfr=df tot = $s_tot
+
1746 wave /sdfr=df weight = $s_weight
+
1747 wave /sdfr=df values = $s_int
+
+
+
1750 azim = azim < 0 ? azim + 360 : azim
+
1751 azim = azim >= 360 ? azim - 360 : azim
+
+
1753 duplicate /free polar, neg_polar
+
+
1755 sort {neg_polar, azim}, polar, azim, tot, weight, values
+
+
1757 setdatafolder saveDF
+
+
+
+
+
+
+
1780 dfref savedf = getdatafolderdfr()
+
+
1782 if (ParamIsDefault(projection))
+
+
+
+
+
1787 string s_prefix = ""
+
1788 string s_int = "values"
+
+
+
1791 string s_polar = s_prefix + "pol"
+
1792 string s_azim = s_prefix + "az"
+
+
1794 wave /sdfr=df /z values = $s_int
+
1795 wave /sdfr=df /z azim = $s_azim
+
1796 wave /sdfr=df /z polar = $s_polar
+
+
+
1799 string s_ster_rad = s_prefix + "ster_rad"
+
1800 duplicate /o polar, $s_ster_rad /wave=ster_rad
+
+
+
1803 string s_ster_x = s_prefix + "ster_x"
+
1804 string s_ster_y = s_prefix + "ster_y"
+
1805 duplicate /o azim, $s_ster_x /wave=ster_x, $s_ster_y /wave=ster_y
+
1806 ster_x = ster_rad * cos(azim * pi / 180)
+
1807 ster_y = ster_rad * sin(azim * pi / 180)
+
+
1809 setdatafolder savedf
+
+
+
+
+
+
+
+
+
+
+
1866 dfref savedf = getdatafolderdfr()
+
+
1868 if (ParamIsDefault(projection))
+
+
+
1871 if (ParamIsDefault(graphtype))
+
+
+
1874 if (ParamIsDefault(do_ticks))
+
+
+
1877 if (ParamIsDefault(do_grids))
+
+
+
1880 if (ParamIsDefault(graphname))
+
1881 if (strlen(nickname) > 0)
+
1882 graphname = nickname
+
+
1884 graphname = GetDataFolder(0)
+
+
+
+
+
+
+
1891 string s_prefix = ""
+
1892 string s_int = "values"
+
+
+
1895 string s_polar = s_prefix + "pol"
+
1896 string s_azim = s_prefix + "az"
+
1897 string s_matrix = s_prefix + "matrix"
+
1898 string s_ster_rad = s_prefix + "ster_rad"
+
+
1900 wave /sdfr=df /z values = $s_int
+
1901 wave /sdfr=df /z azim = $s_azim
+
1902 wave /sdfr=df /z polar = $s_polar
+
1903 wave /sdfr=df /z ster_rad = $s_ster_rad
+
1904 wave /sdfr=df /z matrix = $s_matrix
+
+
+
1907 variable azim_offset = 0
+
1908 if (!(NumberByKey("
version ", note(azim), "=", "\r") >= 1.6))
+
1909 DoAlert /T="display hemi scan" 0, "your dataset doesn't include the
version 1.6 flag. if it was created with an earlier
version that might be okay. please check that the orientation is correct!"
+
+
+
+
+
+
+
1916 if (str2num(GetUserData(graphname, "", "graphtype")) == graphtype)
+
+
+
+
+
1921 killwindow $graphname
+
+
+
+
+
+
+
+
1929 s_trace = WMPolarAppendTrace(graphname, ster_rad, azim, 360)
+
1930 ModifyGraph /W=$graphname mode($s_trace)=2, lsize($s_trace)=2
+
1931 ModifyGraph /W=$graphname zColor($s_trace)={values,*,*,BlueGreenOrange,0}
+
+
1933 ColorScale /W=$graphname /C /N=text0 /E=2 /F=0 /B=1 /A=RB /X=0.00 /Y=0.00 trace=polarY0
+
1934 ColorScale /W=$graphname /C /N=text0 side=2, width=5, heightPct=40, frame=0.50, lblMargin=0
+
1935 ColorScale /W=$graphname /C /N=text0 nticks=2, minor=1, tickLen=4.00, tickThick=0.50
+
+
1937 SetWindow $graphname, userdata(projection)=num2str(projection)
+
1938 SetWindow $graphname, userdata(graphtype)=num2str(graphtype)
+
+
+
+
+
+
1944 s_trace = WMPolarAppendTrace(graphname, ster_rad, azim, 360)
+
1945 ModifyGraph /W=$graphname mode($s_trace)=0, lsize($s_trace)=0
+
1946 AppendImage /L=VertCrossing /B=HorizCrossing matrix
+
+
1948 ColorScale /W=$graphname /C /N=text0 /E=2 /F=0 /B=1 /A=RB /X=0.00 /Y=0.00 image=$s_matrix
+
1949 ColorScale /W=$graphname /C /N=text0 side=2, width=5, heightPct=40, frame=0.50, lblMargin=0
+
1950 ColorScale /W=$graphname /C /N=text0 nticks=2, minor=1, tickLen=4.00, tickThick=0.50
+
+
1952 SetWindow $graphname, userdata(projection)=num2str(projection)
+
1953 SetWindow $graphname, userdata(graphtype)=num2str(graphtype)
+
+
+
+
+
1958 setdatafolder savedf
+
+
+
+
+
+
+
2006 variable angle_offset
+
+
+
2009 dfref savedf = GetDataFolderDFR()
+
+
2011 if (ParamIsDefault(angle_offset))
+
+
+
2014 if (ParamIsDefault(do_ticks))
+
+
+
+
2018 if ((strlen(graphname) == 0) || (wintype(graphname) == 0))
+
2019 Display /k=1 /W=(10,45,360,345)
+
2020 DoWindow /C $graphname
+
2021 graphname = WMNewPolarGraph("", graphname)
+
2022 WMPolarGraphSetVar(graphname, "zeroAngleWhere", angle_offset)
+
+
2024 WMPolarGraphSetVar(graphname, "angleAxisThick", 0.5)
+
2025 WMPolarGraphSetStr(graphname, "doMajorAngleTicks", "manual")
+
2026 WMPolarGraphSetVar(graphname, "majorAngleInc", 30)
+
2027 WMPolarGraphSetVar(graphname, "minorAngleTicks", 2)
+
2028 WMPolarGraphSetStr(graphname, "angleTicksLocation", "Outside")
+
2029 WMPolarGraphSetVar(graphname, "doAngleTickLabelSubRange", 1)
+
2030 WMPolarGraphSetVar(graphname, "angleTickLabelRangeStart", 0)
+
2031 WMPolarGraphSetVar(graphname, "angleTickLabelRangeExtent", 90)
+
2032 WMPolarGraphSetStr(graphname, "angleTickLabelNotation", "%g°")
+
+
2034 WMPolarGraphSetVar(graphname, "doPolarGrids", 0)
+
2035 WMPolarGraphSetVar(graphname, "doRadiusTickLabels", 0)
+
2036 WMPolarGraphSetStr(graphname, "radiusAxesWhere", " Off")
+
2037 WMPolarGraphSetStr(graphname, "radiusTicksLocation", "Off")
+
+
2039 WMPolarGraphSetVar(graphname, "majorTickLength", 2)
+
2040 WMPolarGraphSetVar(graphname, "majorTickThick", 0.5)
+
2041 WMPolarGraphSetVar(graphname, "minorTickLength", 1)
+
2042 WMPolarGraphSetVar(graphname, "minorTickThick", 0.5)
+
2043 WMPolarGraphSetVar(graphname, "tickLabelOpaque", 0)
+
2044 WMPolarGraphSetVar(graphname, "tickLabelFontSize", 7)
+
+
+
+
2048 WMPolarGraphSetStr(graphname, "angleTicksLocation", "Outside")
+
+
2050 WMPolarGraphSetStr(graphname, "angleTicksLocation", "Off")
+
+
+
2053 WMPolarGraphSetVar(graphname, "doMinorAngleTicks", 1)
+
+
2055 WMPolarGraphSetVar(graphname, "doMinorAngleTicks", 0)
+
+
+
2058 DoWindow /T $graphname, graphname
+
+
+
2061 string graphdf = "root:packages:WMPolarGraphs:" + graphname
+
2062 setdatafolder graphdf
+
+
2064 variable /g csrA_theta
+
2065 variable /g csrA_phi
+
2066 variable /g csrB_theta
+
2067 variable /g csrB_phi
+
+
+
+
2071 tb = tb + " \
"A = (%.1f, %.1f)\","
+
2072 tb = tb + graphdf +
":csrA_theta,"
+
2073 tb = tb + graphdf +
":csrA_phi"
+
+
2075 TextBox /W=$graphname /A=LT /B=1 /E=2 /F=0 /N=tb_angles /X=1 /Y=1 /V=0 tb
+
+
2077 tb = tb +
"\"B = (%.1f, %.1f)\","
+
2078 tb = tb + graphdf +
":csrB_theta,"
+
2079 tb = tb + graphdf +
":csrB_phi"
+
+
2081 AppendText /W=$graphname /N=tb_angles tb
+
+
+
+
+
2086 DoWindow /F $graphname
+
+
+
2089 setdatafolder savedf
+
+
+
+
+
+
+
+
2122 if (ParamIsDefault(do_grids))
+
+
+
+
2126 dfref savedf = GetDataFolderDFR()
+
+
2128 string sproj = GetUserData(graphname, "", "projection")
+
2129 variable projection = str2num("0" + sproj)
+
+
2131 SetDrawLayer /W=$graphname ProgFront
+
+
+
2134 SetDrawEnv /W=$graphname xcoord=HorizCrossing, ycoord=VertCrossing
+
2135 SetDrawEnv /W=$graphname linethick= 0.5
+
2136 SetDrawEnv /W=$graphname dash=2
+
2137 SetDrawEnv /W=$graphname fillpat=0
+
2138 SetDrawEnv /W=$graphname fname="default", fsize=7
+
2139 SetDrawEnv /W=$graphname textxjust=1, textyjust=1
+
+
2141 SetDrawEnv /W=$graphname save
+
+
+
2144 DrawLine /W=$graphname 0, -2, 0, 2
+
2145 DrawLine /W=$graphname -2, 0, 2, 0
+
+
+
+
+
+
2151 DrawOval /W=$graphname -radi, radi, radi, -radi
+
+
2153 DrawOval /W=$graphname -radi, radi, radi, -radi
+
+
2155 DrawOval /W=$graphname -radi, radi, radi, -radi
+
+
2157 SetDrawEnv /W=$graphname textxjust= 1,textyjust= 2
+
2158 SetDrawEnv /W=$graphname save
+
+
2160 DrawText /W=$graphname radi, -0.1, "30°"
+
+
2162 DrawText /W=$graphname radi, -0.1, "60°"
+
+
+
2165 setdatafolder savedf
+
+
+
+
+
+
+
+
2195 variable theta_inner
+
+
+
+
+
+
+
+
2203 SetDrawLayer UserFront
+
2204 DrawAction getgroup=$groupname, delete
+
2205 SetDrawEnv gstart, gname=$groupname
+
2206 variable xc, yc, xr, yr
+
+
+
2209 variable r_center = (r_outer + r_inner) / 2
+
2210 variable r_radius = (r_outer - r_inner) / 2
+
2211 xc = r_center * cos(phi * pi / 180)
+
2212 yc = r_center * sin(phi * pi / 180)
+
+
+
2215 SetDrawEnv xcoord=HorizCrossing, ycoord=VertCrossing
+
2216 SetDrawEnv dash=11, fillpat=0
+
2217 DrawOval xc - xr, yc - yr, xc + xr, yc + yr
+
+
+
2220 xc = r_axis * cos(phi * pi / 180)
+
2221 yc = r_axis * sin(phi * pi / 180)
+
+
+
+
2225 SetDrawEnv xcoord=HorizCrossing, ycoord=VertCrossing
+
2226 SetDrawEnv fillfgc=(0,0,0)
+
2227 DrawOval xc - xr, yc - yr, xc + xr, yc + yr
+
+
+
+
+
+
2254 function /s
display_scanlines (nickname, alpha_lo, alpha_hi, m_theta, m_tilt, m_phi, [folding, projection])
+
+
+
+
+
+
+
+
+
+
2264 if (ParamIsDefault(folding))
+
+
+
2267 if (ParamIsDefault(projection))
+
+
+
+
+
2272 dfref saveDF = GetDataFolderDFR()
+
2273 newdatafolder /s/o $nickname
+
2274 string graphname = "graph_" + nickname
+
+
2276 duplicate /free m_tilt, loc_m_tilt
+
2277 loc_m_tilt = -m_tilt
+
+
2279 make /n=1 /d /free d_polar, d_azi
+
2280 variable n_alpha = round(alpha_hi - alpha_lo) + 1
+
2281 make /n=(n_alpha) /d /free analyser
+
2282 setscale /i x alpha_lo, alpha_hi, "°", analyser
+
+
+
+
2286 duplicate /free d_polar, d_radius
+
+
+
+
+
2291 SetWindow $graphname, userdata(projection)=num2str(projection)
+
+
+
+
2295 variable nang = numpnts(m_theta)
+
+
+
+
2299 for (ifold = 0; ifold < folding; ifold += 1)
+
2300 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
+
2301 for (iang = 0; iang < nang; iang += 1)
+
2302 sprintf s_rad, "rad_%d_%d", ifold, iang
+
2303 duplicate /o analyser, $s_rad
+
+
2305 w_rad = d_radius[p][iang]
+
+
2307 sprintf s_azi, "azi_%d_%d", ifold, iang
+
2308 duplicate /o analyser, $s_azi
+
+
2310 w_azi = d_azi[p][iang]
+
+
2312 if (numtype(sum(w_rad)) == 0)
+
2313 s_trace = WMPolarAppendTrace(graphname, w_rad, w_azi, 360)
+
2314 ModifyGraph /w=$graphname mode($s_trace)=0, lsize($s_trace)=0.5
+
+
+
2317 d_azi += 360 / folding
+
+
+
+
+
2322 setdatafolder saveDF
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2373 if (ParamIsDefault(projection))
+
+
+
+
+
+
+
+
+
+
+
+
+
2386 radius = polar < 90 ?
kProjScaleGnom * tan(polar * pi / 180) : inf
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2419 if (ParamIsDefault(projection))
+
+
+
+
+
+
+
2426 radius = sqrt(x^2 + y^2)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2473 if (ParamIsDefault(projection))
+
+
+
2476 if (ParamIsDefault(zeroAngle))
+
+
+
+
+
+
2482 azi = atan(y / x) * 180 / pi
+
+
2484 azi = atan(y / x) * 180 / pi + 180
+
+
+
+
+
+
+
+
+
+
2494 if (numtype(azi) != 0)
+
+
+
+
+
+
+
+
+
+
2515 dfref savedf = GetDataFolderDFR()
+
+
2517 string graphdf = "root:packages:WMPolarGraphs:" + graphname
+
2518 setdatafolder graphdf
+
+
+
+
+
+
+
2525 string sproj = GetUserData(graphname, "", "projection")
+
2526 variable projection = str2num("0" + sproj)
+
+
+
2529 variable x = hcsr(A, graphname)
+
2530 variable y = vcsr(A, graphname)
+
+
2532 csrA_phi =
calc_graph_azi (x, y, projection=projection, zeroAngle=zeroAngleWhere)
+
+
2534 x = hcsr(B, graphname)
+
2535 y = vcsr(B, graphname)
+
+
2537 csrB_phi =
calc_graph_azi (x, y, projection=projection, zeroAngle=zeroAngleWhere)
+
+
2539 setdatafolder savedf
+
+
+
+
2548 STRUCT WMWinHookStruct &s
+
+
2550 Variable hookResult = 0
+
+
+
+
+
+
+
2557 TextBox /W=$s.winname /N=tb_angles /C /V=1
+
+
+
2560 TextBox /W=$s.winname /N=tb_angles /C /V=0
+
+
+
+
+
+
+
+
+
+
2570 variable polar_angle
+
+
+
+
2574 if (ParamIsDefault(graphname))
+
2575 if (strlen(nickname) > 0)
+
2576 graphname = nickname
+
+
2578 graphname = GetDataFolder(0)
+
+
+
+
2582 string s_prefix = ""
+
2583 string s_int = "values"
+
+
+
2586 string s_polar = s_prefix + "pol"
+
2587 string s_azim = s_prefix + "az"
+
2588 wave /sdfr=df /z azim = $s_azim
+
2589 wave /sdfr=df /z polar = $s_polar
+
+
2591 FindLevel /P /Q polar, polar_angle
+
+
2593 variable polar_level = floor(v_levelx)
+
2594 FindLevel /P /Q /R=[polar_level] azim, azim_angle
+
+
2596 variable azim_level = round(v_levelx)
+
2597 string tracename = "polarY0"
+
2598 Cursor /W=$graphname /P $cursorname $traceName azim_level
+
+
+
+
+
+
+
+
+
+
+
+
+
2644 dfref savedf = GetDataFolderDFR()
+
+
2646 if (ParamIsDefault(weights))
+
2647 duplicate /free values, weights
+
+
+
+
2651 string s_prefix = ""
+
2652 string s_int = "values"
+
+
+
2655 string s_totals = s_prefix + "tot"
+
2656 string s_weights = s_prefix + "wt"
+
2657 string s_polar = s_prefix + "pol"
+
2658 string s_azim = s_prefix + "az"
+
2659 string s_index = s_prefix + "index"
+
2660 string s_theta = s_prefix + "th"
+
2661 string s_dphi = s_prefix + "dphi"
+
2662 string s_nphis = s_prefix + "nphis"
+
+
2664 wave /sdfr=df w_polar = $s_polar
+
2665 wave /sdfr=df w_azim = $s_azim
+
2666 wave /sdfr=df w_values = $s_int
+
2667 wave /sdfr=df w_totals = $s_totals
+
2668 wave /sdfr=df w_weights = $s_weights
+
2669 wave /sdfr=df w_index = $s_index
+
2670 wave /sdfr=df w_theta = $s_theta
+
2671 wave /sdfr=df w_dphi = $s_dphi
+
2672 wave /sdfr=df w_nphis = $s_nphis
+
+
+
2675 duplicate /free values, values_copy
+
2676 duplicate /free polar, polar_copy
+
2677 duplicate /free azi, azi_copy
+
2678 duplicate /free weights, weights_copy
+
2679 variable nn = dimsize(values, 0) * max(dimsize(values, 1), 1)
+
2680 redimension /n=(nn) values_copy, polar_copy, azi_copy, weights_copy
+
2681 sort /r polar_copy, polar_copy, azi_copy, values_copy, weights_copy
+
+
2683 make /n=(numpnts(w_theta)) /free /df dfw
+
+
2685 MultiThread dfw =
add_anglescan_worker (p, values_copy, weights_copy, polar_copy, azi_copy, w_polar, w_azim, w_theta, w_index, w_dphi, w_nphis)
+
+
+
2688 for (pp = 0; pp < numpnts(dfw); pp += 1)
+
+
2690 wave df_totals = tdf:w_totals
+
2691 wave df_weights = tdf:w_weights
+
2692 w_totals += df_totals
+
2693 w_weights += df_weights
+
+
2695 w_values = w_weights > 0 ? w_totals / w_weights : nan
+
+
2697 SetDataFolder savedf
+
+
+
2711 threadsafe static function /df
add_anglescan_worker (ith, values, weights, polar, azi, w_polar, w_azim, w_theta, w_index, w_dphi, w_nphis)
+
+
+
+
+
+
+
+
+
+
+
+
+
2724 dfref savedf= GetDataFolderDFR()
+
2725 dfref freedf= NewFreeDataFolder()
+
2726 SetDataFolder freedf
+
2727 make /n=(numpnts(w_polar)) /d w_totals, w_weights
+
+
2729 variable pol = w_theta[ith]
+
2730 variable pol_st = abs(w_theta[1] - w_theta[0])
+
2731 variable pol1 = pol - pol_st / 2
+
2732 variable pol2 = pol + pol_st / 2
+
+
2734 extract /free /indx polar, sel, (pol1 < polar) && (polar <= pol2) && (numtype(values) == 0) && (weights > 0)
+
2735 if (numpnts(sel) > 0)
+
2736 duplicate /free /r=[0, numpnts(sel)-1] azi, azi_slice
+
2737 duplicate /free /r=[0, numpnts(sel)-1] values, values_slice
+
2738 duplicate /free /r=[0, numpnts(sel)-1] weights, weights_slice
+
2739 azi_slice = azi[sel]
+
2740 values_slice = values[sel]
+
2741 weights_slice = weights[sel]
+
2742 add_aziscan_core (values_slice, weights_slice, pol, azi_slice, w_theta, w_azim, w_index, w_dphi, w_totals, w_weights)
+
+
+
2745 SetDataFolder savedf
+
+
+
+
2761 threadsafe static function
add_aziscan_core (values, weights, polar, azi, w_theta, w_azim, w_index, w_dphi, w_totals, w_weights)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2776 variable ipol = BinarySearch(w_theta, polar)
+
+
+
+
+
+
+
2783 d1 = w_index[ipol - 1]
+
+
+
+
2787 d2 = w_index[ipol] - 1
+
2788 variable nd = d2 - d1 + 1
+
2789 variable dphi = w_dphi[ipol]
+
2790 make /n=(nd+1) /free bin_index
+
2791 setscale /i x w_azim[d1] - dphi/2, w_azim[d2] + dphi/2, "deg", bin_index
+
+
+
+
2795 azi = azi < 0 ? azi + 360 : azi
+
2796 azi = azi >= 360 - dphi/2 ? azi - 360 : azi
+
2797 sort azi, values, weights, azi
+
2798 setscale /p x 0, 1, "", values, weights, azi
+
+
2800 bin_index = BinarySearch(azi, x) + 1
+
2801 bin_index = bin_index == -2 ? 0 : bin_index[p]
+
2802 bin_index = bin_index == -1 ? numpnts(azi) : bin_index[p]
+
2803 bin_index[nd] = numpnts(azi)
+
+
+
+
2807 variable v1, v2, w1, w2
+
2808 for (
id = 0;
id < nd;
id += 1)
+
2809 if (bin_index[
id +1] > bin_index[
id ])
+
2810 v1 = w_totals[d1 +
id ]
+
2811 w1 = w_weights[d1 +
id ]
+
2812 if ((numtype(v1) == 2) || (w1 <= 0))
+
+
+
+
2816 v2 = sum(values, bin_index[
id ], bin_index[
id +1] - 1)
+
2817 w2 = sum(weights, bin_index[
id ], bin_index[
id +1] - 1)
+
2818 w_totals[d1 +
id ] = v1 + v2
+
2819 w_weights[d1 +
id ] = w1 + w2
+
+
+
+
+
+
+
+
+
+
+
+
2851 dfref savedf = GetDataFolderDFR()
+
+
2853 duplicate /free values, values_copy
+
2854 duplicate /free azi, azi_copy
+
2855 if (ParamIsDefault(weights))
+
2856 duplicate /free values, weights_copy
+
+
+
2859 duplicate /free weights, weights_copy
+
+
+
+
2863 string s_prefix = ""
+
2864 string s_int = "values"
+
+
+
2867 string s_totals = s_prefix + "tot"
+
2868 string s_weights = s_prefix + "wt"
+
2869 string s_polar = s_prefix + "pol"
+
2870 string s_azim = s_prefix + "az"
+
2871 string s_index = s_prefix + "index"
+
2872 string s_theta = s_prefix + "th"
+
2873 string s_dphi = s_prefix + "dphi"
+
2874 string s_nphis = s_prefix + "nphis"
+
+
2876 wave /sdfr=df w_polar = $s_polar
+
2877 wave /sdfr=df w_azim = $s_azim
+
2878 wave /sdfr=df w_values = $s_int
+
2879 wave /sdfr=df w_totals = $s_totals
+
2880 wave /sdfr=df w_weights = $s_weights
+
2881 wave /sdfr=df w_index = $s_index
+
2882 wave /sdfr=df w_theta = $s_theta
+
2883 wave /sdfr=df w_dphi = $s_dphi
+
2884 wave /sdfr=df w_nphis = $s_nphis
+
+
2886 add_aziscan_core (values_copy, weights_copy, polar, azi_copy, w_theta, w_azim, w_index, w_dphi, w_totals, w_weights)
+
+
2888 w_values = w_weights > 0 ? w_totals / w_weights : nan
+
+
2890 SetDataFolder savedf
+
+
+
+
+
+
+
2924 dfref savedf = GetDataFolderDFR()
+
+
2926 if (ParamIsDefault(projection))
+
+
+
+
2930 string s_prefix = ""
+
2931 string s_int = "values"
+
+
+
+
2935 string s_polar = s_prefix + "pol"
+
2936 string s_azim = s_prefix + "az"
+
2937 string s_matrix = s_prefix + "matrix"
+
2938 string s_ster_rad = s_prefix + "ster_rad"
+
2939 string s_ster_x = s_prefix + "ster_x"
+
2940 string s_ster_y = s_prefix + "ster_y"
+
+
2942 wave /sdfr=df /z values = $s_int
+
2943 wave /sdfr=df /z azim = $s_azim
+
2944 wave /sdfr=df /z polar = $s_polar
+
2945 wave /sdfr=df /z ster_rad = $s_ster_rad
+
2946 wave /sdfr=df /z ster_x = $s_ster_x
+
2947 wave /sdfr=df /z ster_y = $s_ster_y
+
+
2949 variable min_ster_x = wavemin(ster_x)
+
2950 variable max_ster_x = wavemax(ster_x)
+
2951 variable x0 = min_ster_x
+
+
2953 variable dx = (max_ster_x - min_ster_x) / (xn - 1)
+
2954 make /n=(numpnts(ster_x), 3) /free triplet
+
2955 triplet[][0] = ster_x[p]
+
2956 triplet[][1] = ster_y[p]
+
2957 triplet[][2] = values[p]
+
+
+
+
2961 make /n=(size, size) /d /o $(s_prefix + "matrix") /wave=matrix
+
2962 make /n=(size, size) /free mnorm
+
2963 ImageFromXYZ /as {ster_x, ster_y, values}, matrix, mnorm
+
+
2965 matrixfilter NanZapMedian, matrix
+
2966 matrixfilter gauss, matrix
+
+
2968 duplicate /free values, ster_finite
+
2969 ster_finite = (numtype(values) == 0) * (ster_x^2 + ster_y^2)
+
2970 variable ster_max = wavemax(ster_finite)
+
2971 matrix = (x^2 + y^2) <= ster_max ? matrix : nan
+
+
2973 setdatafolder savedf
+
+
+
2986 function quick_pizza_image (data, nickname, theta_offset, tilt_offset, phi_offset, [npolar, nograph, folding])
+
+
+
+
+
2991 variable theta_offset
+
2992 variable tilt_offset
+
+
+
+
+
+
+
+
3000 if (ParamIsDefault(npolar))
+
+
+
3003 if (ParamIsDefault(nograph))
+
+
+
3006 if (ParamIsDefault(folding))
+
+
+
3009 string graphname =
"graph_" + nickname
+
3010 string s_prefix =
""
+
+
+
3013 dfref saveDF = GetDataFolderDFR()
+
3014 dfref dataDF = GetWavesDataFolderDFR(data)
+
3015 setdatafolder dataDF
+
3016 if (DataFolderExists(
":attr" ))
+
+
+
3019 dfref attrDF = GetDataFolderDFR()
+
3020 setdatafolder dataDF
+
3021 newdatafolder /s/o $nickname
+
3022 dfref destDF = GetDataFolderDFR()
+
+
+
3025 variable timerRefNum
+
3026 variable /g xyz_perf_secs
+
3027 timerRefNum = startMSTimer
+
+
3029 wave /sdfr=attrDF ManipulatorTheta
+
3030 wave /sdfr=attrDF ManipulatorTilt
+
3031 wave /sdfr=attrDF ManipulatorPhi
+
3032 duplicate /free ManipulatorTheta, m_theta
+
3033 duplicate /free ManipulatorTilt, m_tilt
+
3034 duplicate /free ManipulatorPhi, m_phi
+
3035 m_theta -= theta_offset
+
3036 m_tilt -= tilt_offset
+
+
+
+
+
3041 make /n=1/d/free d_polar, d_azi
+
+
+
3044 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
+
+
3046 duplicate /free data, values
+
3047 variable nn = dimsize(values, 0) * max(dimsize(values, 1), 1)
+
3048 redimension /n=(nn) values, d_polar, d_azi
+
3049 duplicate /o d_polar, ster_rad, ster_x, ster_y
+
+
3051 variable projection = 1
+
+
+
3054 ster_rad = 2 * tan(d_polar / 2 * pi / 180)
+
+
+
3057 ster_rad = 2 * cos((180 - d_polar) / 2 * pi / 180)
+
+
+
3060 string s_ster_x = s_prefix + "ster_x"
+
3061 string s_ster_y = s_prefix + "ster_y"
+
+
+
3064 make /n=(nn, nn) /d /o matrix
+
3065 make /n=(nn, nn) /free mnorm
+
3066 setscale /i x -2, +2, matrix, mnorm
+
3067 setscale /i y -2, +2, matrix, mnorm
+
+
+
+
+
3072 for (ifold = 0; ifold < folding; ifold += 1)
+
3073 ster_x = ster_rad * cos(d_azi * pi / 180)
+
3074 ster_y = ster_rad * sin(d_azi * pi / 180)
+
3075 ImageFromXYZ {ster_x, ster_y, values}, matrix, mnorm
+
3076 d_azi = d_azi >= 180 ? d_azi + 360 / folding - 180 : d_azi + 360 / folding
+
+
+
+
3080 matrixfilter /n=5 NanZapMedian matrix
+
3081 matrixfilter /n=3 gauss matrix
+
+
+
+
+
3086 modifygraph width={Plan,1,bottom,left}
+
+
+
3089 if (timerRefNum >= 0)
+
3090 xyz_perf_secs = stopMSTimer(timerRefNum) / 1e6
+
+
+
3093 setdatafolder saveDF
+
+
+
+
+
+
+
+
3102 dfref savedf = getdatafolderdfr()
+
+
+
3105 string s_prefix = ""
+
3106 string s_int = "values"
+
+
+
3109 string s_polar = s_prefix + "pol"
+
3110 string s_azim = s_prefix + "az"
+
3111 string s_theta = s_prefix + "th"
+
3112 string s_tot = s_prefix + "tot"
+
3113 string s_weight = s_prefix + "wt"
+
+
3115 wave /sdfr=df theta1 = $s_theta
+
3116 wave /sdfr=df polar1 = $s_polar
+
3117 wave /sdfr=df azim1 = $s_azim
+
3118 wave /sdfr=df tot1 = $s_tot
+
3119 wave /sdfr=df weight1 = $s_weight
+
3120 wave /sdfr=df values1 = $s_int
+
+
3122 save /m="\r\n" /o /p=$pathname /t theta1, polar1, azim1, tot1, weight1, values1 as filename
+
+
3124 setdatafolder saveDF
+
+
+
+
+
+
+
+
3135 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
3144 setdatafolder saveDF
+
+
+
3179 function
import_tpi_scan (nickname, theta, phi, intensity, [folding, npolar, nograph, xpdplot])
+
+
+
+
+
+
+
+
+
+
+
3190 if (ParamIsDefault(npolar))
+
+
+
3193 if (ParamIsDefault(nograph))
+
+
+
3196 if (ParamIsDefault(folding))
+
+
+
3199 if (ParamIsDefault(xpdplot))
+
+
+
+
+
+
+
3206 duplicate /free phi, fold_phi
+
3207 for (ifold = 0; ifold < folding; ifold += 1)
+
3208 fold_phi = fold_phi >= 360 ? fold_phi - 360 : fold_phi
+
+
3210 fold_phi += 360 / folding
+
+
+
+
+
+
+
+
+
+
+
+
3233 string s_prefix = ""
+
3234 string s_int = "values"
+
+
+
3237 string s_totals = s_prefix + "tot"
+
3238 string s_weights = s_prefix + "wt"
+
3239 string s_polar = s_prefix + "pol"
+
+
3241 wave /sdfr=df w_polar = $s_polar
+
3242 wave /sdfr=df w_values = $s_int
+
3243 wave /sdfr=df w_totals = $s_totals
+
3244 wave /sdfr=df w_weights = $s_weights
+
+
3246 w_values = w_polar <= theta_max ? w_totals / w_weights : nan
+
+
+
+
+
+
+
3272 dfref savedf = getdatafolderdfr()
+
3273 string s_prefix = ""
+
3274 string s_int = "values"
+
+
+
3277 string s_totals = s_prefix + "tot"
+
3278 string s_weights = s_prefix + "wt"
+
3279 string s_polar = s_prefix + "pol"
+
3280 string s_azim = s_prefix + "az"
+
3281 string s_index = s_prefix + "index"
+
3282 string s_theta = s_prefix + "th"
+
3283 string s_dphi = s_prefix + "dphi"
+
3284 string s_nphis = s_prefix + "nphis"
+
+
3286 sprintf s_cut, "%s_azi%03u", s_int, round(azim)
+
+
3288 wave /sdfr=df w_polar = $s_polar
+
3289 wave /sdfr=df w_azim = $s_azim
+
3290 wave /sdfr=df w_values = $s_int
+
3291 wave /sdfr=df w_totals = $s_totals
+
3292 wave /sdfr=df w_weights = $s_weights
+
3293 wave /sdfr=df w_index = $s_index
+
3294 wave /sdfr=df w_theta = $s_theta
+
3295 wave /sdfr=df w_dphi = $s_dphi
+
3296 wave /sdfr=df w_nphis = $s_nphis
+
+
3298 variable npol = numpnts(w_theta)
+
+
3300 variable pol_st = abs(w_theta[1] - w_theta[0])
+
+
+
+
+
+
3306 make /n=(npol) /o $s_cut
+
+
3308 setscale /i x w_theta[0], w_theta[numpnts(w_theta)-1], "deg", w_cut
+
3309 make /n=1 /free azi_slice
+
3310 make /n=1 /free values_slice
+
+
3312 for (ipol = 0; ipol < npol; ipol += 1)
+
+
3314 pol1 = pol - pol_st / 2
+
3315 pol2 = pol + pol_st / 2
+
3316 extract /free /indx w_polar, sel, (pol1 < w_polar) && (w_polar <= pol2)
+
+
+
3319 redimension /n=(nsel+2) azi_slice, values_slice
+
3320 azi_slice[1, nsel] = w_azim[sel[p-1]]
+
3321 azi_slice[0] = azi_slice[nsel] - 360
+
3322 azi_slice[nsel+1] = azi_slice[1] + 360
+
3323 values_slice[1, nsel] = w_values[sel[p-1]]
+
3324 values_slice[0] = values_slice[nsel]
+
3325 values_slice[nsel+1] = values_slice[1]
+
3326 w_cut[ipol] = interp(azim, azi_slice, values_slice)
+
+
+
+
+
+
3332 setdatafolder savedf
+
+
+
+
+
+
+
+
3358 dfref savedf = getdatafolderdfr()
+
3359 string s_prefix = ""
+
3360 string s_int = "values"
+
+
+
3363 string s_totals = s_prefix + "tot"
+
3364 string s_weights = s_prefix + "wt"
+
3365 string s_polar = s_prefix + "pol"
+
3366 string s_azim = s_prefix + "az"
+
3367 string s_index = s_prefix + "index"
+
3368 string s_theta = s_prefix + "th"
+
3369 string s_dphi = s_prefix + "dphi"
+
3370 string s_nphis = s_prefix + "nphis"
+
+
3372 sprintf s_cut, "%s_pol%03u", s_int, round(pol)
+
+
3374 wave /sdfr=df w_polar = $s_polar
+
3375 wave /sdfr=df w_azim = $s_azim
+
3376 wave /sdfr=df w_values = $s_int
+
3377 wave /sdfr=df w_totals = $s_totals
+
3378 wave /sdfr=df w_weights = $s_weights
+
3379 wave /sdfr=df w_index = $s_index
+
3380 wave /sdfr=df w_theta = $s_theta
+
3381 wave /sdfr=df w_dphi = $s_dphi
+
3382 wave /sdfr=df w_nphis = $s_nphis
+
+
3384 variable pol_st = abs(w_theta[1] - w_theta[0])
+
+
+
+
3388 pol1 = pol - pol_st / 2
+
3389 pol2 = pol + pol_st / 2
+
3390 extract /free /indx w_polar, sel, (pol1 < w_polar) && (w_polar <= pol2)
+
+
+
+
3394 make /n=(nsel) /o $s_cut
+
+
3396 w_cut = w_values[sel]
+
3397 setscale /i x w_azim[sel[0]], w_azim[sel[nsel-1]], "°", w_cut
+
3398 setdatafolder savedf
+
+
+
3401 setdatafolder savedf
+
+
+
3404 setdatafolder savedf
+
+
+
+
+
+
+
+
+
+
+
3415 dfref save_df = GetDataFolderDFR()
+
3416 dfref dfr = NewFreeDataFolder()
+
+
3418 StatsQuantiles /inan /iw /q /z values
+
3419 wave /z index = w_quantilesindex
+
3420 setdatafolder save_df
+
+
3422 if (waveexists(index))
+
3423 variable imin = round(numpnts(index) * pcmin / 100)
+
3424 variable imax = round(numpnts(index) * (100 - pcmax) / 100)
+
3425 vmin = values[index[imin]]
+
3426 vmax = values[index[imax]]
+
+
3428 variable d = vmax - vmin
+
3429 if ((vmax >= d/4) && (-vmin >= d/4))
+
3430 vmax = min(abs(vmin), abs(vmax))
+
+
+
+
+
3435 vmin = wavemin(values)
+
3436 vmax = wavemax(values)
+
+
+
+
3463 function
set_contrast (pcmin, pcmax, [graphname, colortable, reversecolors, symmetric])
+
+
+
+
+
3468 variable reversecolors
+
+
+
3471 if (ParamIsDefault(graphname))
+
+
+
3474 if (ParamIsDefault(colortable))
+
+
+
3477 if (ParamIsDefault(reversecolors))
+
+
+
3480 if (ParamIsDefault(symmetric))
+
+
+
+
3484 dfref save_df = GetDataFolderDFR()
+
+
+
+
+
+
+
+
+
+
+
+
3496 string traces = TraceNameList(graphname, ";", 1+4)
+
3497 n = ItemsInList(traces, ";")
+
3498 for (i = 0; i < n; i += 1)
+
3499 objname = StringFromList(i, traces, ";")
+
3500 info = TraceInfo(graphname, objname, 0)
+
3501 if (strlen(info) > 0)
+
3502 info = StringByKey("RECREATION", info, ":", ";")
+
3503 info = StringByKey("zColor(x)", info, "=", ";")
+
3504 if (strlen(info) > 2)
+
3505 info = info[1,strlen(info)-2]
+
3506 wname = StringFromList(0, info, ",")
+
+
3508 ctab = StringFromList(3, info, ",")
+
3509 rev = str2num("0" + StringFromList(4, info, ","))
+
3510 if (strlen(colortable) > 0)
+
+
+
+
+
+
3516 ModifyGraph /w=$graphname zColor($objname)={w, vmin, vmax, $ctab, rev}
+
+
+
+
+
+
3522 string images = ImageNameList(graphname,
";" )
+
3523 n = ItemsInList(images, ";")
+
3524 for (i = 0; i < n; i += 1)
+
3525 objname = StringFromList(i, images, ";")
+
3526 wave w = ImageNameToWaveRef(graphname, objname)
+
3527 info = ImageInfo(graphname, objname, 0)
+
3528 if (strlen(info) > 0)
+
3529 info = StringByKey("RECREATION", info, ":", ";")
+
3530 info = StringByKey("ctab", info, "=", ";")
+
3531 if (strlen(info) > 2)
+
3532 info = info[1,strlen(info)-2]
+
3533 ctab = StringFromList(2, info, ",")
+
3534 rev = str2num("0" + StringFromList(3, info, ","))
+
3535 if (strlen(colortable) > 0)
+
+
+
+
+
+
3541 ModifyImage /w=$graphname $objname ctab={vmin, vmax, $ctab, rev}
+
+
+
+
+
+
3547 setdatafolder save_df
+
+
+
+
+
3564 String newname = NameofWave(inwave)+
"_k"
+
3565 Duplicate/O inwave, $newname
+
3566 Wave outwave = $newname
+
3567 Variable rows,columns,xdelta,xoffset,ydelta,yoffset,kmin,kmax,Emax
+
+
3569 rows = DimSize(inwave,0)
+
3570 columns = DimSize(inwave,1)
+
3571 xdelta = DimDelta(inwave,0)
+
3572 xoffset = DimOffset(inwave,0)
+
3573 ydelta = DimDelta(inwave,1)
+
3574 yoffset = DimOffset(inwave,1)
+
3575 Emax= xoffset + xdelta*(rows-1)
+
3576 kmin = 0.5123*sqrt(Emax)*sin(pi/180*(yoffset))
+
3577 kmax = 0.5123*sqrt(Emax)*sin(pi/180*(yoffset+(columns-1)*ydelta))
+
3578 SetScale/I y kmin,kmax,"Ang^-1", outwave
+
+
3580 outwave = interp2D(inwave, x, 180/pi*asin(y/ (0.5123*sqrt(x))))
+
3581 outwave = (NumType(outwave)==2) ? 0 : outwave
+
variable crop_strip(wave strip, variable xlo, variable xhi)
crop a strip at the sides.
variable trim_hemi_scan(string nickname, variable theta_max)
trim a hemispherical scan at grazing angle
variable hemi_add_anglescan(string nickname, wave values, wave polar, wave azi, wave weights=defaultValue)
add arbitrary angle scan data to a hemispherical scan grid.
static variable CalcN_Theta(string HoloMode, variable Theta_in, variable Theta_ran, variable Theta_st)
calculate the number of thetas for a pattern
variable import_tpi_scan(string nickname, wave theta, wave phi, wave intensity, variable folding=defaultValue, variable npolar=defaultValue, variable nograph=defaultValue, variable xpdplot=defaultValue)
import a hemispherical scan from theta-phi-intensity waves and display it
variable pizza_service_2(wave data, string nickname, wave m_theta, wave m_tilt, wave m_phi, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue)
create a pizza plot from a measured (energy-integrated) data strip
variable load_hemi_scan(string nickname, string pathname, string filename)
load a hemispherical scan from an Igor text file
variable normalize_strip_theta(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average polar distribution.
variable normalize_strip_x(wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average X distribution.
static variable check_contrast(wave values, variable pcmin, variable pcmax, variable *vmin, variable *vmax, variable sym)
variable convert_angles_ttpd2polar(wave theta, wave tilt, wave phi, wave data, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
string get_hemi_prefix(wave w)
finds the prefix given any hemi wave
variable make_hemi_grid(variable npol, string nickname, variable xpdplot=defaultValue)
create a hemispherical, constant solid angle grid
variable clear_hemi_grid(string nickname)
clear a hemispherical scan grid
variable rotate_y_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the y axis
threadsafe variable calc_graph_polar(variable x, variable y, variable projection=defaultValue)
calculate polar angle from Cartesian coordinate
static const variable kProjScaleOrtho
string get_hemi_nickname(wave w)
finds the nick name given any hemi wave
wave hemi_azi_cut(string nickname, variable pol)
extract an azimuthal cut from a hemispherical scan
variable normalize_strip_2d(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by a two-dimensional normalization function.
static variable line_average(wave source, wave dest)
threadsafe wave ad_profile_x(wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, new destination wave.
string display_scanlines(string nickname, variable alpha_lo, variable alpha_hi, wave m_theta, wave m_tilt, wave m_phi, variable folding=defaultValue, variable projection=defaultValue)
display a polar graph with lines indicating the angles covered by an angle scan.
threadsafe wave ad_profile_y(wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along Y dimension, new destination wave.
variable normalize_strip_theta_scans(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip piecewise by a smooth polar distribution.
static variable Calc_The_step(variable th, variable Theta_st, string Holomode)
calculate delta-theta for a given theta
variable crop_strip_theta(wave strip, variable theta_lo, variable theta_hi, wave theta, wave tilt, wave phi)
crop a strip in theta.
threadsafe variable calc_graph_radius(variable polar, variable projection=defaultValue)
calculate the projected polar angle
static threadsafe dfr add_anglescan_worker(variable ith, wave values, wave weights, wave polar, wave azi, wave w_polar, wave w_azim, wave w_theta, wave w_index, wave w_dphi, wave w_nphis)
thread worker for hemi_add_anglescan
dfr find_hemi_data(string nickname, string *prefix, string *intwave)
finds the folder, prefix and name of holo waves given their nick name
variable pizza_service(wave data, string nickname, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue, variable xpdplot=defaultValue)
create a pizza plot from a measured (energy-integrated) data strip
variable draw_diffraction_cone(string graphname, string groupname, variable theta_axis, variable theta_inner, variable phi)
draw the circle of a diffraction cone in a stereographic polar graph.
variable interpolate_hemi_scan(string nickname, variable projection=defaultValue)
interpolate a hemispherical scan onto a rectangular grid
static const variable kProjScaleDist
variable cart2polar_wave(wave in, wave out)
variable rotate_hemi_scan(string nickname, variable angle)
azimuthally rotate a hemispherical scan dataset.
static string display_polar_graph(string graphname, variable angle_offset=defaultValue, variable do_ticks=defaultValue)
displays an empty polar graph
variable quick_pizza_image(wave data, string nickname, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable folding=defaultValue)
map angle scan data onto a rectangular grid in stereographic projection
variable set_contrast(variable pcmin, variable pcmax, string graphname=defaultValue, string colortable=defaultValue, variable reversecolors=defaultValue, variable symmetric=defaultValue)
set the pseudocolor contrast by percentile.
static variable calc_nth(variable Theta_st, variable Theta_in, variable th, variable Phi_ran, variable Phi_ref, string Holomode)
calculate the number of phis for a given theta
variable hemi_add_aziscan(string nickname, wave values, variable polar, wave azi, wave weights=defaultValue)
add azimuthal data to a hemispherical scan grid.
static threadsafe variable add_aziscan_core(wave values, wave weights, variable polar, wave azi, wave w_theta, wave w_azim, wave w_index, wave w_dphi, wave w_totals, wave w_weights)
thread worker for hemi_add_anglescan and hemi_add_aziscan
variable convert_angles_ttpa2polar(wave theta, wave tilt, wave phi, wave analyser, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
static const variable kProjScaleGnom
variable save_hemi_scan(string nickname, string pathname, string filename)
save a hemispherical scan to an Igor text file
processing and holographic mapping of angle scanned XPD data.
variable rotate_x_wave(wave inout, variable angle)
rotate a wave of 3-vectors about the x axis.
threadsafe variable calc_graph_azi(variable x, variable y, variable projection=defaultValue, variable zeroAngle=defaultValue)
calculate azimuthal angle from Cartesian coordinate
const variable kProjStereo
variable normalize_strip_thetaphi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by a smooth polar-azimuthal distribution.
variable rotate_z_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the z axis
static const variable kProjScaleStereo
static const variable kProjScaleArea
variable duplicate_hemi_scan(string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue)
duplicate a hemispherical scan dataset.
variable set_polar_graph_cursor(string nickname, string cursorname, variable polar_angle, variable azim_angle, string graphname=defaultValue)
const variable kProjOrtho
variable normalize_strip_phi(wave strip, wave theta, wave phi, variable theta_offset=defaultValue, variable theta_range=defaultValue, variable check=defaultValue)
divide the strip by a sine function in phi (wobble correction).
variable polar2cart_wave(wave in, wave out)
static variable calc_phi_step(variable Theta_in, variable th, variable Theta_st, variable Phi_ran, variable Phi_ref, string Holomode)
calculate delta-phi for a given theta
static variable polar_graph_hook(WMWinHookStruct *s)
polar graph window hook
string prepare_hemi_scan_display(string nickname, variable projection=defaultValue)
create waves for plotting a hemispherical angle scan.
wave hemi_polar_cut(string nickname, variable azim)
extract a polar cut from a hemispherical scan.
variable show_analyser_line(variable theta, variable tilt, variable phi, variable theta_offset, variable tilt_offset, variable phi_offset, variable npolar=defaultValue, variable nograph=defaultValue, variable xpdplot=defaultValue)
calculate and display the line seen by the analyser for a specific emission angle
string strip_append(wave strip1, wave strip2)
append an angle scan strip to another one
variable strip_delete_frames(wave strip, variable qlo, variable qhi, wave theta, wave tilt, wave phi)
delete a contiguous range of frames from a strip.
variable AngleToK(wave inwave)
k-space mapping of 2D angle-energy distribution (scienta image)
static variable update_polar_info(string graphname)
update the angles info based on cursors A and B of a given polar graph window
static string draw_hemi_axes(string graphname, variable do_grids=defaultValue)
draw polar and azimuthal grids in an existing polar graph.
string display_hemi_scan(string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue)
display a plot of a hemispherical angle scan.
PEARL Procedures: pearl-anglescan-tracker.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -99,84 +101,84 @@ $(document).ready(function(){initNavTree('pearl-anglescan-tracker_8ipf.html','')
static variable AfterCompiledHook ()
-
initialize package data once when the procedure is first loaded More...
+
initialize package data once when the procedure is first loaded More... static variable init_package () static variable save_prefs ()
-
save persistent package data to the preferences file. More...
+
save persistent package data to the preferences file. More... static variable load_prefs ()
-
load persistent package data from the preferences file. More...
+
load persistent package data from the preferences file. More... static variable IgorQuitHook (string app)
-
disconnect EPICS channels before Igor quits. More...
+
disconnect EPICS channels before Igor quits. More... variable ast_setup ()
-
set up data structures, display graph, and try to connect to analyser. More...
+
set up data structures, display graph, and try to connect to analyser. More... variable ast_prepare (variable theta_offset=defaultValue, variable tilt_offset=defaultValue, variable phi_offset=defaultValue)
-
prepare for new measurement and clear the data buffer. More...
+
prepare for new measurement and clear the data buffer. More... variable ast_set_processing (string reduction_func, string reduction_params)
-
set the data processing parameters More...
+
set the data processing parameters More... variable ast_add_image (wave image, variable theta, variable tilt, variable phi)
-
process and add a detector image to the tracker scan. More...
+
process and add a detector image to the tracker scan. More... variable ast_export (dfref folder, string nickname, variable xpdplot=defaultValue)
-
export tracker data to a separate, independent data set. More...
+
export tracker data to a separate, independent data set. More... variable ast_import (string nickname)
-
import tracker data from an existing angle scan dataset. More...
+
import tracker data from an existing angle scan dataset. More... variable ast_update_detector (variable theta, variable tilt, variable phi, variable range)
-
update the current position indicator. More...
+
update the current position indicator. More... variable ast_close ()
-
stop tracker, close graph, release data structures. More...
+
stop tracker, close graph, release data structures. More... static variable setup_data () static variable extend_data (variable num_slices)
-
extend the data buffer for the next polar scan More...
+
extend the data buffer for the next polar scan More... static variable setup_detector () static variable add_image_data (wave image, variable theta, variable tilt, variable phi)
-
reduce a detector image and add the result to the data buffer. More...
+
reduce a detector image and add the result to the data buffer. More... static variable process_image_data ()
-
process the data buffer to generate the tracker dataset. More...
+
process the data buffer to generate the tracker dataset. More... static variable update_detector (variable theta, variable tilt, variable phi, variable range)
-
update the current position indicator. More...
+
update the current position indicator. More... static variable setup_graph ()
-
create the graph window. More...
+
create the graph window. More... static variable update_data_graph () static variable update_detector_graph () static variable epics_connect ()
-
connect the angle scan tracker to EPICS More...
+
connect the angle scan tracker to EPICS More... static variable epics_disconnect_chid (string chid_var_name) static variable epics_disconnect () static variable ast_window_hook (WMWinHookStruct *s)
-
window hook More...
+
window hook More... variable ast_callback_data (variable chan)
-
callback function for new analyser data from EPICS. More...
+
callback function for new analyser data from EPICS. More... variable ast_callback_detector (variable chan)
-
callback function for new detector state from EPICS. More...
+
callback function for new detector state from EPICS. More... variable ast_callback_manip (variable chan)
-
callback function for new manipulator position from EPICS. More...
+
callback function for new manipulator position from EPICS. More... static variable bp_capture (WMButtonAction *ba)
@@ -189,16 +191,16 @@ Functions
static variable pmp_data_mouseup (WMPopupAction *pa) static variable export_tracker_data ()
-
export tracker data (with prompt) More...
+
export tracker data (with prompt) More... static variable import_tracker_data ()
-
import tracker data (with prompt) More...
+
import tracker data (with prompt) More... static variable save_tracker_data ()
-
save tracker data to file (with prompt) More...
+
save tracker data to file (with prompt) More... static variable load_tracker_data ()
-
import tracker data from file (with prompt) More...
+
import tracker data from file (with prompt) More... static variable pmp_parameters (WMPopupAction *pa)
@@ -214,10 +216,10 @@ Variables
version static const string package_path = "root:packages:pearl_anglescan_tracker:"
-
data folder path More...
+
data folder path More... static const string prefs_objects = "projection;theta_offset;tilt_offset;phi_offset;reduction_func;reduction_params"
-
semicolon-separated list of persistent variable, string, and wave names More...
+
semicolon-separated list of persistent variable, string, and wave names More...
@@ -279,7 +281,7 @@ Variables
the manipulator angles are corrected by the preset offsets internally.
-
Definition at line 453 of file pearl-anglescan-tracker.ipf .
+
Definition at line 454 of file pearl-anglescan-tracker.ipf .
initialize package data once when the procedure is first loaded
-Definition at line 73 of file pearl-anglescan-tracker.ipf .
+Definition at line 74 of file pearl-anglescan-tracker.ipf .
@@ -362,7 +364,7 @@ Variables
the manipulator angles are corrected by the preset offsets internally.
-Definition at line 285 of file pearl-anglescan-tracker.ipf .
+Definition at line 286 of file pearl-anglescan-tracker.ipf .
@@ -384,7 +386,7 @@ Variables
callback function for new analyser data from EPICS.
-Definition at line 856 of file pearl-anglescan-tracker.ipf .
+Definition at line 857 of file pearl-anglescan-tracker.ipf .
@@ -405,9 +407,9 @@ Variables
@@ -429,7 +431,7 @@ Variables
callback function for new manipulator position from EPICS.
-Definition at line 990 of file pearl-anglescan-tracker.ipf .
+Definition at line 991 of file pearl-anglescan-tracker.ipf .
@@ -450,7 +452,7 @@ Variables
stop tracker, close graph, release data structures.
-Definition at line 360 of file pearl-anglescan-tracker.ipf .
+Definition at line 361 of file pearl-anglescan-tracker.ipf .
@@ -492,7 +494,7 @@ Variables
folder destination folder path nickname name prefix for waves xpdplot xpdplot compatibility, see make_hemi_grid() for details Definition at line 329 of file pearl-anglescan-tracker.ipf .
+Definition at line 330 of file pearl-anglescan-tracker.ipf .
@@ -576,7 +578,7 @@ Variables
-Definition at line 211 of file pearl-anglescan-tracker.ipf .
+Definition at line 212 of file pearl-anglescan-tracker.ipf .
@@ -610,13 +612,13 @@ Variables
the parameters will be effective for subsequent measurements only. previously acquired data is not affected. the processing parameters are saved with the preferences.
Parameters
- reduction_func name of custom reduction function, e.g. "int_linbg_reduction". any user-defined function with the same signature as adh5_default_reduction() is allowed. reduction_func name of custom reduction function, e.g. "int_linbg_reduction". any user-defined function with the same signature as adh5_default_reduction() is allowed. reduction_params parameter string for the reduction function. the format depends on the actual function. for int_linbg_reduction, e.g., "Lcrop=0.1;Hcrop=0.1;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.4".
Definition at line 261 of file pearl-anglescan-tracker.ipf .
+Definition at line 262 of file pearl-anglescan-tracker.ipf .
@@ -637,7 +639,7 @@ Variables
set up data structures, display graph, and try to connect to analyser.
-Definition at line 194 of file pearl-anglescan-tracker.ipf .
+Definition at line 195 of file pearl-anglescan-tracker.ipf .
@@ -691,7 +693,7 @@ Variables
the manipulator angles are corrected by the preset offsets internally.
-Definition at line 349 of file pearl-anglescan-tracker.ipf .
+Definition at line 350 of file pearl-anglescan-tracker.ipf .
@@ -722,7 +724,7 @@ Variables
window hook
disconnects from EPICS when the window is closed.
-Definition at line 841 of file pearl-anglescan-tracker.ipf .
+Definition at line 842 of file pearl-anglescan-tracker.ipf .
@@ -750,7 +752,7 @@ Variables
@@ -777,7 +779,7 @@ Variables
@@ -804,7 +806,7 @@ Variables
@@ -837,7 +839,7 @@ Variables
Returns zero if successful, non-zero if an error occurred Todo: the X03DA channel names are hard-coded. Definition at line 680 of file pearl-anglescan-tracker.ipf .
+Definition at line 681 of file pearl-anglescan-tracker.ipf .
@@ -864,7 +866,7 @@ Variables
@@ -892,7 +894,7 @@ Variables
@@ -921,7 +923,7 @@ Variables
export tracker data (with prompt)
-Definition at line 1105 of file pearl-anglescan-tracker.ipf .
+Definition at line 1106 of file pearl-anglescan-tracker.ipf .
@@ -958,7 +960,7 @@ Variables
-Definition at line 402 of file pearl-anglescan-tracker.ipf .
+Definition at line 403 of file pearl-anglescan-tracker.ipf .
@@ -988,7 +990,7 @@ Variables
disconnect EPICS channels before Igor quits.
-Definition at line 188 of file pearl-anglescan-tracker.ipf .
+Definition at line 189 of file pearl-anglescan-tracker.ipf .
@@ -1017,7 +1019,7 @@ Variables
import tracker data (with prompt)
-Definition at line 1135 of file pearl-anglescan-tracker.ipf .
+Definition at line 1136 of file pearl-anglescan-tracker.ipf .
@@ -1044,7 +1046,7 @@ Variables
@@ -1075,7 +1077,7 @@ Variables
the preferences file is an Igor packed experiment file in a special preferences folder.
this function is called automatically when the procedure is first compiled, or whenever the user clicks the corresponding button.
-Definition at line 163 of file pearl-anglescan-tracker.ipf .
+Definition at line 164 of file pearl-anglescan-tracker.ipf .
@@ -1104,7 +1106,7 @@ Variables
import tracker data from file (with prompt)
-Definition at line 1175 of file pearl-anglescan-tracker.ipf .
+Definition at line 1176 of file pearl-anglescan-tracker.ipf .
@@ -1132,7 +1134,7 @@ Variables
@@ -1160,7 +1162,7 @@ Variables
@@ -1188,7 +1190,7 @@ Variables
@@ -1216,7 +1218,7 @@ Variables
@@ -1245,7 +1247,7 @@ Variables
process the data buffer to generate the tracker dataset.
-Definition at line 507 of file pearl-anglescan-tracker.ipf .
+Definition at line 508 of file pearl-anglescan-tracker.ipf .
@@ -1275,7 +1277,7 @@ Variables
save persistent package data to the preferences file.
this function is called when the user clicks the corresponding button.
-Definition at line 139 of file pearl-anglescan-tracker.ipf .
+Definition at line 140 of file pearl-anglescan-tracker.ipf .
@@ -1304,7 +1306,7 @@ Variables
save tracker data to file (with prompt)
-Definition at line 1164 of file pearl-anglescan-tracker.ipf .
+Definition at line 1165 of file pearl-anglescan-tracker.ipf .
@@ -1331,7 +1333,7 @@ Variables
@@ -1358,7 +1360,7 @@ Variables
@@ -1387,7 +1389,7 @@ Variables
create the graph window.
-Definition at line 594 of file pearl-anglescan-tracker.ipf .
+Definition at line 595 of file pearl-anglescan-tracker.ipf .
@@ -1414,7 +1416,7 @@ Variables
@@ -1441,7 +1443,7 @@ Variables
@@ -1468,7 +1470,7 @@ Variables
@@ -1530,7 +1532,7 @@ Variables
the manipulator angles are corrected by the preset offsets internally.
-Definition at line 559 of file pearl-anglescan-tracker.ipf .
+Definition at line 560 of file pearl-anglescan-tracker.ipf .
@@ -1557,7 +1559,7 @@ Variables
@@ -1584,7 +1586,7 @@ Variables
data folder path
-Definition at line 68 of file pearl-anglescan-tracker.ipf .
+Definition at line 69 of file pearl-anglescan-tracker.ipf .
@@ -1610,7 +1612,7 @@ Variables
semicolon-separated list of persistent variable, string, and wave names
-Definition at line 70 of file pearl-anglescan-tracker.ipf .
+Definition at line 71 of file pearl-anglescan-tracker.ipf .
@@ -1625,21 +1627,40 @@ Variables
+static const string package_name
package name is used as data folder name
PEARL Procedures: pearl-anglescan-tracker.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,77 +87,1182 @@ $(document).ready(function(){initNavTree('pearl-anglescan-tracker_8ipf_source.ht
pearl-anglescan-tracker.ipf
-
Go to the documentation of this file. 3 #pragma IgorVersion = 6.2 4 #pragma ModuleName = PearlAnglescanTracker 5 #include "pearl-area-profiles" ,
version > 1.04
6 #include
"pearl-area-import" ,
version > 1.05
7 #include
"pearl-scienta-preprocess" ,
version > 1.00
8 #include
"pearl-anglescan-process" ,
version >= 1.6
9 #include <New Polar Graphs>
66 static strconstant
package_name =
"pearl_anglescan_tracker" 68 static strconstant
package_path =
"root:packages:pearl_anglescan_tracker:" 70 static strconstant
prefs_objects =
"projection;theta_offset;tilt_offset;phi_offset;reduction_func;reduction_params" 75 dfref savedf = GetDataFolderDFR()
80 if (nvar_exists(init_done))
91 variable /g init_done = 1
99 dfref savedf = getdatafolderdfr()
101 newdatafolder /o/s packages
102 newdatafolder /o/s $package_name
105 string /g graphname = "graph_anglescan_tracker"
106 string /g dataname = "tracker"
107 string /g projection = "stereographic"
110 variable /g theta_offset = 0
111 variable /g tilt_offset = 0
112 variable /g phi_offset = 0
114 string /g reduction_params = "Lcrop=0.1;Hcrop=0.1;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.4"
117 string /g export_folderpath = "root:"
118 variable /g export_format = 1
121 string /g detector_tracename
122 variable /g capturing = 0
123 variable /g buf_size = 0
124 variable /g buf_count = 0
125 variable /g buf_width = 0
128 string path = FunctionPath("")
129 path = ParseFilePath(1, path, ":", 1, 0) + "tracker-sample-picture.png"
130 LoadPict /O/Q path, pict_tracker_sample
140 dfref saveDF = GetDataFolderDFR()
142 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
144 NewPath/O/C/Q tempPackagePrefsPath, fullPath
145 fullPath += ":preferences.pxp"
147 SetDataFolder root:packages
148 SetDataFolder $package_name
151 KillPath/Z tempPackagePrefsPath
164 dfref saveDF = GetDataFolderDFR()
168 NewDataFolder /O/S packages
169 NewDataFolder /O/S $package_name
170 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
173 GetFileFolderInfo /Q /Z fullPath
175 fullPath += ":preferences.pxp"
176 GetFileFolderInfo /Q /Z fullPath
178 LoadData /O /R /Q fullPath
212 variable theta_offset
216 dfref savedf = getdatafolderdfr()
219 if (!ParamIsDefault(theta_offset))
220 nvar v_theta_offset = theta_offset
221 v_theta_offset = theta_offset
223 if (!ParamIsDefault(tilt_offset))
224 nvar v_tilt_offset = tilt_offset
225 v_tilt_offset = tilt_offset
227 if (!ParamIsDefault(phi_offset))
228 nvar v_phi_offset = phi_offset
229 v_phi_offset = phi_offset
242 wave values = $(dataname + "_i")
243 values[numpnts(values) - 1] = 0
262 string reduction_func
263 string reduction_params
265 dfref savedf = getdatafolderdfr()
268 svar red_func = reduction_func
269 svar red_params = reduction_params
271 red_func = reduction_func
272 red_params = reduction_params
312 if (ParamIsDefault(xpdplot))
316 dfref savedf = getdatafolderdfr()
332 dfref savedf = getdatafolderdfr()
361 dfref savedf = getdatafolderdfr()
362 setdatafolder $(package_path)
367 KillWindow $graphname
373 dfref savedf = getdatafolderdfr()
374 setdatafolder $(package_path)
382 make /n=(1,1) /o buf_i
383 make /n=(1) /o buf_th, buf_ph, buf_ti
390 wave values = $(dataname + "_i")
391 values[numpnts(values) - 1] = 0
405 dfref savedf = getdatafolderdfr()
406 setdatafolder $(package_path)
412 variable new_size = buf_size + 91
413 buf_width = num_slices
420 redimension /n=(buf_width,new_size) buf_i
421 redimension /n=(new_size) buf_th, buf_ph, buf_ti
423 buf_i[][buf_size, new_size-1] = nan
424 buf_th[buf_size, new_size-1] = nan
425 buf_ph[buf_size, new_size-1] = nan
426 buf_ti[buf_size, new_size-1] = nan
435 dfref savedf = getdatafolderdfr()
436 setdatafolder $(package_path)
438 make /n=31 /o detector_angle, detector_pol, detector_az, detector_rad
439 setscale /i x -30, 30, "°", detector_angle, detector_pol, detector_az, detector_rad
459 dfref savedf = getdatafolderdfr()
460 setdatafolder $(package_path)
467 svar red_func_name = reduction_func
468 svar red_params = reduction_params
470 variable nx = dimsize(image, 0)
471 string loc_params = red_params
472 wave /wave red_results = red_func(image, loc_params)
473 if (numpnts(red_results) < 1)
478 wave profile1 = red_results[0]
479 nx = numpnts(profile1)
490 if ((buf_count >= buf_size) || (nx > buf_width))
492 setscale /p x dimoffset(profile1,0), dimdelta(profile1,0), waveunits(profile1,0), buf_i
495 buf_i[][buf_count] = profile1[p]
496 buf_th[buf_count] = theta - theta_offset
497 buf_ti[buf_count] = -(tilt - tilt_offset)
498 buf_ph[buf_count] = phi - phi_offset
513 dfref savedf = getdatafolderdfr()
514 setdatafolder $(package_path)
526 duplicate /free /R=[0,buf_width-1][0,buf_count-1] buf_i, buf_n
527 duplicate /free /R=[0,buf_count-1] buf_th, w_th
528 duplicate /free /R=[0,buf_count-1] buf_ti, w_ti
529 duplicate /free /R=[0,buf_count-1] buf_ph, w_ph
535 if (dimoffset(buf_i,0) < -20)
541 make /n=1 /free d_polar, d_azi
544 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
565 dfref savedf = getdatafolderdfr()
566 setdatafolder $(package_path)
571 make /n=1 /free m_theta
572 make /n=1 /free m_tilt
573 make /n=1 /free m_phi
574 m_theta = theta - theta_offset
575 m_tilt = tilt - tilt_offset
577 m_phi = phi - phi_offset
580 wave detector_angle, detector_pol, detector_az, detector_rad
581 setscale /i x -range/2, +range/2, "°", detector_angle
585 redimension /n=(numpnts(detector_pol)) detector_rad
586 detector_rad = 2 * tan(detector_pol / 2 * pi / 180)
588 detector_az = detector_az >= 360 ? detector_az - 360 : detector_az
595 dfref savedf = getdatafolderdfr()
596 setdatafolder $(package_path)
603 svar tracename = detector_tracename
606 tracename = WMPolarAppendTrace(graphname, detector_rad, detector_az, 360)
607 ModifyGraph /w=$graphname lstyle($tracename)=0
608 ModifyGraph /w=$graphname lsize($tracename)=1.5
609 ModifyGraph /w=$graphname zColor($tracename)={detector_angle,*,*,RedWhiteBlue,0}
610 ColorScale /w=$graphname /C /N=text1 trace=$tracename
611 ColorScale /w=$graphname /C /N=text1 /F=0 /B=1 /A=LB /X=0.00 /Y=0.00
612 ColorScale /w=$graphname /C /N=text1 width=1.5, heightPct=20, frame=0.00
613 ColorScale /w=$graphname /C /N=text1 lblMargin=0
614 ColorScale /w=$graphname /C /N=text1 nticks=2, tickLen=2.00, tickThick=0.50
616 TextBox /w=$graphname /C /N=tb_manip /F=0 /B=1 /X=0.00 /Y=0.00 /E=2
"\\{\"manip = (%.1f, %.1f, %.1f)\", " 617 AppendText /w=$graphname /N=tb_manip /NOCR
"root:packages:pearl_anglescan_tracker:curTheta, " 618 AppendText /w=$graphname /N=tb_manip /NOCR
"root:packages:pearl_anglescan_tracker:curTilt, " 619 AppendText /w=$graphname /N=tb_manip /NOCR
"root:packages:pearl_anglescan_tracker:curPhi}" 622 DoWindow /T $graphname,
"Angle Scan Tracker" 625 ControlBar /w=$graphname 21
627 Button b_capture win=$graphname, fColor=(65535,65535,65535), fSize=10
628 Button b_capture win=$graphname, help={
"Start/stop capturing." }
629 PopupMenu pm_params win=$graphname, mode=0, value=
"load preferences;save preferences;reduction parameters;manipulator offsets" , title=
"parameters" 631 PopupMenu pm_params win=$graphname, help={
"Load/save/edit data processing parameters" }
632 PopupMenu pm_data win=$graphname, mode=0, value=
"import;export;load file;save file" , title=
"data" 634 PopupMenu pm_data win=$graphname, help={
"Load/save data from/to independent dataset or file" }
636 SetDrawLayer /w=$graphname ProgFront
637 SetDrawEnv /w=$graphname xcoord=rel, ycoord=rel
638 DrawPict /w=$graphname 0, 0, 1, 1, pict_tracker_sample
646 dfref savedf = getdatafolderdfr()
658 dfref savedf = getdatafolderdfr()
681 dfref savedf = getdatafolderdfr()
688 make /n=(1)/o arraydata, xscale, yscale
689 make /n=(1,1)/o image
690 variable /g ndimensions
691 variable /g arraysize0, arraysize1
693 variable /g colormode
694 string /g controls, monitors
695 string /g xunits, yunits
698 variable /g chidDetectorState = 0
699 variable /g chidArrayData = 0
700 variable /g chidXScale = 0
701 variable /g chidYScale = 0
702 variable /g chidNDimensions = 0
703 variable /g chidArraySize0 = 0
704 variable /g chidArraySize1 = 0
705 variable /g chidDataType = 0
706 variable /g chidColorMode = 0
707 variable /g chidLensMode = 0
708 variable /g chidTheta = 0
709 variable /g chidTilt = 0
710 variable /g chidPhi = 0
711 variable /g curDetectorState = 0
712 variable /g curLensMode = 0
713 variable /g curTheta = 0
714 variable /g curTilt = 0
715 variable /g curPhi = 0
716 variable /g acqTheta = 0
717 variable /g acqTilt = 0
718 variable /g acqPhi = 0
719 variable /g connected = 0
721 string epicsname = "X03DA-SCIENTA:"
722 string imagename = epicsname + "image1:"
723 string camname = epicsname + "cam1:"
724 string manipname = "X03DA-ES2-MA:"
729 pvOpen /Q chidDetectorState, camname +
"DetectorState_RBV" 730 pvOpen /Q chidLensMode, camname +
"LENS_MODE_RBV" 731 pvOpen /Q chidXScale, camname +
"CHANNEL_SCALE_RBV" 732 pvOpen /Q chidYScale, camname +
"SLICE_SCALE_RBV" 733 pvOpen /Q chidArrayData, imagename +
"ArrayData" 734 pvOpen /Q chidNDimensions, imagename +
"NDimensions_RBV" 735 pvOpen /Q chidArraySize0, imagename +
"ArraySize0_RBV" 736 pvOpen /Q chidArraySize1, imagename +
"ArraySize1_RBV" 737 pvOpen /Q chidDataType, imagename +
"DataType_RBV" 738 pvOpen /Q chidColorMode, imagename +
"ColorMode_RBV" 740 pvOpen /Q chidTheta, manipname +
"THT.RBV" 741 pvOpen /Q chidTilt, manipname +
"TLT.RBV" 742 pvOpen /Q chidPhi, manipname +
"PHI.RBV" 749 #elif exists("pvOpen") 751 pvOpen /T=(timeout) chidDetectorState, camname +
"DetectorState_RBV" 752 pvOpen /T=(timeout) chidLensMode, camname +
"LENS_MODE_RBV" 753 pvOpen /T=(timeout) chidXScale, camname +
"CHANNEL_SCALE_RBV" 754 pvOpen /T=(timeout) chidYScale, camname +
"SLICE_SCALE_RBV" 755 pvOpen /T=(timeout) chidArrayData, imagename +
"ArrayData" 756 pvOpen /T=(timeout) chidNDimensions, imagename +
"NDimensions_RBV" 757 pvOpen /T=(timeout) chidArraySize0, imagename +
"ArraySize0_RBV" 758 pvOpen /T=(timeout) chidArraySize1, imagename +
"ArraySize1_RBV" 759 pvOpen /T=(timeout) chidDataType, imagename +
"DataType_RBV" 760 pvOpen /T=(timeout) chidColorMode, imagename +
"ColorMode_RBV" 762 pvOpen /T=(timeout) chidTheta, manipname +
"THT.RBV" 763 pvOpen /T=(timeout) chidTilt, manipname +
"TLT.RBV" 764 pvOpen /T=(timeout) chidPhi, manipname +
"PHI.RBV" 771 #
if exists(
"pvMonitor" )
783 print
"angle scan tracker: online" 785 print
"angle scan tracker: offline" 795 #if exists("pvClose") 796 nvar /z chid = $chid_var_name
797 if (nvar_exists(chid))
807 dfref savedf = GetDataFolderDFR()
831 print "angle scan tracker: offline"
842 STRUCT WMWinHookStruct &s
844 Variable hookResult = 0
864 dfref savedf = GetDataFolderDFR()
866 #if exists("pvGetWave") 896 pvGet chidNDimensions, ndimensions
897 pvGet chidArraySize0, arraysize0
898 pvGet chidArraySize1, arraysize1
899 pvGet chidDataType, datatype
900 pvGet chidColorMode, colormode
903 if (ndimensions != 2)
910 redimension /n=(arraysize0 * arraysize1) arraydata
911 redimension /n=(arraysize0, arraysize1) image
912 redimension /n=(arraysize0) xscale
913 redimension /n=(arraysize1) yscale
917 redimension /b arraydata, image
920 redimension /b/u arraydata, image
923 redimension /w arraydata, image
926 redimension /w/u arraydata, image
929 redimension /i arraydata, image
932 redimension /i/u arraydata, image
935 redimension /s arraydata, image
938 redimension /d arraydata, image
942 pvGetWave chidArrayData, arraydata
943 pvGetWave chidXScale, xscale
944 pvGetWave chidYScale, yscale
946 image = arraydata[p + q * arraysize0]
947 setscale /i x xscale[0], xscale[numpnts(xscale)-1], image
948 setscale /i y yscale[0], yscale[numpnts(yscale)-1], image
964 dfref savedf = GetDataFolderDFR()
968 nvar curDetectorState
977 if (curDetectorState == 1)
993 dfref savedf = GetDataFolderDFR()
997 nvar lensmode = curLensMode
998 nvar theta = curTheta
1017 setdatafolder savedf
1024 STRUCT WMButtonAction &ba
1026 switch( ba.eventCode )
1038 dfref savedf = getdatafolderdfr()
1044 capturing = !capturing
1047 Button b_capture win=$graphname, title="stop"
1049 Button b_capture win=$graphname, title="start"
1052 setdatafolder saveDF
1056 dfref savedf = getdatafolderdfr()
1063 Button b_capture win=$graphname, title="stop"
1065 Button b_capture win=$graphname, title="start"
1068 setdatafolder saveDF
1072 STRUCT WMPopupAction &pa
1074 switch( pa.eventCode )
1086 STRUCT WMPopupAction &pa
1106 dfref savedf = getdatafolderdfr()
1109 svar export_folderpath
1112 string folderpath = export_folderpath
1113 string nickname = ""
1114 variable format = export_format
1116 prompt folderpath, "Folder Path"
1117 prompt nickname, "Nick Name"
1118 prompt format, "Format", popup, "PEARL;XPDplot"
1120 doprompt "Export Parameters", folderpath, nickname, format
1123 export_folderpath = folderpath
1124 export_format = format
1126 newdatafolder /o $folderpath
1127 variable xpdplot = format == 2
1128 ast_export ($folderpath, nickname, xpdplot=xpdplot)
1131 setdatafolder saveDF
1136 dfref savedf = getdatafolderdfr()
1139 svar export_folderpath
1140 string folderpath = export_folderpath
1141 string nickname = ""
1143 dfref dfBefore = GetDataFolderDFR()
1144 Execute /q/z "CreateBrowser prompt=\"Select wave from dataset\", showWaves=1, showVars=0, showStrs=0"
1145 dfref dfAfter = GetDataFolderDFR()
1146 SetDataFolder dfBefore
1148 SVAR list = S_BrowserList
1151 if ((flag != 0) && (ItemsInList(list) >= 1))
1152 string wname = StringFromList(0, list)
1155 dfref df = GetWavesDataFolderDFR(w)
1160 setdatafolder saveDF
1165 dfref savedf = getdatafolderdfr()
1171 setdatafolder saveDF
1176 dfref savedf = getdatafolderdfr()
1179 NewDataFolder /O/S load_data
1182 string wname = StringFromList(0, s_wavenames, ";")
1189 KillDataFolder /Z load_data
1191 setdatafolder saveDF
1195 STRUCT WMPopupAction &pa
1197 switch( pa.eventCode )
1209 STRUCT WMPopupAction &pa
1229 dfref savedf = getdatafolderdfr()
1232 svar pref_func = reduction_func
1233 svar pref_params = reduction_params
1235 string loc_func = pref_func
1236 string loc_params = pref_params
1241 setdatafolder saveDF
1245 dfref savedf = getdatafolderdfr()
1252 variable loc_theta = theta_offset
1253 variable loc_tilt = tilt_offset
1254 variable loc_phi = phi_offset
1256 prompt loc_theta, "theta offset"
1257 prompt loc_tilt, "tilt offset"
1258 prompt loc_phi, "phi offset"
1260 doprompt "manipulator offsets", loc_theta, loc_tilt, loc_phi
1262 theta_offset = loc_theta
1263 tilt_offset = loc_tilt
1264 phi_offset = loc_phi
1267 setdatafolder saveDF
variable ast_set_processing(string reduction_func, string reduction_params)
set the data processing parameters
-
variable ast_close()
stop tracker, close graph, release data structures.
-
variable normalize_strip_theta(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average polar distribution.
-
static variable epics_connect()
connect the angle scan tracker to EPICS
-
static variable update_detector_graph()
-
static variable bp_capture(WMButtonAction *ba)
-
variable crop_strip(wave strip, variable xlo, variable xhi)
crop a strip at the sides.
-
variable make_hemi_grid(variable npol, string nickname, variable xpdplot=defaultValue)
create a hemispherical, constant solid angle grid
-
variable hemi_add_anglescan(string nickname, wave values, wave polar, wave azi, wave weights=defaultValue)
add an arbitrary angle scan to a hemispherical scan grid.
-
static variable setup_detector()
-
static variable pmp_parameters(WMPopupAction *pa)
-
string get_hemi_prefix(wave w)
finds the prefix given any hemi wave
-
string display_hemi_scan(string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue)
display a plot of a hemispherical angle scan.
-
static variable epics_disconnect()
-
static variable update_data_graph()
-
variable ast_setup()
set up data structures, display graph, and try to connect to analyser.
-
variable convert_angles_ttpd2polar(wave theta, wave tilt, wave phi, wave data, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
-
static const string prefs_objects
semicolon-separated list of persistent variable, string, and wave names
-
static variable setup_graph()
create the graph window.
-
static variable import_tracker_data()
import tracker data (with prompt)
-
variable clear_hemi_grid(string nickname)
clear a hemispherical scan grid
-
static variable extend_data(variable num_slices)
extend the data buffer for the next polar scan
-
static variable pmp_data_mouseup(WMPopupAction *pa)
-
variable ast_prepare(variable theta_offset=defaultValue, variable tilt_offset=defaultValue, variable phi_offset=defaultValue)
prepare for new measurement and clear the data buffer.
-
-
static variable setup_data()
-
threadsafe wave int_linbg_reduction(wave source, string *param)
linear-background subtracted integration reduction function.
-
static variable epics_disconnect_chid(string chid_var_name)
-
-
static variable AfterCompiledHook()
initialize package data once when the procedure is first loaded
-
static variable save_prefs()
save persistent package data to the preferences file.
-
static variable edit_offsets()
-
static variable add_image_data(wave image, variable theta, variable tilt, variable phi)
reduce a detector image and add the result to the data buffer.
-
static const string package_path
data folder path
-
static variable load_tracker_data()
import tracker data from file (with prompt)
-
static variable save_tracker_data()
save tracker data to file (with prompt)
-
static variable update_capture()
-
variable ast_export(dfref folder, string nickname, variable xpdplot=defaultValue)
export tracker data to a separate, independent data set.
-
variable ast_update_detector(variable theta, variable tilt, variable phi, variable range)
update the current position indicator.
-
static variable process_image_data()
process the data buffer to generate the tracker dataset.
-
variable save_hemi_scan(string nickname, string pathname, string filename)
save a hemispherical scan to an Igor text file
-
static variable IgorQuitHook(string app)
disconnect EPICS channels before Igor quits.
-
threadsafe wave adh5_default_reduction(wave source, string *param)
function prototype for adh5_load_reduced_detector
-
variable ast_callback_manip(variable chan)
callback function for new manipulator position from EPICS.
-
variable ast_callback_detector(variable chan)
callback function for new detector state from EPICS.
-
static variable pmp_parameters_mouseup(WMPopupAction *pa)
-
variable prompt_func_params(string func_name, string *func_param)
-
variable convert_angles_ttpa2polar(wave theta, wave tilt, wave phi, wave analyser, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
-
variable ast_add_image(wave image, variable theta, variable tilt, variable phi)
process and add a detector image to the tracker scan.
-
static variable pmp_data(WMPopupAction *pa)
-
variable duplicate_hemi_scan(string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue)
duplicate a hemispherical scan dataset.
-
static variable init_package()
-
static variable ast_window_hook(WMWinHookStruct *s)
window hook
-
static variable edit_reduction_params()
-
static variable toggle_capture()
-
variable ast_callback_data(variable chan)
callback function for new analyser data from EPICS.
-
variable ast_import(string nickname)
import tracker data from an existing angle scan dataset.
-
static const string package_name
package name is used as data folder name
-
static variable load_prefs()
load persistent package data from the preferences file.
-
variable normalize_strip_x(wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average X distribution.
-
static variable update_detector(variable theta, variable tilt, variable phi, variable range)
update the current position indicator.
-
static variable export_tracker_data()
export tracker data (with prompt)
+
Go to the documentation of this file. 1 #pragma TextEncoding = "Windows-1252"
+
+
+
4 #pragma IgorVersion = 6.2
+
5 #pragma ModuleName = PearlAnglescanTracker
+
6 #include "pearl-area-profiles" ,
version > 1.04
+
7 #include
"pearl-area-import" ,
version > 1.05
+
8 #include
"pearl-scienta-preprocess" ,
version > 1.00
+
9 #include
"pearl-anglescan-process" ,
version >= 1.6
+
10 #include <New Polar Graphs>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
67 static strconstant
package_name =
"pearl_anglescan_tracker"
+
69 static strconstant
package_path =
"root:packages:pearl_anglescan_tracker:"
+
71 static strconstant
prefs_objects =
"projection;theta_offset;tilt_offset;phi_offset;reduction_func;reduction_params"
+
+
+
+
76 dfref savedf = GetDataFolderDFR()
+
+
+
+
+
81 if (nvar_exists(init_done))
+
+
+
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+
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+
+
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92 variable /g init_done = 1
+
+
+
+
+
+
+
+
100 dfref savedf = getdatafolderdfr()
+
+
102 newdatafolder /o/s packages
+
103 newdatafolder /o/s $package_name
+
+
+
106 string /g graphname = "graph_anglescan_tracker"
+
107 string /g dataname = "tracker"
+
108 string /g projection = "stereographic"
+
+
+
111 variable /g theta_offset = 0
+
112 variable /g tilt_offset = 0
+
113 variable /g phi_offset = 0
+
+
115 string /g reduction_params = "Lcrop=0.1;Hcrop=0.1;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.4"
+
+
+
118 string /g export_folderpath = "root:"
+
119 variable /g export_format = 1
+
+
+
122 string /g detector_tracename
+
123 variable /g capturing = 0
+
124 variable /g buf_size = 0
+
125 variable /g buf_count = 0
+
126 variable /g buf_width = 0
+
+
+
129 string path = FunctionPath("")
+
130 path = ParseFilePath(1, path, ":", 1, 0) + "tracker-sample-picture.png"
+
131 LoadPict /O/Q path, pict_tracker_sample
+
+
+
+
+
+
141 dfref saveDF = GetDataFolderDFR()
+
+
143 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
+
+
145 NewPath/O/C/Q tempPackagePrefsPath, fullPath
+
146 fullPath += ":preferences.pxp"
+
+
148 SetDataFolder root:packages
+
149 SetDataFolder $package_name
+
+
+
152 KillPath/Z tempPackagePrefsPath
+
+
+
+
+
+
165 dfref saveDF = GetDataFolderDFR()
+
+
+
+
169 NewDataFolder /O/S packages
+
170 NewDataFolder /O/S $package_name
+
171 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
+
+
+
174 GetFileFolderInfo /Q /Z fullPath
+
+
176 fullPath += ":preferences.pxp"
+
177 GetFileFolderInfo /Q /Z fullPath
+
+
179 LoadData /O /R /Q fullPath
+
+
+
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+
+
+
+
+
+
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+
+
+
+
+
+
+
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+
+
213 variable theta_offset
+
+
+
+
217 dfref savedf = getdatafolderdfr()
+
+
+
220 if (!ParamIsDefault(theta_offset))
+
221 nvar v_theta_offset = theta_offset
+
222 v_theta_offset = theta_offset
+
+
224 if (!ParamIsDefault(tilt_offset))
+
225 nvar v_tilt_offset = tilt_offset
+
226 v_tilt_offset = tilt_offset
+
+
228 if (!ParamIsDefault(phi_offset))
+
229 nvar v_phi_offset = phi_offset
+
230 v_phi_offset = phi_offset
+
+
+
+
+
+
+
+
+
+
+
+
+
243 wave values = $(dataname + "_i")
+
244 values[numpnts(values) - 1] = 0
+
+
+
+
+
+
+
+
263 string reduction_func
+
264 string reduction_params
+
+
266 dfref savedf = getdatafolderdfr()
+
+
+
269 svar red_func = reduction_func
+
270 svar red_params = reduction_params
+
+
272 red_func = reduction_func
+
273 red_params = reduction_params
+
+
+
+
+
+
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+
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+
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+
+
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313 if (ParamIsDefault(xpdplot))
+
+
+
+
317 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
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+
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333 dfref savedf = getdatafolderdfr()
+
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+
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+
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362 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
368 KillWindow $graphname
+
+
+
+
+
+
374 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
383 make /n=(1,1) /o buf_i
+
384 make /n=(1) /o buf_th, buf_ph, buf_ti
+
+
+
+
+
+
+
391 wave values = $(dataname + "_i")
+
392 values[numpnts(values) - 1] = 0
+
+
+
+
+
+
+
+
406 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
413 variable new_size = buf_size + 91
+
414 buf_width = num_slices
+
+
+
+
+
+
+
421 redimension /n=(buf_width,new_size) buf_i
+
422 redimension /n=(new_size) buf_th, buf_ph, buf_ti
+
+
424 buf_i[][buf_size, new_size-1] = nan
+
425 buf_th[buf_size, new_size-1] = nan
+
426 buf_ph[buf_size, new_size-1] = nan
+
427 buf_ti[buf_size, new_size-1] = nan
+
+
+
+
+
+
+
+
+
436 dfref savedf = getdatafolderdfr()
+
+
+
439 make /n=31 /o detector_angle, detector_pol, detector_az, detector_rad
+
440 setscale /i x -30, 30, "°", detector_angle, detector_pol, detector_az, detector_rad
+
+
+
+
+
+
+
+
+
+
+
+
460 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
468 svar red_func_name = reduction_func
+
469 svar red_params = reduction_params
+
+
471 variable nx = dimsize(image, 0)
+
472 string loc_params = red_params
+
473 wave /wave red_results = red_func(image, loc_params)
+
474 if (numpnts(red_results) < 1)
+
+
+
+
+
479 wave profile1 = red_results[0]
+
480 nx = numpnts(profile1)
+
+
+
+
+
+
+
+
+
+
+
491 if ((buf_count >= buf_size) || (nx > buf_width))
+
+
493 setscale /p x dimoffset(profile1,0), dimdelta(profile1,0), waveunits(profile1,0), buf_i
+
+
+
496 buf_i[][buf_count] = profile1[p]
+
497 buf_th[buf_count] = theta - theta_offset
+
498 buf_ti[buf_count] = -(tilt - tilt_offset)
+
499 buf_ph[buf_count] = phi - phi_offset
+
+
+
+
+
+
+
+
+
+
+
+
+
514 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
+
+
+
+
527 duplicate /free /R=[0,buf_width-1][0,buf_count-1] buf_i, buf_n
+
528 duplicate /free /R=[0,buf_count-1] buf_th, w_th
+
529 duplicate /free /R=[0,buf_count-1] buf_ti, w_ti
+
530 duplicate /free /R=[0,buf_count-1] buf_ph, w_ph
+
+
+
+
+
+
536 if (dimoffset(buf_i,0) < -20)
+
+
+
+
+
+
542 make /n=1 /free d_polar, d_azi
+
+
+
545 d_azi = d_azi >= 360 ? d_azi - 360 : d_azi
+
+
+
+
+
+
+
+
+
+
+
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566 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
572 make /n=1 /free m_theta
+
573 make /n=1 /free m_tilt
+
574 make /n=1 /free m_phi
+
575 m_theta = theta - theta_offset
+
576 m_tilt = tilt - tilt_offset
+
+
578 m_phi = phi - phi_offset
+
+
+
581 wave detector_angle, detector_pol, detector_az, detector_rad
+
582 setscale /i x -range/2, +range/2, "°", detector_angle
+
+
+
+
586 redimension /n=(numpnts(detector_pol)) detector_rad
+
587 detector_rad = 2 * tan(detector_pol / 2 * pi / 180)
+
+
589 detector_az = detector_az >= 360 ? detector_az - 360 : detector_az
+
+
+
+
+
+
596 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
604 svar tracename = detector_tracename
+
+
+
607 tracename = WMPolarAppendTrace(graphname, detector_rad, detector_az, 360)
+
608 ModifyGraph /w=$graphname lstyle($tracename)=0
+
609 ModifyGraph /w=$graphname lsize($tracename)=1.5
+
610 ModifyGraph /w=$graphname zColor($tracename)={detector_angle,*,*,RedWhiteBlue,0}
+
611 ColorScale /w=$graphname /C /N=text1 trace=$tracename
+
612 ColorScale /w=$graphname /C /N=text1 /F=0 /B=1 /A=LB /X=0.00 /Y=0.00
+
613 ColorScale /w=$graphname /C /N=text1 width=1.5, heightPct=20, frame=0.00
+
614 ColorScale /w=$graphname /C /N=text1 lblMargin=0
+
615 ColorScale /w=$graphname /C /N=text1 nticks=2, tickLen=2.00, tickThick=0.50
+
+
617 TextBox /w=$graphname /C /N=tb_manip /F=0 /B=1 /X=0.00 /Y=0.00 /E=2
"\\{\"manip = (%.1f, %.1f, %.1f)\", "
+
618 AppendText /w=$graphname /N=tb_manip /NOCR
"root:packages:pearl_anglescan_tracker:curTheta, "
+
619 AppendText /w=$graphname /N=tb_manip /NOCR
"root:packages:pearl_anglescan_tracker:curTilt, "
+
620 AppendText /w=$graphname /N=tb_manip /NOCR
"root:packages:pearl_anglescan_tracker:curPhi}"
+
+
+
623 DoWindow /T $graphname,
"Angle Scan Tracker"
+
+
+
626 ControlBar /w=$graphname 21
+
+
628 Button b_capture win=$graphname, fColor=(65535,65535,65535), fSize=10
+
629 Button b_capture win=$graphname, help={
"Start/stop capturing." }
+
630 PopupMenu pm_params win=$graphname, mode=0, value=
"load preferences;save preferences;reduction parameters;manipulator offsets" , title=
"parameters"
+
+
632 PopupMenu pm_params win=$graphname, help={
"Load/save/edit data processing parameters" }
+
633 PopupMenu pm_data win=$graphname, mode=0, value=
"import;export;load file;save file" , title=
"data"
+
+
635 PopupMenu pm_data win=$graphname, help={
"Load/save data from/to independent dataset or file" }
+
+
637 SetDrawLayer /w=$graphname ProgFront
+
638 SetDrawEnv /w=$graphname xcoord=rel, ycoord=rel
+
639 DrawPict /w=$graphname 0, 0, 1, 1, pict_tracker_sample
+
+
+
+
+
+
+
+
647 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
+
+
+
659 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
+
+
+
+
+
682 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
689 make /n=(1)/o arraydata, xscale, yscale
+
690 make /n=(1,1)/o image
+
691 variable /g ndimensions
+
692 variable /g arraysize0, arraysize1
+
+
694 variable /g colormode
+
695 string /g controls, monitors
+
696 string /g xunits, yunits
+
+
+
699 variable /g chidDetectorState = 0
+
700 variable /g chidArrayData = 0
+
701 variable /g chidXScale = 0
+
702 variable /g chidYScale = 0
+
703 variable /g chidNDimensions = 0
+
704 variable /g chidArraySize0 = 0
+
705 variable /g chidArraySize1 = 0
+
706 variable /g chidDataType = 0
+
707 variable /g chidColorMode = 0
+
708 variable /g chidLensMode = 0
+
709 variable /g chidTheta = 0
+
710 variable /g chidTilt = 0
+
711 variable /g chidPhi = 0
+
712 variable /g curDetectorState = 0
+
713 variable /g curLensMode = 0
+
714 variable /g curTheta = 0
+
715 variable /g curTilt = 0
+
716 variable /g curPhi = 0
+
717 variable /g acqTheta = 0
+
718 variable /g acqTilt = 0
+
719 variable /g acqPhi = 0
+
720 variable /g connected = 0
+
+
722 string epicsname = "X03DA-SCIENTA:"
+
723 string imagename = epicsname + "image1:"
+
724 string camname = epicsname + "cam1:"
+
725 string manipname = "X03DA-ES2-MA:"
+
+
+
+
+
730 pvOpen /Q chidDetectorState, camname +
"DetectorState_RBV"
+
731 pvOpen /Q chidLensMode, camname +
"LENS_MODE_RBV"
+
732 pvOpen /Q chidXScale, camname +
"CHANNEL_SCALE_RBV"
+
733 pvOpen /Q chidYScale, camname +
"SLICE_SCALE_RBV"
+
734 pvOpen /Q chidArrayData, imagename +
"ArrayData"
+
735 pvOpen /Q chidNDimensions, imagename +
"NDimensions_RBV"
+
736 pvOpen /Q chidArraySize0, imagename +
"ArraySize0_RBV"
+
737 pvOpen /Q chidArraySize1, imagename +
"ArraySize1_RBV"
+
738 pvOpen /Q chidDataType, imagename +
"DataType_RBV"
+
739 pvOpen /Q chidColorMode, imagename +
"ColorMode_RBV"
+
+
741 pvOpen /Q chidTheta, manipname +
"THT.RBV"
+
742 pvOpen /Q chidTilt, manipname +
"TLT.RBV"
+
743 pvOpen /Q chidPhi, manipname +
"PHI.RBV"
+
+
+
+
+
+
+
750 #elif exists("pvOpen")
+
+
752 pvOpen /T=(timeout) chidDetectorState, camname +
"DetectorState_RBV"
+
753 pvOpen /T=(timeout) chidLensMode, camname +
"LENS_MODE_RBV"
+
754 pvOpen /T=(timeout) chidXScale, camname +
"CHANNEL_SCALE_RBV"
+
755 pvOpen /T=(timeout) chidYScale, camname +
"SLICE_SCALE_RBV"
+
756 pvOpen /T=(timeout) chidArrayData, imagename +
"ArrayData"
+
757 pvOpen /T=(timeout) chidNDimensions, imagename +
"NDimensions_RBV"
+
758 pvOpen /T=(timeout) chidArraySize0, imagename +
"ArraySize0_RBV"
+
759 pvOpen /T=(timeout) chidArraySize1, imagename +
"ArraySize1_RBV"
+
760 pvOpen /T=(timeout) chidDataType, imagename +
"DataType_RBV"
+
761 pvOpen /T=(timeout) chidColorMode, imagename +
"ColorMode_RBV"
+
+
763 pvOpen /T=(timeout) chidTheta, manipname +
"THT.RBV"
+
764 pvOpen /T=(timeout) chidTilt, manipname +
"TLT.RBV"
+
765 pvOpen /T=(timeout) chidPhi, manipname +
"PHI.RBV"
+
+
+
+
+
+
+
772 #
if exists(
"pvMonitor" )
+
+
+
+
+
+
+
+
+
+
+
+
784 print
"angle scan tracker: online"
+
+
786 print
"angle scan tracker: offline"
+
+
+
+
+
+
+
+
+
+
796 #if exists("pvClose")
+
797 nvar /z chid = $chid_var_name
+
798 if (nvar_exists(chid))
+
+
+
+
+
+
+
+
+
+
808 dfref savedf = GetDataFolderDFR()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
832 print "angle scan tracker: offline"
+
+
+
+
+
+
+
843 STRUCT WMWinHookStruct &s
+
+
845 Variable hookResult = 0
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
865 dfref savedf = GetDataFolderDFR()
+
+
867 #if exists("pvGetWave")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
897 pvGet chidNDimensions, ndimensions
+
898 pvGet chidArraySize0, arraysize0
+
899 pvGet chidArraySize1, arraysize1
+
900 pvGet chidDataType, datatype
+
901 pvGet chidColorMode, colormode
+
+
+
904 if (ndimensions != 2)
+
+
+
+
+
+
+
911 redimension /n=(arraysize0 * arraysize1) arraydata
+
912 redimension /n=(arraysize0, arraysize1) image
+
913 redimension /n=(arraysize0) xscale
+
914 redimension /n=(arraysize1) yscale
+
+
+
+
918 redimension /b arraydata, image
+
+
+
921 redimension /b/u arraydata, image
+
+
+
924 redimension /w arraydata, image
+
+
+
927 redimension /w/u arraydata, image
+
+
+
930 redimension /i arraydata, image
+
+
+
933 redimension /i/u arraydata, image
+
+
+
936 redimension /s arraydata, image
+
+
+
939 redimension /d arraydata, image
+
+
+
+
943 pvGetWave chidArrayData, arraydata
+
944 pvGetWave chidXScale, xscale
+
945 pvGetWave chidYScale, yscale
+
+
947 image = arraydata[p + q * arraysize0]
+
948 setscale /i x xscale[0], xscale[numpnts(xscale)-1], image
+
949 setscale /i y yscale[0], yscale[numpnts(yscale)-1], image
+
+
+
+
+
+
+
+
+
+
+
+
965 dfref savedf = GetDataFolderDFR()
+
+
+
+
969 nvar curDetectorState
+
+
+
+
+
+
+
+
+
978 if (curDetectorState == 1)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
994 dfref savedf = GetDataFolderDFR()
+
+
+
+
998 nvar lensmode = curLensMode
+
999 nvar theta = curTheta
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1018 setdatafolder savedf
+
+
+
+
+
+
+
1025 STRUCT WMButtonAction &ba
+
+
1027 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1039 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
1045 capturing = !capturing
+
+
+
1048 Button b_capture win=$graphname, title="stop"
+
+
1050 Button b_capture win=$graphname, title="start"
+
+
+
1053 setdatafolder saveDF
+
+
+
+
1057 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
1064 Button b_capture win=$graphname, title="stop"
+
+
1066 Button b_capture win=$graphname, title="start"
+
+
+
1069 setdatafolder saveDF
+
+
+
+
1073 STRUCT WMPopupAction &pa
+
+
1075 switch( pa.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1087 STRUCT WMPopupAction &pa
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1107 dfref savedf = getdatafolderdfr()
+
+
+
1110 svar export_folderpath
+
+
+
1113 string folderpath = export_folderpath
+
1114 string nickname = ""
+
1115 variable format = export_format
+
+
1117 prompt folderpath, "Folder Path"
+
1118 prompt nickname, "Nick Name"
+
1119 prompt format, "Format", popup, "PEARL;XPDplot"
+
+
1121 doprompt "Export Parameters", folderpath, nickname, format
+
+
+
1124 export_folderpath = folderpath
+
1125 export_format = format
+
+
1127 newdatafolder /o $folderpath
+
1128 variable xpdplot = format == 2
+
1129 ast_export ($folderpath, nickname, xpdplot=xpdplot)
+
+
+
1132 setdatafolder saveDF
+
+
+
+
1137 dfref savedf = getdatafolderdfr()
+
+
+
1140 svar export_folderpath
+
1141 string folderpath = export_folderpath
+
1142 string nickname = ""
+
+
1144 dfref dfBefore = GetDataFolderDFR()
+
1145 Execute /q/z "CreateBrowser prompt=\"Select wave from dataset\", showWaves=1, showVars=0, showStrs=0"
+
1146 dfref dfAfter = GetDataFolderDFR()
+
1147 SetDataFolder dfBefore
+
+
1149 SVAR list = S_BrowserList
+
+
+
1152 if ((flag != 0) && (ItemsInList(list) >= 1))
+
1153 string wname = StringFromList(0, list)
+
+
+
1156 dfref df = GetWavesDataFolderDFR(w)
+
+
+
+
+
1161 setdatafolder saveDF
+
+
+
+
1166 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
1172 setdatafolder saveDF
+
+
+
+
1177 dfref savedf = getdatafolderdfr()
+
+
+
1180 NewDataFolder /O/S load_data
+
+
+
1183 string wname = StringFromList(0, s_wavenames, ";")
+
+
+
+
+
+
+
1190 KillDataFolder /Z load_data
+
+
1192 setdatafolder saveDF
+
+
+
+
1196 STRUCT WMPopupAction &pa
+
+
1198 switch( pa.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
1210 STRUCT WMPopupAction &pa
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1230 dfref savedf = getdatafolderdfr()
+
+
+
1233 svar pref_func = reduction_func
+
1234 svar pref_params = reduction_params
+
+
1236 string loc_func = pref_func
+
1237 string loc_params = pref_params
+
+
+
+
+
1242 setdatafolder saveDF
+
+
+
+
1246 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
1253 variable loc_theta = theta_offset
+
1254 variable loc_tilt = tilt_offset
+
1255 variable loc_phi = phi_offset
+
+
1257 prompt loc_theta, "theta offset"
+
1258 prompt loc_tilt, "tilt offset"
+
1259 prompt loc_phi, "phi offset"
+
+
1261 doprompt "manipulator offsets", loc_theta, loc_tilt, loc_phi
+
+
1263 theta_offset = loc_theta
+
1264 tilt_offset = loc_tilt
+
1265 phi_offset = loc_phi
+
+
+
1268 setdatafolder saveDF
+
variable crop_strip(wave strip, variable xlo, variable xhi)
crop a strip at the sides.
variable hemi_add_anglescan(string nickname, wave values, wave polar, wave azi, wave weights=defaultValue)
add arbitrary angle scan data to a hemispherical scan grid.
variable ast_callback_manip(variable chan)
callback function for new manipulator position from EPICS.
static variable save_prefs()
save persistent package data to the preferences file.
variable normalize_strip_theta(wave strip, wave theta, variable theta_offset=defaultValue, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average polar distribution.
static variable setup_detector()
static variable update_capture()
static variable epics_disconnect()
variable ast_update_detector(variable theta, variable tilt, variable phi, variable range)
update the current position indicator.
threadsafe wave int_linbg_reduction(wave source, string *param)
linear-background subtracted integration reduction function.
variable normalize_strip_x(wave strip, variable smooth_method=defaultValue, variable smooth_factor=defaultValue, variable check=defaultValue)
divide the strip by the average X distribution.
variable convert_angles_ttpd2polar(wave theta, wave tilt, wave phi, wave data, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
variable ast_export(dfref folder, string nickname, variable xpdplot=defaultValue)
export tracker data to a separate, independent data set.
string get_hemi_prefix(wave w)
finds the prefix given any hemi wave
variable make_hemi_grid(variable npol, string nickname, variable xpdplot=defaultValue)
create a hemispherical, constant solid angle grid
variable clear_hemi_grid(string nickname)
clear a hemispherical scan grid
static variable bp_capture(WMButtonAction *ba)
variable ast_set_processing(string reduction_func, string reduction_params)
set the data processing parameters
static variable pmp_parameters_mouseup(WMPopupAction *pa)
variable ast_callback_detector(variable chan)
callback function for new detector state from EPICS.
static variable AfterCompiledHook()
initialize package data once when the procedure is first loaded
static variable setup_graph()
create the graph window.
static variable IgorQuitHook(string app)
disconnect EPICS channels before Igor quits.
static variable pmp_data(WMPopupAction *pa)
static variable init_package()
static variable setup_data()
static variable export_tracker_data()
export tracker data (with prompt)
static variable pmp_parameters(WMPopupAction *pa)
static variable toggle_capture()
variable ast_close()
stop tracker, close graph, release data structures.
variable ast_add_image(wave image, variable theta, variable tilt, variable phi)
process and add a detector image to the tracker scan.
variable ast_callback_data(variable chan)
callback function for new analyser data from EPICS.
static variable update_detector_graph()
static variable update_detector(variable theta, variable tilt, variable phi, variable range)
update the current position indicator.
variable ast_import(string nickname)
import tracker data from an existing angle scan dataset.
static const string prefs_objects
semicolon-separated list of persistent variable, string, and wave names
variable ast_setup()
set up data structures, display graph, and try to connect to analyser.
static variable process_image_data()
process the data buffer to generate the tracker dataset.
static variable import_tracker_data()
import tracker data (with prompt)
static variable save_tracker_data()
save tracker data to file (with prompt)
threadsafe wave adh5_default_reduction(wave source, string *param)
function prototype for adh5_load_reduced_detector
variable convert_angles_ttpa2polar(wave theta, wave tilt, wave phi, wave analyser, wave polar, wave azi)
convert angles from TTPA (theta-tilt-phi-analyser) scheme to polar coordinates.
variable ast_prepare(variable theta_offset=defaultValue, variable tilt_offset=defaultValue, variable phi_offset=defaultValue)
prepare for new measurement and clear the data buffer.
static variable pmp_data_mouseup(WMPopupAction *pa)
variable save_hemi_scan(string nickname, string pathname, string filename)
save a hemispherical scan to an Igor text file
static variable load_prefs()
load persistent package data from the preferences file.
variable prompt_func_params(string func_name, string *func_param)
variable duplicate_hemi_scan(string source_nickname, dfref dest_folder, string dest_nickname, variable xpdplot=defaultValue)
duplicate a hemispherical scan dataset.
static variable ast_window_hook(WMWinHookStruct *s)
window hook
static variable update_data_graph()
static variable edit_reduction_params()
static variable epics_connect()
connect the angle scan tracker to EPICS
static variable edit_offsets()
static variable epics_disconnect_chid(string chid_var_name)
static const string package_path
data folder path
static const string package_name
package name is used as data folder name
static variable extend_data(variable num_slices)
extend the data buffer for the next polar scan
static variable load_tracker_data()
import tracker data from file (with prompt)
string display_hemi_scan(string nickname, variable projection=defaultValue, variable graphtype=defaultValue, variable do_ticks=defaultValue, variable do_grids=defaultValue, string graphname=defaultValue)
display a plot of a hemispherical angle scan.
static variable add_image_data(wave image, variable theta, variable tilt, variable phi)
reduce a detector image and add the result to the data buffer.
PEARL Procedures: pearl-area-display.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -92,6 +94,7 @@ $(document).ready(function(){initNavTree('pearl-area-display_8ipf.html','');});
visualization tools for 2D and 3D data.
More...
#include "pearl-compat"#include "pearl-area-profiles"
Go to the source code of this file.
@@ -104,43 +107,43 @@ Namespaces
static string graphname_from_dfref (dfref df, string prefix) compose a valid and unique graph name from a data folder reference More... compose a valid and unique graph name from a data folder reference More... string ad_display (wave image) open a new graph window with a 2D image. More... open a new graph window with a 2D image. More... string ad_display_histogram (wave image) display the histogram of a 2D image. More... display the histogram of a 2D image. More... string ad_display_profiles (wave image, string filter=defaultValue) open a new profiles graph window. More... open a new profiles graph window. More... wave ad_add_overlay (wave image, string rgba=defaultValue) add an overlay on top of the displayed image More... add an overlay on top of the displayed image More... variable ad_update_profiles (wave image) update a profiles graph with new data. More... update a profiles graph with new data. More... variable ad_profiles_cursor_mode (wave image, variable mode) switch cursors on a profiles graph More... switch cursors on a profiles graph More... variable ad_profiles_set_cursor (wave image, string cursorname, variable xa, variable ya, variable pscale=defaultValue) move a cursor to the specified position in a profiles graph. More... move a cursor to the specified position in a profiles graph. More... variable ad_profiles_crosshairs (wave image, variable clear=defaultValue) draw permanent crosshairs in a profiles graph. More... draw permanent crosshairs in a profiles graph. More... static wave get_source_image (wave view) find the source image wave corresponding to the given view. More... find the source image wave corresponding to the given view. More... static dfr make_view_folder (wave source) create a view data folder. More... create a view data folder. More... static dfr get_view_folder (wave source) find the view data folder corresponding to the given source. More... find the view data folder corresponding to the given source. More... static wave get_view_image (wave source) find the view image wave corresponding to the given source. More... find the view image wave corresponding to the given source. More... static variable bp_reset_cursors (WMButtonAction *ba) static variable pmp_export (WMPopupAction *pa) variable ad_profiles_hook (WMWinHookStruct *s) hook function for user events in the profiles window. More... hook function for user events in the profiles window. More... variable ad_calc_cursor_profiles (wave image) calculate profiles, statistics, and histogram of a cross-hair delimited region of interest. More... calculate profiles, statistics, and histogram of a cross-hair delimited region of interest. More... variable ad_calc_profiles (wave image, variable pa, variable qa, variable pb, variable qb) calculate profiles, statistics, and histogram of a rectangular region of interest. More... calculate profiles, statistics, and histogram of a rectangular region of interest. More... variable ad_export_profile (wave view_image, variable dim, variable trace=defaultValue, variable show=defaultValue, variable overwrite=defaultValue) export a profile from a profiles graph to the source data folder. More... export a profile from a profiles graph to the source data folder. More... static variable set_trace_colors (string graphname) variable ad_calc_histogram (wave image) calculate the histogram. More... calculate the histogram. More... variable ad_default_image_filter (wave image, string options) abstract filter function for image display. More... abstract filter function for image display. More... variable ad_box_filter (wave image, string options) boxcar smoothing filter. More... boxcar smoothing filter. More... variable ad_transpose_filter (wave image, string options) transpose image filter. More... transpose image filter. More... string ad_display_brick (wave data) open a new "gizmo" window with three-dimensional data. More... open a new "gizmo" window with three-dimensional data. More... variable ad_brick_slicer (wave data) open a slicer panel for 3D data. More... open a slicer panel for 3D data. More... string ad_display_slice (wave data) display three-dimensional data by 2D slice. More... display three-dimensional data by 2D slice. More... static variable update_slice_info () update controls with data scale limits. More... update controls with data scale limits. More... variable ad_gizmo_set_plane (wave brick, variable dim, variable value) set the position of a slicing plane of a 3D brick in a Gizmo window. More... set the position of a slicing plane of a 3D brick in a Gizmo window. More... variable ad_profiles_set_slice (wave brick, variable dim, variable value) set the position of the slicing plane of a 3D brick in a profiles window. More... set the position of the slicing plane of a 3D brick in a profiles window. More... static variable slp_slice_position (WMSliderAction *sa) set slice coordinate (slider procedure). More... set slice coordinate (slider procedure). More... static variable svp_slice_position (WMSetVariableAction *sva) set slice coordinate (button procedure). More... set slice coordinate (button procedure). More... static variable bp_move_slice (WMButtonAction *ba) move slice (button procedure). More... move slice (button procedure). More... static variable bp_extract_slice (WMButtonAction *ba) export a slice (button procedure). More... export a slice (button procedure). More... static variable bp_move_slice_center (wave brick, variable dim, string posvariable) move the slice to the center of the dimension (button procedure). More... move the slice to the center of the dimension (button procedure). More... static variable ad_slicer_move_bg (WMBackgroundStruct *s) move a slice by one step (background task). More... move a slice by one step (background task). More... variable ad_slicer_init_bg () initialize the slice animation background task. More... initialize the slice animation background task. More... variable ad_slicer_start_bg (wave brick, variable dimension, string posvariable, variable delta) start the animation. More... start the animation. More... variable ad_slicer_stop_bg (string posvariable) stop the animation. More... stop the animation. More...
@@ -267,7 +270,7 @@ Functions
Returns overlay overlay wave. same dimensions and scales as image, but unsigned binary. pixels that are 0 are overlaid with semi-transparent color. other pixels should be 64 (igor's mask convention). Definition at line 329 of file pearl-area-display.ipf .
+Definition at line 331 of file pearl-area-display.ipf .
@@ -311,7 +314,7 @@ Functions
-Definition at line 1103 of file pearl-area-display.ipf .
+Definition at line 1105 of file pearl-area-display.ipf .
@@ -340,7 +343,7 @@ Functions
-Definition at line 1256 of file pearl-area-display.ipf .
+Definition at line 1258 of file pearl-area-display.ipf .
@@ -367,9 +370,9 @@ Functions
-the function expects further objects as created by ad_display_profiles() in the same data folder as the image wave. the most recent profiles graph of the image must exist, and the cursors A and B must be set on the image.
+the function expects further objects as created by ad_display_profiles() in the same data folder as the image wave. the most recent profiles graph of the image must exist, and the cursors A and B must be set on the image.
-Definition at line 785 of file pearl-area-display.ipf .
+Definition at line 787 of file pearl-area-display.ipf .
@@ -392,12 +395,12 @@ Functions
calculate the histogram.
Parameters
- image wave which contains the image data from the detector. the function expects further objects as created by ad_display_histogram() in the same data folder as the image wave. image wave which contains the image data from the detector. the function expects further objects as created by ad_display_histogram() in the same data folder as the image wave.
Definition at line 1066 of file pearl-area-display.ipf .
+Definition at line 1068 of file pearl-area-display.ipf .
@@ -457,10 +460,10 @@ Functions
-the function expects further objects as created by ad_display_profiles() in the same data folder as the image wave.
+the function expects further objects as created by ad_display_profiles() in the same data folder as the image wave.
this function does not require that the graph exists as long as the data folder is complete.
-Definition at line 832 of file pearl-area-display.ipf .
+Definition at line 834 of file pearl-area-display.ipf .
@@ -501,7 +504,7 @@ Functions
Returns the result must be written to the incoming image wave. Definition at line 1089 of file pearl-area-display.ipf .
+Definition at line 1091 of file pearl-area-display.ipf .
@@ -531,7 +534,7 @@ Functions
Returns (string) name of the graph window Definition at line 85 of file pearl-area-display.ipf .
+Definition at line 87 of file pearl-area-display.ipf .
@@ -560,7 +563,7 @@ Functions
Returns name of the gizmo window. Definition at line 1141 of file pearl-area-display.ipf .
+Definition at line 1143 of file pearl-area-display.ipf .
@@ -581,7 +584,7 @@ Functions
display the histogram of a 2D image.
-
the function will create additional objects in the same data folder as the image. this objects are displayed in the graph and are updated by calling ad_calc_profiles() . see the code.
+
the function will create additional objects in the same data folder as the image. this objects are displayed in the graph and are updated by calling ad_calc_profiles() . see the code.
Parameters
image wave which contains the image data from the detector. Returns (string) name of the graph window Definition at line 115 of file pearl-area-display.ipf .
+Definition at line 117 of file pearl-area-display.ipf .
@@ -621,17 +624,17 @@ Functions
open a new profiles graph window.
-
opens an extended graph window with profiles for the specified image. the function copies/creates all necessary data structures in a subfolder of the one which contains the image wave. the data folder name is derived from the image wave name by prefixing with "view_". there can be at most one profiles window of each image wave. the original wave must not be renamed while the graph window is used. to update the graph after modifying the original wave, call ad_update_profiles() .
+
opens an extended graph window with profiles for the specified image. the function copies/creates all necessary data structures in a subfolder of the one which contains the image wave. the data folder name is derived from the image wave name by prefixing with "view_". there can be at most one profiles window of each image wave. the original wave must not be renamed while the graph window is used. to update the graph after modifying the original wave, call ad_update_profiles() .
Parameters
image wave which contains the image data. filter name of a filter function which maps the original data to the displayed data. the function must have the same parameters as ad_default_image_filter() . default: boxcar average (ad_box_filter() ) using parameters view_filter_smoothing_x and _y. filter name of a filter function which maps the original data to the displayed data. the function must have the same parameters as ad_default_image_filter() . default: boxcar average (ad_box_filter() ) using parameters view_filter_smoothing_x and _y.
Returns name of the graph window
-
Definition at line 166 of file pearl-area-display.ipf .
+
Definition at line 168 of file pearl-area-display.ipf .
@@ -652,7 +655,7 @@ Functions
display three-dimensional data by 2D slice.
-
to select the slice data to display, call ad_profiles_set_slice() , or open a ad_brick_slicer() panel. do not modify the content of the created view_ data folder.
+
to select the slice data to display, call ad_profiles_set_slice() , or open a ad_brick_slicer() panel. do not modify the content of the created view_ data folder.
Parameters
data three-dimensional wave. Returns name of the graph window. Definition at line 1404 of file pearl-area-display.ipf .
+Definition at line 1406 of file pearl-area-display.ipf .
@@ -713,7 +716,7 @@ Functions
this function does not require that the show exists as long as the view data folder is complete.
Parameters
- view_image wave which contains the view image (image wave on display in profiles window). the function expects further objects as created by ad_display_profiles() in the same data folder as the view_image wave. view_image wave which contains the view image (image wave on display in profiles window). the function expects further objects as created by ad_display_profiles() in the same data folder as the view_image wave. dim dimension index (0 = x, 1 = y). trace select profile trace:
0 = cursor A
@@ -736,7 +739,7 @@ Functions Definition at line 934 of file pearl-area-display.ipf .
+Definition at line 936 of file pearl-area-display.ipf .
@@ -783,7 +786,7 @@ Functions
Returns 0 if successful, non-zero otherwise Definition at line 1481 of file pearl-area-display.ipf .
+Definition at line 1483 of file pearl-area-display.ipf .
@@ -823,7 +826,7 @@ Functions
-Definition at line 540 of file pearl-area-display.ipf .
+Definition at line 542 of file pearl-area-display.ipf .
@@ -868,7 +871,7 @@ Functions
-Definition at line 427 of file pearl-area-display.ipf .
+Definition at line 429 of file pearl-area-display.ipf .
@@ -890,7 +893,7 @@ Functions
hook function for user events in the profiles window.
-Definition at line 745 of file pearl-area-display.ipf .
+Definition at line 747 of file pearl-area-display.ipf .
@@ -955,7 +958,7 @@ Functions
-Definition at line 488 of file pearl-area-display.ipf .
+Definition at line 490 of file pearl-area-display.ipf .
@@ -1002,7 +1005,7 @@ Functions
Returns 0 if successful, non-zero otherwise Definition at line 1517 of file pearl-area-display.ipf .
+Definition at line 1519 of file pearl-area-display.ipf .
@@ -1023,7 +1026,7 @@ Functions
initialize the slice animation background task.
-Definition at line 1776 of file pearl-area-display.ipf .
+Definition at line 1778 of file pearl-area-display.ipf .
@@ -1053,7 +1056,7 @@ Functions
move a slice by one step (background task).
-Definition at line 1737 of file pearl-area-display.ipf .
+Definition at line 1739 of file pearl-area-display.ipf .
@@ -1106,7 +1109,7 @@ Functions
-Definition at line 1800 of file pearl-area-display.ipf .
+Definition at line 1802 of file pearl-area-display.ipf .
@@ -1134,7 +1137,7 @@ Functions
-Definition at line 1842 of file pearl-area-display.ipf .
+Definition at line 1844 of file pearl-area-display.ipf .
@@ -1174,7 +1177,7 @@ Functions
-Definition at line 1125 of file pearl-area-display.ipf .
+Definition at line 1127 of file pearl-area-display.ipf .
@@ -1197,12 +1200,12 @@ Functions
update a profiles graph with new data.
Parameters
- image wave which contains the image data. must be the same (by data folder and name) wave used with ad_display_profiles() . image wave which contains the image data. must be the same (by data folder and name) wave used with ad_display_profiles() .
Definition at line 375 of file pearl-area-display.ipf .
+Definition at line 377 of file pearl-area-display.ipf .
@@ -1233,7 +1236,7 @@ Functions
export a slice (button procedure).
extract a slice and saves it in a separate wave.
-Definition at line 1671 of file pearl-area-display.ipf .
+Definition at line 1673 of file pearl-area-display.ipf .
@@ -1263,7 +1266,7 @@ Functions
move slice (button procedure).
-Definition at line 1622 of file pearl-area-display.ipf .
+Definition at line 1624 of file pearl-area-display.ipf .
@@ -1309,7 +1312,7 @@ Functions
move the slice to the center of the dimension (button procedure).
-Definition at line 1725 of file pearl-area-display.ipf .
+Definition at line 1727 of file pearl-area-display.ipf .
@@ -1337,7 +1340,7 @@ Functions
@@ -1368,7 +1371,7 @@ Functions
find the source image wave corresponding to the given view.
Returns wave reference of the original data wave. the reference may be invalid if the source wave cannot be found. Definition at line 606 of file pearl-area-display.ipf .
+Definition at line 608 of file pearl-area-display.ipf .
@@ -1400,12 +1403,12 @@ Functions
the result data folder reference may be invalid if no view is currently open. use the built-in DataFolderRefStatus function to check for validity.
Parameters
- source wave which contains the image data. must be the same (by data folder and name) wave used with ad_display_profiles() . source wave which contains the image data. must be the same (by data folder and name) wave used with ad_display_profiles() .
Definition at line 644 of file pearl-area-display.ipf .
+Definition at line 646 of file pearl-area-display.ipf .
@@ -1436,12 +1439,12 @@ Functions
find the view image wave corresponding to the given source.
Parameters
- source wave which contains the image data. must be the same (by data folder and name) wave used with ad_display_profiles() . source wave which contains the image data. must be the same (by data folder and name) wave used with ad_display_profiles() .
Definition at line 667 of file pearl-area-display.ipf .
+Definition at line 669 of file pearl-area-display.ipf .
@@ -1481,7 +1484,7 @@ Functions
compose a valid and unique graph name from a data folder reference
-Definition at line 57 of file pearl-area-display.ipf .
+Definition at line 59 of file pearl-area-display.ipf .
@@ -1511,7 +1514,7 @@ Functions
create a view data folder.
-Definition at line 620 of file pearl-area-display.ipf .
+Definition at line 622 of file pearl-area-display.ipf .
@@ -1539,7 +1542,7 @@ Functions
@@ -1567,7 +1570,7 @@ Functions
@@ -1597,7 +1600,7 @@ Functions
set slice coordinate (slider procedure).
-Definition at line 1558 of file pearl-area-display.ipf .
+Definition at line 1560 of file pearl-area-display.ipf .
@@ -1627,7 +1630,7 @@ Functions
set slice coordinate (button procedure).
-Definition at line 1590 of file pearl-area-display.ipf .
+Definition at line 1592 of file pearl-area-display.ipf .
@@ -1655,7 +1658,7 @@ Functions
@@ -1685,7 +1688,7 @@ Functions
update controls with data scale limits.
current folder must be slicer info
-Definition at line 1445 of file pearl-area-display.ipf .
+Definition at line 1447 of file pearl-area-display.ipf .
@@ -1695,9 +1698,9 @@ Functions
diff --git a/doc/html/pearl-area-display_8ipf_source.html b/doc/html/pearl-area-display_8ipf_source.html
index 692424d..92bf0d6 100644
--- a/doc/html/pearl-area-display_8ipf_source.html
+++ b/doc/html/pearl-area-display_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-area-display.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,44 +87,1585 @@ $(document).ready(function(){initNavTree('pearl-area-display_8ipf_source.html','
pearl-area-display.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.2 3 #pragma ModuleName = PearlAreaDisplay 5 #include "pearl-compat" 63 name = GetDataFolder(1, df)
64 name = ReplaceString(
"root:" , name,
"" )
65 name = name[0, strlen(name) - 2]
66 name = ReplaceString(" ", name, "")
68 if (CheckName(name, 6))
69 name = UniqueName(name, 6, 0)
89 dfref savedf = GetDataFolderDFR()
90 dfref imagedf = GetWavesDataFolderDFR(image)
93 string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
94 string graphtitle = dfname + " View"
96 svar graphname = view_graphname
97 display /k=1/n=$graphname as graphtitle
99 appendimage /w=$graphname image
118 dfref savedf = GetDataFolderDFR()
119 dfref imagedf = GetWavesDataFolderDFR(image)
120 string s_imagedf = GetDataFolder(1, imagedf)
121 setdatafolder imagedf
125 string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
126 string graphtitle = dfname + " Histogram"
128 svar graphname = hist_graphname
129 display /k=1/n=$graphname as graphtitle
131 appendtograph /w=$graphname hist
133 ModifyGraph /w=$graphname rgb(hist)=(39168,0,0)
134 ModifyGraph /w=$graphname mode=6
135 ModifyGraph /w=$graphname mirror=1
136 ModifyGraph /w=$graphname minor=1
137 ModifyGraph /w=$graphname axThick=0.5
138 ModifyGraph /w=$graphname lblPosMode=1,lblPos=30,lblMargin=0
139 ModifyGraph /w=$graphname btLen=4
140 ModifyGraph /w=$graphname margin(left)=45,margin(bottom)=35,margin(top)=10,margin(right)=10
141 ModifyGraph /w=$graphname gfSize=10
142 Label /w=$graphname bottom "value"
143 Label /w=$graphname left "
# pixels" 169 variable show_legend = 0
171 if (WaveDims(image) != 2)
172 abort
"ad_display_profiles: image wave must be two-dimensional." 174 if (ParamIsDefault(filter))
175 filter =
"ad_box_filter" 179 dfref savedf = GetDataFolderDFR()
180 dfref imagedf = GetWavesDataFolderDFR(image)
181 string s_imagedf = GetDataFolder(1, imagedf)
182 setdatafolder imagedf
184 newdatafolder /o/s $s_viewdf
185 dfref viewdf = GetDataFolderDFR()
186 s_viewdf = GetDataFolder(1, viewdf)
189 string /g sourcepath = GetWavesDataFolder(image, 2)
190 string viewname = "view_image"
191 duplicate /o image, $viewname /wave=view
192 make /n=(3,3)/o xprofiles
193 make /n=(3,3)/o yprofiles
194 string /g view_filter
195 string /g view_filter_options
197 view_filter_options = ""
198 variable /g view_filter_smoothing_x = 1
199 variable /g view_filter_smoothing_y = 1
200 variable /g view_cursor_mode = 0
201 string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
202 string graphtitle = dfname + NameOfWave(image) + " Profiles"
204 svar graphname = prof_graphname
205 variable /g graph_avg
206 variable /g graph_min
207 variable /g graph_max
208 variable /g graph_sum
209 variable /g graph_sdev
212 display /k=1 /n=$graphname /w=(100,100,500,400) as graphtitle
214 AppendToGraph /w=$graphname /L=xprofiles xprofiles[*][0],xprofiles[*][1],xprofiles[*][2]
215 AppendToGraph /w=$graphname /VERT/B=yprofiles yprofiles[*][0],yprofiles[*][1],yprofiles[*][2]
216 AppendImage /w=$graphname view
217 string imgname = StringFromList(0, ImageNameList(graphname, ";"))
218 ModifyImage /w=$graphname $imgname ctab= {*,*,BlueGreenOrange,0}
219 ModifyGraph /w=$graphname rgb(xprofiles)=(39168,0,0),rgb(yprofiles)=(39168,0,0)
220 ModifyGraph /w=$graphname rgb(xprofiles#1)=(0,26112,0),rgb(yprofiles#1)=(0,26112,0)
221 ModifyGraph /w=$graphname rgb(xprofiles#2)=(0,9472,39168),rgb(yprofiles#2)=(0,9472,39168)
222 ModifyGraph /w=$graphname mirror(xprofiles)=2,mirror(bottom)=3,mirror(yprofiles)=2,mirror(left)=3
223 ModifyGraph /w=$graphname nticks=3
224 ModifyGraph /w=$graphname minor=1
225 ModifyGraph /w=$graphname axThick=0.5
226 ModifyGraph /w=$graphname lblPosMode=1,lblPos=30,lblMargin=0
227 ModifyGraph /w=$graphname btLen=4
228 ModifyGraph /w=$graphname freePos(xprofiles)=0
229 ModifyGraph /w=$graphname freePos(yprofiles)=0
230 ModifyGraph /w=$graphname axisEnab(xprofiles)={0.64,1}
231 ModifyGraph /w=$graphname axisEnab(bottom)={0,0.6}
232 ModifyGraph /w=$graphname axisEnab(yprofiles)={0.64,1}
233 ModifyGraph /w=$graphname axisEnab(left)={0,0.6}
234 ModifyGraph /w=$graphname zero(left)=8
235 ModifyGraph /w=$graphname margin(left)=40,margin(bottom)=30,margin(top)=20,margin(right)=40
236 ModifyGraph /w=$graphname gfSize=10
239 string labels = note(image)
241 lab = StringByKey(
"AxisLabelX" , labels,
"=" ,
"\r" )
245 Label /w=$graphname bottom lab +
" (\\U)" 246 lab = StringByKey(
"AxisLabelY" , labels,
"=" ,
"\r" )
250 Label /w=$graphname left lab +
" (\\U)" 251 lab = StringByKey(
"AxisLabelD" , labels,
"=" ,
"\r" )
255 Label /w=$graphname xprofiles lab +
" (\\U)" 256 Label /w=$graphname yprofiles lab +
" (\\U)" 260 Legend /w=$graphname/C/N=text0/J/F=2/D=0.5/T={28}/A=RT/X=0.00/Y=0.00
"\\s(xprofiles)\tprofile A" 261 AppendText /w=$graphname
"\\s(xprofiles#1)\tprofile B" 262 AppendText /w=$graphname
"\\s(xprofiles#2)\tROI average" 263 AppendText /w=$graphname
"min\t\\{" + s_viewdf +
"graph_min}" 264 AppendText /w=$graphname
"max\t\\{" + s_viewdf +
"graph_max}" 265 AppendText /w=$graphname
"sum\t\\{" + s_viewdf +
"graph_sum}" 266 AppendText /w=$graphname
"avg\t\\{" + s_viewdf +
"graph_avg}" 267 AppendText /w=$graphname
"sdev\t\\{" + s_viewdf +
"graph_sdev}" 269 TextBox /w=$graphname /C/N=text0 /F=0 /B=1 /X=1.00 /Y=1.00
270 lab = StringByKey(
"Dataset" , labels,
"=" ,
"\r" )
272 AppendText /w=$graphname lab
274 AppendText /w=$graphname
"sum\t\\{" + s_viewdf +
"graph_sum}" 275 AppendText /w=$graphname
"avg\t\\{" + s_viewdf +
"graph_avg}" 276 AppendText /w=$graphname
"sdev\t\\{" + s_viewdf +
"graph_sdev}" 280 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 A $imgname 0,0
281 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 B $imgname DimSize(view, 0)-1, DimSize(view, 1)-1
283 pcurs = floor(DimSize(xprofiles, 0) / 3)
284 Cursor /w=$graphname /A=0 /P /S=1 /H=0 C xprofiles#2 pcurs
285 pcurs = floor(DimSize(xprofiles, 0) * 2 / 3)
286 Cursor /w=$graphname /A=0 /P /S=1 /H=0 D xprofiles#2 pcurs
287 pcurs = floor(DimSize(yprofiles, 0) / 3)
288 Cursor /w=$graphname /A=0 /P /S=1 /H=0 E yprofiles#2 pcurs
289 pcurs = floor(DimSize(yprofiles, 0) * 2 / 3)
290 Cursor /w=$graphname /A=0 /P /S=1 /H=0 F yprofiles#2 pcurs
291 ShowInfo /w=$graphname /CP=0
294 ControlBar /w=$graphname 21
296 Button b_reset_cursors win=$graphname, fColor=(65535,65535,65535),fSize=10
298 SetVariable sv_smoothing_x win=$graphname, title=
"X smoothing" ,pos={130,2},bodyWidth=40
299 SetVariable sv_smoothing_x win=$graphname, value=view_filter_smoothing_x,limits={1,100,1}
301 SetVariable sv_smooting_y win=$graphname, title=
"Y smoothing" ,pos={240,2},bodyWidth=40
302 SetVariable sv_smooting_y win=$graphname, value=view_filter_smoothing_y,limits={1,100,1}
305 PopupMenu pm_export win=$graphname, mode=0,title=
"Export" 306 PopupMenu pm_export win=$graphname, value=
"X profile;Y profile;X profile (collate);Y profile (collate)" 308 PopupMenu pm_export win=$graphname, help={
"Export profile of selected area and display in graph. Collate mode = display all profiles in same graph." }
333 if (ParamIsDefault(rgba))
334 rgba =
"65535,65532,16385,32767" 335 elseif (ItemsInList(rgba,
"," ) == 3)
339 dfref savedf = GetDataFolderDFR()
341 dfref viewdf = GetWavesDataFolderDFR(view_image)
342 svar /sdfr=viewdf graphname = prof_graphname
345 string overlayname = "view_overlay"
346 duplicate /o image, $overlayname /wave=overlay
347 redimension /b/u overlay
350 string imagenames = ImageNameList(graphname, ";")
351 if (whichlistItem(overlayname, imagenames, ";") < 0)
352 AppendImage /w=$graphname $overlayname
353 rgba = replacestring("(", rgba, "")
354 rgba = replacestring(")", rgba, "")
355 variable rr = str2num(StringFromList(0, rgba, ","))
356 variable gg = str2num(StringFromList(1, rgba, ","))
357 variable bb = str2num(StringFromList(2, rgba, ","))
358 variable aa = str2num(StringFromList(3, rgba, ","))
359 #if IgorVersion() >= 8 360 ModifyImage /w=$graphname $overlayname
explicit =1,eval={0,rr,gg,bb,aa},eval={255,-1,-1,-1}
362 ModifyImage /w=$graphname $overlayname
explicit =1,eval={0,rr,gg,bb},eval={255,-1,-1,-1}
380 if (DataFolderRefStatus(viewdf) == 0)
383 dfref savedf = GetDataFolderDFR()
387 string viewname = "view_image"
388 duplicate /o image, $viewname /wave=view
389 string overlayname = "view_overlay"
390 wave /z overlay = $overlayname
391 if (waveexists(overlay))
392 redimension /n=(dimsize(view,0), dimsize(view,1)) overlay
397 svar view_filter_options
398 nvar smoothing_x = view_filter_smoothing_x
399 nvar smoothing_y = view_filter_smoothing_y
401 view_filter_options = ReplaceNumberByKey("SmoothingX", view_filter_options, smoothing_x, "=", ";")
402 view_filter_options = ReplaceNumberByKey("SmoothingY", view_filter_options, smoothing_y, "=", ";")
403 filterfunc(view, view_filter_options)
431 dfref savedf = GetDataFolderDFR()
433 dfref viewdf = GetWavesDataFolderDFR(view_image)
434 svar /sdfr=viewdf graphname = prof_graphname
435 nvar /sdfr=viewdf cursor_mode = view_cursor_mode
436 wave /sdfr=viewdf xprofiles, yprofiles
438 variable dx = DimSize(view_image, 0)
439 variable dy = DimSize(view_image, 1)
442 Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 A view_image 0, 0
443 Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
444 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 C view_image round(0.2 * dx) -1, 0
445 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 D view_image round(0.8 * dx) -1, 0
446 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 E view_image round(0.4 * dx) -1, 0
447 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 F view_image round(0.6 * dx) -1, 0
449 ShowInfo /w=$graphname /CP=0
453 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 A view_image 0,0
454 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
456 pcurs = floor(DimSize(xprofiles, 0) / 3)
457 Cursor /w=$graphname /A=0 /P /S=1 /H=0 C xprofiles
#2 pcurs 458 pcurs = floor(DimSize(xprofiles, 0) * 2 / 3)
459 Cursor /w=$graphname /A=0 /P /S=1 /H=0 D xprofiles
#2 pcurs 460 pcurs = floor(DimSize(yprofiles, 0) / 3)
461 Cursor /w=$graphname /A=0 /P /S=1 /H=0 E yprofiles
#2 pcurs 462 pcurs = floor(DimSize(yprofiles, 0) * 2 / 3)
463 Cursor /w=$graphname /A=0 /P /S=1 /H=0 F yprofiles
#2 pcurs 464 ShowInfo /w=$graphname /CP=0
494 if (ParamIsDefault(pscale))
499 dfref savedf = GetDataFolderDFR()
501 dfref viewdf = GetWavesDataFolderDFR(view_image)
502 svar /sdfr=viewdf graphname = prof_graphname
509 pa = round((xa - DimOffset(view_image, 0)) / DimDelta(view_image, 0))
510 qa = round((ya - DimOffset(view_image, 1)) / DimDelta(view_image, 1))
513 pa = min(pa, DimSize(view_image, 0) - 1)
515 qa = min(qa, DimSize(view_image, 1) - 1)
517 Cursor /i /p /w=$graphname $cursorname view_image pa, qa
544 if (ParamIsDefault(clear))
550 dfref viewdf = GetWavesDataFolderDFR(view_image)
551 svar /sdfr=viewdf graphname = prof_graphname
553 string cursors = "A;B"
554 string colors = "39168,0,0;0,26112,0"
559 string groupname = "crosshairs"
564 SetDrawEnv /W=$graphname push
565 DrawAction /w=$graphname getgroup=$groupname, delete, begininsert
566 SetDrawEnv /w=$graphname gstart, gname=$groupname
568 SetDrawEnv /W=$graphname dash=4
569 SetDrawEnv /W=$graphname linethick=0.5
571 ncursors = ItemsInList(cursors, ";")
572 for (icursor=0; icursor < ncursors; icursor += 1)
573 cursorname = StringFromList(icursor, cursors, ";")
574 color = StringFromList(icursor, colors, ";")
575 rgb.red = str2num(StringFromList(0, color, ","))
576 rgb.green = str2num(StringFromList(1, color, ","))
577 rgb.blue = str2num(StringFromList(2, color, ","))
578 if (strlen(CsrInfo($cursorname, graphname)) > 0)
579 xx = hcsr($cursorname, graphname)
580 yy = vcsr($cursorname, graphname)
581 SetDrawEnv /W=$graphname linefgc=(rgb.red, rgb.green, rgb.blue)
582 SetDrawEnv /W=$graphname save
583 SetDrawEnv /W=$graphname xcoord=bottom, ycoord=prel
584 DrawLine /W=$graphname xx, 0, xx, 1
585 SetDrawEnv /W=$graphname xcoord=prel, ycoord=left
586 DrawLine /W=$graphname 0, yy, 1, yy
590 SetDrawEnv /w=$graphname gstop
591 DrawAction /w=$graphname endinsert
592 SetDrawEnv /W=$graphname pop
593 SetDrawEnv /W=$graphname save
595 DrawAction /w=$graphname getgroup=$groupname, delete
609 dfref viewdf = GetWavesDataFolderDFR(view)
610 svar /z /sdfr=viewdf sourcepath
611 if (svar_exists(sourcepath))
612 wave /z img = $sourcepath
624 dfref savedf = GetDataFolderDFR()
625 dfref imagedf = GetWavesDataFolderDFR(source)
626 string s_imagedf = GetDataFolder(1, imagedf)
627 setdatafolder imagedf
629 newdatafolder /o/s $s_viewdf
630 dfref viewdf = GetDataFolderDFR()
648 dfref savedf = GetDataFolderDFR()
649 dfref imagedf = GetWavesDataFolderDFR(source)
651 setdatafolder imagedf
653 if (DataFolderExists(s_viewdf))
654 setdatafolder $s_viewdf
655 viewdf = GetDataFolderDFR()
671 string viewname = "view_image"
672 wave /sdfr=viewdf view = $viewname
678 STRUCT WMButtonAction &ba
680 switch( ba.eventCode )
682 string imgname = StringFromList(0, ImageNameList(ba.win, ";"))
683 wave /z image = ImageNameToWaveRef(ba.win, imgname)
684 if (waveexists(image))
685 Cursor /i/p A $imgname 0,0
686 Cursor /i/p B $imgname DimSize(image, 0)-1, DimSize(image, 1)-1
697 STRUCT WMSetVariableAction &sva
701 switch( sva.eventCode )
705 imglist = ImageNameList(sva.win, ";")
706 wave /z img = ImageNameToWaveRef(sva.win, StringFromList(0, imglist))
709 if (WaveExists(source))
722 STRUCT WMPopupAction &pa
724 switch( pa.eventCode )
726 variable popNum = pa.popNum
728 string imgname = StringFromList(0, ImageNameList(pa.win, ";"))
729 wave /z image = ImageNameToWaveRef(pa.win, imgname)
730 if (waveexists(image) && (popNum >= 1) && (popNum <= 2))
732 elseif (waveexists(image) && (popNum >= 3) && (popNum <= 4))
746 struct WMWinHookStruct &s
747 variable hookresult = 0
754 imglist = ImageNameList(s.winName, ";")
755 wave /z img = ImageNameToWaveRef(s.winName, StringFromList(0, imglist))
757 viewdf = GetWavesDataFolderDFR(img)
758 cmd = "killdatafolder /z " + GetDataFolder(1, viewdf)
763 imglist = ImageNameList(s.winName, ";")
764 wave /z img = ImageNameToWaveRef(s.winName, StringFromList(0, imglist))
788 dfref savedf = GetDataFolderDFR()
789 dfref imagedf = GetWavesDataFolderDFR(image)
790 setdatafolder imagedf
792 svar graphname = prof_graphname
795 if (strlen(CsrInfo(A, graphname)) > 0)
796 pa = pcsr(A, graphname)
797 qa = qcsr(A, graphname)
804 if (strlen(CsrInfo(B, graphname)) > 0)
805 pb = pcsr(B, graphname)
806 qb = qcsr(B, graphname)
808 pb = DimSize(image, 0) - 1
809 qb = DimSize(image, 1) - 1
837 dfref savedf = GetDataFolderDFR()
838 dfref imagedf = GetWavesDataFolderDFR(image)
839 setdatafolder imagedf
850 redimension /n=(dimsize(image,0), 3) xprofiles
851 setscale /p x dimoffset(image,0), dimdelta(image,0), WaveUnits(image,0), xprofiles
852 setscale d 0, 0, waveunits(image,-1), xprofiles
853 xprofiles[][0] = image[p][qa]
854 xprofiles[][1] = image[p][qb]
857 note xprofiles, "SourceWave=" + nameofwave(image)
858 note xprofiles, "SourceDimension=0"
859 note xprofiles, "SourceIndex0=" + num2str(qa)
860 note xprofiles, "SourceIndex1=" + num2str(qb)
867 for (qq = q0; qq <= q1; qq += 1)
868 xprofiles[][2] += image[p][qq]
870 xprofiles[][2] /= q1 - q0 + 1
873 redimension /n=(dimsize(image,1), 3) yprofiles
874 setscale /p x dimoffset(image,1), dimdelta(image,1), WaveUnits(image,1), yprofiles
875 setscale d 0, 0, waveunits(image,-1), yprofiles
876 yprofiles[][0] = image[pa][p]
877 yprofiles[][1] = image[pb][p]
880 note yprofiles, "SourceWave=" + nameofwave(image)
881 note yprofiles, "SourceDimension=1"
882 note yprofiles, "SourceIndex0=" + num2str(pa)
883 note yprofiles, "SourceIndex1=" + num2str(pb)
890 for (pp = p0; pp <= p1; pp += 1)
891 yprofiles[][2] += image[pp][p]
893 yprofiles[][2] /= p1 - p0 + 1
896 Duplicate /r=[p0,p1][q0,q1]/o image, roi_image
897 WaveStats /Q roi_image
901 graph_sum = v_avg * v_npnts
906 if (waveexists(hist))
907 Histogram /B=3 roi_image, hist
941 dfref savedf = GetDataFolderDFR()
943 if (ParamIsDefault(trace))
946 if (ParamIsDefault(show))
949 if (ParamIsDefault(overwrite))
954 dfref imagedf = GetWavesDataFolderDFR(view_image)
958 wave /sdfr=imagedf profiles=xprofiles
962 wave /sdfr=imagedf profiles=yprofiles
968 string graphname_string = "export_graph_" + dim_label
969 svar /z /sdfr=imagedf linked_graphname = $graphname_string
973 if (WaveExists(source_image))
974 dfref sourcedf = GetWavesDataFolderDFR(source_image)
975 setdatafolder sourcedf
981 string profile_note = note(profiles)
986 variable index_width = ceil(log(DimSize(view_image, 1 - dim)))
987 variable index0 = NumberByKey("SourceIndex0", profile_note, "=", "\r")
988 variable index1 = NumberByKey("SourceIndex1", profile_note, "=", "\r")
989 name_dim = "_" + dim_label
990 sprintf name_index, "%0*u_%0*u", index_width, index0, index_width, index1
991 name_base = NameOfWave(source_image)
992 name_base = name_base[0, min(strlen(name_base), 31 - strlen(name_index) - strlen(name_dim) - 1)]
993 profile_name = name_base + name_dim + name_index
994 if ((overwrite == 0) && (CheckName(profile_name, 1)))
995 profile_name = UniqueName(profile_name + "_", 1, 0)
999 duplicate /o /r=[][trace] profiles, $profile_name /wave=dest_profile
1000 redimension /n=(dimsize(profiles, 0)) dest_profile
1001 profile_note = ReplaceStringByKey("SourceWave", profile_note, NameOfWave(source_image), "=", "\r")
1002 note /k dest_profile
1003 note dest_profile, profile_note
1004 print "created", GetWavesDataFolder(dest_profile, 2)
1011 graphname = "export_profiles_" + dim_label
1012 graphtitle = UpperStr(dim_label) + " Profiles"
1015 if (svar_exists(linked_graphname) && (ItemsInList(WinList(linked_graphname, ";", "WIN:1"), ";") >= 1))
1016 graphname = linked_graphname
1018 graphname = GetWavesDataFolder(source_image, 0) + name_dim
1020 graphtitle = UpperStr(dim_label) + " Profiles: " + GetWavesDataFolder(source_image, 2)
1023 if ((ItemsInList(WinList(graphname, ";", "WIN:1"), ";") >= 1))
1024 appendtograph /w=$graphname dest_profile
1026 setdatafolder imagedf
1027 display /k=1 /n=$graphname dest_profile as graphtitle
1029 ModifyGraph /w=$graphname mirror=1,nticks=3,minor=1
1030 ModifyGraph /w=$graphname axThick=0.5,btLen=4
1031 ModifyGraph /w=$graphname gfSize=10
1032 ModifyGraph /w=$graphname grid=2,gridHair=0,gridRGB=(52224,52224,52224)
1033 Legend /w=$graphname /C/N=legend0/F=0/B=1/A=LT/X=0.00/Y=0.00
1036 string /g $graphname_string = graphname
1041 setdatafolder savedf
1048 ModifyGraph /w=$graphname /z rgb[0]=(0, 0, 0)
1049 ModifyGraph /w=$graphname /z rgb[1]=(65535, 16385, 16385)
1050 ModifyGraph /w=$graphname /z rgb[2]=(2, 39321, 1)
1051 ModifyGraph /w=$graphname /z rgb[3]=(0, 0, 65535)
1052 ModifyGraph /w=$graphname /z rgb[4]=(39321, 1, 31457)
1053 ModifyGraph /w=$graphname /z rgb[5]=(48059, 48059, 48059)
1054 ModifyGraph /w=$graphname /z rgb[6]=(65535, 32768, 32768)
1055 ModifyGraph /w=$graphname /z rgb[7]=(0, 65535, 0)
1056 ModifyGraph /w=$graphname /z rgb[8]=(16385,65535,65535)
1057 ModifyGraph /w=$graphname /z rgb[9]=(65535, 32768, 58981)
1069 dfref savedf = GetDataFolderDFR()
1070 dfref imagedf = GetWavesDataFolderDFR(image)
1071 setdatafolder imagedf
1074 Histogram /B=3 image, hist
1076 setdatafolder savedf
1107 variable xsmoothing = NumberByKey("SmoothingX", options, "=", ";")
1108 variable ysmoothing = NumberByKey("SmoothingY", options, "=", ";")
1110 if ((NumType(xsmoothing) == 0) && (xsmoothing >= 2))
1111 Smooth /B /DIM=0 /E=3 xsmoothing, image
1113 if ((NumType(ysmoothing) == 0) && (ysmoothing >= 2))
1114 Smooth /B /DIM=1 /E=3 ysmoothing, image
1129 MatrixTranspose image
1144 if(exists("NewGizmo") != 4)
1145 abort "Gizmo XOP must be installed."
1147 if (WaveDims(data) != 3)
1151 dfref savedf = GetDataFolderDFR()
1152 dfref datadf = GetWavesDataFolderDFR(data)
1153 string s_datadf = GetDataFolder(1, datadf)
1156 setdatafolder viewdf
1157 string dfname = ReplaceString("root:", s_datadf, "")
1158 string graphtitle = dfname + " Gizmo"
1160 svar graphname = gizmo_graphname
1162 if ((strlen(graphname) > 0) && (wintype(graphname) == 13))
1163 setdatafolder savedf
1167 variable nx = dimsize(data, 0)
1168 variable ny = dimsize(data, 1)
1169 variable nz = dimsize(data, 2)
1176 setdatafolder datadf
1177 sprintf cmd, "NewGizmo /k=1 /n=%s /w=(100,100,500,400) /t=\"%s\"", graphname, graphtitle
1179 cmd = "AppendToGizmo /D Axes=BoxAxes, name=axes0"
1182 obj = "surface_xmid"
1183 pp = round(nx / 2 - 1)
1184 sprintf cmd, "AppendToGizmo /D surface=%s, name=%s", nameofwave(data), obj
1186 sprintf cmd, "ModifyGizmo modifyObject=%s, property={srcMode, 128}
", obj 1188 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={plane, %d}
", obj, pp 1190 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCtab, BlueGreenOrange}
", obj 1192 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={SurfaceCTABScaling,128}
", obj 1194 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCTABAlpha, 1.0}
", obj 1197 obj = " surface_ymid
" 1198 pp = round(ny / 2 - 1) 1199 sprintf cmd, " AppendToGizmo /D surface=%s, name=%s
", nameofwave(data), obj 1201 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={srcMode, 64}
", obj 1203 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={plane, %d}
", obj, pp 1205 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCtab, BlueGreenOrange}
", obj 1207 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={SurfaceCTABScaling,128}
", obj 1209 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCTABAlpha, 1.0}
", obj 1212 obj = " surface_zmid
" 1213 pp = round(nz / 2 - 1) 1214 sprintf cmd, " AppendToGizmo /D surface=%s, name=%s
", nameofwave(data), obj 1216 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={srcMode, 32}
", obj 1218 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={plane, %d}
", obj, pp 1220 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCtab, BlueGreenOrange}
", obj 1222 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={SurfaceCTABScaling,128}
", obj 1224 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCTABAlpha, 1.0}
", obj 1228 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={-1,axisScalingMode,1}
", obj 1230 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={-1,axisColor,0,0,0,1}
", obj 1232 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={0,ticks,3}
", obj 1234 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={1,ticks,3}
", obj 1236 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={2,ticks,3}
", obj 1238 sprintf cmd, " ModifyGizmo modifyObject=%s
property ={Clipped,0}
", obj 1240 sprintf cmd, " ModifyGizmo modifyObject=%s
property ={-1,fontScaleFactor,2}
", obj 1243 sprintf cmd, " ModifyGizmo showAxisCue=1
" 1246 setdatafolder savedf 1256 function ad_brick_slicer(data) 1259 // data folders and references 1260 dfref savedf = GetDataFolderDFR() 1261 dfref datadf = GetWavesDataFolderDFR(data) 1262 string s_datadf = GetDataFolder(1, datadf) 1263 dfref viewdf = make_view_folder(data) 1265 setdatafolder viewdf 1266 svar /z ex_panel = slicer_panelname 1267 if (svar_exists(ex_panel)) 1268 string panels = WinList(" SlicerPanel*
", " ;
", " WIN:64
") 1269 if (WhichListItem(ex_panel, panels, " ;
") >= 0) 1270 dowindow /f $(StringFromList(0, panels, " ;
")) 1275 variable /g x_slice_pos 1276 variable /g y_slice_pos 1277 variable /g z_slice_pos 1278 variable /g slab_thickness 1279 string /g brick_path = getwavesdatafolder(data, 2) 1280 variable /g x_autoinc = 0 1281 variable /g y_autoinc = 0 1282 variable /g z_autoinc = 0 1285 string labels = note(data) 1286 string xlabel = StringByKey(" AxisLabelX
", labels, " =
", " \r
") 1287 if (!strlen(xlabel)) 1290 string ylabel = StringByKey(" AxisLabelY
", labels, " =
", " \r
") 1291 if (!strlen(ylabel)) 1294 string zlabel = StringByKey(" AxisLabelZ
", labels, " =
", " \r
") 1295 if (!strlen(zlabel)) 1298 string dlabel = StringByKey(" Dataset
", labels, " =
", " \r
") 1299 if (!strlen(dlabel)) 1300 dlabel = NameOfWave(data) 1303 // this section copied from slicer panel 1304 NewPanel /k=1 /W=(500,600,890,940) /N=SlicerPanel as " Brick Slicer
" 1305 string /g slicer_panelname = S_name 1306 string panel = s_name 1308 GroupBox g_xslice win=$panel,pos={8,8},size={376,96},title=xlabel 1309 Slider sl_xslice_position win=$panel,pos={16,32},size={240,56},proc=PearlAreaDisplay#slp_slice_position 1310 Slider sl_xslice_position win=$panel,limits={0,100,1},variable=x_slice_pos,vert= 0 1311 SetVariable sv_xslice_position win=$panel,pos={20,80},size={92,16},proc=PearlAreaDisplay#svp_slice_position,title=" X
" 1312 SetVariable sv_xslice_position win=$panel,limits={0,100,1},value=x_slice_pos 1313 Button b_xslice_center win=$panel,pos={122,80},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W618
" 1314 Button b_xslice_center win=$panel,help={" reset to center position
"} 1315 Button b_xslice_extract win=$panel,pos={288,80},size={68,20},proc=PearlAreaDisplay#bp_extract_slice,title=" extract slice
" 1316 Button b_xslice_extract win=$panel,help={" extract
this slice to a separate wave
"} 1317 //CheckBox cb_xslab_active win=$panel,pos={288,80},size={80,16},title=" Display X Slab
" 1318 //CheckBox cb_xslab_active win=$panel,value= 0 1319 TitleBox tb_xslice_animation win=$panel,pos={288,32},size={356,16},title=" animation
",frame=0 1320 TitleBox tb_xslice_animation win=$panel,anchor= MC 1321 Button b_xslice_back win=$panel,pos={288,48},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W646
" 1322 Button b_xslice_back win=$panel,help={" animate backwards
"} 1323 Button b_xslice_forward win=$panel,pos={312,48},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W649
" 1324 Button b_xslice_forward win=$panel,help={" animate forward
"} 1325 Button b_xslice_stop win=$panel,pos={336,48},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W616
" 1326 Button b_xslice_stop win=$panel,help={" stop animation
"} 1328 GroupBox g_yslice win=$panel,pos={8,108},size={376,96},title=ylabel 1329 Slider sl_yslice_position win=$panel,pos={16,132},size={240,56},proc=PearlAreaDisplay#slp_slice_position 1330 Slider sl_yslice_position win=$panel,limits={0,100,1},variable=y_slice_pos,vert= 0 1331 SetVariable sv_yslice_position win=$panel,pos={20,180},size={92,16},proc=PearlAreaDisplay#svp_slice_position,title=" Y
" 1332 SetVariable sv_yslice_position win=$panel,limits={0,100,1},value=y_slice_pos 1333 Button b_yslice_center win=$panel,pos={122,180},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W618
" 1334 Button b_yslice_center win=$panel,help={" reset to center position
"} 1335 Button b_yslice_extract win=$panel,pos={288,180},size={68,20},proc=PearlAreaDisplay#bp_extract_slice,title=" extract slice
" 1336 Button b_yslice_extract win=$panel,help={" extract
this slice to a separate wave
"} 1337 //CheckBox cb_yslab_active win=$panel,pos={288,180},size={80,16},title=" Display Y Slab
" 1338 //CheckBox cb_yslab_active win=$panel,value= 0 1339 TitleBox tb_yslice_animation win=$panel,pos={288,132},size={356,16},title=" animation
",frame=0 1340 TitleBox tb_yslice_animation win=$panel,anchor= MC 1341 Button b_yslice_back win=$panel,pos={288,148},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W646
" 1342 Button b_yslice_back win=$panel,help={" animate backwards
"} 1343 Button b_yslice_forward win=$panel,pos={312,148},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W649
" 1344 Button b_yslice_forward win=$panel,help={" animate forward
"} 1345 Button b_yslice_stop win=$panel,pos={336,148},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W616
" 1346 Button b_yslice_stop win=$panel,help={" stop animation
"} 1348 GroupBox g_zslice win=$panel,pos={8,208},size={376,96},title=zlabel 1349 Slider sl_zslice_position win=$panel,pos={16,232},size={240,56},proc=PearlAreaDisplay#slp_slice_position 1350 Slider sl_zslice_position win=$panel,limits={0,100,1},variable=z_slice_pos,vert= 0 1351 SetVariable sv_zslice_position win=$panel,pos={20,280},size={92,16},proc=PearlAreaDisplay#svp_slice_position,title=" Z
" 1352 SetVariable sv_zslice_position win=$panel,limits={0,100,1},value=z_slice_pos 1353 Button b_zslice_center win=$panel,pos={122,280},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W618
" 1354 Button b_zslice_center win=$panel,help={" reset to center position
"} 1355 Button b_zslice_extract win=$panel,pos={288,280},size={68,20},proc=PearlAreaDisplay#bp_extract_slice,title=" extract slice
" 1356 Button b_zslice_extract win=$panel,help={" extract
this slice to a separate wave
"} 1357 //CheckBox cb_zslab_active win=$panel,pos={288,280},size={80,16},title=" Display Z Slab
" 1358 //CheckBox cb_zslab_active win=$panel,value= 0 1359 TitleBox tb_zslice_animation win=$panel,pos={288,232},size={356,16},title=" animation
",frame=0 1360 TitleBox tb_zslice_animation win=$panel,anchor= MC 1361 Button b_zslice_back win=$panel,pos={288,248},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W646
" 1362 Button b_zslice_back win=$panel,help={" animate backwards
"} 1363 Button b_zslice_forward win=$panel,pos={312,248},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W649
" 1364 Button b_zslice_forward win=$panel,help={" animate forward
"} 1365 Button b_zslice_stop win=$panel,pos={336,248},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W616
" 1366 Button b_zslice_stop win=$panel,help={" stop animation
"} 1368 TitleBox t_slicerpath win=$panel,pos={8,316},size={128,20},disable=2,title=dlabel 1369 //SetVariable setvar0 win=$panel,pos={240,316},size={120,16},title=" slab thickness
" 1370 //SetVariable setvar0 win=$panel,limits={1,inf,1},value=slab_thickness 1372 // update control limits and move slicing planes to the center 1373 setwindow $panel, userdata(control_datafolder) = GetDataFolder(1, viewdf) 1374 setwindow $panel, userdata(brick_path) = brick_path 1376 x_slice_pos = dimoffset(data, 0) + dimsize(data, 0) * dimdelta(data, 0) / 2 1377 y_slice_pos = dimoffset(data, 1) + dimsize(data, 1) * dimdelta(data, 1) / 2 1378 z_slice_pos = dimoffset(data, 2) + dimsize(data, 2) * dimdelta(data, 2) / 2 1380 svar /z /sdfr=viewdf gizmo_graphname 1381 if (svar_exists(gizmo_graphname) && (strlen(gizmo_graphname) > 0) && (wintype(gizmo_graphname) == 13)) 1382 ad_gizmo_set_plane(data, 0, x_slice_pos) 1383 ad_gizmo_set_plane(data, 1, y_slice_pos) 1384 ad_gizmo_set_plane(data, 2, z_slice_pos) 1386 svar /z /sdfr=viewdf slice_graphname 1387 if (svar_exists(slice_graphname) && (strlen(slice_graphname) > 0) && (wintype(slice_graphname) == 1)) 1388 ad_profiles_set_slice(data, 2, z_slice_pos) 1392 setdatafolder savedf 1404 function /s ad_display_slice(data) 1407 if (WaveDims(data) != 3) 1411 dfref savedf = GetDataFolderDFR() 1412 dfref datadf = GetWavesDataFolderDFR(data) 1413 string s_datadf = GetDataFolder(1, datadf) 1414 dfref viewdf = make_view_folder(data) 1416 setdatafolder viewdf 1417 string dfname = ReplaceString(" root:
", s_datadf, " ") 1418 dfname = dfname[0, strlen(dfname) - 2] 1419 string graphtitle = dfname + " Slice
" 1421 if (exists(" slice_graphname
") != 2) 1422 string /g slice_graphname = " " 1424 string /g slice_wavename = PearlCleanupName(" slice_
" + NameOfWave(data)) 1425 svar graphname = slice_graphname 1426 svar slicename = slice_wavename 1428 make /n=(1,1)/o $slicename 1429 wave slice = $slicename 1430 if ((strlen(graphname) == 0) || (wintype(graphname) != 1)) 1431 graphname = ad_display_profiles(slice) 1433 variable z_slice_pos = dimoffset(data, 2) + dimsize(data, 2) * dimdelta(data, 2) / 2 1434 ad_profiles_set_slice(data, 2, z_slice_pos) 1435 ad_profiles_set_cursor(slice, " A
", -inf, -inf, pscale=1) 1436 ad_profiles_set_cursor(slice, " B
", +inf, +inf, pscale=1) 1438 setdatafolder savedf 1445 static function update_slice_info() 1446 dfref savedf = GetDataFolderDFR() 1449 //svar slicer_panelname 1450 wave brick = $brick_path 1452 //dowindow /F $slicer_panelname 1453 variable lo, hi, inc 1454 lo = dimoffset(brick, 0) 1455 inc = dimdelta(brick, 0) 1456 hi = lo + inc * (dimsize(brick, 0) - 1) 1457 Slider sl_xslice_position,limits={lo,hi,inc} 1458 SetVariable sv_xslice_position,limits={lo,hi,inc} 1459 lo = dimoffset(brick, 1) 1460 inc = dimdelta(brick, 1) 1461 hi = lo + inc * (dimsize(brick, 1) - 1) 1462 Slider sl_yslice_position,limits={lo,hi,inc} 1463 SetVariable sv_yslice_position,limits={lo,hi,inc} 1464 lo = dimoffset(brick, 2) 1465 inc = dimdelta(brick, 2) 1466 hi = lo + inc * (dimsize(brick, 2) - 1) 1467 Slider sl_zslice_position,limits={lo,hi,inc} 1468 SetVariable sv_zslice_position,limits={lo,hi,inc} 1470 setdatafolder savedf 1481 function ad_gizmo_set_plane(brick, dim, value) 1486 dfref savedf = GetDataFolderDFR() 1487 dfref datadf = GetWavesDataFolderDFR(brick) 1488 dfref viewdf = get_view_folder(brick) 1489 svar /z /sdfr=viewdf graphname=gizmo_graphname 1491 variable pp = round((value - dimoffset(brick, dim)) / dimdelta(brick, dim)) 1492 if ((pp < 0) || (pp >= dimsize(brick, dim))) 1493 return -1 // requested value out of range 1496 if (svar_exists(graphname) && (strlen(graphname) > 0) && (wintype(graphname) == 13)) 1498 string obj = " surface_
" + axes[dim] + " mid
" 1500 sprintf cmd, " ModifyGizmo /N=%s ModifyObject=%s,
property ={plane, %d}
", graphname, obj, pp 1503 return -2 // gizmo window not found 1517 function ad_profiles_set_slice(brick, dim, value) 1522 dfref savedf = GetDataFolderDFR() 1523 dfref datadf = GetWavesDataFolderDFR(brick) 1524 dfref viewdf = get_view_folder(brick) 1525 svar /z /sdfr=viewdf graphname = slice_graphname 1526 svar /z /sdfr=viewdf slicename = slice_wavename 1528 variable pp = round((value - dimoffset(brick, dim)) / dimdelta(brick, dim)) 1529 if ((pp < 0) || (pp >= dimsize(brick, dim))) 1530 return -1 // requested value out of range 1533 if (svar_exists(graphname) && (strlen(graphname) > 0) && (wintype(graphname) == 1)) 1534 setdatafolder viewdf 1537 wave wdest = ad_extract_slab_x(brick, pp, pp, slicename) 1538 ad_update_profiles(wdest) 1541 wave wdest = ad_extract_slab_y(brick, pp, pp, slicename) 1542 ad_update_profiles(wdest) 1545 wave wdest = ad_extract_slab_z(brick, pp, pp, slicename) 1546 ad_update_profiles(wdest) 1550 return -2 // graph window not found 1553 setdatafolder savedf 1558 static function slp_slice_position(sa) : SliderControl 1559 STRUCT WMSliderAction &sa 1561 dfref savedf = GetDataFolderDFR() 1563 switch( sa.eventCode ) 1564 case -1: // control being killed 1567 if( sa.eventCode & 1 ) // value set 1568 string control_datafolder = GetUserData(sa.win, " ", " control_datafolder
") 1569 setdatafolder control_datafolder 1570 string brick_path = GetUserData(sa.win, " ", " brick_path
") 1571 string axis = StringFromList(1, sa.ctrlName, " _
") 1572 variable dim = char2num(axis[0]) - char2num(" x
") 1574 wave /z brick = $brick_path 1575 if (WaveExists(brick)) 1576 ad_gizmo_set_plane(brick, dim, sa.curval) 1577 ad_profiles_set_slice(brick, dim, sa.curval) 1579 Abort " can
't find original wave " + brick_path 1585 setdatafolder savedf 1590 static function svp_slice_position(sva) : SetVariableControl 1591 STRUCT WMSetVariableAction &sva 1593 dfref savedf = GetDataFolderDFR() 1595 switch( sva.eventCode ) 1597 case 2: // Enter key 1598 case 3: // Live update 1599 string control_datafolder = GetUserData(sva.win, "", "control_datafolder") 1600 setdatafolder control_datafolder 1601 string brick_path = GetUserData(sva.win, "", "brick_path") 1602 string axis = StringFromList(1, sva.ctrlName, "_") 1603 variable dim = char2num(axis[0]) - char2num("x") 1605 wave /z brick = $brick_path 1606 if (WaveExists(brick)) 1607 ad_gizmo_set_plane(brick, dim, sva.dval) 1608 ad_profiles_set_slice(brick, dim, sva.dval) 1610 Abort "can' t find original wave
" + brick_path 1613 case -1: // control being killed 1617 setdatafolder savedf 1622 static function bp_move_slice(ba) : ButtonControl 1623 STRUCT WMButtonAction &ba 1625 dfref savedf = GetDataFolderDFR() 1627 switch( ba.eventCode ) 1629 string control_datafolder = GetUserData(ba.win, " ", " control_datafolder
") 1630 setdatafolder control_datafolder 1631 string brick_path = GetUserData(ba.win, " ", " brick_path
") 1632 string axis = StringFromList(1, ba.ctrlName, " _
") 1633 string cmd = StringFromList(2, ba.ctrlName, " _
") 1634 variable dim = char2num(axis[0]) - char2num(" x
") 1635 string posvariable = getdatafolder(1) + axis[0] + " _slice_pos
" 1636 nvar pos = $(posvariable) 1638 wave /z brick = $brick_path 1639 if (WaveExists(brick)) 1642 ad_slicer_start_bg(brick, dim, posvariable, dimdelta(brick, dim)) 1645 ad_slicer_start_bg(brick, dim, posvariable, -dimdelta(brick, dim)) 1648 ad_slicer_stop_bg(posvariable) 1649 bp_move_slice_center(brick, dim, posvariable) 1652 ad_slicer_stop_bg(posvariable) 1656 ad_slicer_stop_bg(posvariable) 1657 Abort " can
't find original wave " + brick_path 1660 case -1: // control being killed 1664 setdatafolder savedf 1671 static function bp_extract_slice(ba) : ButtonControl 1672 STRUCT WMButtonAction &ba 1674 dfref savedf = GetDataFolderDFR() 1676 switch( ba.eventCode ) 1678 string control_datafolder = GetUserData(ba.win, "", "control_datafolder") 1679 setdatafolder control_datafolder 1680 string brick_path = GetUserData(ba.win, "", "brick_path") 1681 wave brick = $brick_path 1682 dfref brickdf = GetWavesDataFolderDFR(brick) 1684 string axis = StringFromList(1, ba.ctrlName, "_") 1685 string cmd = StringFromList(2, ba.ctrlName, "_") 1686 variable dim = char2num(axis[0]) - char2num("x") 1687 string posvariable = getdatafolder(1) + axis[0] + "_slice_pos" 1689 nvar pos = $(posvariable) 1690 variable pp = round((pos - dimoffset(brick, dim)) / dimdelta(brick, dim)) 1691 if ((pp < 0) || (pp >= dimsize(brick, dim))) 1692 return -1 // requested value out of range 1695 variable dig = ceil(log(dimsize(brick, dim))) 1697 sprintf slicename, "%s_%s%0*u", NameOfWave(brick), axis[0], dig, pp 1698 setdatafolder brickdf 1701 wave wdest = ad_extract_slab_x(brick, pp, pp, slicename) 1704 wave wdest = ad_extract_slab_y(brick, pp, pp, slicename) 1707 wave wdest = ad_extract_slab_z(brick, pp, pp, slicename) 1712 sprintf msg, "%s=%g", axis[0], pos 1716 case -1: // control being killed 1720 setdatafolder savedf 1725 static function bp_move_slice_center(brick, dim, posvariable) 1730 nvar pos = $posvariable 1731 pos = dimoffset(brick, dim) + dimdelta(brick, dim) * dimsize(brick, dim) / 2 1732 ad_gizmo_set_plane(brick, dim, pos) 1733 ad_profiles_set_slice(brick, dim, pos) 1737 static function ad_slicer_move_bg(s) 1738 STRUCT WMBackgroundStruct &s 1740 dfref savedf = GetDataFolderDFR() 1741 setdatafolder root:pearl_area:slicer 1742 wave /t bg_brickpaths 1743 wave /t bg_graphnames 1744 wave /t bg_variablepaths 1749 variable nn = numpnts(bg_brickpaths) 1753 for (ii = 0; ii < nn; ii += 1) 1754 wave /z brick = $bg_brickpaths[ii] 1755 nvar /z pos = $bg_variablepaths[ii] 1756 dim = bg_dimensions[0] 1757 pos += bg_increments[ii] 1758 // wrap around at limits 1759 pp = round((pos - dimoffset(brick, dim)) / dimdelta(brick, dim)) 1761 pos = dimoffset(brick, dim) + dimdelta(brick, dim) * (dimsize(brick, dim) - 1) 1762 elseif (pp >= dimsize(brick, dim) - 0.5) 1763 pos = dimoffset(brick, dim) 1765 if (waveexists(brick)) 1766 ad_gizmo_set_plane(brick, dim, pos) 1767 ad_profiles_set_slice(brick, dim, pos) 1771 setdatafolder savedf 1776 function ad_slicer_init_bg() 1777 dfref savedf = GetDataFolderDFR() 1779 newdatafolder /o/s pearl_area 1780 newdatafolder /o/s slicer 1782 make /n=0/o/t bg_brickpaths 1783 make /n=0/o/t bg_variablepaths 1784 make /n=0/o/i/u bg_dimensions 1785 make /n=0/o bg_increments 1787 CtrlNamedBackground ad_slicer, period = 30, proc = PearlAreaDisplay#ad_slicer_move_bg 1789 setdatafolder savedf 1800 function ad_slicer_start_bg(brick, dimension, posvariable, delta) 1801 wave brick // 3D data wave 1802 variable dimension // dimension to animate, 0, 1, or 2 1803 string posvariable // full path to the global position variable 1804 variable delta // step increment, should be +/- dimdelta 1806 dfref savedf = GetDataFolderDFR() 1807 setdatafolder root:pearl_area:slicer 1808 wave /t bg_brickpaths 1809 wave /t bg_variablepaths 1813 // create entry in ad_slicer background task table 1815 FindValue /TEXT=posvariable /TXOP=4 /Z bg_variablepaths 1819 idx = numpnts(bg_variablepaths) 1820 InsertPoints idx, 1, bg_brickpaths, bg_variablepaths, bg_dimensions, bg_increments 1823 // set background task 1824 bg_brickpaths[idx] = GetWavesDataFolder(brick, 2) 1825 bg_variablepaths[idx] = posvariable 1826 bg_dimensions[idx] = dimension 1827 bg_increments[idx] = delta 1829 // start background task 1830 if (numpnts(bg_variablepaths) > 0) 1831 CtrlNamedBackground ad_slicer, start 1834 setdatafolder savedf 1842 function ad_slicer_stop_bg(posvariable) 1845 dfref savedf = GetDataFolderDFR() 1846 setdatafolder root:pearl_area:slicer 1847 wave /t bg_brickpaths 1848 wave /t bg_variablepaths 1852 // find entry in ad_slicer background task table 1853 FindValue /TEXT=posvariable /TXOP=4 /Z bg_variablepaths 1855 DeletePoints v_value, 1, bg_brickpaths, bg_variablepaths, bg_dimensions, bg_increments 1858 // stop background task if task table is empty 1859 if (numpnts(bg_variablepaths) == 0) 1860 CtrlNamedBackground ad_slicer, stop 1863 setdatafolder savedf variable ad_profiles_cursor_mode(wave image, variable mode)
switch cursors on a profiles graph
-
static variable set_trace_colors(string graphname)
-
variable ad_profiles_crosshairs(wave image, variable clear=defaultValue)
draw permanent crosshairs in a profiles graph.
-
variable ad_update_profiles(wave image)
update a profiles graph with new data.
-
variable ad_default_image_filter(wave image, string options)
abstract filter function for image display.
-
static variable svp_smoothing(WMSetVariableAction *sva)
-
static dfr get_view_folder(wave source)
find the view data folder corresponding to the given source.
-
variable ad_calc_histogram(wave image)
calculate the histogram.
-
static dfr make_view_folder(wave source)
create a view data folder.
-
string PearlCleanupName(string name)
-
variable ad_calc_profiles(wave image, variable pa, variable qa, variable pb, variable qb)
calculate profiles, statistics, and histogram of a rectangular region of interest.
-
variable ad_profiles_set_cursor(wave image, string cursorname, variable xa, variable ya, variable pscale=defaultValue)
move a cursor to the specified position in a profiles graph.
-
static wave get_view_image(wave source)
find the view image wave corresponding to the given source.
-
instant visualization of angle scan and manipulator position.
-
static variable pmp_export(WMPopupAction *pa)
-
static wave get_source_image(wave view)
find the source image wave corresponding to the given view.
-
string ad_display_histogram(wave image)
display the histogram of a 2D image.
-
string ad_display(wave image)
open a new graph window with a 2D image.
-
static string graphname_from_dfref(dfref df, string prefix)
compose a valid and unique graph name from a data folder reference
-
wave ad_add_overlay(wave image, string rgba=defaultValue)
add an overlay on top of the displayed image
-
variable ad_calc_cursor_profiles(wave image)
calculate profiles, statistics, and histogram of a cross-hair delimited region of interest...
-
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
-
static variable bp_reset_cursors(WMButtonAction *ba)
-
variable ad_export_profile(wave view_image, variable dim, variable trace=defaultValue, variable show=defaultValue, variable overwrite=defaultValue)
export a profile from a profiles graph to the source data folder.
-
variable ad_transpose_filter(wave image, string options)
transpose image filter.
-
string ad_display_slice(wave data)
display three-dimensional data by 2D slice.
-
variable ad_box_filter(wave image, string options)
boxcar smoothing filter.
-
string ad_display_brick(wave data)
open a new "gizmo" window with three-dimensional data.
-
variable ad_profiles_hook(WMWinHookStruct *s)
hook function for user events in the profiles window.
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.2
+
4 #pragma ModuleName = PearlAreaDisplay
+
+
6 #include "pearl-compat"
+
7 #include "pearl-area-profiles"
+
+
+
+
+
+
+
+
+
+
+
65 name = GetDataFolder(1, df)
+
66 name = ReplaceString(
"root:" , name,
"" )
+
67 name = name[0, strlen(name) - 2]
+
68 name = ReplaceString(" ", name, "")
+
+
70 if (CheckName(name, 6))
+
71 name = UniqueName(name, 6, 0)
+
+
+
+
+
+
+
+
+
+
91 dfref savedf = GetDataFolderDFR()
+
92 dfref imagedf = GetWavesDataFolderDFR(image)
+
+
+
95 string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
+
96 string graphtitle = dfname + " View"
+
+
98 svar graphname = view_graphname
+
99 display /k=1/n=$graphname as graphtitle
+
+
101 appendimage /w=$graphname image
+
+
+
+
+
+
+
+
+
120 dfref savedf = GetDataFolderDFR()
+
121 dfref imagedf = GetWavesDataFolderDFR(image)
+
122 string s_imagedf = GetDataFolder(1, imagedf)
+
123 setdatafolder imagedf
+
+
+
+
127 string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
+
128 string graphtitle = dfname + " Histogram"
+
+
130 svar graphname = hist_graphname
+
131 display /k=1/n=$graphname as graphtitle
+
+
133 appendtograph /w=$graphname hist
+
+
135 ModifyGraph /w=$graphname rgb(hist)=(39168,0,0)
+
136 ModifyGraph /w=$graphname mode=6
+
137 ModifyGraph /w=$graphname mirror=1
+
138 ModifyGraph /w=$graphname minor=1
+
139 ModifyGraph /w=$graphname axThick=0.5
+
140 ModifyGraph /w=$graphname lblPosMode=1,lblPos=30,lblMargin=0
+
141 ModifyGraph /w=$graphname btLen=4
+
142 ModifyGraph /w=$graphname margin(left)=45,margin(bottom)=35,margin(top)=10,margin(right)=10
+
143 ModifyGraph /w=$graphname gfSize=10
+
144 Label /w=$graphname bottom "value"
+
145 Label /w=$graphname left "
# pixels"
+
+
+
+
+
+
+
+
+
+
+
171 variable show_legend = 0
+
+
173 if (WaveDims(image) != 2)
+
174 abort
"ad_display_profiles: image wave must be two-dimensional."
+
+
176 if (ParamIsDefault(filter))
+
177 filter =
"ad_box_filter"
+
+
+
+
181 dfref savedf = GetDataFolderDFR()
+
182 dfref imagedf = GetWavesDataFolderDFR(image)
+
183 string s_imagedf = GetDataFolder(1, imagedf)
+
184 setdatafolder imagedf
+
+
186 newdatafolder /o/s $s_viewdf
+
187 dfref viewdf = GetDataFolderDFR()
+
188 s_viewdf = GetDataFolder(1, viewdf)
+
+
+
191 string /g sourcepath = GetWavesDataFolder(image, 2)
+
192 string viewname = "view_image"
+
193 duplicate /o image, $viewname /wave=view
+
194 make /n=(3,3)/o xprofiles
+
195 make /n=(3,3)/o yprofiles
+
196 string /g view_filter
+
197 string /g view_filter_options
+
+
199 view_filter_options = ""
+
200 variable /g view_filter_smoothing_x = 1
+
201 variable /g view_filter_smoothing_y = 1
+
202 variable /g view_cursor_mode = 0
+
203 string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
+
204 string graphtitle = dfname + NameOfWave(image) + " Profiles"
+
+
206 svar graphname = prof_graphname
+
207 variable /g graph_avg
+
208 variable /g graph_min
+
209 variable /g graph_max
+
210 variable /g graph_sum
+
211 variable /g graph_sdev
+
+
+
214 display /k=1 /n=$graphname /w=(100,100,500,400) as graphtitle
+
+
216 AppendToGraph /w=$graphname /L=xprofiles xprofiles[*][0],xprofiles[*][1],xprofiles[*][2]
+
217 AppendToGraph /w=$graphname /VERT/B=yprofiles yprofiles[*][0],yprofiles[*][1],yprofiles[*][2]
+
218 AppendImage /w=$graphname view
+
219 string imgname = StringFromList(0, ImageNameList(graphname, ";"))
+
220 ModifyImage /w=$graphname $imgname ctab= {*,*,BlueGreenOrange,0}
+
221 ModifyGraph /w=$graphname rgb(xprofiles)=(39168,0,0),rgb(yprofiles)=(39168,0,0)
+
222 ModifyGraph /w=$graphname rgb(xprofiles#1)=(0,26112,0),rgb(yprofiles#1)=(0,26112,0)
+
223 ModifyGraph /w=$graphname rgb(xprofiles#2)=(0,9472,39168),rgb(yprofiles#2)=(0,9472,39168)
+
224 ModifyGraph /w=$graphname mirror(xprofiles)=2,mirror(bottom)=3,mirror(yprofiles)=2,mirror(left)=3
+
225 ModifyGraph /w=$graphname nticks=3
+
226 ModifyGraph /w=$graphname minor=1
+
227 ModifyGraph /w=$graphname axThick=0.5
+
228 ModifyGraph /w=$graphname lblPosMode=1,lblPos=30,lblMargin=0
+
229 ModifyGraph /w=$graphname btLen=4
+
230 ModifyGraph /w=$graphname freePos(xprofiles)=0
+
231 ModifyGraph /w=$graphname freePos(yprofiles)=0
+
232 ModifyGraph /w=$graphname axisEnab(xprofiles)={0.64,1}
+
233 ModifyGraph /w=$graphname axisEnab(bottom)={0,0.6}
+
234 ModifyGraph /w=$graphname axisEnab(yprofiles)={0.64,1}
+
235 ModifyGraph /w=$graphname axisEnab(left)={0,0.6}
+
236 ModifyGraph /w=$graphname zero(left)=8
+
237 ModifyGraph /w=$graphname margin(left)=40,margin(bottom)=30,margin(top)=20,margin(right)=40
+
238 ModifyGraph /w=$graphname gfSize=10
+
+
+
241 string labels = note(image)
+
+
243 lab = StringByKey(
"AxisLabelX" , labels,
"=" ,
"\r" )
+
+
+
+
247 Label /w=$graphname bottom lab + " (\\U)"
+
248 lab = StringByKey("AxisLabelY", labels, "=", "\r")
+
+
+
+
252 Label /w=$graphname left lab + " (\\U)"
+
253 lab = StringByKey("AxisLabelD", labels, "=", "\r")
+
+
+
+
257 Label /w=$graphname xprofiles lab + " (\\U)"
+
258 Label /w=$graphname yprofiles lab + " (\\U)"
+
+
+
+
262 Legend /w=$graphname/C/N=text0/J/F=2/D=0.5/T={28}/A=RT/X=0.00/Y=0.00
"\\s(xprofiles)\tprofile A"
+
263 AppendText /w=$graphname
"\\s(xprofiles#1)\tprofile B"
+
264 AppendText /w=$graphname
"\\s(xprofiles#2)\tROI average"
+
265 AppendText /w=$graphname
"min\t\\{" + s_viewdf +
"graph_min}"
+
266 AppendText /w=$graphname
"max\t\\{" + s_viewdf +
"graph_max}"
+
267 AppendText /w=$graphname
"sum\t\\{" + s_viewdf +
"graph_sum}"
+
268 AppendText /w=$graphname
"avg\t\\{" + s_viewdf +
"graph_avg}"
+
269 AppendText /w=$graphname
"sdev\t\\{" + s_viewdf +
"graph_sdev}"
+
+
271 TextBox /w=$graphname /C/N=text0 /F=0 /B=1 /X=1.00 /Y=1.00
+
272 lab = StringByKey(
"Dataset" , labels,
"=" ,
"\r" )
+
+
274 AppendText /w=$graphname lab
+
+
276 AppendText /w=$graphname "sum\t\\{
" + s_viewdf + " graph_sum}
"
+
277 AppendText /w=$graphname " avg\t\\{
" + s_viewdf + " graph_avg}
"
+
278 AppendText /w=$graphname " sdev\t\\{
" + s_viewdf + " graph_sdev}
"
+
+
+
281 // interactive elements
+
282 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 A $imgname 0,0
+
283 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 B $imgname DimSize(view, 0)-1, DimSize(view, 1)-1
+
+
285 pcurs = floor(DimSize(xprofiles, 0) / 3)
+
286 Cursor /w=$graphname /A=0 /P /S=1 /H=0 C xprofiles#2 pcurs
+
287 pcurs = floor(DimSize(xprofiles, 0) * 2 / 3)
+
288 Cursor /w=$graphname /A=0 /P /S=1 /H=0 D xprofiles#2 pcurs
+
289 pcurs = floor(DimSize(yprofiles, 0) / 3)
+
290 Cursor /w=$graphname /A=0 /P /S=1 /H=0 E yprofiles#2 pcurs
+
291 pcurs = floor(DimSize(yprofiles, 0) * 2 / 3)
+
292 Cursor /w=$graphname /A=0 /P /S=1 /H=0 F yprofiles#2 pcurs
+
293 ShowInfo /w=$graphname /CP=0
+
+
295 SetWindow $graphname, hook(ad_profiles_hook)=ad_profiles_hook
+
296 ControlBar /w=$graphname 21
+
297 Button b_reset_cursors win=$graphname, title=" reset cursors
",pos={0,0},size={70,20},proc=PearlAreaDisplay#bp_reset_cursors
+
298 Button b_reset_cursors win=$graphname, fColor=(65535,65535,65535),fSize=10
+
+
300 SetVariable sv_smoothing_x win=$graphname, title=" X smoothing
",pos={130,2},bodyWidth=40
+
301 SetVariable sv_smoothing_x win=$graphname, value=view_filter_smoothing_x,limits={1,100,1}
+
302 SetVariable sv_smoothing_x win=$graphname, proc=PearlAreaDisplay#svp_smoothing
+
303 SetVariable sv_smooting_y win=$graphname, title=" Y smoothing
",pos={240,2},bodyWidth=40
+
304 SetVariable sv_smooting_y win=$graphname, value=view_filter_smoothing_y,limits={1,100,1}
+
305 SetVariable sv_smooting_y win=$graphname, proc=PearlAreaDisplay#svp_smoothing
+
+
307 PopupMenu pm_export win=$graphname, mode=0,title=" Export
"
+
308 PopupMenu pm_export win=$graphname, value=" X profile;Y profile;X profile (collate);Y profile (collate)
"
+
309 PopupMenu pm_export win=$graphname, pos={308,0},bodyWidth=60,proc=PearlAreaDisplay#pmp_export
+
310 PopupMenu pm_export win=$graphname, help={" Export profile of selected area and display in graph. Collate mode = display all profiles in same graph.
"}
+
+
+
313 ad_update_profiles(image)
+
+
+
+
+
+
331 function /wave ad_add_overlay(image, [rgba])
+
+
+
+
335 if (ParamIsDefault(rgba))
+
336 rgba = " 65535,65532,16385,32767
"
+
337 elseif (ItemsInList(rgba, " ,
") == 3)
+
+
+
+
341 dfref savedf = GetDataFolderDFR()
+
342 wave view_image = get_view_image(image)
+
343 dfref viewdf = GetWavesDataFolderDFR(view_image)
+
344 svar /sdfr=viewdf graphname = prof_graphname
+
+
+
347 string overlayname = " view_overlay
"
+
348 duplicate /o image, $overlayname /wave=overlay
+
349 redimension /b/u overlay
+
+
+
352 string imagenames = ImageNameList(graphname, " ;
")
+
353 if (whichlistItem(overlayname, imagenames, " ;
") < 0)
+
354 AppendImage /w=$graphname $overlayname
+
355 rgba = replacestring(" (
", rgba, " ")
+
356 rgba = replacestring(" )
", rgba, " ")
+
357 variable rr = str2num(StringFromList(0, rgba, " ,
"))
+
358 variable gg = str2num(StringFromList(1, rgba, " ,
"))
+
359 variable bb = str2num(StringFromList(2, rgba, " ,
"))
+
360 variable aa = str2num(StringFromList(3, rgba, " ,
"))
+
361 #if IgorVersion() >= 8
+
362 ModifyImage /w=$graphname $overlayname explicit=1,eval={0,rr,gg,bb,aa},eval={255,-1,-1,-1}
+
+
364 ModifyImage /w=$graphname $overlayname explicit=1,eval={0,rr,gg,bb},eval={255,-1,-1,-1}
+
+
+
+
+
+
+
+
377 function ad_update_profiles(image)
+
+
+
380 // data folders and references
+
381 dfref viewdf = get_view_folder(image)
+
382 if (DataFolderRefStatus(viewdf) == 0)
+
383 return -1 // data folder not found
+
+
385 dfref savedf = GetDataFolderDFR()
+
+
+
+
389 string viewname = " view_image
"
+
390 duplicate /o image, $viewname /wave=view
+
391 string overlayname = " view_overlay
"
+
392 wave /z overlay = $overlayname
+
393 if (waveexists(overlay))
+
394 redimension /n=(dimsize(view,0), dimsize(view,1)) overlay
+
+
+
+
+
399 svar view_filter_options
+
400 nvar smoothing_x = view_filter_smoothing_x
+
401 nvar smoothing_y = view_filter_smoothing_y
+
402 funcref ad_default_image_filter filterfunc = $view_filter
+
403 view_filter_options = ReplaceNumberByKey(" SmoothingX
", view_filter_options, smoothing_x, " =
", " ;
")
+
404 view_filter_options = ReplaceNumberByKey(" SmoothingY
", view_filter_options, smoothing_y, " =
", " ;
")
+
405 filterfunc(view, view_filter_options)
+
+
407 ad_calc_cursor_profiles(view)
+
+
+
+
+
+
429 function ad_profiles_cursor_mode(image, mode)
+
+
+
+
433 dfref savedf = GetDataFolderDFR()
+
434 wave view_image = get_view_image(image)
+
435 dfref viewdf = GetWavesDataFolderDFR(view_image)
+
436 svar /sdfr=viewdf graphname = prof_graphname
+
437 nvar /sdfr=viewdf cursor_mode = view_cursor_mode
+
438 wave /sdfr=viewdf xprofiles, yprofiles
+
+
440 variable dx = DimSize(view_image, 0)
+
441 variable dy = DimSize(view_image, 1)
+
+
443 case 1: // background selection
+
444 Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 A view_image 0, 0
+
445 Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
+
446 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 C view_image round(0.2 * dx) -1, 0
+
447 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 D view_image round(0.8 * dx) -1, 0
+
448 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 E view_image round(0.4 * dx) -1, 0
+
449 Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 F view_image round(0.6 * dx) -1, 0
+
+
451 ShowInfo /w=$graphname /CP=0
+
+
+
+
455 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 A view_image 0,0
+
456 Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
+
+
458 pcurs = floor(DimSize(xprofiles, 0) / 3)
+
459 Cursor /w=$graphname /A=0 /P /S=1 /H=0 C xprofiles#2 pcurs
+
460 pcurs = floor(DimSize(xprofiles, 0) * 2 / 3)
+
461 Cursor /w=$graphname /A=0 /P /S=1 /H=0 D xprofiles#2 pcurs
+
462 pcurs = floor(DimSize(yprofiles, 0) / 3)
+
463 Cursor /w=$graphname /A=0 /P /S=1 /H=0 E yprofiles#2 pcurs
+
464 pcurs = floor(DimSize(yprofiles, 0) * 2 / 3)
+
465 Cursor /w=$graphname /A=0 /P /S=1 /H=0 F yprofiles#2 pcurs
+
466 ShowInfo /w=$graphname /CP=0
+
+
+
+
+
+
+
+
490 function ad_profiles_set_cursor(image, cursorname, xa, ya, [pscale])
+
+
+
+
+
+
496 if (ParamIsDefault(pscale))
+
+
+
+
500 // data folders and references
+
501 dfref savedf = GetDataFolderDFR()
+
502 wave view_image = get_view_image(image)
+
503 dfref viewdf = GetWavesDataFolderDFR(view_image)
+
504 svar /sdfr=viewdf graphname = prof_graphname
+
+
+
+
+
+
+
511 pa = round((xa - DimOffset(view_image, 0)) / DimDelta(view_image, 0))
+
512 qa = round((ya - DimOffset(view_image, 1)) / DimDelta(view_image, 1))
+
+
+
515 pa = min(pa, DimSize(view_image, 0) - 1)
+
+
517 qa = min(qa, DimSize(view_image, 1) - 1)
+
+
519 Cursor /i /p /w=$graphname $cursorname view_image pa, qa
+
+
+
+
+
+
535 // the lines can be removed manually using the draw toolbox, or by calling this function with @c clean=1.
+
542 function ad_profiles_crosshairs(image, [clear])
+
+
+
+
546 if (ParamIsDefault(clear))
+
+
+
+
550 // data folders and references
+
551 wave view_image = get_view_image(image)
+
552 dfref viewdf = GetWavesDataFolderDFR(view_image)
+
553 svar /sdfr=viewdf graphname = prof_graphname
+
+
555 string cursors = " A;B
"
+
556 string colors = " 39168,0,0;0,26112,0
"
+
+
+
+
+
561 string groupname = " crosshairs
"
+
+
+
+
+
566 SetDrawEnv /W=$graphname push
+
567 DrawAction /w=$graphname getgroup=$groupname, delete, begininsert
+
568 SetDrawEnv /w=$graphname gstart, gname=$groupname
+
+
570 SetDrawEnv /W=$graphname dash=4
+
571 SetDrawEnv /W=$graphname linethick=0.5
+
+
573 ncursors = ItemsInList(cursors, " ;
")
+
574 for (icursor=0; icursor < ncursors; icursor += 1)
+
575 cursorname = StringFromList(icursor, cursors, " ;
")
+
576 color = StringFromList(icursor, colors, " ;
")
+
577 rgb.red = str2num(StringFromList(0, color, " ,
"))
+
578 rgb.green = str2num(StringFromList(1, color, " ,
"))
+
579 rgb.blue = str2num(StringFromList(2, color, " ,
"))
+
580 if (strlen(CsrInfo($cursorname, graphname)) > 0)
+
581 xx = hcsr($cursorname, graphname)
+
582 yy = vcsr($cursorname, graphname)
+
583 SetDrawEnv /W=$graphname linefgc=(rgb.red, rgb.green, rgb.blue)
+
584 SetDrawEnv /W=$graphname save
+
585 SetDrawEnv /W=$graphname xcoord=bottom, ycoord=prel
+
586 DrawLine /W=$graphname xx, 0, xx, 1
+
587 SetDrawEnv /W=$graphname xcoord=prel, ycoord=left
+
588 DrawLine /W=$graphname 0, yy, 1, yy
+
+
+
+
592 SetDrawEnv /w=$graphname gstop
+
593 DrawAction /w=$graphname endinsert
+
594 SetDrawEnv /W=$graphname pop
+
595 SetDrawEnv /W=$graphname save
+
+
597 DrawAction /w=$graphname getgroup=$groupname, delete
+
+
+
+
+
+
608 static function /wave get_source_image(view)
+
609 wave view // image wave displayed in a profiles window
+
+
611 dfref viewdf = GetWavesDataFolderDFR(view)
+
612 svar /z /sdfr=viewdf sourcepath
+
613 if (svar_exists(sourcepath))
+
614 wave /z img = $sourcepath
+
+
+
+
+
+
+
622 static function /df make_view_folder(source)
+
623 wave source // wave which contains the raw data from the detector.
+
+
625 // data folders and references
+
626 dfref savedf = GetDataFolderDFR()
+
627 dfref imagedf = GetWavesDataFolderDFR(source)
+
628 string s_imagedf = GetDataFolder(1, imagedf)
+
629 setdatafolder imagedf
+
630 string s_viewdf = PearlCleanupName(" view_
" + NameOfWave(source))
+
631 newdatafolder /o/s $s_viewdf
+
632 dfref viewdf = GetDataFolderDFR()
+
+
+
+
+
+
646 static function /df get_view_folder(source)
+
+
+
649 // data folders and references
+
650 dfref savedf = GetDataFolderDFR()
+
651 dfref imagedf = GetWavesDataFolderDFR(source)
+
+
653 setdatafolder imagedf
+
654 string s_viewdf = PearlCleanupName(" view_
" + NameOfWave(source))
+
655 if (DataFolderExists(s_viewdf))
+
656 setdatafolder $s_viewdf
+
657 viewdf = GetDataFolderDFR()
+
+
+
+
+
+
+
669 static function /wave get_view_image(source)
+
+
+
672 dfref viewdf = get_view_folder(source)
+
673 string viewname = " view_image
"
+
674 wave /sdfr=viewdf view = $viewname
+
+
+
+
+
679 static function bp_reset_cursors(ba) : ButtonControl
+
680 STRUCT WMButtonAction &ba
+
+
682 switch( ba.eventCode )
+
+
684 string imgname = StringFromList(0, ImageNameList(ba.win, " ;
"))
+
685 wave /z image = ImageNameToWaveRef(ba.win, imgname)
+
686 if (waveexists(image))
+
687 Cursor /i/p A $imgname 0,0
+
688 Cursor /i/p B $imgname DimSize(image, 0)-1, DimSize(image, 1)-1
+
+
+
691 case -1: // control being killed
+
+
+
+
+
+
+
698 static function svp_smoothing(sva) : SetVariableControl
+
699 STRUCT WMSetVariableAction &sva
+
+
+
+
703 switch( sva.eventCode )
+
+
+
706 case 3: // Live update
+
707 imglist = ImageNameList(sva.win, " ;
")
+
708 wave /z img = ImageNameToWaveRef(sva.win, StringFromList(0, imglist))
+
+
710 wave source = get_source_image(img)
+
711 if (WaveExists(source))
+
712 ad_update_profiles(source)
+
+
+
+
716 case -1: // control being killed
+
+
+
+
+
+
+
723 static function pmp_export(pa) : PopupMenuControl
+
724 STRUCT WMPopupAction &pa
+
+
726 switch( pa.eventCode )
+
+
728 variable popNum = pa.popNum
+
+
730 string imgname = StringFromList(0, ImageNameList(pa.win, " ;
"))
+
731 wave /z image = ImageNameToWaveRef(pa.win, imgname)
+
732 if (waveexists(image) && (popNum >= 1) && (popNum <= 2))
+
733 ad_export_profile(image, popNum - 1, show=1)
+
734 elseif (waveexists(image) && (popNum >= 3) && (popNum <= 4))
+
735 ad_export_profile(image, popNum - 3, show=2)
+
+
+
+
739 case -1: // control being killed
+
+
+
+
+
+
+
747 function ad_profiles_hook(s)
+
748 struct WMWinHookStruct &s
+
749 variable hookresult = 0
+
+
+
+
+
+
755 case 2: // delete data folder after window is killed
+
756 imglist = ImageNameList(s.winName, " ;
")
+
757 wave /z img = ImageNameToWaveRef(s.winName, StringFromList(0, imglist))
+
+
759 viewdf = GetWavesDataFolderDFR(img)
+
760 cmd = " killdatafolder /z
" + GetDataFolder(1, viewdf)
+
+
+
+
764 case 7: // update profiles when cursor is moved
+
765 imglist = ImageNameList(s.winName, " ;
")
+
766 wave /z img = ImageNameToWaveRef(s.winName, StringFromList(0, imglist))
+
+
768 ad_calc_cursor_profiles(img)
+
+
+
+
+
+
+
+
+
+
+
787 function ad_calc_cursor_profiles(image)
+
+
+
790 dfref savedf = GetDataFolderDFR()
+
791 dfref imagedf = GetWavesDataFolderDFR(image)
+
792 setdatafolder imagedf
+
+
794 svar graphname = prof_graphname
+
+
796 variable pa, qa // point coordinates cursor A
+
797 if (strlen(CsrInfo(A, graphname)) > 0)
+
798 pa = pcsr(A, graphname)
+
799 qa = qcsr(A, graphname)
+
+
+
+
+
+
805 variable pb, qb // point coordinates cursor B
+
806 if (strlen(CsrInfo(B, graphname)) > 0)
+
807 pb = pcsr(B, graphname)
+
808 qb = qcsr(B, graphname)
+
+
810 pb = DimSize(image, 0) - 1
+
811 qb = DimSize(image, 1) - 1
+
+
+
814 ad_calc_profiles(image, pa, qa, pb, qb)
+
+
+
+
834 function ad_calc_profiles(image, pa, qa, pb, qb)
+
+
+
+
+
839 dfref savedf = GetDataFolderDFR()
+
840 dfref imagedf = GetWavesDataFolderDFR(image)
+
841 setdatafolder imagedf
+
+
+
+
+
+
+
+
+
+
851 // horizontal profiles at crosshairs
+
852 redimension /n=(dimsize(image,0), 3) xprofiles
+
853 setscale /p x dimoffset(image,0), dimdelta(image,0), WaveUnits(image,0), xprofiles
+
854 setscale d 0, 0, waveunits(image,-1), xprofiles
+
855 xprofiles[][0] = image[p][qa]
+
856 xprofiles[][1] = image[p][qb]
+
+
+
859 note xprofiles, " SourceWave=
" + nameofwave(image)
+
860 note xprofiles, " SourceDimension=0
"
+
861 note xprofiles, " SourceIndex0=
" + num2str(qa)
+
862 note xprofiles, " SourceIndex1=
" + num2str(qb)
+
+
864 // average horizontal profile between crosshairs
+
+
+
+
+
869 for (qq = q0; qq <= q1; qq += 1)
+
870 xprofiles[][2] += image[p][qq]
+
+
872 xprofiles[][2] /= q1 - q0 + 1
+
+
874 // vertical profiles at crosshairs
+
875 redimension /n=(dimsize(image,1), 3) yprofiles
+
876 setscale /p x dimoffset(image,1), dimdelta(image,1), WaveUnits(image,1), yprofiles
+
877 setscale d 0, 0, waveunits(image,-1), yprofiles
+
878 yprofiles[][0] = image[pa][p]
+
879 yprofiles[][1] = image[pb][p]
+
+
+
882 note yprofiles, " SourceWave=
" + nameofwave(image)
+
883 note yprofiles, " SourceDimension=1
"
+
884 note yprofiles, " SourceIndex0=
" + num2str(pa)
+
885 note yprofiles, " SourceIndex1=
" + num2str(pb)
+
+
887 // average vertical profile between crosshairs
+
+
+
+
+
892 for (pp = p0; pp <= p1; pp += 1)
+
893 yprofiles[][2] += image[pp][p]
+
+
895 yprofiles[][2] /= p1 - p0 + 1
+
+
897 // statistics between crosshairs
+
898 Duplicate /r=[p0,p1][q0,q1]/o image, roi_image
+
899 WaveStats /Q roi_image
+
+
+
+
903 graph_sum = v_avg * v_npnts
+
+
+
+
+
908 if (waveexists(hist))
+
909 Histogram /B=3 roi_image, hist
+
+
+
+
+
+
936 function ad_export_profile(view_image, dim, [trace, show, overwrite])
+
+
+
+
+
+
+
943 dfref savedf = GetDataFolderDFR()
+
+
945 if (ParamIsDefault(trace))
+
+
+
948 if (ParamIsDefault(show))
+
+
+
951 if (ParamIsDefault(overwrite))
+
+
+
+
+
956 dfref imagedf = GetWavesDataFolderDFR(view_image)
+
+
+
+
960 wave /sdfr=imagedf profiles=xprofiles
+
+
+
+
964 wave /sdfr=imagedf profiles=yprofiles
+
+
+
+
968 return -1 // invalid argument
+
+
970 string graphname_string = " export_graph_
" + dim_label
+
971 svar /z /sdfr=imagedf linked_graphname = $graphname_string
+
+
+
974 wave /z source_image = get_source_image(view_image)
+
975 if (WaveExists(source_image))
+
976 dfref sourcedf = GetWavesDataFolderDFR(source_image)
+
977 setdatafolder sourcedf
+
+
979 return -2 // invalid source data folder
+
+
+
982 // format dest wave name
+
983 string profile_note = note(profiles)
+
+
+
+
+
988 variable index_width = ceil(log(DimSize(view_image, 1 - dim)))
+
989 variable index0 = NumberByKey(" SourceIndex0
", profile_note, " =
", " \r
")
+
990 variable index1 = NumberByKey(" SourceIndex1
", profile_note, " =
", " \r
")
+
991 name_dim = " _
" + dim_label
+
992 sprintf name_index, " %0*u_%0*u
", index_width, index0, index_width, index1
+
993 name_base = NameOfWave(source_image)
+
994 name_base = name_base[0, min(strlen(name_base), 31 - strlen(name_index) - strlen(name_dim) - 1)]
+
995 profile_name = name_base + name_dim + name_index
+
996 if ((overwrite == 0) && (CheckName(profile_name, 1)))
+
997 profile_name = UniqueName(profile_name + " _
", 1, 0)
+
+
+
+
1001 duplicate /o /r=[][trace] profiles, $profile_name /wave=dest_profile
+
1002 redimension /n=(dimsize(profiles, 0)) dest_profile
+
1003 profile_note = ReplaceStringByKey(" SourceWave
", profile_note, NameOfWave(source_image), " =
", " \r
")
+
1004 note /k dest_profile
+
1005 note dest_profile, profile_note
+
1006 print " created
", GetWavesDataFolder(dest_profile, 2)
+
+
+
+
+
+
1012 // common graph for all profiles of a dimension
+
1013 graphname = " export_profiles_
" + dim_label
+
1014 graphtitle = UpperStr(dim_label) + " Profiles
"
+
+
1016 // one graph per source image
+
1017 if (svar_exists(linked_graphname) && (ItemsInList(WinList(linked_graphname, " ;
", " WIN:1
"), " ;
") >= 1))
+
1018 graphname = linked_graphname
+
+
1020 graphname = GetWavesDataFolder(source_image, 0) + name_dim
+
+
1022 graphtitle = UpperStr(dim_label) + " Profiles:
" + GetWavesDataFolder(source_image, 2)
+
+
+
1025 if ((ItemsInList(WinList(graphname, " ;
", " WIN:1
"), " ;
") >= 1))
+
1026 appendtograph /w=$graphname dest_profile
+
+
1028 setdatafolder imagedf
+
1029 display /k=1 /n=$graphname dest_profile as graphtitle
+
+
1031 ModifyGraph /w=$graphname mirror=1,nticks=3,minor=1
+
1032 ModifyGraph /w=$graphname axThick=0.5,btLen=4
+
1033 ModifyGraph /w=$graphname gfSize=10
+
1034 ModifyGraph /w=$graphname grid=2,gridHair=0,gridRGB=(52224,52224,52224)
+
1035 Legend /w=$graphname /C/N=legend0/F=0/B=1/A=LT/X=0.00/Y=0.00
+
+
+
1038 string /g $graphname_string = graphname
+
+
+
+
+
1043 setdatafolder savedf
+
+
+
+
1047 static function set_trace_colors(graphname)
+
+
+
1050 ModifyGraph /w=$graphname /z rgb[0]=(0, 0, 0)
+
1051 ModifyGraph /w=$graphname /z rgb[1]=(65535, 16385, 16385)
+
1052 ModifyGraph /w=$graphname /z rgb[2]=(2, 39321, 1)
+
1053 ModifyGraph /w=$graphname /z rgb[3]=(0, 0, 65535)
+
1054 ModifyGraph /w=$graphname /z rgb[4]=(39321, 1, 31457)
+
1055 ModifyGraph /w=$graphname /z rgb[5]=(48059, 48059, 48059)
+
1056 ModifyGraph /w=$graphname /z rgb[6]=(65535, 32768, 32768)
+
1057 ModifyGraph /w=$graphname /z rgb[7]=(0, 65535, 0)
+
1058 ModifyGraph /w=$graphname /z rgb[8]=(16385,65535,65535)
+
1059 ModifyGraph /w=$graphname /z rgb[9]=(65535, 32768, 58981)
+
+
+
1068 function ad_calc_histogram(image)
+
+
+
1071 dfref savedf = GetDataFolderDFR()
+
1072 dfref imagedf = GetWavesDataFolderDFR(image)
+
1073 setdatafolder imagedf
+
+
+
1076 Histogram /B=3 image, hist
+
+
1078 setdatafolder savedf
+
+
+
1091 function ad_default_image_filter(image, options)
+
+
+
+
+
1105 function ad_box_filter(image, options)
+
+
+
+
1109 variable xsmoothing = NumberByKey(" SmoothingX
", options, " =
", " ;
")
+
1110 variable ysmoothing = NumberByKey(" SmoothingY
", options, " =
", " ;
")
+
+
1112 if ((NumType(xsmoothing) == 0) && (xsmoothing >= 2))
+
1113 Smooth /B /DIM=0 /E=3 xsmoothing, image
+
+
1115 if ((NumType(ysmoothing) == 0) && (ysmoothing >= 2))
+
1116 Smooth /B /DIM=1 /E=3 ysmoothing, image
+
+
+
+
1127 function ad_transpose_filter(image, options)
+
+
+
+
1131 MatrixTranspose image
+
+
+
+
1135 // ################### 3D DATA ##################
+
+
1143 function /s ad_display_brick(data)
+
+
+
1146 if(exists(" NewGizmo
") != 4)
+
1147 abort " Gizmo XOP must be installed.
"
+
+
1149 if (WaveDims(data) != 3)
+
1150 abort " ad_display_brick: data must be three-dimensional.
"
+
+
+
1153 dfref savedf = GetDataFolderDFR()
+
1154 dfref datadf = GetWavesDataFolderDFR(data)
+
1155 string s_datadf = GetDataFolder(1, datadf)
+
1156 dfref viewdf = make_view_folder(data)
+
+
1158 setdatafolder viewdf
+
1159 string dfname = ReplaceString(" root:
", s_datadf, " ")
+
1160 string graphtitle = dfname + " Gizmo
"
+
1161 string /g gizmo_graphname = graphname_from_dfref(datadf, " giz_
")
+
1162 svar graphname = gizmo_graphname
+
+
1164 if ((strlen(graphname) > 0) && (wintype(graphname) == 13))
+
1165 setdatafolder savedf
+
1166 return graphname // gizmo window exists
+
+
+
1169 variable nx = dimsize(data, 0)
+
1170 variable ny = dimsize(data, 1)
+
1171 variable nz = dimsize(data, 2)
+
+
+
+
+
+
1177 // igor does not allow calling gizmo functions directly
+
1178 setdatafolder datadf
+
1179 sprintf cmd, " NewGizmo /k=1 /n=%s /w=(100,100,500,400) /t=\
"%s\"" , graphname, graphtitle
+
+
1181 cmd =
"AppendToGizmo /D Axes=BoxAxes, name=axes0"
+
+
+
1184 obj =
"surface_xmid"
+
1185 pp = round(nx / 2 - 1)
+
1186 sprintf cmd,
"AppendToGizmo /D surface=%s, name=%s" , nameofwave(data), obj
+
+
1188 sprintf cmd,
"ModifyGizmo modifyObject=%s, property={srcMode, 128}" , obj
+
+
1190 sprintf cmd,
"ModifyGizmo ModifyObject=%s, property={plane, %d}" , obj, pp
+
+
1192 sprintf cmd,
"ModifyGizmo modifyObject=%s, property={surfaceCtab, BlueGreenOrange}" , obj
+
+
1194 sprintf cmd,
"ModifyGizmo ModifyObject=%s, property={SurfaceCTABScaling,128}" , obj
+
+
1196 sprintf cmd,
"ModifyGizmo modifyObject=%s, property={surfaceCTABAlpha, 1.0}" , obj
+
+
+
1199 obj =
"surface_ymid"
+
1200 pp = round(ny / 2 - 1)
+
1201 sprintf cmd, "AppendToGizmo /D surface=%s, name=%s", nameofwave(data), obj
+
+
1203 sprintf cmd, "ModifyGizmo modifyObject=%s, property={srcMode, 64}
", obj
+
+
1205 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={plane, %d}
", obj, pp
+
+
1207 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCtab, BlueGreenOrange}
", obj
+
+
1209 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={SurfaceCTABScaling,128}
", obj
+
+
1211 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCTABAlpha, 1.0}
", obj
+
+
+
1214 obj = " surface_zmid
"
+
1215 pp = round(nz / 2 - 1)
+
1216 sprintf cmd, " AppendToGizmo /D surface=%s, name=%s
", nameofwave(data), obj
+
+
1218 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={srcMode, 32}
", obj
+
+
1220 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={plane, %d}
", obj, pp
+
+
1222 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCtab, BlueGreenOrange}
", obj
+
+
1224 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={SurfaceCTABScaling,128}
", obj
+
+
1226 sprintf cmd, " ModifyGizmo modifyObject=%s,
property ={surfaceCTABAlpha, 1.0}
", obj
+
+
+
+
1230 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={-1,axisScalingMode,1}
", obj
+
+
1232 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={-1,axisColor,0,0,0,1}
", obj
+
+
1234 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={0,ticks,3}
", obj
+
+
1236 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={1,ticks,3}
", obj
+
+
1238 sprintf cmd, " ModifyGizmo ModifyObject=%s,
property ={2,ticks,3}
", obj
+
+
1240 sprintf cmd, " ModifyGizmo modifyObject=%s
property ={Clipped,0}
", obj
+
+
1242 sprintf cmd, " ModifyGizmo modifyObject=%s
property ={-1,fontScaleFactor,2}
", obj
+
+
+
1245 sprintf cmd, " ModifyGizmo showAxisCue=1
"
+
+
+
1248 setdatafolder savedf
+
+
+
+
1258 function ad_brick_slicer(data)
+
+
+
1261 // data folders and references
+
1262 dfref savedf = GetDataFolderDFR()
+
1263 dfref datadf = GetWavesDataFolderDFR(data)
+
1264 string s_datadf = GetDataFolder(1, datadf)
+
1265 dfref viewdf = make_view_folder(data)
+
+
1267 setdatafolder viewdf
+
1268 svar /z ex_panel = slicer_panelname
+
1269 if (svar_exists(ex_panel))
+
1270 string panels = WinList(" SlicerPanel*
", " ;
", " WIN:64
")
+
1271 if (WhichListItem(ex_panel, panels, " ;
") >= 0)
+
1272 dowindow /f $(StringFromList(0, panels, " ;
"))
+
+
+
+
+
1277 variable /g x_slice_pos
+
1278 variable /g y_slice_pos
+
1279 variable /g z_slice_pos
+
1280 variable /g slab_thickness
+
1281 string /g brick_path = getwavesdatafolder(data, 2)
+
1282 variable /g x_autoinc = 0
+
1283 variable /g y_autoinc = 0
+
1284 variable /g z_autoinc = 0
+
+
+
1287 string labels = note(data)
+
1288 string xlabel = StringByKey(" AxisLabelX
", labels, " =
", " \r
")
+
1289 if (!strlen(xlabel))
+
+
+
1292 string ylabel = StringByKey(" AxisLabelY
", labels, " =
", " \r
")
+
1293 if (!strlen(ylabel))
+
+
+
1296 string zlabel = StringByKey(" AxisLabelZ
", labels, " =
", " \r
")
+
1297 if (!strlen(zlabel))
+
+
+
1300 string dlabel = StringByKey(" Dataset
", labels, " =
", " \r
")
+
1301 if (!strlen(dlabel))
+
1302 dlabel = NameOfWave(data)
+
+
+
1305 // this section copied from slicer panel
+
1306 NewPanel /k=1 /W=(500,600,890,940) /N=SlicerPanel as " Brick Slicer
"
+
1307 string /g slicer_panelname = S_name
+
1308 string panel = s_name
+
+
1310 GroupBox g_xslice win=$panel,pos={8,8},size={376,96},title=xlabel
+
1311 Slider sl_xslice_position win=$panel,pos={16,32},size={240,56},proc=PearlAreaDisplay#slp_slice_position
+
1312 Slider sl_xslice_position win=$panel,limits={0,100,1},variable=x_slice_pos,vert= 0
+
1313 SetVariable sv_xslice_position win=$panel,pos={20,80},size={92,16},proc=PearlAreaDisplay#svp_slice_position,title=" X
"
+
1314 SetVariable sv_xslice_position win=$panel,limits={0,100,1},value=x_slice_pos
+
1315 Button b_xslice_center win=$panel,pos={122,80},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W618
"
+
1316 Button b_xslice_center win=$panel,help={" reset to center position
"}
+
1317 Button b_xslice_extract win=$panel,pos={288,80},size={68,20},proc=PearlAreaDisplay#bp_extract_slice,title=" extract slice
"
+
1318 Button b_xslice_extract win=$panel,help={" extract
this slice to a separate wave
"}
+
1319 //CheckBox cb_xslab_active win=$panel,pos={288,80},size={80,16},title=" Display X Slab
"
+
1320 //CheckBox cb_xslab_active win=$panel,value= 0
+
1321 TitleBox tb_xslice_animation win=$panel,pos={288,32},size={356,16},title=" animation
",frame=0
+
1322 TitleBox tb_xslice_animation win=$panel,anchor= MC
+
1323 Button b_xslice_back win=$panel,pos={288,48},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W646
"
+
1324 Button b_xslice_back win=$panel,help={" animate backwards
"}
+
1325 Button b_xslice_forward win=$panel,pos={312,48},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W649
"
+
1326 Button b_xslice_forward win=$panel,help={" animate forward
"}
+
1327 Button b_xslice_stop win=$panel,pos={336,48},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W616
"
+
1328 Button b_xslice_stop win=$panel,help={" stop animation
"}
+
+
1330 GroupBox g_yslice win=$panel,pos={8,108},size={376,96},title=ylabel
+
1331 Slider sl_yslice_position win=$panel,pos={16,132},size={240,56},proc=PearlAreaDisplay#slp_slice_position
+
1332 Slider sl_yslice_position win=$panel,limits={0,100,1},variable=y_slice_pos,vert= 0
+
1333 SetVariable sv_yslice_position win=$panel,pos={20,180},size={92,16},proc=PearlAreaDisplay#svp_slice_position,title=" Y
"
+
1334 SetVariable sv_yslice_position win=$panel,limits={0,100,1},value=y_slice_pos
+
1335 Button b_yslice_center win=$panel,pos={122,180},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W618
"
+
1336 Button b_yslice_center win=$panel,help={" reset to center position
"}
+
1337 Button b_yslice_extract win=$panel,pos={288,180},size={68,20},proc=PearlAreaDisplay#bp_extract_slice,title=" extract slice
"
+
1338 Button b_yslice_extract win=$panel,help={" extract
this slice to a separate wave
"}
+
1339 //CheckBox cb_yslab_active win=$panel,pos={288,180},size={80,16},title=" Display Y Slab
"
+
1340 //CheckBox cb_yslab_active win=$panel,value= 0
+
1341 TitleBox tb_yslice_animation win=$panel,pos={288,132},size={356,16},title=" animation
",frame=0
+
1342 TitleBox tb_yslice_animation win=$panel,anchor= MC
+
1343 Button b_yslice_back win=$panel,pos={288,148},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W646
"
+
1344 Button b_yslice_back win=$panel,help={" animate backwards
"}
+
1345 Button b_yslice_forward win=$panel,pos={312,148},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W649
"
+
1346 Button b_yslice_forward win=$panel,help={" animate forward
"}
+
1347 Button b_yslice_stop win=$panel,pos={336,148},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W616
"
+
1348 Button b_yslice_stop win=$panel,help={" stop animation
"}
+
+
1350 GroupBox g_zslice win=$panel,pos={8,208},size={376,96},title=zlabel
+
1351 Slider sl_zslice_position win=$panel,pos={16,232},size={240,56},proc=PearlAreaDisplay#slp_slice_position
+
1352 Slider sl_zslice_position win=$panel,limits={0,100,1},variable=z_slice_pos,vert= 0
+
1353 SetVariable sv_zslice_position win=$panel,pos={20,280},size={92,16},proc=PearlAreaDisplay#svp_slice_position,title=" Z
"
+
1354 SetVariable sv_zslice_position win=$panel,limits={0,100,1},value=z_slice_pos
+
1355 Button b_zslice_center win=$panel,pos={122,280},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W618
"
+
1356 Button b_zslice_center win=$panel,help={" reset to center position
"}
+
1357 Button b_zslice_extract win=$panel,pos={288,280},size={68,20},proc=PearlAreaDisplay#bp_extract_slice,title=" extract slice
"
+
1358 Button b_zslice_extract win=$panel,help={" extract
this slice to a separate wave
"}
+
1359 //CheckBox cb_zslab_active win=$panel,pos={288,280},size={80,16},title=" Display Z Slab
"
+
1360 //CheckBox cb_zslab_active win=$panel,value= 0
+
1361 TitleBox tb_zslice_animation win=$panel,pos={288,232},size={356,16},title=" animation
",frame=0
+
1362 TitleBox tb_zslice_animation win=$panel,anchor= MC
+
1363 Button b_zslice_back win=$panel,pos={288,248},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W646
"
+
1364 Button b_zslice_back win=$panel,help={" animate backwards
"}
+
1365 Button b_zslice_forward win=$panel,pos={312,248},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W649
"
+
1366 Button b_zslice_forward win=$panel,help={" animate forward
"}
+
1367 Button b_zslice_stop win=$panel,pos={336,248},size={20,20},proc=PearlAreaDisplay#bp_move_slice,title=" \\W616
"
+
1368 Button b_zslice_stop win=$panel,help={" stop animation
"}
+
+
1370 TitleBox t_slicerpath win=$panel,pos={8,316},size={128,20},disable=2,title=dlabel
+
1371 //SetVariable setvar0 win=$panel,pos={240,316},size={120,16},title=" slab thickness
"
+
1372 //SetVariable setvar0 win=$panel,limits={1,inf,1},value=slab_thickness
+
+
1374 // update control limits and move slicing planes to the center
+
1375 setwindow $panel, userdata(control_datafolder) = GetDataFolder(1, viewdf)
+
1376 setwindow $panel, userdata(brick_path) = brick_path
+
+
1378 x_slice_pos = dimoffset(data, 0) + dimsize(data, 0) * dimdelta(data, 0) / 2
+
1379 y_slice_pos = dimoffset(data, 1) + dimsize(data, 1) * dimdelta(data, 1) / 2
+
1380 z_slice_pos = dimoffset(data, 2) + dimsize(data, 2) * dimdelta(data, 2) / 2
+
+
1382 svar /z /sdfr=viewdf gizmo_graphname
+
1383 if (svar_exists(gizmo_graphname) && (strlen(gizmo_graphname) > 0) && (wintype(gizmo_graphname) == 13))
+
1384 ad_gizmo_set_plane(data, 0, x_slice_pos)
+
1385 ad_gizmo_set_plane(data, 1, y_slice_pos)
+
1386 ad_gizmo_set_plane(data, 2, z_slice_pos)
+
+
1388 svar /z /sdfr=viewdf slice_graphname
+
1389 if (svar_exists(slice_graphname) && (strlen(slice_graphname) > 0) && (wintype(slice_graphname) == 1))
+
1390 ad_profiles_set_slice(data, 2, z_slice_pos)
+
+
+
+
1394 setdatafolder savedf
+
+
+
1406 function /s ad_display_slice(data)
+
+
+
1409 if (WaveDims(data) != 3)
+
+
+
+
1413 dfref savedf = GetDataFolderDFR()
+
1414 dfref datadf = GetWavesDataFolderDFR(data)
+
1415 string s_datadf = GetDataFolder(1, datadf)
+
1416 dfref viewdf = make_view_folder(data)
+
+
1418 setdatafolder viewdf
+
1419 string dfname = ReplaceString(" root:
", s_datadf, " ")
+
1420 dfname = dfname[0, strlen(dfname) - 2]
+
1421 string graphtitle = dfname + " Slice
"
+
+
1423 if (exists(" slice_graphname
") != 2)
+
1424 string /g slice_graphname = " "
+
+
1426 string /g slice_wavename = PearlCleanupName(" slice_
" + NameOfWave(data))
+
1427 svar graphname = slice_graphname
+
1428 svar slicename = slice_wavename
+
+
1430 make /n=(1,1)/o $slicename
+
1431 wave slice = $slicename
+
1432 if ((strlen(graphname) == 0) || (wintype(graphname) != 1))
+
1433 graphname = ad_display_profiles(slice)
+
+
1435 variable z_slice_pos = dimoffset(data, 2) + dimsize(data, 2) * dimdelta(data, 2) / 2
+
1436 ad_profiles_set_slice(data, 2, z_slice_pos)
+
1437 ad_profiles_set_cursor(slice, " A
", -inf, -inf, pscale=1)
+
1438 ad_profiles_set_cursor(slice, " B
", +inf, +inf, pscale=1)
+
+
1440 setdatafolder savedf
+
+
+
+
1447 static function update_slice_info()
+
1448 dfref savedf = GetDataFolderDFR()
+
+
+
1451 //svar slicer_panelname
+
1452 wave brick = $brick_path
+
+
1454 //dowindow /F $slicer_panelname
+
1455 variable lo, hi, inc
+
1456 lo = dimoffset(brick, 0)
+
1457 inc = dimdelta(brick, 0)
+
1458 hi = lo + inc * (dimsize(brick, 0) - 1)
+
1459 Slider sl_xslice_position,limits={lo,hi,inc}
+
1460 SetVariable sv_xslice_position,limits={lo,hi,inc}
+
1461 lo = dimoffset(brick, 1)
+
1462 inc = dimdelta(brick, 1)
+
1463 hi = lo + inc * (dimsize(brick, 1) - 1)
+
1464 Slider sl_yslice_position,limits={lo,hi,inc}
+
1465 SetVariable sv_yslice_position,limits={lo,hi,inc}
+
1466 lo = dimoffset(brick, 2)
+
1467 inc = dimdelta(brick, 2)
+
1468 hi = lo + inc * (dimsize(brick, 2) - 1)
+
1469 Slider sl_zslice_position,limits={lo,hi,inc}
+
1470 SetVariable sv_zslice_position,limits={lo,hi,inc}
+
+
1472 setdatafolder savedf
+
+
+
1483 function ad_gizmo_set_plane(brick, dim, value)
+
+
+
+
+
1488 dfref savedf = GetDataFolderDFR()
+
1489 dfref datadf = GetWavesDataFolderDFR(brick)
+
1490 dfref viewdf = get_view_folder(brick)
+
1491 svar /z /sdfr=viewdf graphname=gizmo_graphname
+
+
1493 variable pp = round((value - dimoffset(brick, dim)) / dimdelta(brick, dim))
+
1494 if ((pp < 0) || (pp >= dimsize(brick, dim)))
+
1495 return -1 // requested value out of range
+
+
+
1498 if (svar_exists(graphname) && (strlen(graphname) > 0) && (wintype(graphname) == 13))
+
+
1500 string obj = " surface_
" + axes[dim] + " mid
"
+
+
1502 sprintf cmd, " ModifyGizmo /N=%s ModifyObject=%s,
property ={plane, %d}
", graphname, obj, pp
+
+
+
1505 return -2 // gizmo window not found
+
+
+
+
+
+
1519 function ad_profiles_set_slice(brick, dim, value)
+
+
+
+
+
1524 dfref savedf = GetDataFolderDFR()
+
1525 dfref datadf = GetWavesDataFolderDFR(brick)
+
1526 dfref viewdf = get_view_folder(brick)
+
1527 svar /z /sdfr=viewdf graphname = slice_graphname
+
1528 svar /z /sdfr=viewdf slicename = slice_wavename
+
+
1530 variable pp = round((value - dimoffset(brick, dim)) / dimdelta(brick, dim))
+
1531 if ((pp < 0) || (pp >= dimsize(brick, dim)))
+
1532 return -1 // requested value out of range
+
+
+
1535 if (svar_exists(graphname) && (strlen(graphname) > 0) && (wintype(graphname) == 1))
+
1536 setdatafolder viewdf
+
+
+
1539 wave wdest = ad_extract_slab_x(brick, pp, pp, slicename)
+
1540 ad_update_profiles(wdest)
+
+
+
1543 wave wdest = ad_extract_slab_y(brick, pp, pp, slicename)
+
1544 ad_update_profiles(wdest)
+
+
+
1547 wave wdest = ad_extract_slab_z(brick, pp, pp, slicename)
+
1548 ad_update_profiles(wdest)
+
+
+
+
1552 return -2 // graph window not found
+
+
+
1555 setdatafolder savedf
+
+
+
+
1560 static function slp_slice_position(sa) : SliderControl
+
1561 STRUCT WMSliderAction &sa
+
+
1563 dfref savedf = GetDataFolderDFR()
+
+
1565 switch( sa.eventCode )
+
1566 case -1: // control being killed
+
+
+
1569 if( sa.eventCode & 1 ) // value set
+
1570 string control_datafolder = GetUserData(sa.win, " ", " control_datafolder
")
+
1571 setdatafolder control_datafolder
+
1572 string brick_path = GetUserData(sa.win, " ", " brick_path
")
+
1573 string axis = StringFromList(1, sa.ctrlName, " _
")
+
1574 variable dim = char2num(axis[0]) - char2num(" x
")
+
+
1576 wave /z brick = $brick_path
+
1577 if (WaveExists(brick))
+
1578 ad_gizmo_set_plane(brick, dim, sa.curval)
+
1579 ad_profiles_set_slice(brick, dim, sa.curval)
+
+
1581 Abort " can
't find original wave " + brick_path
+
+
+
+
+
+
1587 setdatafolder savedf
+
+
+
+
1592 static function svp_slice_position(sva) : SetVariableControl
+
1593 STRUCT WMSetVariableAction &sva
+
+
1595 dfref savedf = GetDataFolderDFR()
+
+
1597 switch( sva.eventCode )
+
+
1599 case 2: // Enter key
+
1600 case 3: // Live update
+
1601 string control_datafolder = GetUserData(sva.win, "", "control_datafolder")
+
1602 setdatafolder control_datafolder
+
1603 string brick_path = GetUserData(sva.win, "", "brick_path")
+
1604 string axis = StringFromList(1, sva.ctrlName, "_")
+
1605 variable dim = char2num(axis[0]) - char2num("x")
+
+
1607 wave /z brick = $brick_path
+
1608 if (WaveExists(brick))
+
1609 ad_gizmo_set_plane(brick, dim, sva.dval)
+
1610 ad_profiles_set_slice(brick, dim, sva.dval)
+
+
1612 Abort "can' t find original wave
" + brick_path
+
+
+
1615 case -1: // control being killed
+
+
+
+
1619 setdatafolder savedf
+
+
+
+
1624 static function bp_move_slice(ba) : ButtonControl
+
1625 STRUCT WMButtonAction &ba
+
+
1627 dfref savedf = GetDataFolderDFR()
+
+
1629 switch( ba.eventCode )
+
+
1631 string control_datafolder = GetUserData(ba.win, " ", " control_datafolder
")
+
1632 setdatafolder control_datafolder
+
1633 string brick_path = GetUserData(ba.win, " ", " brick_path
")
+
1634 string axis = StringFromList(1, ba.ctrlName, " _
")
+
1635 string cmd = StringFromList(2, ba.ctrlName, " _
")
+
1636 variable dim = char2num(axis[0]) - char2num(" x
")
+
1637 string posvariable = getdatafolder(1) + axis[0] + " _slice_pos
"
+
1638 nvar pos = $(posvariable)
+
+
1640 wave /z brick = $brick_path
+
1641 if (WaveExists(brick))
+
+
+
1644 ad_slicer_start_bg(brick, dim, posvariable, dimdelta(brick, dim))
+
+
+
1647 ad_slicer_start_bg(brick, dim, posvariable, -dimdelta(brick, dim))
+
+
+
1650 ad_slicer_stop_bg(posvariable)
+
1651 bp_move_slice_center(brick, dim, posvariable)
+
+
+
1654 ad_slicer_stop_bg(posvariable)
+
+
+
+
1658 ad_slicer_stop_bg(posvariable)
+
1659 Abort " can
't find original wave " + brick_path
+
+
+
1662 case -1: // control being killed
+
+
+
+
1666 setdatafolder savedf
+
+
+
+
1673 static function bp_extract_slice(ba) : ButtonControl
+
1674 STRUCT WMButtonAction &ba
+
+
1676 dfref savedf = GetDataFolderDFR()
+
+
1678 switch( ba.eventCode )
+
+
1680 string control_datafolder = GetUserData(ba.win, "", "control_datafolder")
+
1681 setdatafolder control_datafolder
+
1682 string brick_path = GetUserData(ba.win, "", "brick_path")
+
1683 wave brick = $brick_path
+
1684 dfref brickdf = GetWavesDataFolderDFR(brick)
+
+
1686 string axis = StringFromList(1, ba.ctrlName, "_")
+
1687 string cmd = StringFromList(2, ba.ctrlName, "_")
+
1688 variable dim = char2num(axis[0]) - char2num("x")
+
1689 string posvariable = getdatafolder(1) + axis[0] + "_slice_pos"
+
+
1691 nvar pos = $(posvariable)
+
1692 variable pp = round((pos - dimoffset(brick, dim)) / dimdelta(brick, dim))
+
1693 if ((pp < 0) || (pp >= dimsize(brick, dim)))
+
1694 return -1 // requested value out of range
+
+
+
1697 variable dig = ceil(log(dimsize(brick, dim)))
+
+
1699 sprintf slicename, "%s_%s%0*u", NameOfWave(brick), axis[0], dig, pp
+
1700 setdatafolder brickdf
+
+
+
1703 wave wdest = ad_extract_slab_x(brick, pp, pp, slicename)
+
+
+
1706 wave wdest = ad_extract_slab_y(brick, pp, pp, slicename)
+
+
+
1709 wave wdest = ad_extract_slab_z(brick, pp, pp, slicename)
+
+
+
+
+
1714 sprintf msg, "%s=%g", axis[0], pos
+
+
+
+
1718 case -1: // control being killed
+
+
+
+
1722 setdatafolder savedf
+
+
+
+
1727 static function bp_move_slice_center(brick, dim, posvariable)
+
+
+
+
+
1732 nvar pos = $posvariable
+
1733 pos = dimoffset(brick, dim) + dimdelta(brick, dim) * dimsize(brick, dim) / 2
+
1734 ad_gizmo_set_plane(brick, dim, pos)
+
1735 ad_profiles_set_slice(brick, dim, pos)
+
+
+
1739 static function ad_slicer_move_bg(s)
+
1740 STRUCT WMBackgroundStruct &s
+
+
1742 dfref savedf = GetDataFolderDFR()
+
1743 setdatafolder root:pearl_area:slicer
+
1744 wave /t bg_brickpaths
+
1745 wave /t bg_graphnames
+
1746 wave /t bg_variablepaths
+
+
+
+
+
1751 variable nn = numpnts(bg_brickpaths)
+
+
+
+
1755 for (ii = 0; ii < nn; ii += 1)
+
1756 wave /z brick = $bg_brickpaths[ii]
+
1757 nvar /z pos = $bg_variablepaths[ii]
+
1758 dim = bg_dimensions[0]
+
1759 pos += bg_increments[ii]
+
1760 // wrap around at limits
+
1761 pp = round((pos - dimoffset(brick, dim)) / dimdelta(brick, dim))
+
+
1763 pos = dimoffset(brick, dim) + dimdelta(brick, dim) * (dimsize(brick, dim) - 1)
+
1764 elseif (pp >= dimsize(brick, dim) - 0.5)
+
1765 pos = dimoffset(brick, dim)
+
+
1767 if (waveexists(brick))
+
1768 ad_gizmo_set_plane(brick, dim, pos)
+
1769 ad_profiles_set_slice(brick, dim, pos)
+
+
+
+
1773 setdatafolder savedf
+
+
+
+
1778 function ad_slicer_init_bg()
+
1779 dfref savedf = GetDataFolderDFR()
+
+
1781 newdatafolder /o/s pearl_area
+
1782 newdatafolder /o/s slicer
+
+
1784 make /n=0/o/t bg_brickpaths
+
1785 make /n=0/o/t bg_variablepaths
+
1786 make /n=0/o/i/u bg_dimensions
+
1787 make /n=0/o bg_increments
+
+
1789 CtrlNamedBackground ad_slicer, period = 30, proc = PearlAreaDisplay#ad_slicer_move_bg
+
+
1791 setdatafolder savedf
+
+
+
+
1802 function ad_slicer_start_bg(brick, dimension, posvariable, delta)
+
1803 wave brick // 3D data wave
+
1804 variable dimension // dimension to animate, 0, 1, or 2
+
1805 string posvariable // full path to the global position variable
+
1806 variable delta // step increment, should be +/- dimdelta
+
+
1808 dfref savedf = GetDataFolderDFR()
+
1809 setdatafolder root:pearl_area:slicer
+
1810 wave /t bg_brickpaths
+
1811 wave /t bg_variablepaths
+
+
+
+
1815 // create entry in ad_slicer background task table
+
+
1817 FindValue /TEXT=posvariable /TXOP=4 /Z bg_variablepaths
+
+
+
+
1821 idx = numpnts(bg_variablepaths)
+
1822 InsertPoints idx, 1, bg_brickpaths, bg_variablepaths, bg_dimensions, bg_increments
+
+
+
1825 // set background task
+
1826 bg_brickpaths[idx] = GetWavesDataFolder(brick, 2)
+
1827 bg_variablepaths[idx] = posvariable
+
1828 bg_dimensions[idx] = dimension
+
1829 bg_increments[idx] = delta
+
+
1831 // start background task
+
1832 if (numpnts(bg_variablepaths) > 0)
+
1833 CtrlNamedBackground ad_slicer, start
+
+
+
1836 setdatafolder savedf
+
+
+
+
1844 function ad_slicer_stop_bg(posvariable)
+
+
+
1847 dfref savedf = GetDataFolderDFR()
+
1848 setdatafolder root:pearl_area:slicer
+
1849 wave /t bg_brickpaths
+
1850 wave /t bg_variablepaths
+
+
+
+
1854 // find entry in ad_slicer background task table
+
1855 FindValue /TEXT=posvariable /TXOP=4 /Z bg_variablepaths
+
+
1857 DeletePoints v_value, 1, bg_brickpaths, bg_variablepaths, bg_dimensions, bg_increments
+
+
+
1860 // stop background task if task table is empty
+
1861 if (numpnts(bg_variablepaths) == 0)
+
1862 CtrlNamedBackground ad_slicer, stop
+
+
+
1865 setdatafolder savedf
+
+
string ad_display_slice(wave data)
display three-dimensional data by 2D slice.
static string graphname_from_dfref(dfref df, string prefix)
compose a valid and unique graph name from a data folder reference
variable ad_calc_histogram(wave image)
calculate the histogram.
string ad_display_histogram(wave image)
display the histogram of a 2D image.
string ad_display(wave image)
open a new graph window with a 2D image.
string PearlCleanupName(string name)
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
PEARL Procedures: pearl-area-import.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -106,83 +108,83 @@ Namespaces
static variable BeforeFileOpenHook (variable refNum, string fileName, string path, string type, string creator, variable kind) callback function for drag&drop of HDF5 files into Igor. More... callback function for drag&drop of HDF5 files into Igor. More... string ad_suggest_foldername (string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue) generate the name of a data folder based on a file name. More... generate the name of a data folder based on a file name. More... variable ad_load_dialog (string APathName) load area detector data files selected in a file dialog window More... load area detector data files selected in a file dialog window More... string adh5_load_complete (string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue) import everything from a HDF5 file created by the Area Detector software. More... import everything from a HDF5 file created by the Area Detector software. More... string adh5_load_reduced (string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable load_data=defaultValue, variable load_attr=defaultValue, variable progress=defaultValue) load and reduce a dataset from a HDF5 file created by the Area Detector software. More... load and reduce a dataset from a HDF5 file created by the Area Detector software. More... string adh5_load_preview (string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue) load a single image from a HDF5 file created by the Area Detector software. More... load a single image from a HDF5 file created by the Area Detector software. More... string adh5_load_info (string APathName, string AFileName) load descriptive info from a HDF5 file created by the Area Detector software. More... load descriptive info from a HDF5 file created by the Area Detector software. More... variable adh5_load_detector (variable fileID, string detectorpath) load the detector dataset from the open HDF5 file. More... load the detector dataset from the open HDF5 file. More... variable adh5_redim (wave data) redimension a multi-dimensional area detector array loaded from HDF5. More... redimension a multi-dimensional area detector array loaded from HDF5. More... static dfr GetAttrDataFolderDFR (wave data) find the attributes data folder of an area detector dataset. More... find the attributes data folder of an area detector dataset. More... variable adh5_scale (wave data, string source=defaultValue) set the dimension scales of an area detector dataset. More... set the dimension scales of an area detector dataset. More... variable adh5_load_detector_slabs (variable fileID, string detectorpath, variable progress=defaultValue) load the detector dataset from the open HDF5 file. More... load the detector dataset from the open HDF5 file. More... variable adh5_load_detector_image (variable fileID, string detectorpath, variable dim2start, variable dim2count, variable dim3start, variable dim3count) load a single image from the detector dataset of the open HDF5 file More... load a single image from the detector dataset of the open HDF5 file More... string adh5_list_reduction_funcs () get a list of functions which can be used as reduction functions. More... get a list of functions which can be used as reduction functions. More... threadsafe wave adh5_default_reduction (wave source, string *param) function prototype for adh5_load_reduced_detector More... function prototype for adh5_load_reduced_detector More... threadsafe variable adh5_setup_profile (wave image, wave profile, variable dim) set up a one-dimensional wave for a line profile based on a 2D original wave. More... set up a one-dimensional wave for a line profile based on a 2D original wave. More... string adh5_test_reduction_func (wave source, funcref reduction_func, string reduction_param, string result_prefix) wrapper function for testing reduction functions from the command line. More... wrapper function for testing reduction functions from the command line. More... variable adh5_reduce_brick (wave source, funcref reduction_func, string reduction_param, string result_prefix, variable progress=defaultValue, variable nthreads=defaultValue) reduce a three-dimensional intensity distribution More... reduce a three-dimensional intensity distribution More... static threadsafe variable reduce_brick_worker (funcref reduction_func) thread worker for adh5_reduce_brick More... thread worker for adh5_reduce_brick More... threadsafe variable adh5_get_result_waves (wave results, string result_prefix, variable start_index) copy waves from wave reference wave into current data folder More... copy waves from wave reference wave into current data folder More... variable adh5_load_reduced_detector (variable fileID, string detectorpath, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue) load a reduced detector dataset from the open HDF5 file. More... load a reduced detector dataset from the open HDF5 file. More... static threadsafe variable reduce_slab_worker (funcref reduction_func) static threadsafe wave reduce_slab_image (wave slabdata, wave image, funcref reduction_func, string reduction_param) variable adh5_loadattr_all (variable fileID, string attributespath) load an NDAttributes group from an open HDF5 file into the current data folder. More... load an NDAttributes group from an open HDF5 file into the current data folder. More... static variable read_attribute_info (string datawavename, string source, variable *idest) sub-function of adh5_loadattr_all. More... sub-function of adh5_loadattr_all. More... variable adh5_scale_scienta (wave data) set the energy and angle scales of an area detector dataset from the Scienta analyser. More... set the energy and angle scales of an area detector dataset from the Scienta analyser. More... variable adh5_scale_scan (wave data) scales the extra dimensions of an area detector dataset according to the EPICS scan More... scales the extra dimensions of an area detector dataset according to the EPICS scan More... HDF5 file import from EPICS area detectors such as CCD cameras, 2D electron analysers
as of Igor 6.3, Igor can open datasets of up to rank 4. i.e. the extra dimension Y of the file plugin cannot be used. the extra dimensions N and X are supported.
Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch Copyright 2013-18 Paul Scherrer Institut Copyright 2013-20 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-area-import.ipf .
@@ -221,7 +223,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
Definition at line 167 of file pearl-area-import.ipf .
+Definition at line 171 of file pearl-area-import.ipf .
@@ -276,7 +278,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 106 of file pearl-area-import.ipf .
+Definition at line 110 of file pearl-area-import.ipf .
@@ -309,7 +311,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); function prototype for adh5_load_reduced_detector
this is a prototype of custom functions that convert (reduce) a two-dimensional detector image into one or more one-dimensional waves. data processing can be tuned with a set of parameters.
reduction functions have a fixed signature (function arguments) so that the file import functions can call them efficiently on a series of detector images. pearl procedures comes with a number of pre-defined reduction functions but you may as well implement your own functions. if you write your own function, you must use the same declaration and arguments as this function except for the function name. you can do many things in a reduction function, e.g. integration over a region of interest, curve fitting, etc.
-each destination wave is a one-dimensional intensity distribution. the function must redimension each of these waves to one of the image dimensions by calling the adh5_setup_profile() function. this function will also copy the scale information and dimension labels, which is important for the proper scaling of the result.
+each destination wave is a one-dimensional intensity distribution. the function must redimension each of these waves to one of the image dimensions by calling the adh5_setup_profile() function. this function will also copy the scale information and dimension labels, which is important for the proper scaling of the result.
the meaning of the data in the result waves is up to the particular function, e.g. dest1 could hold the mean value and dest2 the one-sigma error, or dest1 could hold the X-profile, and dest2 the Y-profile.
Parameters
@@ -320,7 +322,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns a free wave containing references of the result waves. the result waves should as well be free waves. if an error occurred, the reference wave is empty. Definition at line 1111 of file pearl-area-import.ipf .
+Definition at line 1115 of file pearl-area-import.ipf .
@@ -367,7 +369,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 1430 of file pearl-area-import.ipf .
+Definition at line 1463 of file pearl-area-import.ipf .
@@ -389,7 +391,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); get a list of functions which can be used as reduction functions.
the function evaluates only the function arguments, it may thus include functions which are not suitable as reduction functions.
-Definition at line 1041 of file pearl-area-import.ipf .
+Definition at line 1045 of file pearl-area-import.ipf .
@@ -450,7 +452,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 207 of file pearl-area-import.ipf .
+Definition at line 211 of file pearl-area-import.ipf .
@@ -490,7 +492,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 581 of file pearl-area-import.ipf .
+Definition at line 585 of file pearl-area-import.ipf .
@@ -558,7 +560,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 945 of file pearl-area-import.ipf .
+Definition at line 949 of file pearl-area-import.ipf .
@@ -606,7 +608,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns 0 if successful, non-zero if an error occurred. Definition at line 780 of file pearl-area-import.ipf .
+Definition at line 784 of file pearl-area-import.ipf .
@@ -647,7 +649,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 497 of file pearl-area-import.ipf .
+Definition at line 501 of file pearl-area-import.ipf .
@@ -709,7 +711,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 387 of file pearl-area-import.ipf .
+Definition at line 391 of file pearl-area-import.ipf .
@@ -784,7 +786,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); ANickName destination folder name (top level under root) APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed AFileName if empty a dialog box shows up reduction_func custom reduction function (any user-defined function which has the same parameters as adh5_default_reduction() ) reduction_func custom reduction function (any user-defined function which has the same parameters as adh5_default_reduction() ) reduction_param parameter string for the reduction function load_data 1 (default): load data; 0: do not load data load_attr 1 (default): load attributes; 0: do not load attributes for proper wave scaling, the attributes must be loaded Definition at line 302 of file pearl-area-import.ipf .
+Definition at line 306 of file pearl-area-import.ipf .
@@ -854,7 +856,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
fileID ID of open HDF5 file from HDF5OpenFile detectorpath path to detector group in the HDF5 file reduction_func custom reduction function (any user-defined function which has the same parameters as adh5_default_reduction() ) reduction_func custom reduction function (any user-defined function which has the same parameters as adh5_default_reduction() ) reduction_param parameter string for the reduction function progress 1 (default): show progress window; 0: do not show progress window nthreads -1 (default): use as many threads as there are processor cores (in addition to main thread) 0: use main thread only (e.g. for debugging the reduction function) >= 1: use a fixed number of (additional) threads Definition at line 1466 of file pearl-area-import.ipf .
+Definition at line 1499 of file pearl-area-import.ipf .
@@ -902,7 +904,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 1790 of file pearl-area-import.ipf .
+Definition at line 1823 of file pearl-area-import.ipf .
@@ -932,7 +934,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 626 of file pearl-area-import.ipf .
+Definition at line 630 of file pearl-area-import.ipf .
@@ -993,12 +995,13 @@ Licensed under the Apache License, Version 2.0 (the "License"); source source wave. three-dimensional intensity distribution (image). the scales are carried over to the result waves. reduction_func name of the reduction function to apply to the source data. reduction_param string with reduction parameters as required by the specific reduction function. result_prefix name prefix of result waves. a numeric index is appended to distinguish the results. the index starts at 1. existing waves are overwritten. result_prefix name prefix of result waves. a numeric index is appended to distinguish the results. the index starts at 1. existing waves are overwritten.
+Returns result code: 0 for success, < 0 for error Definition at line 1198 of file pearl-area-import.ipf .
+Definition at line 1203 of file pearl-area-import.ipf .
@@ -1031,7 +1034,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); set the dimension scales of an area detector dataset.
the intrinsic dimensions 0 and 1 are scaled according to the data source (currently supported: Prosilica cameras, Scienta electron analyser). the extra dimensions are scaled according to the scan. the latter requires that the positioner names and position values are available.
-Definition at line 726 of file pearl-area-import.ipf .
+Definition at line 730 of file pearl-area-import.ipf .
@@ -1055,7 +1058,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); the scan positioner name and its values must be available
Todo: incomplete Definition at line 2030 of file pearl-area-import.ipf .
+Definition at line 2063 of file pearl-area-import.ipf .
@@ -1078,7 +1081,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); set the energy and angle scales of an area detector dataset from the Scienta analyser.
the dimension labels of the energy and angle scales must be set correctly: AD_Dim0 = energy dimension; AD_Dim1 = angle dimension. these dimensions must be the first two dimensions of a multi-dimensional dataset. normally, AD_Dim0 is the X dimension, and AD_Dim1 the Y dimension.
-Definition at line 1925 of file pearl-area-import.ipf .
+Definition at line 1958 of file pearl-area-import.ipf .
@@ -1117,7 +1120,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); set up a one-dimensional wave for a line profile based on a 2D original wave.
redimensions the profile wave to the given dimension. copies the scale and dimension label of the given dimension.
-Definition at line 1134 of file pearl-area-import.ipf .
+Definition at line 1138 of file pearl-area-import.ipf .
@@ -1172,7 +1175,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns a copy of the reduction_param string, possibly modified by the reduction function. Definition at line 1167 of file pearl-area-import.ipf .
+Definition at line 1171 of file pearl-area-import.ipf .
@@ -1236,7 +1239,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); callback function for drag&drop of HDF5 files into Igor.
-Definition at line 42 of file pearl-area-import.ipf .
+Definition at line 46 of file pearl-area-import.ipf .
@@ -1274,7 +1277,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns data folder reference of the attributes folder. the reference may be invalid (and default to root) if the folder cannot be found, cf. built-in DataFolderRefStatus function. Definition at line 707 of file pearl-area-import.ipf .
+Definition at line 711 of file pearl-area-import.ipf .
@@ -1329,7 +1332,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 1872 of file pearl-area-import.ipf .
+Definition at line 1905 of file pearl-area-import.ipf .
@@ -1360,7 +1363,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); thread worker for adh5_reduce_brick
this function polls job data folders from thread group 0 and calls the reduction function on their contents. the result waves have prefix "redw_" and are saved in the job folder.
-Definition at line 1377 of file pearl-area-import.ipf .
+Definition at line 1410 of file pearl-area-import.ipf .
@@ -1410,7 +1413,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
@@ -1438,7 +1441,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-area-import.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,49 +87,1791 @@ $(document).ready(function(){initNavTree('pearl-area-import_8ipf_source.html',''
pearl-area-import.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.2 3 #pragma ModuleName = PearlAreaImport 4 #include <HDF5 Browser> 5 #include "pearl-compat" 6 #include "pearl-gui-tools" 44 string fileName, path, type, creator
46 variable handledOpen = 0
51 string FileExt = LowerStr(ParseFilePath(4, FileName, ":", 0, 0))
55 svar /z cnn = gsCustomNickName
57 if (exists("gvNickNameIndex") != 2)
58 variable/g gvNickNameIndex = 1
60 nvar nni = gvNickNameIndex
61 NickName = cnn + num2str(nni)
65 if (stringmatch(FileExt, "h5") == 1)
69 string /g s_latest_datafile = result
70 string /g s_latest_nickname = nickname
72 handledOpen = strlen(result) > 0
112 if (ParamIsDefault(ignoredate))
115 if (ParamIsDefault(unique))
119 string basename = ParseFilePath(3, filename, ":", 0, 0)
120 string extension = ParseFilePath(4, filename, ":", 0, 0)
124 if (strsearch(basename, "scienta", 0, 2) >= 0)
126 elseif (strsearch(basename, "pshell", 0, 2) >= 0)
128 elseif (strsearch(basename, "OP-SL", 0, 2) >= 0)
130 elseif (strsearch(basename, "ES-PS", 0, 2) >= 0)
135 if (ParamIsDefault(sourcename))
136 sourcename = autosource
139 variable nparts = ItemsInList(basename, "-")
141 string datepart = StringFromList(1, basename, "-")
142 variable l_datepart = strlen(datepart)
144 datepart = datepart[l_datepart-6, l_datepart-1]
146 string indexpart = StringFromList(2, basename, "-")
148 sprintf nickname, "%s_%s", sourcename, indexpart
150 sprintf nickname, "%s_%s_%s", sourcename, datepart, indexpart
156 if (unique && CheckName(nickname, 11))
157 nickname = UniqueName(nickname + "_", 11, 0)
171 string message = "Select data files"
173 string filefilters = "Area Detector HDF5 Files (*.h5):.h5;"
174 filefilters += "All Files:.*;"
176 PathInfo /S $APathName
177 Open /D /R /F=filefilters /M=message /MULT=1 refNum
178 filepaths = S_fileName
180 dfref saveDF = GetDataFolderDFR()
183 if (strlen(filepaths) > 0)
184 variable nfiles = ItemsInList(filepaths, "\r")
186 for(ifile = 0; ifile < nfiles; ifile += 1)
187 String path = StringFromList(ifile, filepaths, "\r")
214 if (ParamIsDefault(load_data))
217 if (ParamIsDefault(load_attr))
221 dfref saveDF = GetDataFolderDFR()
223 newdatafolder /s/o $("root:" + ANickName)
227 string instrumentpath = "/entry/instrument/"
228 string detectorpath = instrumentpath + "detector/"
229 string attributespath = instrumentpath + "NDAttributes/"
235 variable /g adh5_perf_secs
236 timerRefNum = startMSTimer
239 #if Exists("HDF5OpenFile") 240 HDF5OpenFile /P=$APathName/R fileID as AFileName
242 AFileName = s_path + s_filename
243 print
"loading " + s_filename +
"\r" 249 newdatafolder /o/s attr
255 if (waveexists(data))
265 Abort
"HDF5 XOP not loaded." 268 if (timerRefNum >= 0)
269 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
302 function /s
adh5_load_reduced (ANickName, APathName, AFileName, reduction_func, reduction_param, [load_data, load_attr, progress])
308 string reduction_param
314 if (ParamIsDefault(load_data))
317 if (ParamIsDefault(load_attr))
320 if (ParamIsDefault(progress))
324 dfref saveDF = GetDataFolderDFR()
326 newdatafolder /s/o $("root:" + ANickName)
330 string instrumentpath = "/entry/instrument/"
331 string detectorpath = instrumentpath + "detector/"
332 string attributespath = instrumentpath + "NDAttributes/"
338 variable /g adh5_perf_secs
339 timerRefNum = startMSTimer
342 #if Exists("HDF5OpenFile") 343 HDF5OpenFile /P=$APathName/R fileID as AFileName
345 AFileName = s_path + s_filename
346 print
"loading " + s_filename +
"\r" 349 newdatafolder /o/s attr
362 Abort
"HDF5 XOP not loaded." 365 if (timerRefNum >= 0)
366 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
394 if (ParamIsDefault(load_data))
397 if (ParamIsDefault(load_attr))
401 dfref saveDF = GetDataFolderDFR()
403 newdatafolder /o/s pearl_area
404 newdatafolder /o/s preview
408 string instrumentpath = "/entry/instrument/"
409 string detectorpath = instrumentpath + "detector/"
410 string attributespath = instrumentpath + "NDAttributes/"
416 variable /g adh5_perf_secs
417 timerRefNum = startMSTimer
420 #if Exists("HDF5OpenFile") 421 HDF5OpenFile /P=$APathName/R/Z fileID as AFileName
423 AFileName = s_path + s_filename
426 datasetname = detectorpath +
"data" 427 STRUCT HDF5DataInfo di
429 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
431 print
"error accessing detector/data" 435 print
"error: rank of dataset < 2" 439 variable dim2start = 0, dim2count = 1, dim3start = 0, dim3count = 1
441 dim2start = floor(di.dims[di.ndims - 3] / 2)
445 dim3start = floor(di.dims[di.ndims - 4] / 2)
452 string destpath = GetDataFolder(1, saveDF) + ANickName
453 if (waveexists(data))
454 duplicate /o data, $destpath
455 wave /z data = $destpath
461 newdatafolder /o/s attr
465 if (waveexists(data))
472 print "error opening file " + AFileName
476 Abort
"HDF5 XOP not loaded." 479 if (timerRefNum >= 0)
480 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
501 dfref saveDF = GetDataFolderDFR()
505 string instrumentpath = "/entry/instrument/"
506 string detectorpath = instrumentpath + "detector/"
507 string attributespath = instrumentpath + "NDAttributes/"
517 #if Exists("HDF5OpenFile") 518 HDF5OpenFile /P=$APathName/R/Z fileID as AFileName
520 AFileName = s_path + s_filename
523 datasetname = detectorpath +
"data" 524 STRUCT HDF5DataInfo di
526 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
528 print
"error accessing detector/data" 532 for (idim = 0; idim < di.ndims; idim += 1)
533 sprintf s,
"dim %u: %u points" , idim, di.dims[idim]
534 if (strlen(s_info) > 0)
535 s_info = s_info +
"\r" + s
541 dfref df = NewFreeDataFolder()
545 for (idim = 1; idim < 5; idim += 1)
546 sprintf s, "Scan%uActive", idim
548 if (waveexists(w) && (numpnts(w) > 0) && (w[0] > 0))
549 sprintf s, "Scan%uPositioner1", idim
551 sprintf s, "scan %u: %s", idim, wt[0]
552 if (strlen(s_info) > 0)
553 s_info = s_info + "\r" + s
562 print "error opening file " + AFileName
566 Abort
"HDF5 XOP not loaded." 586 #if Exists("HDF5LoadData") 591 datasetname = detectorpath +
"data" 592 STRUCT HDF5DataInfo di
594 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
596 print
"error accessing detector/data" 600 print
"error: rank of dataset < 2" 604 HDF5LoadData /O /Q /Z fileID, datasetname
608 Abort
"HDF5 XOP not loaded." 629 duplicate /free data, tempdata
630 variable nd = wavedims(tempdata)
631 variable nx = dimsize(tempdata, nd - 1)
632 variable ny = dimsize(tempdata, nd - 2)
633 variable nz = dimsize(tempdata, nd - 3)
634 variable nt = dimsize(tempdata, nd - 4)
639 redimension /n=(ny) data
640 setdimlabel 0, -1, AD_Dim1, data
641 data = tempdata[p][0]
643 redimension /n=(nx) data
644 setdimlabel 0, -1, AD_Dim0, data
645 data = tempdata[0][p]
647 redimension /n=(nx,ny) data
648 setdimlabel 0, -1, AD_Dim0, data
649 setdimlabel 1, -1, AD_Dim1, data
650 data = tempdata[q][p]
655 redimension /n=(ny,nz) data
656 setdimlabel 0, -1, AD_Dim1, data
657 setdimlabel 1, -1, AD_DimN, data
658 multithread data = tempdata[q][p][0]
660 redimension /n=(nx,nz) data
661 setdimlabel 0, -1, AD_Dim0, data
662 setdimlabel 1, -1, AD_DimN, data
663 multithread data = tempdata[q][0][p]
665 redimension /n=(nx,ny) data
666 setdimlabel 0, -1, AD_Dim0, data
667 setdimlabel 1, -1, AD_Dim1, data
668 multithread data = tempdata[0][q][p]
670 redimension /n=(nx,ny,nz) data
671 setdimlabel 0, -1, AD_Dim0, data
672 setdimlabel 1, -1, AD_Dim1, data
673 setdimlabel 2, -1, AD_DimN, data
674 multithread data = tempdata[r][q][p]
680 redimension /n=(nx,ny,nt) data
681 setdimlabel 0, -1, AD_Dim0, data
682 setdimlabel 1, -1, AD_Dim1, data
683 setdimlabel 2, -1, AD_DimX, data
684 multithread data = tempdata[r][0][q][p]
686 redimension /n=(nx,ny,nz,nt) data
687 setdimlabel 0, -1, AD_Dim0, data
688 setdimlabel 1, -1, AD_Dim1, data
689 setdimlabel 2, -1, AD_DimN, data
690 setdimlabel 3, -1, AD_DimX, data
691 multithread data = tempdata[s][r][q][p]
710 dfref dataDF = GetWavesDataFolderDFR(data)
711 dfref attrDF = dataDF:attr
712 if (DataFolderRefStatus(attrDF) == 0)
730 dfref saveDF = GetDataFolderDFR()
731 dfref dataDF = GetWavesDataFolderDFR(data)
734 if (ParamIsDefault(source))
736 wave /SDFR=attrDF /Z AcquisitionMode
737 wave /SDFR=attrDF /T /Z Manufacturer
739 if (waveexists(Manufacturer) && (numpnts(Manufacturer) >= 1))
740 strswitch(Manufacturer[0])
748 elseif (waveexists(AcquisitionMode) && (numpnts(AcquisitionMode) >= 1))
749 if (stringmatch(note(AcquisitionMode), "*SCIENTA*"))
785 if (ParamIsDefault(progress))
791 #if Exists("HDF5LoadData") 796 datasetname = detectorpath +
"data" 797 STRUCT HDF5DataInfo di
799 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
801 print
"error accessing detector/data" 805 print
"error: rank of dataset < 2" 810 variable idx, idy, idz, idt, izt
816 variable nx, ny, nz, nt, nzt
822 make /n=(nx,ny,nz,nt) /o data
823 string dim_labels =
"AD_Dim0;AD_Dim1;AD_DimN;AD_DimX;AD_DimY" 825 dim_label = StringFromList(0, dim_labels,
";" )
826 setdimlabel 0, -1, $dim_label, data
827 dim_labels = RemoveFromList(dim_label, dim_labels,
";" )
828 dim_label = StringFromList(0, dim_labels, ";")
829 setdimlabel 1, -1, $dim_label, data
830 dim_labels = RemoveFromList(dim_label, dim_labels, ";")
834 for (
id = idy - 1; (
id >= 0) && (nz == 1);
id -= 1)
838 dim_label = StringFromList(0, dim_labels, ";")
839 setdimlabel 2, -1, $dim_label, data
841 dim_labels = RemoveListItem(0, dim_labels, ";")
843 for (
id = idz - 1; (
id >= 0) && (nt == 1);
id -= 1)
847 dim_label = StringFromList(0, dim_labels, ";")
848 setdimlabel 3, -1, $dim_label, data
850 dim_labels = RemoveListItem(0, dim_labels, ";")
852 redimension /n=(nx,ny,nz,nt) data
869 HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4))
875 slab[idx][%Block] = nx
876 slab[idy][%Block] = ny
879 for (iz = 0; iz < nz; iz += 1)
880 for (it = 0; it < nt; it += 1)
881 slab[idz][%Start] = iz
882 slab[idt][%Start] = it
883 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname
885 switch (WaveDims(slabdata))
887 data[][][iz][it] = slabdata[q][p]
890 data[][][iz][it] = slabdata[0][q][p]
893 data[][][iz][it] = slabdata[0][0][q][p]
911 redimension /n=(nx,ny) data
913 redimension /n=(nx,ny,nz) data
920 Abort
"HDF5 XOP not loaded." 954 #if Exists("HDF5LoadData") 959 datasetname = detectorpath +
"data" 960 STRUCT HDF5DataInfo di
962 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
964 print
"error accessing detector/data" 968 print
"error: rank of dataset < 1" 973 variable idx, idy, idz, idt
975 idy = di.ndims >= 2 ? di.ndims - 2 : 1
976 idz = di.ndims >= 3 ? di.ndims - 3 : 2
977 idt = di.ndims >= 4 ? di.ndims - 4 : 3
981 ny = di.ndims >= 2 ? di.dims[idy] : 1
983 variable dim2end = dim2start + dim2count - 1
984 variable dim3end = dim3start + dim3count - 1
988 HDF5MakeHyperslabWave(GetDataFolder(1) +
"slab" , max(di.ndims, 4))
994 slab[idx][%Block] = nx
995 slab[idy][%Block] = ny
997 make /n=(nx,ny)/o/d data
1001 for (iz = dim2start; iz <= dim2end; iz += 1)
1002 for (it = dim3start; it <= dim3end; it += 1)
1003 slab[idz][%Start] = iz
1004 slab[idt][%Start] = it
1005 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname
1007 switch (WaveDims(slabdata))
1013 data += slabdata[q][p]
1017 data += slabdata[0][q][p]
1021 data += slabdata[0][0][q][p]
1028 setdimlabel 0, -1, AD_Dim0, data
1029 setdimlabel 1, -1, AD_Dim1, data
1032 Abort
"HDF5 XOP not loaded." 1042 string all_funcs = FunctionList("*", ";", "KIND:6,NPARAMS:2,VALTYPE:8")
1046 variable nn = ItemsInList(all_funcs, ";")
1053 for (ii = 0; ii < nn; ii += 1)
1054 funcname = StringFromList(ii, all_funcs, ";")
1055 info = FunctionInfo(funcname)
1056 accept = (NumberByKey("RETURNTYPE", info, ":", ";") == 0x4000)
1057 accept = accept && (cmpstr(StringByKey("THREADSAFE", info, ":", ";"), "yes") == 0)
1058 accept = accept && (NumberByKey("N_PARAMS", info, ":", ";") == 2)
1059 accept = accept && (NumberByKey("N_OPT_PARAMS", info, ":", ";") == 0)
1062 accept = accept && (NumberByKey("PARAM_0_TYPE", info, ":", ";") == 0x4002)
1063 accept = accept && (NumberByKey("PARAM_1_TYPE", info, ":", ";") == 0x3000)
1066 result = AddListItem(funcname, result, ";")
1070 result = SortList(result, ";", 4)
1117 make /n=0 /free dest1, dest2
1123 make /n=2 /free /wave results
1139 redimension /n=(dimsize(image, dim)) profile
1140 setscale /p x dimoffset(image, dim), dimdelta(image, dim), waveunits(image, dim), profile
1141 setscale d 0, 0, waveunits(image, -1), profile
1142 setdimlabel 0, -1, $getdimlabel(image, dim, -1), profile
1170 string reduction_param
1171 string result_prefix
1173 wave /wave results = reduction_func(source, reduction_param)
1176 return reduction_param
1198 function
adh5_reduce_brick (source, reduction_func, reduction_param, result_prefix, [progress, nthreads])
1201 string reduction_param
1202 string result_prefix
1207 if (ParamIsDefault(progress))
1210 if (ParamIsDefault(nthreads))
1216 variable nx, ny, nz, nt
1217 nx = dimsize(source, 0)
1218 ny = dimsize(source, 1)
1219 nz = dimsize(source, 2)
1223 variable nzt = max(nz, 1) * max(nt, 1)
1228 nthreads = ThreadProcessorCount
1231 variable threadGroupID = ThreadGroupCreate(nthreads)
1233 for (ithread = 0; ithread < nthreads; ithread += 1)
1237 make /n=(nzt) /df /free processing_folders
1248 make /n=0 /free /wave result_waves
1251 for (iz = 0; iz < max(nz, 1); iz += 1)
1252 for (it = 0; it < max(nt, 1); it += 1)
1253 dfname = "processing_" + num2str(izt)
1254 newdatafolder /s $dfname
1255 ad_extract_slab (source, nan, nan, nan, nan, iz, iz, "image", pscale=1)
1259 variable /g r_index = iz
1260 variable /g s_index = it
1261 string /g func_param = reduction_param
1265 ThreadGroupPutDF threadGroupID, :
1267 processing_folders[izt] = GetDataFolderDFR()
1268 string param = reduction_param
1269 wave /wave reduced_waves = reduction_func(image, param)
1270 variable /g func_result = numpnts(reduced_waves)
1272 WaveClear image, reduced_waves
1292 for (izt = 0; (izt < nzt) && (result == 0); izt += 1)
1295 dfr = ThreadGroupGetDFR(threadGroupID, 1000)
1296 if (DatafolderRefStatus(dfr) != 0)
1300 if (update_progress_panel(izt))
1307 dfr = processing_folders[izt]
1309 if (update_progress_panel(izt))
1320 nvar rr = dfr:r_index
1321 nvar ss = dfr:s_index
1322 nvar func_result = dfr:func_result
1324 if (func_result < 1)
1329 if (numpnts(result_waves) == 0)
1330 redimension /n=(func_result) result_waves
1331 for (iw = 0; iw < func_result; iw += 1)
1332 sw = "redw_" + num2str(iw)
1333 wave profile = dfr:$sw
1334 sw = "ReducedData" + num2str(iw+1)
1335 make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
1337 setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
1338 setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
1339 setscale /p y dimoffset(source, 2), dimdelta(source, 2), waveunits(source, 2), data
1340 setscale /p z dimoffset(source, 3), dimdelta(source, 3), waveunits(source, 3), data
1341 setscale d 0, 0, waveunits(profile, -1), data
1342 result_waves[iw] = data
1345 for (iw = 0; iw < func_result; iw += 1)
1346 sw = "redw_" + num2str(iw)
1347 wave profile = dfr:$sw
1348 wave data = result_waves[iw]
1349 data[][rr][ss] = profile[p]
1354 variable tstatus = ThreadGroupRelease(threadGroupID)
1359 for (izt = 0; izt < nzt; izt += 1)
1360 KillDataFolder /Z processing_folders[izt]
1382 dfref dfr = ThreadGroupGetDFR(0, 1000)
1383 if (DataFolderRefStatus(dfr) == 0)
1393 wave image = dfr:image
1394 svar func_param = dfr:func_param
1395 nvar rr = dfr:r_index
1396 nvar ss = dfr:s_index
1399 newdatafolder /s outDF
1400 variable /g r_index = rr
1401 variable /g s_index = ss
1402 string param = func_param
1403 wave /wave reduced_waves = reduction_func(image, param)
1404 variable /g func_result = numpnts(reduced_waves)
1408 WaveClear image, reduced_waves
1409 ThreadGroupPutDF 0, :
1432 string result_prefix
1433 variable start_index
1435 variable nw = numpnts(results)
1438 for (iw = 0; iw < nw; iw += 1)
1439 sw = result_prefix + num2str(iw + start_index)
1440 duplicate /o results[iw], $sw
1470 string reduction_param
1474 if (ParamIsDefault(progress))
1477 if (ParamIsDefault(nthreads))
1483 #if Exists("HDF5LoadData") 1488 datasetname = detectorpath +
"data" 1489 STRUCT HDF5DataInfo di
1490 InitHDF5DataInfo(di)
1491 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
1493 print
"error accessing detector/data" 1497 print
"error: rank of dataset < 2" 1502 variable idx, idy, idz, idt
1508 variable nx, ny, nz, nt
1516 for (
id = idy - 1; (
id >= 0) && (nz == 1);
id -= 1)
1517 if (di.dims[
id ] > 1)
1522 for (
id = idz - 1; (
id >= 0) && (nt == 1);
id -= 1)
1523 if (di.dims[
id ] > 1)
1535 variable nzt = nz * nt
1539 HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4))
1545 slab[idx][%Block] = nx
1546 slab[idy][%Block] = ny
1550 nthreads = ThreadProcessorCount
1553 variable threadGroupID = ThreadGroupCreate(nthreads)
1555 for (ithread = 0; ithread < nthreads; ithread += 1)
1559 make /n=(nzt) /df /free processing_folders
1566 make /n=(nx,ny)/d image_template
1567 setdimlabel 0, -1, AD_Dim0, image_template
1568 setdimlabel 1, -1, AD_Dim1, image_template
1575 make /n=0 /free /wave result_waves
1578 for (iz = 0; iz < nz; iz += 1)
1579 for (it = 0; it < nt; it += 1)
1581 slab[idz][%Start] = iz
1582 slab[idt][%Start] = it
1583 dfname = "processing_" + num2str(izt)
1584 newdatafolder /s $dfname
1585 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname
1588 duplicate image_template, image
1589 variable /g r_index = iz
1590 variable /g s_index = it
1591 string /g func_param = reduction_param
1595 ThreadGroupPutDF threadGroupID, :
1597 processing_folders[izt] = GetDataFolderDFR()
1599 wave /wave reduced_waves =
reduce_slab_image (slabdata, image, reduction_func, func_param)
1600 variable /g func_result = numpnts(reduced_waves)
1602 WaveClear slabdata, image, reduced_waves
1609 if (update_progress_panel(izt))
1617 killwaves /z slab, image_template
1619 update_progress_panel(0, message="Processing data (step 2 of 2)...")
1623 for (izt = 0; (izt < nzt) && (result == 0); izt += 1)
1626 dfr = ThreadGroupGetDFR(threadGroupID, 1000)
1627 if (DatafolderRefStatus(dfr) != 0)
1631 if (update_progress_panel(izt))
1638 dfr = processing_folders[izt]
1640 if (update_progress_panel(izt))
1651 nvar rr = dfr:r_index
1652 nvar ss = dfr:s_index
1653 nvar func_result = dfr:func_result
1655 if (func_result < 1)
1660 if (numpnts(result_waves) == 0)
1661 redimension /n=(func_result) result_waves
1662 for (iw = 0; iw < func_result; iw += 1)
1663 sw = "redw_" + num2str(iw)
1664 wave profile = dfr:$sw
1665 sw = "ReducedData" + num2str(iw+1)
1666 make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
1668 setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
1669 setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
1670 setscale d 0, 0, waveunits(profile, -1), data
1671 result_waves[iw] = data
1674 for (iw = 0; iw < func_result; iw += 1)
1675 sw = "redw_" + num2str(iw)
1676 wave profile = dfr:$sw
1677 wave data = result_waves[iw]
1678 data[][rr][ss] = profile[p]
1683 variable tstatus = ThreadGroupRelease(threadGroupID)
1688 for (izt = 0; izt < nzt; izt += 1)
1689 KillDataFolder /Z processing_folders[izt]
1694 nw = numpnts(result_waves)
1695 for (iw = 0; iw < nw; iw += 1)
1696 wave data = result_waves[iw]
1698 redimension /n=(dimsize(data, 0)) data
1700 redimension /n=(dimsize(data, 0),nz) data
1701 setdimlabel 1, -1, AD_DimN, data
1703 setdimlabel 1, -1, AD_DimN, data
1704 setdimlabel 2, -1, AD_DimX, data
1713 Abort
"HDF5 XOP not loaded." 1723 dfref dfr = ThreadGroupGetDFR(0, 1000)
1724 if (DataFolderRefStatus(dfr) == 0)
1734 wave slabdata = dfr:slabdata
1735 wave image = dfr:image
1736 svar func_param = dfr:func_param
1737 nvar rr = dfr:r_index
1738 nvar ss = dfr:s_index
1741 newdatafolder /s outDF
1742 variable /g r_index = rr
1743 variable /g s_index = ss
1744 wave /wave reduced_waves =
reduce_slab_image (slabdata, image, reduction_func, func_param)
1745 variable /g func_result = numpnts(reduced_waves)
1749 WaveClear slabdata, image, reduced_waves
1750 ThreadGroupPutDF 0, :
1757 threadsafe static function /wave
reduce_slab_image (slabdata, image, reduction_func, reduction_param)
1761 string reduction_param
1763 switch (WaveDims(slabdata))
1765 image = slabdata[q][p]
1768 image = slabdata[0][q][p]
1771 image = slabdata[0][0][q][p]
1775 return reduction_func(image, reduction_param)
1792 string attributespath
1798 #if Exists("HDF5LoadData") 1801 HDF5ListGroup /F /TYPE=2 fileID, attributespath
1802 string h5datasets = S_HDF5ListGroup
1803 HDF5ListAttributes /TYPE=1 /Z fileID, attributespath
1804 string h5attributes = S_HDF5ListAttributes
1806 variable nds = ItemsInList(h5datasets,
";" )
1807 variable na = ItemsInList(h5attributes, ";")
1814 make /n=(nds+na) /t /o IN, ID, IV, IU
1816 for (ids = 0; ids < nds; ids += 1)
1817 datasetname = StringFromList(ids, h5datasets, ";")
1818 HDF5LoadData /O/Q fileID, datasetname
1820 datawavename = StringFromList(0, s_wavenames)
1824 HDF5LoadData /A="source"/O/Q/TYPE=2 fileID, datasetname
1827 s_source = source[0]
1836 nds = ItemsInList(h5attributes, ";")
1840 for (ids = 0; ids < nds; ids += 1)
1841 datasetname = StringFromList(ids, h5attributes, ";")
1842 HDF5LoadData /A=datasetname/O/Q/TYPE=1 fileID, attributespath
1844 datawavename = StringFromList(0, s_wavenames)
1849 redimension /n=(idest) IN, ID, IV, IU
1850 sort {IN, ID}, IN, ID, IV, IU
1854 Abort
"HDF5 XOP not loaded." 1890 if (exists(datawavename) == 1)
1891 if (strlen(source) > 0)
1892 Note $datawavename,
"PV=" + source
1894 switch (WaveType($datawavename, 1))
1896 wave w_attr = $datawavename
1897 n_attr = numpnts(w_attr)
1898 sprintf s_attr,
"%.12g" , w_attr[0]
1901 wave /t wt_attr = $datawavename
1902 n_attr = numpnts(wt_attr)
1910 ID[idest] = datawavename
1928 dfref saveDF = GetDataFolderDFR()
1930 dfref dataDF = GetWavesDataFolderDFR(data)
1933 wave /SDFR=attrDF LensMode
1934 wave /SDFR=attrDF /Z ChannelBegin, ChannelEnd
1935 wave /SDFR=attrDF /Z SliceBegin, SliceEnd
1938 variable ELow, EHigh, ALow, AHigh
1942 strswitch(GetDimLabel(data, 0, -1))
1952 strswitch(GetDimLabel(data, 1, -1))
1965 ELow = dimoffset(data, EDim)
1966 EHigh = dimoffset(data, EDim) + dimdelta(data, EDim) * (dimsize(data, EDim) - 1)
1970 ALow = dimoffset(data, ADim)
1971 AHigh = dimoffset(data, ADim) + dimdelta(data, ADim) * (dimsize(data, ADim) - 1)
1976 if (waveexists(LensMode) && (numpnts(LensMode) >= 1))
1992 if (waveexists(ChannelBegin) && waveexists(ChannelEnd) && (numpnts(ChannelBegin) >= 1) && (numpnts(ChannelEnd) >= 1))
1993 ELow = ChannelBegin[0]
1994 EHigh = ChannelEnd[0]
1996 if (waveexists(SliceBegin) && waveexists(SliceEnd) && (numpnts(SliceBegin) >= 1) && (numpnts(SliceEnd) >= 1))
1997 ALow = SliceBegin[0]
2004 setscale /i x ELow, EHigh, EUnit, data
2007 setscale /i y ELow, EHigh, EUnit, data
2012 setscale /i x ALow, AHigh, AUnit, data
2015 setscale /i y ALow, AHigh, AUnit, data
2019 setscale d 0, 0, "arb.", data
2021 setdatafolder saveDF
2033 dfref saveDF = GetDataFolderDFR()
2035 dfref dataDF = GetWavesDataFolderDFR(data)
2036 wave /SDFR=dataDF AcquisitionMode, DetectorMode, EnergyMode
2038 wave /SDFR=dataDF /z Scan1Active, Scan2Active
2039 wave /SDFR=dataDF /t /z Scan1Positioner1, Scan1Readback1
2040 wave /SDFR=dataDF /t /z Scan1Positioner2, Scan1Readback2
2041 wave /SDFR=dataDF /t /z Scan2Positioner1, Scan2Readback1
2042 wave /SDFR=dataDF /t /z Scan2Positioner2, Scan2Readback2
2048 strswitch(GetDimLabel(data, 0, -1))
2050 setscale /i x zscale[0], zscale[numpnts(zscale)-1], "", data
2053 strswitch(GetDimLabel(data, 1, -1))
2055 setscale /i y zscale[0], zscale[numpnts(zscale)-1], "", data
2058 strswitch(GetDimLabel(data, 2, -1))
2060 setscale /i z zscale[0], zscale[numpnts(zscale)-1], "", data
2064 setdatafolder saveDF
string adh5_load_preview(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
load a single image from a HDF5 file created by the Area Detector software.
-
-
-
string adh5_load_info(string APathName, string AFileName)
load descriptive info from a HDF5 file created by the Area Detector software.
-
variable ad_load_dialog(string APathName)
load area detector data files selected in a file dialog window
-
threadsafe wave ad_profile_x_w(wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
-
static variable read_attribute_info(string datawavename, string source, variable *idest)
sub-function of adh5_loadattr_all.
-
string PearlCleanupName(string name)
-
static dfr GetAttrDataFolderDFR(wave data)
find the attributes data folder of an area detector dataset.
-
threadsafe variable adh5_setup_profile(wave image, wave profile, variable dim)
set up a one-dimensional wave for a line profile based on a 2D original wave.
-
threadsafe variable adh5_get_result_waves(wave results, string result_prefix, variable start_index)
copy waves from wave reference wave into current data folder
-
variable adh5_scale_scienta(wave data)
set the energy and angle scales of an area detector dataset from the Scienta analyser.
-
string adh5_test_reduction_func(wave source, funcref reduction_func, string reduction_param, string result_prefix)
wrapper function for testing reduction functions from the command line.
-
variable adh5_loadattr_all(variable fileID, string attributespath)
load an NDAttributes group from an open HDF5 file into the current data folder.
-
variable adh5_scale_scan(wave data)
scales the extra dimensions of an area detector dataset according to the EPICS scan ...
-
static threadsafe variable reduce_brick_worker(funcref reduction_func)
thread worker for adh5_reduce_brick
-
variable adh5_reduce_brick(wave source, funcref reduction_func, string reduction_param, string result_prefix, variable progress=defaultValue, variable nthreads=defaultValue)
reduce a three-dimensional intensity distribution
-
string ad_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
generate the name of a data folder based on a file name.
-
threadsafe wave ad_profile_y_w(wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
-
string adh5_load_complete(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
import everything from a HDF5 file created by the Area Detector software.
-
variable adh5_load_reduced_detector(variable fileID, string detectorpath, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue)
load a reduced detector dataset from the open HDF5 file.
-
string adh5_load_reduced(string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable load_data=defaultValue, variable load_attr=defaultValue, variable progress=defaultValue)
load and reduce a dataset from a HDF5 file created by the Area Detector software. ...
-
variable adh5_redim(wave data)
redimension a multi-dimensional area detector array loaded from HDF5.
-
threadsafe wave adh5_default_reduction(wave source, string *param)
function prototype for adh5_load_reduced_detector
-
variable adh5_load_detector_slabs(variable fileID, string detectorpath, variable progress=defaultValue)
load the detector dataset from the open HDF5 file.
-
variable adh5_scale(wave data, string source=defaultValue)
set the dimension scales of an area detector dataset.
-
-
variable adh5_load_detector(variable fileID, string detectorpath)
load the detector dataset from the open HDF5 file.
-
static threadsafe wave reduce_slab_image(wave slabdata, wave image, funcref reduction_func, string reduction_param)
-
static variable BeforeFileOpenHook(variable refNum, string fileName, string path, string type, string creator, variable kind)
callback function for drag&drop of HDF5 files into Igor.
-
string adh5_list_reduction_funcs()
get a list of functions which can be used as reduction functions.
-
variable adh5_load_detector_image(variable fileID, string detectorpath, variable dim2start, variable dim2count, variable dim3start, variable dim3count)
load a single image from the detector dataset of the open HDF5 file
-
threadsafe wave ad_extract_slab(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue)
2D cut through 3D dataset, integrate in normal dimension
-
static threadsafe variable reduce_slab_worker(funcref reduction_func)
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.36
+
4 #pragma ModuleName = PearlAreaImport
+
+
6 #if IgorVersion() < 9.00
+
7 #include <HDF5 Browser>
+
+
9 #include "pearl-compat"
+
10 #include "pearl-gui-tools"
+
+
+
+
+
+
+
+
+
+
+
+
+
48 string fileName, path, type, creator
+
+
50 variable handledOpen = 0
+
+
+
+
+
55 string FileExt = LowerStr(ParseFilePath(4, FileName, ":", 0, 0))
+
+
+
+
59 svar /z cnn = gsCustomNickName
+
+
61 if (exists("gvNickNameIndex") != 2)
+
62 variable/g gvNickNameIndex = 1
+
+
64 nvar nni = gvNickNameIndex
+
65 NickName = cnn + num2str(nni)
+
+
+
+
69 if (stringmatch(FileExt, "h5") == 1)
+
+
+
+
73 string /g s_latest_datafile = result
+
74 string /g s_latest_nickname = nickname
+
+
76 handledOpen = strlen(result) > 0
+
+
+
+
+
+
+
+
+
+
+
+
+
+
116 if (ParamIsDefault(ignoredate))
+
+
+
119 if (ParamIsDefault(unique))
+
+
+
+
123 string basename = ParseFilePath(3, filename, ":", 0, 0)
+
124 string extension = ParseFilePath(4, filename, ":", 0, 0)
+
+
+
+
128 if (strsearch(basename, "scienta", 0, 2) >= 0)
+
+
130 elseif (strsearch(basename, "pshell", 0, 2) >= 0)
+
+
132 elseif (strsearch(basename, "OP-SL", 0, 2) >= 0)
+
+
134 elseif (strsearch(basename, "ES-PS", 0, 2) >= 0)
+
+
+
+
+
139 if (ParamIsDefault(sourcename))
+
140 sourcename = autosource
+
+
+
143 variable nparts = ItemsInList(basename, "-")
+
+
145 string datepart = StringFromList(1, basename, "-")
+
146 variable l_datepart = strlen(datepart)
+
+
148 datepart = datepart[l_datepart-6, l_datepart-1]
+
+
150 string indexpart = StringFromList(2, basename, "-")
+
+
152 sprintf nickname, "%s_%s", sourcename, indexpart
+
+
154 sprintf nickname, "%s_%s_%s", sourcename, datepart, indexpart
+
+
+
+
+
+
160 if (unique && CheckName(nickname, 11))
+
161 nickname = UniqueName(nickname + "_", 11, 0)
+
+
+
+
+
+
+
+
+
+
175 string message = "Select data files"
+
+
177 string filefilters = "Area Detector HDF5 Files (*.h5):.h5;"
+
178 filefilters += "All Files:.*;"
+
+
180 PathInfo /S $APathName
+
181 Open /D /R /F=filefilters /M=message /MULT=1 refNum
+
182 filepaths = S_fileName
+
+
184 dfref saveDF = GetDataFolderDFR()
+
+
+
187 if (strlen(filepaths) > 0)
+
188 variable nfiles = ItemsInList(filepaths, "\r")
+
+
190 for(ifile = 0; ifile < nfiles; ifile += 1)
+
191 String path = StringFromList(ifile, filepaths, "\r")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
218 if (ParamIsDefault(load_data))
+
+
+
221 if (ParamIsDefault(load_attr))
+
+
+
+
225 dfref saveDF = GetDataFolderDFR()
+
+
227 newdatafolder /s/o $("root:" + ANickName)
+
+
+
+
231 string instrumentpath = "/entry/instrument/"
+
232 string detectorpath = instrumentpath + "detector/"
+
233 string attributespath = instrumentpath + "NDAttributes/"
+
+
+
+
+
+
239 variable /g adh5_perf_secs
+
240 timerRefNum = startMSTimer
+
+
+
243 #if Exists("HDF5OpenFile")
+
244 HDF5OpenFile /P=$APathName/R fileID as AFileName
+
+
246 AFileName = s_path + s_filename
+
247 print
"loading " + s_filename +
"\r"
+
+
+
+
+
+
253 newdatafolder /o/s attr
+
+
+
+
+
+
259 if (waveexists(data))
+
+
+
+
+
+
+
+
+
+
269 Abort
"HDF5 XOP not loaded."
+
+
+
272 if (timerRefNum >= 0)
+
273 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
+
+
+
+
+
+
+
306 function /s
adh5_load_reduced (ANickName, APathName, AFileName, reduction_func, reduction_param, [load_data, load_attr, progress])
+
+
+
+
+
+
312 string reduction_param
+
+
+
+
+
+
318 if (ParamIsDefault(load_data))
+
+
+
321 if (ParamIsDefault(load_attr))
+
+
+
324 if (ParamIsDefault(progress))
+
+
+
+
328 dfref saveDF = GetDataFolderDFR()
+
+
330 newdatafolder /s/o $("root:" + ANickName)
+
+
+
+
334 string instrumentpath = "/entry/instrument/"
+
335 string detectorpath = instrumentpath + "detector/"
+
336 string attributespath = instrumentpath + "NDAttributes/"
+
+
+
+
+
+
342 variable /g adh5_perf_secs
+
343 timerRefNum = startMSTimer
+
+
+
346 #if Exists("HDF5OpenFile")
+
347 HDF5OpenFile /P=$APathName/R fileID as AFileName
+
+
349 AFileName = s_path + s_filename
+
350 print
"loading " + s_filename +
"\r"
+
+
+
353 newdatafolder /o/s attr
+
+
+
+
+
+
+
+
+
+
+
+
+
366 Abort
"HDF5 XOP not loaded."
+
+
+
369 if (timerRefNum >= 0)
+
370 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
+
+
+
+
+
+
+
+
+
+
+
+
+
+
398 if (ParamIsDefault(load_data))
+
+
+
401 if (ParamIsDefault(load_attr))
+
+
+
+
405 dfref saveDF = GetDataFolderDFR()
+
+
407 newdatafolder /o/s pearl_area
+
408 newdatafolder /o/s preview
+
+
+
+
412 string instrumentpath = "/entry/instrument/"
+
413 string detectorpath = instrumentpath + "detector/"
+
414 string attributespath = instrumentpath + "NDAttributes/"
+
+
+
+
+
+
420 variable /g adh5_perf_secs
+
421 timerRefNum = startMSTimer
+
+
+
424 #if Exists("HDF5OpenFile")
+
425 HDF5OpenFile /P=$APathName/R/Z fileID as AFileName
+
+
427 AFileName = s_path + s_filename
+
+
+
430 datasetname = detectorpath +
"data"
+
431 STRUCT HDF5DataInfo di
+
+
433 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
+
+
435 print
"error accessing detector/data"
+
+
+
+
439 print
"error: rank of dataset < 2"
+
+
+
+
443 variable dim2start = 0, dim2count = 1, dim3start = 0, dim3count = 1
+
+
445 dim2start = floor(di.dims[di.ndims - 3] / 2)
+
+
+
+
449 dim3start = floor(di.dims[di.ndims - 4] / 2)
+
+
+
+
+
+
+
456 string destpath = GetDataFolder(1, saveDF) + ANickName
+
457 if (waveexists(data))
+
458 duplicate /o data, $destpath
+
459 wave /z data = $destpath
+
+
+
+
+
+
465 newdatafolder /o/s attr
+
+
+
+
469 if (waveexists(data))
+
+
+
+
+
+
+
476 print "error opening file " + AFileName
+
+
+
+
480 Abort
"HDF5 XOP not loaded."
+
+
+
483 if (timerRefNum >= 0)
+
484 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
+
+
+
+
+
+
+
+
+
+
+
505 dfref saveDF = GetDataFolderDFR()
+
+
+
+
509 string instrumentpath = "/entry/instrument/"
+
510 string detectorpath = instrumentpath + "detector/"
+
511 string attributespath = instrumentpath + "NDAttributes/"
+
+
+
+
+
+
+
+
+
+
521 #if Exists("HDF5OpenFile")
+
522 HDF5OpenFile /P=$APathName/R/Z fileID as AFileName
+
+
524 AFileName = s_path + s_filename
+
+
+
527 datasetname = detectorpath +
"data"
+
528 STRUCT HDF5DataInfo di
+
+
530 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
+
+
532 print
"error accessing detector/data"
+
+
+
+
536 for (idim = 0; idim < di.ndims; idim += 1)
+
537 sprintf s,
"dim %u: %u points" , idim, di.dims[idim]
+
538 if (strlen(s_info) > 0)
+
539 s_info = s_info +
"\r" + s
+
+
+
+
+
+
545 dfref df = NewFreeDataFolder()
+
+
+
+
549 for (idim = 1; idim < 5; idim += 1)
+
550 sprintf s, "Scan%uActive", idim
+
+
552 if (waveexists(w) && (numpnts(w) > 0) && (w[0] > 0))
+
553 sprintf s, "Scan%uPositioner1", idim
+
+
555 sprintf s, "scan %u: %s", idim, wt[0]
+
556 if (strlen(s_info) > 0)
+
557 s_info = s_info + "\r" + s
+
+
+
+
+
+
+
+
+
566 print "error opening file " + AFileName
+
+
+
+
570 Abort
"HDF5 XOP not loaded."
+
+
+
+
+
+
+
+
+
+
+
+
590 #if Exists("HDF5LoadData")
+
+
+
+
+
595 datasetname = detectorpath +
"data"
+
596 STRUCT HDF5DataInfo di
+
+
598 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
+
+
600 print
"error accessing detector/data"
+
+
+
+
604 print
"error: rank of dataset < 2"
+
+
+
+
608 HDF5LoadData /O /Q /Z fileID, datasetname
+
+
+
+
612 Abort
"HDF5 XOP not loaded."
+
+
+
+
+
+
+
633 duplicate /free data, tempdata
+
634 variable nd = wavedims(tempdata)
+
635 variable nx = dimsize(tempdata, nd - 1)
+
636 variable ny = dimsize(tempdata, nd - 2)
+
637 variable nz = dimsize(tempdata, nd - 3)
+
638 variable nt = dimsize(tempdata, nd - 4)
+
+
+
+
+
643 redimension /n=(ny) data
+
644 setdimlabel 0, -1, AD_Dim1, data
+
645 data = tempdata[p][0]
+
+
647 redimension /n=(nx) data
+
648 setdimlabel 0, -1, AD_Dim0, data
+
649 data = tempdata[0][p]
+
+
651 redimension /n=(nx,ny) data
+
652 setdimlabel 0, -1, AD_Dim0, data
+
653 setdimlabel 1, -1, AD_Dim1, data
+
654 data = tempdata[q][p]
+
+
+
+
+
659 redimension /n=(ny,nz) data
+
660 setdimlabel 0, -1, AD_Dim1, data
+
661 setdimlabel 1, -1, AD_DimN, data
+
662 multithread data = tempdata[q][p][0]
+
+
664 redimension /n=(nx,nz) data
+
665 setdimlabel 0, -1, AD_Dim0, data
+
666 setdimlabel 1, -1, AD_DimN, data
+
667 multithread data = tempdata[q][0][p]
+
+
669 redimension /n=(nx,ny) data
+
670 setdimlabel 0, -1, AD_Dim0, data
+
671 setdimlabel 1, -1, AD_Dim1, data
+
672 multithread data = tempdata[0][q][p]
+
+
674 redimension /n=(nx,ny,nz) data
+
675 setdimlabel 0, -1, AD_Dim0, data
+
676 setdimlabel 1, -1, AD_Dim1, data
+
677 setdimlabel 2, -1, AD_DimN, data
+
678 multithread data = tempdata[r][q][p]
+
+
+
+
+
+
684 redimension /n=(nx,ny,nt) data
+
685 setdimlabel 0, -1, AD_Dim0, data
+
686 setdimlabel 1, -1, AD_Dim1, data
+
687 setdimlabel 2, -1, AD_DimX, data
+
688 multithread data = tempdata[r][0][q][p]
+
+
690 redimension /n=(nx,ny,nz,nt) data
+
691 setdimlabel 0, -1, AD_Dim0, data
+
692 setdimlabel 1, -1, AD_Dim1, data
+
693 setdimlabel 2, -1, AD_DimN, data
+
694 setdimlabel 3, -1, AD_DimX, data
+
695 multithread data = tempdata[s][r][q][p]
+
+
+
+
+
+
+
+
+
714 dfref dataDF = GetWavesDataFolderDFR(data)
+
715 dfref attrDF = dataDF:attr
+
716 if (DataFolderRefStatus(attrDF) == 0)
+
+
+
+
+
+
+
+
+
+
+
734 dfref saveDF = GetDataFolderDFR()
+
735 dfref dataDF = GetWavesDataFolderDFR(data)
+
+
+
738 if (ParamIsDefault(source))
+
+
740 wave /SDFR=attrDF /Z AcquisitionMode
+
741 wave /SDFR=attrDF /T /Z Manufacturer
+
+
743 if (waveexists(Manufacturer) && (numpnts(Manufacturer) >= 1))
+
744 strswitch(Manufacturer[0])
+
+
+
+
+
+
+
+
752 elseif (waveexists(AcquisitionMode) && (numpnts(AcquisitionMode) >= 1))
+
753 if (stringmatch(note(AcquisitionMode), "*SCIENTA*"))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
789 if (ParamIsDefault(progress))
+
+
+
+
+
+
795 #if Exists("HDF5LoadData")
+
+
+
+
+
800 datasetname = detectorpath +
"data"
+
801 STRUCT HDF5DataInfo di
+
+
803 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
+
+
805 print
"error accessing detector/data"
+
+
+
+
809 print
"error: rank of dataset < 2"
+
+
+
+
+
814 variable idx, idy, idz, idt, izt
+
+
+
+
+
+
820 variable nx, ny, nz, nt, nzt
+
+
+
+
+
+
826 make /n=(nx,ny,nz,nt) /o data
+
827 string dim_labels =
"AD_Dim0;AD_Dim1;AD_DimN;AD_DimX;AD_DimY"
+
+
829 dim_label = StringFromList(0, dim_labels,
";" )
+
830 setdimlabel 0, -1, $dim_label, data
+
831 dim_labels = RemoveFromList(dim_label, dim_labels,
";" )
+
832 dim_label = StringFromList(0, dim_labels, ";")
+
833 setdimlabel 1, -1, $dim_label, data
+
834 dim_labels = RemoveFromList(dim_label, dim_labels, ";")
+
+
+
+
838 for (
id = idy - 1; (
id >= 0) && (nz == 1);
id -= 1)
+
+
+
+
842 dim_label = StringFromList(0, dim_labels, ";")
+
843 setdimlabel 2, -1, $dim_label, data
+
+
845 dim_labels = RemoveListItem(0, dim_labels, ";")
+
+
847 for (
id = idz - 1; (
id >= 0) && (nt == 1);
id -= 1)
+
+
+
+
851 dim_label = StringFromList(0, dim_labels, ";")
+
852 setdimlabel 3, -1, $dim_label, data
+
+
854 dim_labels = RemoveListItem(0, dim_labels, ";")
+
+
856 redimension /n=(nx,ny,nz,nt) data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
873 HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4))
+
+
+
+
+
+
879 slab[idx][%Block] = nx
+
880 slab[idy][%Block] = ny
+
+
+
883 for (iz = 0; iz < nz; iz += 1)
+
884 for (it = 0; it < nt; it += 1)
+
885 slab[idz][%Start] = iz
+
886 slab[idt][%Start] = it
+
887 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname
+
+
889 switch (WaveDims(slabdata))
+
+
891 data[][][iz][it] = slabdata[q][p]
+
+
+
894 data[][][iz][it] = slabdata[0][q][p]
+
+
+
897 data[][][iz][it] = slabdata[0][0][q][p]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
915 redimension /n=(nx,ny) data
+
+
917 redimension /n=(nx,ny,nz) data
+
+
+
+
+
+
+
924 Abort
"HDF5 XOP not loaded."
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
958 #if Exists("HDF5LoadData")
+
+
+
+
+
963 datasetname = detectorpath +
"data"
+
964 STRUCT HDF5DataInfo di
+
+
966 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
+
+
968 print
"error accessing detector/data"
+
+
+
+
972 print
"error: rank of dataset < 1"
+
+
+
+
+
977 variable idx, idy, idz, idt
+
+
979 idy = di.ndims >= 2 ? di.ndims - 2 : 1
+
980 idz = di.ndims >= 3 ? di.ndims - 3 : 2
+
981 idt = di.ndims >= 4 ? di.ndims - 4 : 3
+
+
+
+
985 ny = di.ndims >= 2 ? di.dims[idy] : 1
+
+
987 variable dim2end = dim2start + dim2count - 1
+
988 variable dim3end = dim3start + dim3count - 1
+
+
+
+
992 HDF5MakeHyperslabWave(GetDataFolder(1) +
"slab" , max(di.ndims, 4))
+
+
+
+
+
+
998 slab[idx][%Block] = nx
+
999 slab[idy][%Block] = ny
+
+
1001 make /n=(nx,ny)/o/d data
+
+
+
+
1005 for (iz = dim2start; iz <= dim2end; iz += 1)
+
1006 for (it = dim3start; it <= dim3end; it += 1)
+
1007 slab[idz][%Start] = iz
+
1008 slab[idt][%Start] = it
+
1009 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname
+
+
1011 switch (WaveDims(slabdata))
+
+
+
+
+
+
1017 data += slabdata[q][p]
+
+
+
+
1021 data += slabdata[0][q][p]
+
+
+
+
1025 data += slabdata[0][0][q][p]
+
+
+
+
+
+
+
1032 setdimlabel 0, -1, AD_Dim0, data
+
1033 setdimlabel 1, -1, AD_Dim1, data
+
+
+
1036 Abort
"HDF5 XOP not loaded."
+
+
+
+
+
1046 string all_funcs = FunctionList("*", ";", "KIND:6,NPARAMS:2,VALTYPE:8")
+
+
+
+
1050 variable nn = ItemsInList(all_funcs, ";")
+
+
+
+
+
+
+
1057 for (ii = 0; ii < nn; ii += 1)
+
1058 funcname = StringFromList(ii, all_funcs, ";")
+
1059 info = FunctionInfo(funcname)
+
1060 accept = (NumberByKey("RETURNTYPE", info, ":", ";") == 0x4000)
+
1061 accept = accept && (cmpstr(StringByKey("THREADSAFE", info, ":", ";"), "yes") == 0)
+
1062 accept = accept && (NumberByKey("N_PARAMS", info, ":", ";") == 2)
+
1063 accept = accept && (NumberByKey("N_OPT_PARAMS", info, ":", ";") == 0)
+
+
+
1066 accept = accept && (NumberByKey("PARAM_0_TYPE", info, ":", ";") == 0x4002)
+
1067 accept = accept && (NumberByKey("PARAM_1_TYPE", info, ":", ";") == 0x3000)
+
+
+
1070 result = AddListItem(funcname, result, ";")
+
+
+
+
1074 result = SortList(result, ";", 4)
+
+
+
+
+
+
+
+
+
+
1121 make /n=0 /free dest1, dest2
+
+
+
+
+
+
1127 make /n=2 /free /wave results
+
+
+
+
+
+
+
+
+
+
+
1143 redimension /n=(dimsize(image, dim)) profile
+
1144 setscale /p x dimoffset(image, dim), dimdelta(image, dim), waveunits(image, dim), profile
+
1145 setscale d 0, 0, waveunits(image, -1), profile
+
1146 setdimlabel 0, -1, $getdimlabel(image, dim, -1), profile
+
+
+
+
+
+
1174 string reduction_param
+
1175 string result_prefix
+
+
1177 wave /wave results = reduction_func(source, reduction_param)
+
+
+
1180 return reduction_param
+
+
+
1203 function
adh5_reduce_brick (source, reduction_func, reduction_param, result_prefix, [progress, nthreads])
+
+
+
1206 string reduction_param
+
1207 string result_prefix
+
+
+
+
+
1212 if (ParamIsDefault(progress))
+
+
+
1215 if (ParamIsDefault(nthreads))
+
+
+
+
1219 dfref base_df = GetDataFolderDFR()
+
+
1221 string wavenames = ""
+
+
+
1224 variable nx, ny, nz, nt
+
1225 nx = dimsize(source, 0)
+
1226 ny = dimsize(source, 1)
+
1227 nz = dimsize(source, 2)
+
+
+
+
1231 variable nzt = max(nz, 1) * max(nt, 1)
+
+
+
+
1235 nthreads = ThreadProcessorCount
+
+
+
1238 variable threadGroupID = ThreadGroupCreate(nthreads)
+
+
1240 for (ithread = 0; ithread < nthreads; ithread += 1)
+
+
+
+
1244 make /n=(nzt) /df /free processing_folders
+
+
+
+
+
+
+
+
+
1253 variable n_recvd = 0
+
+
+
+
+
+
1259 make /n=0 /free /wave result_waves
+
+
+
+
+
+
+
1266 if (n_sent < max(1, nthreads) * 10 + n_recvd)
+
+
+
+
1270 dfname = "processing_" + num2str(n_sent)
+
1271 NewDataFolder /s $dfname
+
1272 ad_extract_slab (source, nan, nan, nan, nan, iz, iz, "image", pscale=1)
+
+
1274 variable /g r_index = iz
+
1275 variable /g s_index = it
+
1276 string /g func_param = reduction_param
+
+
+
+
+
1281 ThreadGroupPutDF threadGroupID, :
+
+
+
1284 processing_folders[n_sent] = GetDataFolderDFR()
+
1285 string param = func_param
+
1286 wave /wave reduced_waves = reduction_func(image, param)
+
1287 variable /g func_result = numpnts(reduced_waves)
+
+
1289 WaveClear image, reduced_waves
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1303 tmo = min(100, tmo + 10)
+
+
+
+
+
+
1309 dfr = ThreadGroupGetDFR(threadGroupID, tmo)
+
+
1311 dfr = processing_folders[n_recvd]
+
1312 processing_folders[n_recvd] = $""
+
+
+
1315 if (DatafolderRefStatus(dfr) != 0)
+
+
1317 nvar rr = dfr:r_index
+
1318 nvar ss = dfr:s_index
+
1319 nvar func_result = dfr:func_result
+
+
1321 if (func_result < 1)
+
1322 print "error during data reduction."
+
+
+
+
+
+
1328 if (numpnts(result_waves) == 0)
+
1329 redimension /n=(func_result) result_waves
+
1330 for (iw = 0; iw < func_result; iw += 1)
+
1331 sw = "redw_" + num2str(iw)
+
1332 wave profile = dfr:$sw
+
1333 sw = "ReducedData" + num2str(iw+1)
+
1334 make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
+
+
1336 setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
+
1337 setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
+
1338 setscale /p y dimoffset(source, 2), dimdelta(source, 2), waveunits(source, 2), data
+
1339 setscale /p z dimoffset(source, 3), dimdelta(source, 3), waveunits(source, 3), data
+
1340 setscale d 0, 0, waveunits(profile, -1), data
+
1341 note data, note(profile)
+
1342 result_waves[iw] = data
+
+
+
+
+
1347 for (iw = 0; iw < func_result; iw += 1)
+
1348 sw = "redw_" + num2str(iw)
+
1349 wave profile = dfr:$sw
+
1350 wave data = result_waves[iw]
+
1351 data[][rr][ss] = profile[p]
+
+
+
+
1355 KillDataFolder /Z dfr
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1370 while ((n_recvd < nzt) && (result == 0))
+
+
+
+
1374 variable tstatus = ThreadGroupRelease(threadGroupID)
+
+
1376 print "error: thread did not terminate properly."
+
+
+
+
+
+
1382 nw = numpnts(result_waves)
+
+
1384 for (iw = 0; iw < nw; iw += 1)
+
1385 wave /z data = result_waves[iw]
+
1386 if (WaveExists(data))
+
+
1388 redimension /n=(-1, 0, 0) data
+
+
1390 redimension /n=(-1, nz, 0) data
+
+
1392 wavenames += nameofwave(data) + ";"
+
+
+
+
+
+
+
+
1400 setdatafolder base_df
+
+
+
+
+
+
+
+
+
1415 dfref dfr = ThreadGroupGetDFR(0, 1000)
+
1416 if (DataFolderRefStatus(dfr) == 0)
+
+
+
+
+
+
+
+
+
+
1426 wave image = dfr:image
+
1427 svar func_param = dfr:func_param
+
1428 nvar rr = dfr:r_index
+
1429 nvar ss = dfr:s_index
+
+
+
1432 newdatafolder /s outDF
+
1433 variable /g r_index = rr
+
1434 variable /g s_index = ss
+
1435 string param = func_param
+
1436 wave /wave reduced_waves = reduction_func(image, param)
+
1437 variable /g func_result = numpnts(reduced_waves)
+
+
+
+
1441 WaveClear image, reduced_waves
+
1442 ThreadGroupPutDF 0, :
+
+
+
+
+
+
+
+
+
1465 string result_prefix
+
1466 variable start_index
+
+
1468 variable nw = numpnts(results)
+
+
+
1471 for (iw = 0; iw < nw; iw += 1)
+
1472 sw = result_prefix + num2str(iw + start_index)
+
1473 duplicate /o results[iw], $sw
+
+
+
+
+
+
+
+
1503 string reduction_param
+
+
+
+
1507 if (ParamIsDefault(progress))
+
+
+
1510 if (ParamIsDefault(nthreads))
+
+
+
+
+
+
1516 #if Exists("HDF5LoadData")
+
+
+
+
+
1521 datasetname = detectorpath +
"data"
+
1522 STRUCT HDF5DataInfo di
+
1523 InitHDF5DataInfo(di)
+
1524 variable err = HDF5DatasetInfo(fileID, datasetname, 0, di)
+
+
1526 print
"error accessing detector/data"
+
+
+
+
1530 print
"error: rank of dataset < 2"
+
+
+
+
+
1535 variable idx, idy, idz, idt
+
+
+
+
+
+
1541 variable nx, ny, nz, nt
+
+
+
+
+
+
+
+
1549 for (
id = idy - 1; (
id >= 0) && (nz == 1);
id -= 1)
+
1550 if (di.dims[
id ] > 1)
+
+
+
+
+
1555 for (
id = idz - 1; (
id >= 0) && (nt == 1);
id -= 1)
+
1556 if (di.dims[
id ] > 1)
+
+
+
+
+
+
+
+
+
+
+
+
1568 variable nzt = nz * nt
+
+
+
+
1572 HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4))
+
+
+
+
+
+
1578 slab[idx][%Block] = nx
+
1579 slab[idy][%Block] = ny
+
+
+
+
1583 nthreads = ThreadProcessorCount
+
+
+
1586 variable threadGroupID = ThreadGroupCreate(nthreads)
+
+
1588 for (ithread = 0; ithread < nthreads; ithread += 1)
+
+
+
+
1592 make /n=(nzt) /df /free processing_folders
+
+
+
+
+
+
+
1599 make /n=(nx,ny)/d image_template
+
1600 setdimlabel 0, -1, AD_Dim0, image_template
+
1601 setdimlabel 1, -1, AD_Dim1, image_template
+
+
+
+
+
+
+
1608 make /n=0 /free /wave result_waves
+
+
+
1611 for (iz = 0; iz < nz; iz += 1)
+
1612 for (it = 0; it < nt; it += 1)
+
+
1614 slab[idz][%Start] = iz
+
1615 slab[idt][%Start] = it
+
1616 dfname = "processing_" + num2str(izt)
+
1617 newdatafolder /s $dfname
+
1618 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname
+
+
+
1621 duplicate image_template, image
+
1622 variable /g r_index = iz
+
1623 variable /g s_index = it
+
1624 string /g func_param = reduction_param
+
+
+
+
1628 ThreadGroupPutDF threadGroupID, :
+
+
1630 processing_folders[izt] = GetDataFolderDFR()
+
+
1632 wave /wave reduced_waves =
reduce_slab_image (slabdata, image, reduction_func, func_param)
+
1633 variable /g func_result = numpnts(reduced_waves)
+
+
1635 WaveClear slabdata, image, reduced_waves
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1650 killwaves /z slab, image_template
+
+
+
+
+
+
1656 for (izt = 0; (izt < nzt) && (result == 0); izt += 1)
+
+
+
1659 dfr = ThreadGroupGetDFR(threadGroupID, 1000)
+
1660 if (DatafolderRefStatus(dfr) != 0)
+
+
+
+
+
+
+
+
+
+
+
1671 dfr = processing_folders[izt]
+
+
+
+
+
+
+
+
+
+
+
+
+
1684 nvar rr = dfr:r_index
+
1685 nvar ss = dfr:s_index
+
1686 nvar func_result = dfr:func_result
+
+
1688 if (func_result < 1)
+
+
+
+
+
1693 if (numpnts(result_waves) == 0)
+
1694 redimension /n=(func_result) result_waves
+
1695 for (iw = 0; iw < func_result; iw += 1)
+
1696 sw = "redw_" + num2str(iw)
+
1697 wave profile = dfr:$sw
+
1698 sw = "ReducedData" + num2str(iw+1)
+
1699 make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
+
+
1701 setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
+
1702 setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
+
1703 setscale d 0, 0, waveunits(profile, -1), data
+
1704 result_waves[iw] = data
+
+
+
1707 for (iw = 0; iw < func_result; iw += 1)
+
1708 sw = "redw_" + num2str(iw)
+
1709 wave profile = dfr:$sw
+
1710 wave data = result_waves[iw]
+
1711 data[][rr][ss] = profile[p]
+
+
+
+
+
1716 variable tstatus = ThreadGroupRelease(threadGroupID)
+
+
+
+
+
1721 for (izt = 0; izt < nzt; izt += 1)
+
1722 KillDataFolder /Z processing_folders[izt]
+
+
+
+
+
1727 nw = numpnts(result_waves)
+
1728 for (iw = 0; iw < nw; iw += 1)
+
1729 wave data = result_waves[iw]
+
+
1731 redimension /n=(dimsize(data, 0)) data
+
+
1733 redimension /n=(dimsize(data, 0),nz) data
+
1734 setdimlabel 1, -1, AD_DimN, data
+
+
1736 setdimlabel 1, -1, AD_DimN, data
+
1737 setdimlabel 2, -1, AD_DimX, data
+
+
+
+
+
+
+
+
+
1746 Abort
"HDF5 XOP not loaded."
+
+
+
+
+
+
+
+
+
+
1756 dfref dfr = ThreadGroupGetDFR(0, 1000)
+
1757 if (DataFolderRefStatus(dfr) == 0)
+
+
+
+
+
+
+
+
+
+
1767 wave slabdata = dfr:slabdata
+
1768 wave image = dfr:image
+
1769 svar func_param = dfr:func_param
+
1770 nvar rr = dfr:r_index
+
1771 nvar ss = dfr:s_index
+
+
+
1774 newdatafolder /s outDF
+
1775 variable /g r_index = rr
+
1776 variable /g s_index = ss
+
1777 wave /wave reduced_waves =
reduce_slab_image (slabdata, image, reduction_func, func_param)
+
1778 variable /g func_result = numpnts(reduced_waves)
+
+
+
+
1782 WaveClear slabdata, image, reduced_waves
+
1783 ThreadGroupPutDF 0, :
+
+
+
+
+
+
+
1790 threadsafe static function /wave
reduce_slab_image (slabdata, image, reduction_func, reduction_param)
+
+
+
+
1794 string reduction_param
+
+
1796 switch (WaveDims(slabdata))
+
+
1798 image = slabdata[q][p]
+
+
+
1801 image = slabdata[0][q][p]
+
+
+
1804 image = slabdata[0][0][q][p]
+
+
+
+
1808 return reduction_func(image, reduction_param)
+
+
+
+
+
1825 string attributespath
+
+
+
+
+
+
1831 #if Exists("HDF5LoadData")
+
+
+
1834 HDF5ListGroup /F /TYPE=2 fileID, attributespath
+
1835 string h5datasets = S_HDF5ListGroup
+
1836 HDF5ListAttributes /TYPE=1 /Z fileID, attributespath
+
1837 string h5attributes = S_HDF5ListAttributes
+
+
1839 variable nds = ItemsInList(h5datasets,
";" )
+
1840 variable na = ItemsInList(h5attributes, ";")
+
+
+
+
+
+
+
1847 make /n=(nds+na) /t /o IN, ID, IV, IU
+
+
1849 for (ids = 0; ids < nds; ids += 1)
+
1850 datasetname = StringFromList(ids, h5datasets, ";")
+
1851 HDF5LoadData /O/Q fileID, datasetname
+
+
1853 datawavename = StringFromList(0, s_wavenames)
+
+
+
+
1857 HDF5LoadData /A="source"/O/Q/TYPE=2 fileID, datasetname
+
+
+
1860 s_source = source[0]
+
+
+
+
+
+
+
+
+
1869 nds = ItemsInList(h5attributes, ";")
+
+
+
+
1873 for (ids = 0; ids < nds; ids += 1)
+
1874 datasetname = StringFromList(ids, h5attributes, ";")
+
1875 HDF5LoadData /A=datasetname/O/Q/TYPE=1 fileID, attributespath
+
+
1877 datawavename = StringFromList(0, s_wavenames)
+
+
+
+
+
1882 redimension /n=(idest) IN, ID, IV, IU
+
1883 sort {IN, ID}, IN, ID, IV, IU
+
+
+
+
1887 Abort
"HDF5 XOP not loaded."
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1923 if (exists(datawavename) == 1)
+
1924 if (strlen(source) > 0)
+
1925 Note $datawavename,
"PV=" + source
+
+
1927 switch (WaveType($datawavename, 1))
+
+
1929 wave w_attr = $datawavename
+
1930 n_attr = numpnts(w_attr)
+
1931 sprintf s_attr,
"%.12g" , w_attr[0]
+
+
+
1934 wave /t wt_attr = $datawavename
+
1935 n_attr = numpnts(wt_attr)
+
+
+
+
+
+
+
+
1943 ID[idest] = datawavename
+
+
+
+
+
+
+
+
+
+
+
1961 dfref saveDF = GetDataFolderDFR()
+
+
1963 dfref dataDF = GetWavesDataFolderDFR(data)
+
+
+
1966 wave /SDFR=attrDF LensMode
+
1967 wave /SDFR=attrDF /Z ChannelBegin, ChannelEnd
+
1968 wave /SDFR=attrDF /Z SliceBegin, SliceEnd
+
+
+
1971 variable ELow, EHigh, ALow, AHigh
+
+
+
+
1975 strswitch(GetDimLabel(data, 0, -1))
+
+
+
+
+
+
+
+
+
+
1985 strswitch(GetDimLabel(data, 1, -1))
+
+
+
+
+
+
+
+
+
+
+
+
+
1998 ELow = dimoffset(data, EDim)
+
1999 EHigh = dimoffset(data, EDim) + dimdelta(data, EDim) * (dimsize(data, EDim) - 1)
+
+
+
+
2003 ALow = dimoffset(data, ADim)
+
2004 AHigh = dimoffset(data, ADim) + dimdelta(data, ADim) * (dimsize(data, ADim) - 1)
+
+
+
+
+
2009 if (waveexists(LensMode) && (numpnts(LensMode) >= 1))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2025 if (waveexists(ChannelBegin) && waveexists(ChannelEnd) && (numpnts(ChannelBegin) >= 1) && (numpnts(ChannelEnd) >= 1))
+
2026 ELow = ChannelBegin[0]
+
2027 EHigh = ChannelEnd[0]
+
+
2029 if (waveexists(SliceBegin) && waveexists(SliceEnd) && (numpnts(SliceBegin) >= 1) && (numpnts(SliceEnd) >= 1))
+
2030 ALow = SliceBegin[0]
+
+
+
+
+
+
+
2037 setscale /i x ELow, EHigh, EUnit, data
+
+
+
2040 setscale /i y ELow, EHigh, EUnit, data
+
+
+
+
+
2045 setscale /i x ALow, AHigh, AUnit, data
+
+
+
2048 setscale /i y ALow, AHigh, AUnit, data
+
+
+
+
2052 setscale d 0, 0, "arb.", data
+
+
2054 setdatafolder saveDF
+
+
+
+
+
+
2066 dfref saveDF = GetDataFolderDFR()
+
+
2068 dfref dataDF = GetWavesDataFolderDFR(data)
+
2069 wave /SDFR=dataDF AcquisitionMode, DetectorMode, EnergyMode
+
+
2071 wave /SDFR=dataDF /z Scan1Active, Scan2Active
+
2072 wave /SDFR=dataDF /t /z Scan1Positioner1, Scan1Readback1
+
2073 wave /SDFR=dataDF /t /z Scan1Positioner2, Scan1Readback2
+
2074 wave /SDFR=dataDF /t /z Scan2Positioner1, Scan2Readback1
+
2075 wave /SDFR=dataDF /t /z Scan2Positioner2, Scan2Readback2
+
+
+
+
+
+
2081 strswitch(GetDimLabel(data, 0, -1))
+
+
2083 setscale /i x zscale[0], zscale[numpnts(zscale)-1], "", data
+
+
+
2086 strswitch(GetDimLabel(data, 1, -1))
+
+
2088 setscale /i y zscale[0], zscale[numpnts(zscale)-1], "", data
+
+
+
2091 strswitch(GetDimLabel(data, 2, -1))
+
+
2093 setscale /i z zscale[0], zscale[numpnts(zscale)-1], "", data
+
+
+
+
2097 setdatafolder saveDF
+
string adh5_list_reduction_funcs()
get a list of functions which can be used as reduction functions.
static threadsafe variable reduce_slab_worker(funcref reduction_func)
string adh5_load_preview(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
load a single image from a HDF5 file created by the Area Detector software.
string adh5_load_info(string APathName, string AFileName)
load descriptive info from a HDF5 file created by the Area Detector software.
variable ad_load_dialog(string APathName)
load area detector data files selected in a file dialog window
threadsafe variable adh5_get_result_waves(wave results, string result_prefix, variable start_index)
copy waves from wave reference wave into current data folder
static variable read_attribute_info(string datawavename, string source, variable *idest)
sub-function of adh5_loadattr_all.
threadsafe wave ad_profile_x_w(wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
variable adh5_scale_scienta(wave data)
set the energy and angle scales of an area detector dataset from the Scienta analyser.
string adh5_test_reduction_func(wave source, funcref reduction_func, string reduction_param, string result_prefix)
wrapper function for testing reduction functions from the command line.
static dfr GetAttrDataFolderDFR(wave data)
find the attributes data folder of an area detector dataset.
threadsafe variable adh5_setup_profile(wave image, wave profile, variable dim)
set up a one-dimensional wave for a line profile based on a 2D original wave.
variable adh5_loadattr_all(variable fileID, string attributespath)
load an NDAttributes group from an open HDF5 file into the current data folder.
variable adh5_scale_scan(wave data)
scales the extra dimensions of an area detector dataset according to the EPICS scan
variable adh5_reduce_brick(wave source, funcref reduction_func, string reduction_param, string result_prefix, variable progress=defaultValue, variable nthreads=defaultValue)
reduce a three-dimensional intensity distribution
static threadsafe variable reduce_brick_worker(funcref reduction_func)
thread worker for adh5_reduce_brick
string ad_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
generate the name of a data folder based on a file name.
string adh5_load_complete(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
import everything from a HDF5 file created by the Area Detector software.
threadsafe wave ad_profile_y_w(wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
threadsafe wave adh5_default_reduction(wave source, string *param)
function prototype for adh5_load_reduced_detector
threadsafe wave ad_extract_slab(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue)
2D cut through 3D dataset, integrate in normal dimension
variable adh5_redim(wave data)
redimension a multi-dimensional area detector array loaded from HDF5.
variable adh5_load_detector_slabs(variable fileID, string detectorpath, variable progress=defaultValue)
load the detector dataset from the open HDF5 file.
string adh5_load_reduced(string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable load_data=defaultValue, variable load_attr=defaultValue, variable progress=defaultValue)
load and reduce a dataset from a HDF5 file created by the Area Detector software.
variable adh5_load_reduced_detector(variable fileID, string detectorpath, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue)
load a reduced detector dataset from the open HDF5 file.
string PearlCleanupName(string name)
variable adh5_load_detector(variable fileID, string detectorpath)
load the detector dataset from the open HDF5 file.
variable adh5_scale(wave data, string source=defaultValue)
set the dimension scales of an area detector dataset.
static variable BeforeFileOpenHook(variable refNum, string fileName, string path, string type, string creator, variable kind)
callback function for drag&drop of HDF5 files into Igor.
static threadsafe wave reduce_slab_image(wave slabdata, wave image, funcref reduction_func, string reduction_param)
variable adh5_load_detector_image(variable fileID, string detectorpath, variable dim2start, variable dim2count, variable dim3start, variable dim3count)
load a single image from the detector dataset of the open HDF5 file
PEARL Procedures: pearl-area-profiles.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -103,19 +105,19 @@ Namespaces
threadsafe wave ad_extract_rod (wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable sdev=defaultValue, variable pscale=defaultValue) 1D cut through 3D dataset, integrate in normal dimensions More... 1D cut through 3D dataset, integrate in normal dimensions More... threadsafe wave ad_extract_rod_x (wave dataset, variable q1, variable q2, variable r1, variable r2, string destname, variable noavg=defaultValue, variable sdev=defaultValue) 1D cut through 3D dataset along X dimension. More... 1D cut through 3D dataset along X dimension. More... threadsafe wave ad_extract_rod_y (wave dataset, variable p1, variable p2, variable r1, variable r2, string destname, variable noavg=defaultValue, variable sdev=defaultValue) 1D cut through 3D dataset along Y dimension. More... 1D cut through 3D dataset along Y dimension. More... threadsafe wave ad_extract_rod_z (wave dataset, variable p1, variable p2, variable q1, variable q2, string destname, variable noavg=defaultValue, variable sdev=defaultValue) 1D cut through 3D dataset along Z dimension. More... 1D cut through 3D dataset along Z dimension. More... threadsafe wave ad_extract_slab (wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue) 2D cut through 3D dataset, integrate in normal dimension More... 2D cut through 3D dataset, integrate in normal dimension More... threadsafe wave ad_extract_slab_x (wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue) threadsafe wave ad_extract_slab_z (wave dataset, variable r1, variable r2, string destname, variable noavg=defaultValue) threadsafe wave ad_profile_x (wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue) 1D cut through 2D dataset along X dimension, new destination wave. More... 1D cut through 2D dataset along X dimension, new destination wave. More... threadsafe wave ad_profile_x_w (wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue) 1D cut through 2D dataset along X dimension, existing destination wave. More... 1D cut through 2D dataset along X dimension, existing destination wave. More... threadsafe wave ad_profile_y (wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue) 1D cut through 2D dataset along Y dimension, new destination wave. More... 1D cut through 2D dataset along Y dimension, new destination wave. More... threadsafe wave ad_profile_y_w (wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue) 1D cut through 2D dataset along X dimension, existing destination wave. More... 1D cut through 2D dataset along X dimension, existing destination wave. More... threadsafe variable calc_y_profile_mins (wave image) variable ad_collect_multiscan_y (wave dataset, wave positions, wave destwave, variable noavg=defaultValue) collect profiles from a multi-scan. More... collect profiles from a multi-scan. More... profile extraction for multi-dimensional datasets acquired from area detectors.
Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
-
Copyright 2013-15 Paul Scherrer Institut Copyright 2013-15 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-area-profiles.ipf .
@@ -192,7 +194,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); collect profiles from a multi-scan.
Warning experimental: name and interface of this function may change. Definition at line 621 of file pearl-area-profiles.ipf .
+Definition at line 622 of file pearl-area-profiles.ipf .
Definition at line 54 of file pearl-area-profiles.ipf .
+Definition at line 55 of file pearl-area-profiles.ipf .
@@ -361,9 +363,9 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 313 of file pearl-area-profiles.ipf .
+Definition at line 314 of file pearl-area-profiles.ipf .
@@ -644,7 +646,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); 1D cut through 2D dataset along X dimension, new destination wave.
-Definition at line 480 of file pearl-area-profiles.ipf .
+Definition at line 481 of file pearl-area-profiles.ipf .
@@ -840,7 +842,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); 1D cut through 2D dataset along X dimension, existing destination wave.
-Definition at line 504 of file pearl-area-profiles.ipf .
+Definition at line 505 of file pearl-area-profiles.ipf .
@@ -890,7 +892,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); 1D cut through 2D dataset along Y dimension, new destination wave.
-Definition at line 542 of file pearl-area-profiles.ipf .
+Definition at line 543 of file pearl-area-profiles.ipf .
@@ -940,7 +942,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); 1D cut through 2D dataset along X dimension, existing destination wave.
-Definition at line 567 of file pearl-area-profiles.ipf .
+Definition at line 568 of file pearl-area-profiles.ipf .
@@ -960,7 +962,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-area-profiles.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,29 +87,589 @@ $(document).ready(function(){initNavTree('pearl-area-profiles_8ipf_source.html',
pearl-area-profiles.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlAreaProfiles 54 threadsafe
function /wave
ad_extract_rod (dataset, x1, x2, y1, y2, z1, z2, destname, [noavg, sdev, pscale])
56 variable x1, x2, y1, y2, z1, z2
62 if (wavedims(dataset) != 3)
65 if (ParamIsDefault(noavg))
68 if (ParamIsDefault(sdev))
71 if (ParamIsDefault(pscale))
75 variable p1, p2, q1, q2, r1, r2
84 p1 = round((x1 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
85 p2 = round((x2 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
86 q1 = round((y1 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
87 q2 = round((y2 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
88 r1 = round((z1 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
89 r2 = round((z2 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
92 if ((numtype(p1) == 2) || (numtype(p2) == 2))
93 return
ad_extract_rod_x (dataset, min(q1, q2), max(q1, q2), min(r1, r2), max(r1, r2), destname, noavg=noavg, sdev=sdev)
94 elseif ((numtype(q1) == 2) || (numtype(q2) == 2))
95 return
ad_extract_rod_y (dataset, min(p1, p2), max(p1, p2), min(r1, r2), max(r1, r2), destname, noavg=noavg, sdev=sdev)
96 elseif ((numtype(r1) == 2) || (numtype(r2) == 2))
97 return
ad_extract_rod_z (dataset, min(p1, p2), max(p1, p2), min(q1, q2), max(q1, q2), destname, noavg=noavg, sdev=sdev)
106 threadsafe function /wave
ad_extract_rod_x (dataset, q1, q2, r1, r2, destname, [noavg, sdev])
108 variable q1, q2, r1, r2
114 if (ParamIsDefault(noavg))
117 if (ParamIsDefault(sdev))
120 variable avg = !noavg && !sdev
123 q2 = min(q2, dimsize(dataset, 1) - 1)
125 r2 = min(r2, dimsize(dataset, 2) - 1)
127 if (strlen(destname) > 0)
128 duplicate /r=[][q1,q1][r1,r1]/o dataset, $destname
129 wave w_dest = $destname
131 duplicate /r=[][q1,q1][r1,r1] /free dataset, w_dest
133 redimension /n=(dimsize(w_dest, 0)) w_dest
134 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), w_dest
139 for (qq = q1; qq <= q2; qq += 1)
140 for (rr = r1; rr <= r2; rr += 1)
141 w_dest += dataset[p][qq][rr]
147 duplicate /free w_dest, w_squares
149 for (qq = q1; qq <= q2; qq += 1)
150 for (rr = r1; rr <= r2; rr += 1)
151 w_squares += dataset[p][qq][rr]^2
159 w_dest = sqrt( (w_squares - w_dest^2 / nn) / (nn - 1) )
168 threadsafe function /wave
ad_extract_rod_y (dataset, p1, p2, r1, r2, destname, [noavg, sdev])
170 variable p1, p2, r1, r2
176 if (ParamIsDefault(noavg))
179 if (ParamIsDefault(sdev))
182 variable avg = !noavg && !sdev
185 p2 = min(p2, dimsize(dataset, 0) - 1)
187 r2 = min(r2, dimsize(dataset, 2) - 1)
189 if (strlen(destname) > 0)
190 duplicate /r=[p1,p1][][r1,r1]/o dataset, $destname
191 wave w_dest = $destname
193 duplicate /r=[p1,p1][][r1,r1] /free dataset, w_dest
195 redimension /n=(dimsize(w_dest, 1)) w_dest
196 setscale /p x dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), w_dest
201 for (pp = p1; pp <= p2; pp += 1)
202 for (rr = r1; rr <= r2; rr += 1)
203 w_dest += dataset[pp][p][rr]
209 duplicate /free w_dest, w_squares
211 for (pp = p1; pp <= p2; pp += 1)
212 for (rr = r1; rr <= r2; rr += 1)
213 w_squares += dataset[pp][p][rr]^2
222 w_dest = sqrt( (w_squares - w_dest^2 / nn) / (nn - 1) )
231 threadsafe function /wave
ad_extract_rod_z (dataset, p1, p2, q1, q2, destname, [noavg, sdev])
233 variable p1, p2, q1, q2
239 if (ParamIsDefault(noavg))
242 if (ParamIsDefault(sdev))
245 variable avg = !noavg && !sdev
248 p2 = min(p2, dimsize(dataset, 0) - 1)
250 q2 = min(q2, dimsize(dataset, 1) - 1)
252 if (strlen(destname) > 0)
253 duplicate /r=[p1,p1][q1,q1][]/o dataset, $destname
254 wave w_dest = $destname
256 duplicate /r=[p1,p1][q1,q1][] /free dataset, w_dest
258 redimension /n=(dimsize(w_dest, 2)) w_dest
259 setscale /p x dimoffset(dataset, 2), dimdelta(dataset, 2), waveunits(dataset, 2), w_dest
264 for (pp = p1; pp <= p2; pp += 1)
265 for (qq = q1; qq <= q2; qq += 1)
266 w_dest += dataset[pp][qq][p]
272 duplicate /free w_dest, w_squares
274 for (pp = p1; pp <= p2; pp += 1)
275 for (qq = q1; qq <= q2; qq += 1)
276 w_squares += dataset[pp][qq][p]^2
285 w_dest = sqrt( (w_squares - w_dest^2 / nn) / (nn - 1) )
313 threadsafe function /wave
ad_extract_slab (dataset, x1, x2, y1, y2, z1, z2, destname, [noavg, pscale])
315 variable x1, x2, y1, y2, z1, z2
320 if (wavedims(dataset) != 3)
323 if (ParamIsDefault(noavg))
326 if (ParamIsDefault(pscale))
330 variable p1, p2, q1, q2, r1, r2
339 p1 = round((x1 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
340 p2 = round((x2 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
341 q1 = round((y1 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
342 q2 = round((y2 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
343 r1 = round((z1 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
344 r2 = round((z2 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
347 if ((numtype(p1) < 2) && (numtype(p2) < 2))
348 return
ad_extract_slab_x (dataset, min(p1, p2), max(p1, p2), destname, noavg=noavg)
349 elseif ((numtype(q1) < 2) && (numtype(q2) < 2))
350 return
ad_extract_slab_y (dataset, min(q1, q2), max(q1, q2), destname, noavg=noavg)
351 elseif ((numtype(r1) < 2) && (numtype(r2) < 2))
352 return
ad_extract_slab_z (dataset, min(r1, r2), max(r1, r2), destname, noavg=noavg)
367 if (ParamIsDefault(noavg))
371 p2 = min(p2, dimsize(dataset, 0) - 1)
373 if (strlen(destname) > 0)
374 duplicate /r=[p1,p1][][]/o dataset, $destname
375 wave w_dest = $destname
377 duplicate /r=[p1,p1][][] /free dataset, w_dest
379 redimension /n=(dimsize(w_dest, 1), dimsize(w_dest, 2)) w_dest
380 setscale /p x dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), w_dest
381 setscale /p y dimoffset(dataset, 2), dimdelta(dataset, 2), waveunits(dataset, 2), w_dest
386 for (pp = p1; pp <= p2; pp += 1)
387 w_dest += dataset[pp][p][q]
407 if (ParamIsDefault(noavg))
411 q2 = min(q2, dimsize(dataset, 1) - 1)
413 if (strlen(destname) > 0)
414 duplicate /r=[][q1,q1][]/o dataset, $destname
415 wave w_dest = $destname
417 duplicate /r=[][q1,q1][] /free dataset, w_dest
419 redimension /n=(dimsize(w_dest, 0), dimsize(w_dest, 2)) w_dest
420 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), w_dest
421 setscale /p y dimoffset(dataset, 2), dimdelta(dataset, 2), waveunits(dataset, 2), w_dest
426 for (qq = q1; qq <= q2; qq += 1)
427 w_dest += dataset[p][qq][q]
447 if (ParamIsDefault(noavg))
451 r2 = min(r2, dimsize(dataset, 2) - 1)
453 if (strlen(destname) > 0)
454 duplicate /r=[][][r1,r1]/o dataset, $destname
455 wave w_dest = $destname
457 duplicate /r=[][][r1,r1] /free dataset, w_dest
459 redimension /n=(dimsize(w_dest, 0), dimsize(w_dest, 1)) w_dest
460 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), w_dest
461 setscale /p y dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), w_dest
466 for (rr = r1; rr <= r2; rr += 1)
467 w_dest += dataset[p][q][rr]
480 threadsafe function /wave
ad_profile_x (dataset, q1, q2, destname, [noavg])
488 if (ParamIsDefault(noavg))
492 if (strlen(destname) > 0)
493 duplicate /r=[0,0][] /o dataset, $destname
494 wave w_dest = $destname
496 duplicate /r=[0,0][] /free dataset, w_dest
511 if (ParamIsDefault(noavg))
515 redimension /n=(dimsize(dataset, 0)) destwave
516 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), destwave
517 setscale d 0, 0, waveunits(dataset, -1), destwave
523 q2 = min(q2, dimsize(dataset, 1) - 1)
528 for (qq = q1; qq <= q2; qq += 1)
529 destwave += dataset[p][qq]
542 threadsafe function /wave
ad_profile_y (dataset, p1, p2, destname, [noavg])
550 if (ParamIsDefault(noavg))
554 if (strlen(destname) > 0)
555 duplicate /r=[][0,0] /o dataset, $destname
556 wave w_dest = $destname
558 duplicate /r=[][0,0] /free dataset, w_dest
560 MatrixTranspose w_dest
574 if (ParamIsDefault(noavg))
578 redimension /n=(dimsize(dataset, 1)) destwave
579 setscale /p x dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), destwave
580 setscale d 0, 0, waveunits(dataset, -1), destwave
586 p2 = min(p2, dimsize(dataset, 0) - 1)
591 for (pp = p1; pp <= p2; pp += 1)
592 destwave += dataset[pp][p]
607 wave yminlocs =
ad_profile_x (image, 0, 0, "ymins", noavg=1)
608 variable nx = dimsize(image, 0)
610 for (ix = 0; ix < nx; ix += 1)
612 wavestats /q/m=1 profile
613 yminlocs[ix] = v_minloc
627 variable tol = (wavemax(positions) - wavemin(positions)) / numpnts(positions) / 100
629 duplicate /free positions, positions_sorted
630 sort positions_sorted, positions_sorted
631 duplicate /free positions_sorted, positions_diff
632 differentiate /p /meth=2 positions_sorted /d=positions_diff
633 positions_diff[0] = 1
634 extract /free positions_sorted, positions_unique, positions_diff > tol
635 variable n_unique = numpnts(positions_unique)
636 redimension /n=(dimsize(dataset, 0), n_unique) destwave
640 for (i = 0; i < n_unique; i += 1)
641 extract /free dataset, data_extract, abs(positions[q] - positions_unique[i]) < tol
642 nx = dimsize(dataset, 0)
643 ny = dimsize(data_extract, 0) / nx
644 redimension /n=(nx, ny) data_extract
645 wave profile =
ad_profile_x (data_extract, -inf, inf, "", noavg=noavg)
646 destwave[][i] = profile[p]
threadsafe wave ad_extract_slab_x(wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue)
-
threadsafe wave ad_extract_rod_x(wave dataset, variable q1, variable q2, variable r1, variable r2, string destname, variable noavg=defaultValue, variable sdev=defaultValue)
1D cut through 3D dataset along X dimension.
-
threadsafe wave ad_profile_y(wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along Y dimension, new destination wave.
-
threadsafe wave ad_profile_x_w(wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
-
threadsafe wave ad_extract_slab_z(wave dataset, variable r1, variable r2, string destname, variable noavg=defaultValue)
-
variable ad_collect_multiscan_y(wave dataset, wave positions, wave destwave, variable noavg=defaultValue)
collect profiles from a multi-scan.
-
threadsafe wave ad_extract_slab_y(wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue)
-
threadsafe wave ad_extract_rod_z(wave dataset, variable p1, variable p2, variable q1, variable q2, string destname, variable noavg=defaultValue, variable sdev=defaultValue)
1D cut through 3D dataset along Z dimension.
-
threadsafe wave ad_profile_y_w(wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
-
threadsafe wave ad_extract_rod_y(wave dataset, variable p1, variable p2, variable r1, variable r2, string destname, variable noavg=defaultValue, variable sdev=defaultValue)
1D cut through 3D dataset along Y dimension.
-
threadsafe variable calc_y_profile_mins(wave image)
-
threadsafe wave ad_profile_x(wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, new destination wave.
-
threadsafe wave ad_extract_rod(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable sdev=defaultValue, variable pscale=defaultValue)
1D cut through 3D dataset, integrate in normal dimensions
-
threadsafe wave ad_extract_slab(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue)
2D cut through 3D dataset, integrate in normal dimension
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.1
+
4 #pragma ModuleName = PearlAreaProfiles
+
+
+
+
+
55 threadsafe
function /wave
ad_extract_rod (dataset, x1, x2, y1, y2, z1, z2, destname, [noavg, sdev, pscale])
+
+
57 variable x1, x2, y1, y2, z1, z2
+
+
+
+
+
+
63 if (wavedims(dataset) != 3)
+
+
+
66 if (ParamIsDefault(noavg))
+
+
+
69 if (ParamIsDefault(sdev))
+
+
+
72 if (ParamIsDefault(pscale))
+
+
+
+
76 variable p1, p2, q1, q2, r1, r2
+
+
+
+
+
+
+
+
+
85 p1 = round((x1 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
+
86 p2 = round((x2 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
+
87 q1 = round((y1 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
+
88 q2 = round((y2 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
+
89 r1 = round((z1 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
+
90 r2 = round((z2 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
+
+
+
93 if ((numtype(p1) == 2) || (numtype(p2) == 2))
+
94 return
ad_extract_rod_x (dataset, min(q1, q2), max(q1, q2), min(r1, r2), max(r1, r2), destname, noavg=noavg, sdev=sdev)
+
95 elseif ((numtype(q1) == 2) || (numtype(q2) == 2))
+
96 return
ad_extract_rod_y (dataset, min(p1, p2), max(p1, p2), min(r1, r2), max(r1, r2), destname, noavg=noavg, sdev=sdev)
+
97 elseif ((numtype(r1) == 2) || (numtype(r2) == 2))
+
98 return
ad_extract_rod_z (dataset, min(p1, p2), max(p1, p2), min(q1, q2), max(q1, q2), destname, noavg=noavg, sdev=sdev)
+
+
+
+
+
+
107 threadsafe function /wave
ad_extract_rod_x (dataset, q1, q2, r1, r2, destname, [noavg, sdev])
+
+
109 variable q1, q2, r1, r2
+
+
+
+
+
+
115 if (ParamIsDefault(noavg))
+
+
+
118 if (ParamIsDefault(sdev))
+
+
+
121 variable avg = !noavg && !sdev
+
+
+
124 q2 = min(q2, dimsize(dataset, 1) - 1)
+
+
126 r2 = min(r2, dimsize(dataset, 2) - 1)
+
+
128 if (strlen(destname) > 0)
+
129 duplicate /r=[][q1,q1][r1,r1]/o dataset, $destname
+
130 wave w_dest = $destname
+
+
132 duplicate /r=[][q1,q1][r1,r1] /free dataset, w_dest
+
+
134 redimension /n=(dimsize(w_dest, 0)) w_dest
+
135 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), w_dest
+
+
+
+
+
140 for (qq = q1; qq <= q2; qq += 1)
+
141 for (rr = r1; rr <= r2; rr += 1)
+
142 w_dest += dataset[p][qq][rr]
+
+
+
+
+
+
148 duplicate /free w_dest, w_squares
+
+
150 for (qq = q1; qq <= q2; qq += 1)
+
151 for (rr = r1; rr <= r2; rr += 1)
+
152 w_squares += dataset[p][qq][rr]^2
+
+
+
+
+
+
+
+
160 w_dest = sqrt( (w_squares - w_dest^2 / nn) / (nn - 1) )
+
+
+
+
+
+
169 threadsafe function /wave
ad_extract_rod_y (dataset, p1, p2, r1, r2, destname, [noavg, sdev])
+
+
171 variable p1, p2, r1, r2
+
+
+
+
+
+
177 if (ParamIsDefault(noavg))
+
+
+
180 if (ParamIsDefault(sdev))
+
+
+
183 variable avg = !noavg && !sdev
+
+
+
186 p2 = min(p2, dimsize(dataset, 0) - 1)
+
+
188 r2 = min(r2, dimsize(dataset, 2) - 1)
+
+
190 if (strlen(destname) > 0)
+
191 duplicate /r=[p1,p1][][r1,r1]/o dataset, $destname
+
192 wave w_dest = $destname
+
+
194 duplicate /r=[p1,p1][][r1,r1] /free dataset, w_dest
+
+
196 redimension /n=(dimsize(w_dest, 1)) w_dest
+
197 setscale /p x dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), w_dest
+
+
+
+
+
202 for (pp = p1; pp <= p2; pp += 1)
+
203 for (rr = r1; rr <= r2; rr += 1)
+
204 w_dest += dataset[pp][p][rr]
+
+
+
+
+
+
210 duplicate /free w_dest, w_squares
+
+
212 for (pp = p1; pp <= p2; pp += 1)
+
213 for (rr = r1; rr <= r2; rr += 1)
+
214 w_squares += dataset[pp][p][rr]^2
+
+
+
+
+
+
+
+
+
223 w_dest = sqrt( (w_squares - w_dest^2 / nn) / (nn - 1) )
+
+
+
+
+
+
232 threadsafe function /wave
ad_extract_rod_z (dataset, p1, p2, q1, q2, destname, [noavg, sdev])
+
+
234 variable p1, p2, q1, q2
+
+
+
+
+
+
240 if (ParamIsDefault(noavg))
+
+
+
243 if (ParamIsDefault(sdev))
+
+
+
246 variable avg = !noavg && !sdev
+
+
+
249 p2 = min(p2, dimsize(dataset, 0) - 1)
+
+
251 q2 = min(q2, dimsize(dataset, 1) - 1)
+
+
253 if (strlen(destname) > 0)
+
254 duplicate /r=[p1,p1][q1,q1][]/o dataset, $destname
+
255 wave w_dest = $destname
+
+
257 duplicate /r=[p1,p1][q1,q1][] /free dataset, w_dest
+
+
259 redimension /n=(dimsize(w_dest, 2)) w_dest
+
260 setscale /p x dimoffset(dataset, 2), dimdelta(dataset, 2), waveunits(dataset, 2), w_dest
+
+
+
+
+
265 for (pp = p1; pp <= p2; pp += 1)
+
266 for (qq = q1; qq <= q2; qq += 1)
+
267 w_dest += dataset[pp][qq][p]
+
+
+
+
+
+
273 duplicate /free w_dest, w_squares
+
+
275 for (pp = p1; pp <= p2; pp += 1)
+
276 for (qq = q1; qq <= q2; qq += 1)
+
277 w_squares += dataset[pp][qq][p]^2
+
+
+
+
+
+
+
+
+
286 w_dest = sqrt( (w_squares - w_dest^2 / nn) / (nn - 1) )
+
+
+
+
+
+
314 threadsafe function /wave
ad_extract_slab (dataset, x1, x2, y1, y2, z1, z2, destname, [noavg, pscale])
+
+
316 variable x1, x2, y1, y2, z1, z2
+
+
+
+
+
321 if (wavedims(dataset) != 3)
+
+
+
324 if (ParamIsDefault(noavg))
+
+
+
327 if (ParamIsDefault(pscale))
+
+
+
+
331 variable p1, p2, q1, q2, r1, r2
+
+
+
+
+
+
+
+
+
340 p1 = round((x1 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
+
341 p2 = round((x2 - DimOffset(dataset, 0)) / DimDelta(dataset, 0))
+
342 q1 = round((y1 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
+
343 q2 = round((y2 - DimOffset(dataset, 1)) / DimDelta(dataset, 1))
+
344 r1 = round((z1 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
+
345 r2 = round((z2 - DimOffset(dataset, 2)) / DimDelta(dataset, 2))
+
+
+
348 if ((numtype(p1) < 2) && (numtype(p2) < 2))
+
349 return
ad_extract_slab_x (dataset, min(p1, p2), max(p1, p2), destname, noavg=noavg)
+
350 elseif ((numtype(q1) < 2) && (numtype(q2) < 2))
+
351 return
ad_extract_slab_y (dataset, min(q1, q2), max(q1, q2), destname, noavg=noavg)
+
352 elseif ((numtype(r1) < 2) && (numtype(r2) < 2))
+
353 return
ad_extract_slab_z (dataset, min(r1, r2), max(r1, r2), destname, noavg=noavg)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
368 if (ParamIsDefault(noavg))
+
+
+
+
372 p2 = min(p2, dimsize(dataset, 0) - 1)
+
+
374 if (strlen(destname) > 0)
+
375 duplicate /r=[p1,p1][][]/o dataset, $destname
+
376 wave w_dest = $destname
+
+
378 duplicate /r=[p1,p1][][] /free dataset, w_dest
+
+
380 redimension /n=(dimsize(w_dest, 1), dimsize(w_dest, 2)) w_dest
+
381 setscale /p x dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), w_dest
+
382 setscale /p y dimoffset(dataset, 2), dimdelta(dataset, 2), waveunits(dataset, 2), w_dest
+
+
+
+
+
387 for (pp = p1; pp <= p2; pp += 1)
+
388 w_dest += dataset[pp][p][q]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
408 if (ParamIsDefault(noavg))
+
+
+
+
412 q2 = min(q2, dimsize(dataset, 1) - 1)
+
+
414 if (strlen(destname) > 0)
+
415 duplicate /r=[][q1,q1][]/o dataset, $destname
+
416 wave w_dest = $destname
+
+
418 duplicate /r=[][q1,q1][] /free dataset, w_dest
+
+
420 redimension /n=(dimsize(w_dest, 0), dimsize(w_dest, 2)) w_dest
+
421 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), w_dest
+
422 setscale /p y dimoffset(dataset, 2), dimdelta(dataset, 2), waveunits(dataset, 2), w_dest
+
+
+
+
+
427 for (qq = q1; qq <= q2; qq += 1)
+
428 w_dest += dataset[p][qq][q]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
448 if (ParamIsDefault(noavg))
+
+
+
+
452 r2 = min(r2, dimsize(dataset, 2) - 1)
+
+
454 if (strlen(destname) > 0)
+
455 duplicate /r=[][][r1,r1]/o dataset, $destname
+
456 wave w_dest = $destname
+
+
458 duplicate /r=[][][r1,r1] /free dataset, w_dest
+
+
460 redimension /n=(dimsize(w_dest, 0), dimsize(w_dest, 1)) w_dest
+
461 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), w_dest
+
462 setscale /p y dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), w_dest
+
+
+
+
+
467 for (rr = r1; rr <= r2; rr += 1)
+
468 w_dest += dataset[p][q][rr]
+
+
+
+
+
+
+
+
+
+
+
481 threadsafe function /wave
ad_profile_x (dataset, q1, q2, destname, [noavg])
+
+
+
+
+
+
+
+
489 if (ParamIsDefault(noavg))
+
+
+
+
493 if (strlen(destname) > 0)
+
494 duplicate /r=[0,0][] /o dataset, $destname
+
495 wave w_dest = $destname
+
+
497 duplicate /r=[0,0][] /free dataset, w_dest
+
+
+
+
+
+
+
+
+
+
+
+
+
512 if (ParamIsDefault(noavg))
+
+
+
+
516 redimension /n=(dimsize(dataset, 0)) destwave
+
517 setscale /p x dimoffset(dataset, 0), dimdelta(dataset, 0), waveunits(dataset, 0), destwave
+
518 setscale d 0, 0, waveunits(dataset, -1), destwave
+
+
+
+
+
+
524 q2 = min(q2, dimsize(dataset, 1) - 1)
+
+
+
+
+
529 for (qq = q1; qq <= q2; qq += 1)
+
530 destwave += dataset[p][qq]
+
+
+
+
+
+
+
+
+
+
+
543 threadsafe function /wave
ad_profile_y (dataset, p1, p2, destname, [noavg])
+
+
+
+
+
+
+
+
551 if (ParamIsDefault(noavg))
+
+
+
+
555 if (strlen(destname) > 0)
+
556 duplicate /r=[][0,0] /o dataset, $destname
+
557 wave w_dest = $destname
+
+
559 duplicate /r=[][0,0] /free dataset, w_dest
+
+
561 MatrixTranspose w_dest
+
+
+
+
+
+
+
+
+
+
+
+
575 if (ParamIsDefault(noavg))
+
+
+
+
579 redimension /n=(dimsize(dataset, 1)) destwave
+
580 setscale /p x dimoffset(dataset, 1), dimdelta(dataset, 1), waveunits(dataset, 1), destwave
+
581 setscale d 0, 0, waveunits(dataset, -1), destwave
+
+
+
+
+
+
587 p2 = min(p2, dimsize(dataset, 0) - 1)
+
+
+
+
+
592 for (pp = p1; pp <= p2; pp += 1)
+
593 destwave += dataset[pp][p]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
608 wave yminlocs =
ad_profile_x (image, 0, 0, "ymins", noavg=1)
+
609 variable nx = dimsize(image, 0)
+
+
611 for (ix = 0; ix < nx; ix += 1)
+
+
613 wavestats /q/m=1 profile
+
614 yminlocs[ix] = v_minloc
+
+
+
+
+
+
+
+
+
+
628 variable tol = (wavemax(positions) - wavemin(positions)) / numpnts(positions) / 100
+
+
630 duplicate /free positions, positions_sorted
+
631 sort positions_sorted, positions_sorted
+
632 duplicate /free positions_sorted, positions_diff
+
633 differentiate /p /meth=2 positions_sorted /d=positions_diff
+
634 positions_diff[0] = 1
+
635 extract /free positions_sorted, positions_unique, positions_diff > tol
+
636 variable n_unique = numpnts(positions_unique)
+
637 redimension /n=(dimsize(dataset, 0), n_unique) destwave
+
+
+
+
641 for (i = 0; i < n_unique; i += 1)
+
642 extract /free dataset, data_extract, abs(positions[q] - positions_unique[i]) < tol
+
643 nx = dimsize(dataset, 0)
+
644 ny = dimsize(data_extract, 0) / nx
+
645 redimension /n=(nx, ny) data_extract
+
646 wave profile =
ad_profile_x (data_extract, -inf, inf, "", noavg=noavg)
+
647 destwave[][i] = profile[p]
+
+
threadsafe variable calc_y_profile_mins(wave image)
threadsafe wave ad_profile_x(wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, new destination wave.
threadsafe wave ad_profile_x_w(wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
threadsafe wave ad_profile_y(wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue)
1D cut through 2D dataset along Y dimension, new destination wave.
threadsafe wave ad_extract_rod_x(wave dataset, variable q1, variable q2, variable r1, variable r2, string destname, variable noavg=defaultValue, variable sdev=defaultValue)
1D cut through 3D dataset along X dimension.
threadsafe wave ad_extract_rod_z(wave dataset, variable p1, variable p2, variable q1, variable q2, string destname, variable noavg=defaultValue, variable sdev=defaultValue)
1D cut through 3D dataset along Z dimension.
variable ad_collect_multiscan_y(wave dataset, wave positions, wave destwave, variable noavg=defaultValue)
collect profiles from a multi-scan.
threadsafe wave ad_extract_slab_z(wave dataset, variable r1, variable r2, string destname, variable noavg=defaultValue)
threadsafe wave ad_extract_rod(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable sdev=defaultValue, variable pscale=defaultValue)
1D cut through 3D dataset, integrate in normal dimensions
threadsafe wave ad_profile_y_w(wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
threadsafe wave ad_extract_slab(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue)
2D cut through 3D dataset, integrate in normal dimension
threadsafe wave ad_extract_slab_y(wave dataset, variable q1, variable q2, string destname, variable noavg=defaultValue)
threadsafe wave ad_extract_slab_x(wave dataset, variable p1, variable p2, string destname, variable noavg=defaultValue)
threadsafe wave ad_extract_rod_y(wave dataset, variable p1, variable p2, variable r1, variable r2, string destname, variable noavg=defaultValue, variable sdev=defaultValue)
1D cut through 3D dataset along Y dimension.
PEARL Procedures: pearl-arpes.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -114,7 +116,7 @@ Namespaces
static variable AfterCompiledHook () initializes package data once when the procedure is first loaded More... initializes package data once when the procedure is first loaded More... variable UnloadPearlArpesPackage () Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch Copyright 2012-18 Paul Scherrer Institut Copyright 2012-18 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-arpes.ipf .
@@ -160,7 +162,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); initializes package data once when the procedure is first loaded
-Definition at line 77 of file pearl-arpes.ipf .
+Definition at line 78 of file pearl-arpes.ipf .
@@ -179,7 +181,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-arpes.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,17 +87,55 @@ $(document).ready(function(){initNavTree('pearl-arpes_8ipf_source.html','');});
pearl-arpes.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlArpes 5 #include "pearl-area-display" 6 #include "pearl-area-profiles" 7 #include "pearl-area-import" 8 #include "pearl-pshell-import" 9 #include "pearl-compat" 10 #include "pearl-data-explorer" 11 #include "pearl-anglescan-process" 12 #include "pearl-anglescan-panel" 13 #include "pearl-anglescan-tracker" 14 #include "pearl-scienta-preprocess" 17 #include "pearl-area-live" 18 #include "pearl-epics" 19 #include "pearl-arpes-scans" 20 #include "pearl-sample-tracker" 21 #include "pearl-scienta-countrate" 79 dfref savefolder = GetDataFolderDFR()
85 execute /p/q/z "DELETEINCLUDE \"pearl-arpes\""
86 execute /p/q/z "COMPILEPROCEDURES "
variable UnloadPearlArpesPackage()
-
static variable AfterCompiledHook()
initializes package data once when the procedure is first loaded
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.1
+
4 #pragma ModuleName = PearlArpes
+
+
6 #include "pearl-area-display"
+
7 #include "pearl-area-profiles"
+
8 #include "pearl-area-import"
+
9 #include "pearl-pshell-import"
+
10 #include "pearl-compat"
+
11 #include "pearl-data-explorer"
+
12 #include "pearl-anglescan-process"
+
13 #include "pearl-anglescan-panel"
+
14 #include "pearl-anglescan-tracker"
+
15 #include "pearl-scienta-preprocess"
+
+
+
18 #include "pearl-area-live"
+
19 #include "pearl-epics"
+
20 #include "pearl-arpes-scans"
+
21 #include "pearl-sample-tracker"
+
22 #include "pearl-scienta-live"
+
+
+
+
+
+
+
+
80 dfref savefolder = GetDataFolderDFR()
+
+
+
+
+
+
86 execute /p/q/z "DELETEINCLUDE \"pearl-arpes\""
+
87 execute /p/q/z "COMPILEPROCEDURES "
+
static variable AfterCompiledHook()
initializes package data once when the procedure is first loaded
variable UnloadPearlArpesPackage()
PEARL Procedures: pearl-compat.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -131,7 +133,7 @@ Functions
@@ -141,9 +143,9 @@ Functions
diff --git a/doc/html/pearl-compat_8ipf_source.html b/doc/html/pearl-compat_8ipf_source.html
index 2508edc..37e5096 100644
--- a/doc/html/pearl-compat_8ipf_source.html
+++ b/doc/html/pearl-compat_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-compat.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,16 +87,58 @@ $(document).ready(function(){initNavTree('pearl-compat_8ipf_source.html','');});
pearl-compat.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlCompat 50 #if IgorVersion() >= 8.00 52 return CleanupName(name, 0, 31)
54 return CleanupName(name, 0)
string PearlCleanupName(string name)
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.1
+
4 #pragma ModuleName = PearlCompat
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
51 #if IgorVersion() >= 8.00
+
+
53 return CleanupName(name, 0, 31)
+
+
55 return CleanupName(name, 0)
+
+
+
string PearlCleanupName(string name)
PEARL Procedures: pearl-data-explorer.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -82,17 +84,14 @@ $(document).ready(function(){initNavTree('pearl-data-explorer_8ipf.html','');});
-
-
preview and import panel for PEARL data
-More...
-
#include "pearl-area-import"
+
#include <HierarchicalListWidget>#include "pearl-area-import"#include "pearl-area-profiles"#include "pearl-area-display"#include "pearl-compat"
Go to the source code of this file.
variable pearl_data_explorer () show the pearl data explorer window More... static variable init_package () initialize the global variables of the data explorer. More... static variable save_prefs () save persistent package data to the preferences file. More... save persistent package data to the preferences file. More... static variable load_prefs () static variable pearl_file_type (string filename) check whether a file can be imported by this module. More... check whether a file can be imported by this module. More... static variable update_filepath () update the file path after path change More... static variable update_filelist () read a list of PEARL files from the file system More... read a list of PEARL files from the file system More... static variable update_datasets () static variable get_file_info (string filename) load the internal structure of a file More... static variable attributes_notebook (string filename) load attributes More... static variable extract_attributes (dfref attr_df, dfref dest_df=defaultValue, wave attr_filter=defaultValue, variable include_datawaves=defaultValue, variable include_infowaves=defaultValue) extract summary from attribute waves More... variable test_attributes_notebook () static variable create_attributes_notebook (wave attr_names, wave attr_values, string title) static variable notebook_add_attributes (string notebook_name, wave attr_filter, wave attr_names, wave attr_values) static variable set_elog_attributes (dfref file_df, string filename=defaultValue, string graphname=defaultValue) send general metadata to ELOG panel - if available More... static variable preview_file (string filename) static wave preview_pshell_file (string filename) load the preview of a PShell HDF5 file. More... load the preview of a PShell HDF5 file. More... static wave preview_hdf_file (string filename) load the preview of a PEARL HDF5 file. More... load the preview of a PEARL HDF5 file. More... static wave preview_itx_file (string filename) load the preview of a general ITX file. More... load the preview of a general ITX file. More... static wave preview_mtrx_file (string filename) load the preview of a Matrix STM file. More... static variable extract_preview_image (wave data, wave preview) extract a preview image from a wave of arbitrary dimension More... static variable preview_dataset (string datasetname) static variable preview_datafolder () preview data in the current data folder More... static variable preview_setscale_x (wave data, wave preview) static variable preview_attributes (dfref attr_folder, dfref dest_folder=defaultValue, wave attr_filter=defaultValue, variable include_datawaves=defaultValue, variable include_infowaves=defaultValue) static variable display_dataset (string datasetname) variable test_attributes_notebook () static variable attributes_notebook (wave attr_names, wave attr_values, string title) static variable notebook_add_attributes (string notebook_name, wave attr_filter, wave attr_names, wave attr_values) static variable display_dataset (dfref file_df, string dataset) displays the graph of a loaded dataset in its own window More... static string show_preview_graph (wave data, wave xdata=defaultValue) static string display_preview_trace (wave xtrace, wave ytrace) static variable load_selected_files (string options=defaultValue) load the selected files More... static variable load_file (string filename, string options=defaultValue) static variable load_file (string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue) load one file More... static variable prompt_hdf_options (string *options) variable prompt_default_process (string *param) prototype for prompting for processing function parameters. More... prototype for prompting for processing function parameters. More... variable prompt_func_params (string func_name, string *func_param) static dfr load_pshell_file (string filename, string options=defaultValue) static dfr load_hdf_file (string filename, string options=defaultValue) static dfr load_itx_file (string filename, string options=defaultValue) static dfr load_mtrx_file (string filename, string options=defaultValue) load a matrix (STM) data file More... static dfr load_pshell_file (string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue) load a pshell file More... static dfr load_hdf_file (string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue) static dfr load_itx_file (string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue) string itx_suggest_foldername (string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue) suggest the name of a data folder based on an igor-text file name More... void PearlDataExplorer () static variable update_controls () update controls state More... static variable bp_load_prefs (WMButtonAction *ba) static variable bp_save_prefs (WMButtonAction *ba) static string shorten_filepath (string long_path, variable max_len) shorten a file path for display More... static variable bp_browse_filepath (WMButtonAction *ba) static variable bp_update_filelist (WMButtonAction *ba) static variable bp_load_files (WMButtonAction *ba) static variable bp_load_files_opt (WMButtonAction *ba) static string pm_reduction_values () items for data reduction popup More... static variable pmp_reduction_func (WMPopupAction *pa) static variable bp_reduction_params (WMButtonAction *ba) static variable bp_load_options (WMButtonAction *ba) static variable selected_file (string file, variable do_preview) actions after a file has been selected More... static variable bp_file_next (WMButtonAction *ba) static variable bp_file_prev (WMButtonAction *ba) static variable lbp_filelist (WMListboxAction *lba) static variable bp_update_datasets (WMButtonAction *ba) static variable bp_dataset_folder (WMButtonAction *ba) static variable bp_dataset_display (WMButtonAction *ba) static variable bp_dataset_next (WMButtonAction *ba) static variable bp_dataset_prev (WMButtonAction *ba) static variable lbp_datasets (WMListboxAction *lba) static variable bp_attr_notebook (WMButtonAction *ba) static variable hlp_setup () static variable hl_contents_clear () static variable hl_contents_update (dfref file_df) populate the contents list box with the internal directory of a HDF5 file More... static dfr get_pshell_info (string path_name, string file_name, dfref dest_df=defaultValue) static variable hl_add_objects (string parent_path, string objects) populate the contents list box with the given hierarchical paths More... static variable hl_expand_scans () static variable hl_default_selection () static variable hlp_contents_open (string HostWindow, string ListControlName, string ContainerPath) static variable hlp_contents_selection (string HostWindow, string ListControlName, string SelectedItem, variable EventCode) static variable goto_dataset_folder (string filename, string datapath) open data folder corresponding to a file and data path More... static variable bp_goto_dataset (WMButtonAction *ba) "goto DF" button More... static variable bp_display_dataset (WMButtonAction *ba) "display dataset" button More... static variable send_to_elog () send file metadata to the ELOG panel More... static variable bp_elog (WMButtonAction *ba)
-
-
preview and import panel for PEARL data
-
preview and import panel for PEARL data:
-area detector (HDF5) files from scienta analyser and prosilica cameras (if HDF5.xop is installed).
-igor text files from s-scans and otf-scans.
-pshell (HDF5) data files (if HDF5.xop is installed).
-matrix STM files (if MatrixFileReader.xop is installed).
-
-
-
Definition in file pearl-data-explorer.ipf .
-
-
-
◆
+
+
+
◆
@@ -257,6 +284,377 @@ Variables
static variable attributes_notebook
(
+ string
+ filename )
+
+
+
+
+static
+
+
+
+
+◆
+
+
+
+
+
+
+ static variable bp_attr_notebook
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_browse_filepath
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_display_dataset
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_elog
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_file_next
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_file_prev
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_goto_dataset
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
+
"goto DF" button
+
the button selects the data folder of the selected file and dataset. an error message is shown if the data folder doesn't exist.
+
+
Definition at line 2231 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_load_options
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_load_prefs
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_reduction_params
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_save_prefs
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable bp_update_filelist
+ (
+ WMButtonAction *
+ ba )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable create_attributes_notebook
+ (
wave
attr_names ,
@@ -285,404 +683,12 @@ Variables
-◆
-
-
-
-
-
-
- static variable bp_attr_notebook
- (
- WMButtonAction *
- ba )
-
-
-
-
-static
-
-
-
-
◆
-
-
-
-
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- static variable bp_browse_filepath
- (
- WMButtonAction *
- ba )
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◆
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- static variable bp_dataset_display
- (
- WMButtonAction *
- ba )
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◆
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- static variable bp_dataset_folder
- (
- WMButtonAction *
- ba )
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◆
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- static variable bp_dataset_next
- (
- WMButtonAction *
- ba )
-
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-
-static
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◆
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- static variable bp_dataset_prev
- (
- WMButtonAction *
- ba )
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◆
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- static variable bp_file_next
- (
- WMButtonAction *
- ba )
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◆
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- (
- WMButtonAction *
- ba )
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◆
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- (
- WMButtonAction *
- ba )
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◆
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- (
- WMButtonAction *
- ba )
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◆
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- (
- WMButtonAction *
- ba )
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◆
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- (
- WMButtonAction *
- ba )
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◆
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- (
- WMButtonAction *
- ba )
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◆ ◆
@@ -693,9 +699,19 @@ Variables
static variable display_dataset
(
- string
- datasetname )
+ dfref
+ file_df ,
+
+ string
+ dataset
+
+ )
+
@@ -705,7 +721,9 @@ Variables
◆
+
+
+
+
+
+
+ static variable extract_attributes
+ (
+ dfref
+ attr_df ,
+
+ dfref
+ dest_df = defaultValue,
+
+ wave
+ attr_filter = defaultValue,
+
+ variable
+ include_datawaves = defaultValue,
+
+ variable
+ include_infowaves = defaultValue
+
+ )
+
+
+
+
+static
+
+
+
+
+
extract summary from attribute waves
+
by default, all existing attributes are copied. if a text wave attr_filter exists in the pear_explorer folder, only the attributes referenced therein are copied. to set up a filter, duplicate the attr_names wave of a template dataset, and remove unwanted items.
+
Parameters
+
+ attr_df data folder which contains the original data, e.g. the attr, diags or snaps folder in pshell files. dest_df destination folder. the output is written to the attr_names and attr_values waves. default = package folder. attr_filter (text wave) list of attributes allowed in the output. default = use attr_filter of package folder. include_datawaves
+1 (default) include data waves (any numeric wave which has a PV=name note).
+0 don't include attributes from data waves.
+
+include_infowaves
+1 (default) include attributes from info waves (IN, ID, IV, IU).
+0 don't include attributes from info waves.
+
+
+
+
+
+
Definition at line 347 of file pearl-data-explorer.ipf .
◆
+
+
+
+
+
+
+ static variable get_file_info
+ (
+ string
+ filename )
+
+
+
+
+static
+
+
+
+
+
load the internal structure of a file
+
this loads metadata for updating the panels.
+
for a pshell file, metadata includes:
+list of all datasets with types and dimensions
+general group
+
+
Returns 0 if successful -1 if no data was loaded because the file was not recognized, -2 if no data is found in file
+
+
Definition at line 273 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static dfr get_pshell_info
+ (
+ string
+ path_name ,
+
+ string
+ file_name ,
+
+ dfref
+ dest_df = defaultValue
+
+ )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable goto_dataset_folder
+ (
+ string
+ filename ,
+
+ string
+ datapath
+
+ )
+
+
+
+
+static
+
+
+
+
+
open data folder corresponding to a file and data path
+
the function tries to find where a given dataset has been loaded and selects the corresponding data folder. the data folder must exist (after previous import from the file), else an error code is returned and the folder selection will be the closest accessible parent folder of the target.
+
Parameters
+
+ filename file name (without path). h5 and otf.itx files are supported. datapath dataset or group path inside the hdf5 file.
+
+
+
Returns 0 if successful, -1 if the file type is unknown -2 if the data path can't be found in the tree.
+
+
Definition at line 2175 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static variable hl_add_objects
+ (
+ string
+ parent_path ,
+
+ string
+ objects
+
+ )
+
+
+
+
+static
+
+
+
+
+
populate the contents list box with the given hierarchical paths
+
Returns the number of top-level objects
+
+
Definition at line 2029 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static variable hl_contents_clear
+ (
+ )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable hl_contents_update
+ (
+ dfref
+ file_df )
+
+
+
+
+static
+
+
+
+
+
populate the contents list box with the internal directory of a HDF5 file
+
Returns the number of top-level objects
+
+
Definition at line 1966 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static variable hl_default_selection
+ (
+ )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable hl_expand_scans
+ (
+ )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable hlp_contents_open
+ (
+ string
+ HostWindow ,
+
+ string
+ ListControlName ,
+
+ string
+ ContainerPath
+
+ )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable hlp_contents_selection
+ (
+ string
+ HostWindow ,
+
+ string
+ ListControlName ,
+
+ string
+ SelectedItem ,
+
+ variable
+ EventCode
+
+ )
+
+
+
+
+static
+
+
+
+
◆
+
+
+
+
+
+
+ static variable hlp_setup
+ (
+ )
+
+
+
+
+static
+
+
+
-
initialize the global variables of the data explorer.
-
initializes the global variables and data folder for this procedure file must be called once before the panel is created warning: this function overwrites previous values
-
-
Definition at line 56 of file pearl-data-explorer.ipf .
+
Definition at line 61 of file pearl-data-explorer.ipf .
-
Definition at line 1258 of file pearl-data-explorer.ipf .
+
suggest the name of a data folder based on an igor-text file name
+
if the file name follows the naming convention source-date-index.extension, the function tries to generate the nick name as source_date_index. otherwise it's just a cleaned up version of the file name.
+
igor text is used by the on-the-fly scan tool.
+
Parameters
+
+ filename file name, including extension. can also include a folder path (which is ignored). the extension is currently ignored, but may be used in a later version. ignoredate if non-zero, the nick name will not include the date part. defaults to zero sourcename nick name of the data source. the function tries to detect the source from the file name. this option can be used to override auto-detection. allowed values: sscan, otf unique if non-zero, the resulting name is made a unique data folder name in the current data folder. defaults to zero
+
+
-
◆
-
-
-
-
-
-
- static variable lbp_datasets
- (
- WMListboxAction *
- lba )
-
-
-
-
-static
-
-
-
◆ ◆
@@ -932,7 +1414,19 @@ Variables
string
- options = defaultValue options = defaultValue,
+ dfref
+ dest_df = defaultValue,
+
+ variable
+ quiet = defaultValue
-
Definition at line 996 of file pearl-data-explorer.ipf .
+
load one file
+
this can be a PShell, HDF5, or ITX file.
+
Note this function may change the current data folder!
+
Parameters
+
+ options key:value; list of load options. the recognized keys are: mode, reduction_func and reduction_params. see main text for a description of possible values. by default (options not specified), options are read from `s_hdf_options. if the option string is empty, the user is prompted for options.dest_df destination data folder. default: a new folder derived from file name under root. quiet
+0 (default) print mode and parameters to history.
+1 do not print to history.
+
+
+
+
+
+
Definition at line 1064 of file pearl-data-explorer.ipf .
-◆ ◆
@@ -970,7 +1480,19 @@ Variables
string
- options = defaultValue options = defaultValue,
+ dfref
+ dest_df = defaultValue,
+
+ variable
+ quiet = defaultValue
-◆ ◆
@@ -1008,45 +1530,19 @@ Variables
string
- options = defaultValue
- )
-
-
-
-
-static
-
-
-
-
-◆
-
-
-
-
-
-
- static dfr load_mtrx_file
- (
- string
- filename , options = defaultValue,
string
- options = defaultValue dfref
+ dest_df = defaultValue,
+
+ variable
+ quiet = defaultValue
@@ -1090,12 +1584,12 @@ Variables
◆ ◆
@@ -1113,7 +1607,19 @@ Variables
string
- options = defaultValue options = defaultValue,
+ dfref
+ dest_df = defaultValue,
+
+ variable
+ quiet = defaultValue
-
Definition at line 1090 of file pearl-data-explorer.ipf .
+
load a pshell file
+
if options is not specified, the complete file is loaded. if options is an empty string, the package default options are used.
+
data selection is extracted from the datasets list box.
+
the file can be loaded in one of the following modes (mode key of the options argument):
+
+load_complete load all datasets regardless of selection. load_scan load default datasets of selected scans. load_region load default datasets of selected regions. load_dataset load selected datasets. load_diags load diagnostic datasets of selected scans.
+
3-dimensional datasets can be loaded with dimension reduction. in this case, the name of the reduction function must be given under the reduction_func key. the reduction parameters are prompted for if a prompt function for the reduction function is found. the default reduction parameters are the most recent parameters s_reduction_params stored in the package data folder.
+
+reduction_func:... name of the reduction function.
+
if a reduction function is specified, default reduction parameters are read from s_reduction_params in the package data folder, and the user is prompted to review/update the parameters.
+
Parameters
+
+ options key:value; list of load options. the recognized keys are: mode, reduction_func and reduction_params. see main text for a description of possible values. by default (options not specified), options are read from `s_hdf_options. if the option string is empty, the user is prompted for options.dest_df destination data folder. default: a new folder derived from file name under root. quiet
+0 (default) print mode and parameters to history.
+1 do not print to history.
+
+
+
+
+
Returns data folder reference of the loaded data. this is the folder which contains the scan sub-folders.
+
+
Definition at line 1188 of file pearl-data-explorer.ipf .
@@ -1156,7 +1692,11 @@ Variables
@@ -1206,7 +1746,7 @@ Variables
@@ -1225,7 +1765,10 @@ Variables
-
Definition at line 45 of file pearl-data-explorer.ipf .
+
show the pearl data explorer window
+
create a pearl data explorer window or bring the existing one to the front. if a new window is created, also initialize all package variables and load package preferences.
+
+
Definition at line 47 of file pearl-data-explorer.ipf .
1 PShell file (HDF5, name starts with psh_)
2 area detector HDF5 file
3 Igor text (itx) file
-4 Matrix STM file (*_mtrx)
Definition at line 163 of file pearl-data-explorer.ipf .
+Definition at line 199 of file pearl-data-explorer.ipf .
@@ -1283,12 +1825,12 @@ Variables
-◆ ◆
@@ -1297,39 +1839,10 @@ Variables
- static variable preview_attributes
+ static string pm_reduction_values
(
- dfref
- attr_folder ,
-
- )
dfref
- dest_folder = defaultValue,
-
- wave
- attr_filter = defaultValue,
-
- variable
- include_datawaves = defaultValue,
-
- variable
- include_infowaves = defaultValue
-
- )
-
@@ -1339,7 +1852,37 @@ Variables
+
+◆
+
+
+
+
+
+
+ static variable pmp_reduction_func
+ (
+ WMPopupAction *
+ pa )
+
+
+
+
+static
+
+
+
◆
-
-
-
-
-
-
- static variable preview_dataset
- (
- string
- datasetname )
-
-
-
-
-static
-
-
-
load the preview of a PEARL HDF5 file.
-
the preview is an arbitrary detector image extracted from the file, see adh5_load_preview() . the preview is loaded to the preview_image wave in the pear_explorer data folder.
+
the preview is an arbitrary detector image extracted from the file, see adh5_load_preview() . the preview is loaded to the preview_image wave in the pear_explorer data folder.
the s_file_info string is updated with information about the scan dimensions.
Parameters
@@ -1461,7 +1979,7 @@ Variables
Returns wave reference of the preview image Definition at line 365 of file pearl-data-explorer.ipf .
+Definition at line 717 of file pearl-data-explorer.ipf .
@@ -1501,47 +2019,7 @@ Variables
Returns wave reference of the preview trace. empty wave reference if the function failed. Definition at line 416 of file pearl-data-explorer.ipf .
-
-
-
-◆
-
-
-
-
-
-
- static wave preview_mtrx_file
- (
- string
- filename )
-
-
-
-
-static
-
-
-
-
-
load the preview of a Matrix STM file.
-
the preview is loaded to the preview_image wave in the pearl_explorer data folder.
-
the s_file_info string is updated with information about the scan dimensions.
-
this function requires the MatrixFileReader.xop and pearl-matrix-import.ipf to be loaded. otherwise it will return an empty wave reference.
-
Parameters
-
- filename name of a file in the directory specified by the pearl_explorer_filepath path object.
-
-
-
Returns wave reference of the preview image. empty wave reference if the function failed.
-
-
Definition at line 452 of file pearl-data-explorer.ipf .
+
Definition at line 762 of file pearl-data-explorer.ipf .
load the preview of a PShell HDF5 file.
-
the preview is an arbitrary detector image extracted from the file, see adh5_load_preview() . the preview is loaded to the preview_image wave in the pear_explorer data folder.
+
the preview is an arbitrary detector image extracted from the file, see adh5_load_preview() . the preview is loaded to the preview_image wave in the pear_explorer data folder.
the s_file_info string is updated with information about the scan dimensions.
Parameters
@@ -1643,7 +2121,7 @@ Variables
prompt functions must have the same name as the corresponding reduction function with the prefix "prompt_". be aware of the limited length of function names in Igor.
this function is a prototype. it does nothing but returns OK.
-Definition at line 1070 of file pearl-data-explorer.ipf .
+Definition at line 1130 of file pearl-data-explorer.ipf .
@@ -1673,7 +2151,7 @@ Variables
@@ -1701,7 +2179,7 @@ Variables
@@ -1731,7 +2209,204 @@ Variables
save persistent package data to the preferences file.
this function is called when the user clicks the corresponding button. the data saved in the file are: data file path, attributes filter
-Definition at line 102 of file pearl-data-explorer.ipf .
+Definition at line 139 of file pearl-data-explorer.ipf .
+
+
+
+◆
+
+
+
+
+
+
+ static variable selected_file
+ (
+ string
+ file ,
+
+ variable
+ do_preview
+
+ )
+
+
+
+
+static
+
+
+
+
+
actions after a file has been selected
+
+load metadata
+load preview if requested
+
+
Parameters
+
+ file name of selected file do_preview enable/disable loading of preview data non-zero: load preview, zero: don't load preview
+
+
+
+
Definition at line 1791 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static variable send_to_elog
+ (
+ )
+
+
+
+
+static
+
+
+
+
+
send file metadata to the ELOG panel
+
metadate is looked up in the following locations:
+data folder if it exists
+file info folder inside package folder
+package folder if it contains preview data from the selected file (???)
+
+
+
Definition at line 2295 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static variable set_elog_attributes
+ (
+ dfref
+ file_df ,
+
+ string
+ filename = defaultValue,
+
+ string
+ graphname = defaultValue
+
+ )
+
+
+
+
+static
+
+
+
+
+
send general metadata to ELOG panel - if available
+
the following metatdata are sent. they must be present as strings in the specified data folder:
+
+
+ELOG parameter global string function argument
+
+file s_filepath filename
+
+graph attachment graphname
+
+author authors
+
+p-group pgroup
+
+project proposal
+
+sample sample
+
+
Parameters
+
+ file_df data folder that contains the metadata. filename override file path read from s_filepath global string variable. if neither is declared, the file name is reset to empty field. graphname select this graph window for attaching. default: do not change the selection.
+
+
+
+
Definition at line 568 of file pearl-data-explorer.ipf .
+
+
+
◆
+
+
+
+
+
+
+ static string shorten_filepath
+ (
+ string
+ long_path ,
+
+ variable
+ max_len
+
+ )
+
+
+
+
+static
+
+
+
+
+
shorten a file path for display
+
Note the result is not a valid path any more!
+
+
Definition at line 1651 of file pearl-data-explorer.ipf .
◆ ◆
@@ -1802,7 +2477,7 @@ Variables
- static variable update_datasets
+ static variable update_controls
(
)
@@ -1843,9 +2520,39 @@ Variables
read a list of PEARL files from the file system
-
wtFiles and wSelectedFiles in the package data folder are updated. only files for which pearl_file_type() returns non-zero are listed.
+
wtFiles and wSelectedFiles in the package data folder are updated. only files for which pearl_file_type() returns non-zero are listed.
-
Definition at line 186 of file pearl-data-explorer.ipf .
+
Definition at line 231 of file pearl-data-explorer.ipf .
+
+
+
+◆
+
+
+
+
+
+
+ static variable update_filepath
+ (
+ )
+
+
+
+
+static
+
+
+
+
+
update the file path after path change
+
read the path info from pearl_explorer_filepath and update the path control
+
+
Definition at line 218 of file pearl-data-explorer.ipf .
◆
-
-
-
-
-
-
- const string ks_filematch_mtrx = "*_mtrx"
-
-
-
-
-static
-
-
-
◆
-
-
-
-
-
-
- const string package_name = "pearl_explorer"
-
-
-
-
-static
-
-
-
◆ static const string package_name
package name is used as data folder name
PEARL Procedures: pearl-data-explorer.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,89 +87,2191 @@ $(document).ready(function(){initNavTree('pearl-data-explorer_8ipf_source.html',
pearl-data-explorer.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlDataExplorer 5 #include "pearl-area-import" 6 #include "pearl-area-profiles" 7 #include "pearl-area-display" 8 #include "pearl-compat" 9 #include "pearl-pshell-import" 10 #if exists("MFR_OpenResultFile") 11 #include "pearl-matrix-import" 58 dfref savefolder = GetDataFolderDFR()
60 newdatafolder /o/s packages
61 newdatafolder /o/s $package_name
62 if (exists("v_InitPanelDone") == 2)
63 SetDataFolder savefolder
68 make /o/n=0/i wSelectedFiles,wSelectedDatasets
69 make /o/n=0/t wtDatasets
70 make /o/n=0/t wtPositioners,wtDetectors
71 make /o/n=0/i wSelectedPositioners,wSelectedDetectors
73 make /o/n=(1,1) preview_image
74 make /o/n=0 preview_trace
75 make /o/n=0/t attr_names, attr_values, attr_filter, attr_filter_summary
78 string /g s_filepath = ""
79 string /g s_hdf_options = ""
80 string /g s_reduction_params = ""
81 string /g s_preview_pvs = ""
83 s_preview_pvs = "*OP:CURRENT*;*Stats*Total*;*KEITHLEY*READOUT;*CADC*"
86 string /g s_preview_file = ""
87 string /g s_preview_source = ""
88 string /g s_profiles_graph = ""
89 string /g s_preview_trace_graph = ""
90 string /g s_file_info = ""
92 variable/g v_InitPanelDone = 1
94 SetDataFolder savefolder
103 dfref saveDF = GetDataFolderDFR()
104 dfref df = $package_path
105 if (DataFolderRefStatus(df) == 1)
106 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
108 NewPath/O/C/Q tempPackagePrefsPath, fullPath
109 fullPath += ":preferences.pxp"
111 string objects = "attr_filter;attr_filter_summary;s_filepath;s_hdf_options;s_reduction_params;s_preview_pvs"
112 SaveData /O /Q /J=objects fullPath
113 KillPath/Z tempPackagePrefsPath
121 dfref saveDF = GetDataFolderDFR()
125 NewDataFolder /O/S packages
126 NewDataFolder /O/S $package_name
127 dfref packageDF = GetDataFolderDFR()
128 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
131 GetFileFolderInfo /Q /Z fullPath
133 fullPath += ":preferences.pxp"
134 GetFileFolderInfo /Q /Z fullPath
136 LoadData /O /R /Q fullPath
142 svar /sdfr=packageDF filepath = s_filepath
143 NewPath /O/Z pearl_explorer_filepath, filepath
172 #if exists("MFR_OpenResultFile") 187 dfref saveDF = GetDataFolderDFR()
191 wave wSelectedFiles = $(
package_path + "wSelectedFiles")
194 PathInfo pearl_explorer_filepath
196 all_files = IndexedFile(pearl_explorer_filepath, -1, "????")
197 nn = ItemsInList(all_files)
203 make /n=(nn) /t /free wtAllFiles
204 wtAllFiles = StringFromList(p, all_files)
206 Sort /A /R wtFiles, wtFiles
208 redimension /n=(numpnts(wtFiles)) wSelectedFiles
218 dfref saveDF = GetDataFolderDFR()
221 dfref rootdf = GetDataFolderDFR()
222 setdatafolder $package_path
223 dfref privatedf = GetDataFolderDFR()
226 wave wSelectedDatasets
227 variable maxdf = CountObjectsDFR(rootdf, 4)
228 redimension /n=(maxdf) wtDatasets
235 sdf = GetIndexedObjNameDFR(rootdf, 4, idf)
236 if (strlen(sdf) >= 1)
239 svar /z importer = pearl_explorer_import
240 if (svar_exists(importer))
241 wtDatasets[ndf] = sdf
250 redimension /n=(ndf) wtDatasets, wSelectedDatasets
251 wSelectedDatasets = 0
252 sort wtDatasets, wtDatasets
260 dfref saveDF = GetDataFolderDFR()
280 if (WaveExists(image))
283 if (exists("
PearlElog #set_panel_attributes") == 6) 285 sprintf cmd,
"PearlElog#set_panel_attributes(\"\", \"File=%s\")" , ParseFilePath(0, filename,
":" , 1, 0)
287 if (strlen(graphname) > 0)
288 sprintf cmd, "
PearlElog #set_panel_graphs(\"\", \"%s\")", graphname 312 dfref saveDF = GetDataFolderDFR()
314 setdatafolder $package_path
315 dfref previewDF = GetDataFolderDFR()
317 svar s_preview_source
319 if (! svar_exists(s_file_info))
320 string /g s_file_info
323 dfref tempDF = NewFreeDataFolder()
328 s_preview_file = filename
329 s_preview_source = ""
331 wave /z data = $dataname
332 if (waveexists(data))
333 duplicate /o data, previewDF:preview_image
335 print "no data found in file " + filename
338 if (strlen(s_preview_file) > 0)
344 dfref attrDF = tempDF:attr
345 if (DataFolderRefStatus(attrDF))
350 wave /z /sdfr=previewDF preview_image
368 dfref saveDF = GetDataFolderDFR()
369 setdatafolder $package_path
371 svar s_preview_source
373 s_preview_file = filename
374 s_preview_source = ""
375 wave /z preview_image
378 if (! svar_exists(s_file_info))
379 string /g s_file_info
381 if (strlen(s_preview_file) > 0)
387 if (DataFolderExists("attr"))
419 dfref saveDF = GetDataFolderDFR()
420 setdatafolder $package_path
422 svar s_preview_source
425 dfref dataDF = newfreedatafolder()
427 LoadWave /t/p=pearl_explorer_filepath/q filename
428 s_preview_file = s_filename
429 s_preview_source = ""
455 #if exists("MFR_OpenResultFile") 456 dfref saveDF = GetDataFolderDFR()
457 setdatafolder $package_path
458 variable /g V_MatrixFileReaderOverwrite = 1
459 variable /g V_MatrixFileReaderFolder = 0
460 variable /g V_MatrixFileReaderDouble = 0
462 svar s_preview_source
466 if (strlen(datanames) > 0)
467 s_preview_file = filename
469 dataname = StringFromList(0, datanames)
470 wave data = $dataname
471 duplicate /o $dataname, preview_image
472 s_preview_source = StringByKey("Dataset", note(data), "=", "\r")
475 if (svar_exists(s_file_info))
480 variable n = ItemsInList(datanames)
482 for (i = 0; i < n; i += 1)
483 s = StringFromList(i, datanames)
487 wave /z preview_image
490 wave /z preview_image = $
"" 503 switch (WaveDims(data))
505 redimension /n=(numpnts(data)) preview
509 redimension /n=(dimsize(data, 0), dimsize(data, 1)) preview
513 redimension /n=(dimsize(data, 0), dimsize(data, 1)) preview
514 z1 = floor(DimSize(data, 2) / 2)
516 wave slab =
ad_extract_slab (data, nan, nan, nan, nan, z1, z2,
"" , pscale=1)
523 switch (WaveDims(data))
527 setscale /p y dimoffset(data, 1), dimdelta(data, 1), waveunits(data, 1), preview
529 setscale /p x dimoffset(data, 0), dimdelta(data, 0), waveunits(data, 0), preview
530 setscale d 0, 0, waveunits(data, -1), preview
537 dfref saveDF = GetDataFolderDFR()
539 if (!DataFolderExists("root:" + datasetname))
543 setdatafolder $datasetname
544 dfref datadf = GetDataFolderDFR()
547 setdatafolder $package_path
549 svar s_preview_source
551 if (WaveExists(data))
552 s_preview_file = datasetname
553 s_preview_source = ""
558 s_preview_file = datasetname
566 if (DataFolderExists("attr"))
579 dfref saveDF = GetDataFolderDFR()
581 setdatafolder $package_path
583 svar s_preview_source
592 string d_names = WaveList("*", ";", "DP:1")
593 variable nw = ItemsInList(d_names, ";")
594 variable npv = ItemsInList(s_preview_pvs, ";")
596 string wname, wnote, pv_name, pv_match
597 for (iw = 0; iw < nw; iw += 1)
598 wname = StringFromList(iw, d_names, ";")
600 pv_name = StringByKey("PV", wnote, "=", "\r")
602 for (ipv = 0; ipv < npv; ipv += 1)
603 pv_match = StringFromList(ipv, s_preview_pvs)
604 if (StringMatch(pv_name, pv_match))
606 s_preview_source = pv_name
628 if ((DimOffset(preview, 0) == 0) && (DimDelta(preview, 0) == 1))
629 string xname = StringByKey("Axis1", note(data), "=", "\r")
630 wave /z xwave = $xname
631 if (WaveExists(xwave))
633 variable monotonic = 0
634 duplicate /free xwave, xdiff
635 differentiate /p xwave /D=xdiff
636 duplicate /free xdiff, xflag
638 monotonic = sum(xflag) > numpnts(xwave) * 0.9
640 monotonic = monotonic || (sum(xflag) > numpnts(xwave) * 0.9)
642 setscale /i x xwave[0], xwave[numpnts(xwave)-1], waveunits(xwave, -1), preview
648 static function
preview_attributes (attr_folder, [dest_folder, attr_filter, include_datawaves, include_infowaves])
658 variable include_datawaves
660 variable include_infowaves
663 dfref saveDF = GetDataFolderDFR()
664 setdatafolder $package_path
666 if (ParamIsDefault(dest_folder))
667 dest_folder = GetDataFolderDFR()
669 if (ParamIsDefault(attr_filter))
670 wave /t /z attr_filter
672 if (ParamIsDefault(include_datawaves))
673 include_datawaves = 1
675 if (ParamIsDefault(include_infowaves))
676 include_infowaves = 1
679 setdatafolder dest_folder
680 wave /t /z attr_names, attr_values
681 if (!WaveExists(attr_names) || !WaveExists(attr_values))
682 make /n=(1) /o /t attr_names, attr_values
687 setdatafolder attr_folder
703 if (WaveExists(IN) && include_infowaves)
708 if (include_datawaves)
709 string waves = WaveList("*", ";", "")
710 string exceptions = "ID;IN;IU;IV"
711 waves = RemoveFromList(exceptions, waves)
712 nw = ItemsInList(waves, ";")
717 if (WaveExists(attr_filter) && (numpnts(attr_filter) >= 1))
718 nattr = numpnts(attr_filter)
719 redimension /n=(nattr) attr_names
720 attr_names = attr_filter
723 redimension /n=(ninfo) attr_names
724 attr_names = SelectString(strlen(ID[p]) >= 0, IN[p], ID[p])
729 redimension /n=(nattr) attr_names
730 for (iw = 0; iw < nw; iw +=1 )
731 sw = StringFromList(iw, waves, ";")
732 ss = StringByKey("PV", note($sw), "=", "\r")
733 FindValue /text=sw attr_names
734 if ((v_value < 0) && (strlen(ss) >= 0))
735 attr_names[iattr] = sw
741 redimension /n=(nattr) attr_names, attr_values
742 sort attr_names, attr_names
745 for (iattr = 0; iattr < nattr; iattr += 1)
746 sw = attr_names[iattr]
749 FindValue /text=sw ID
751 attr_values[iattr] = IV[v_value]
753 FindValue /text=sw IN
755 attr_values[iattr] = IV[v_value]
761 switch (WaveType($sw, 1))
764 if (WaveExists(w) && (numpnts(w) >= 1))
765 sprintf ss, "%g", w[0]
766 attr_values[iattr] = ss
771 if (WaveExists(wt) && (numpnts(wt) >= 1))
772 attr_values[iattr] = wt[0]
786 dfref saveDF = GetDataFolderDFR()
788 if (!DataFolderExists("root:" + datasetname))
792 setdatafolder $datasetname
793 dfref datadf = GetDataFolderDFR()
795 if (!WaveExists(data))
799 if (WaveExists(data))
800 switch(WaveDims(data))
816 dfref df = GetDataFolderDFR()
817 wave /t /sdfr=df attr_names
818 wave /t /sdfr=df attr_values
827 dfref saveDF = GetDataFolderDFR()
828 setdatafolder $package_path
829 wave /t/z attr_filter, attr_filter_summary
832 if (WinType(name) == 5)
833 Notebook $name selection={startOfFile, endOfFile}
834 Notebook $name text=
"" 836 NewNotebook /F=1 /K=1 /N=$name as title
837 GetWindow $name wsize
838 v_right = v_left + 260
839 v_bottom = v_top + 360
840 MoveWindow /W=$name v_left, v_top, v_right, v_bottom
841 Notebook $name tabs={2*72}
845 if (WaveExists(attr_filter_summary) && (numpnts(attr_filter_summary) >= 1))
846 notebook $name fStyle=1, text=
"Summary\r\r" 847 notebook $name fStyle=0
849 notebook $name text=
"\r" 853 notebook $name fStyle=1, text=
"All Attributes\r\r" 854 notebook $name fStyle=0
856 notebook $name selection={startOfFile,startOfFile}, findText={
"" ,1}
863 wave /t /z attr_filter
867 variable nw = numpnts(attr_names)
872 variable do_filter = WaveExists(attr_filter)
874 for (iw = 0; iw < nw; iw += 1)
877 FindValue /text=sw attr_filter
882 sprintf ss,
"%s\t%s\r" , attr_names[iw], attr_values[iw]
883 notebook $notebook_name text=ss
893 dfref saveDF = GetDataFolderDFR()
894 setdatafolder $package_path
896 svar s_profiles_graph
898 svar s_preview_source
899 svar s_preview_trace_graph
901 if ((strlen(s_profiles_graph) > 0) && (WinType(s_profiles_graph) == 1))
902 KillWindow $s_profiles_graph
904 if ((strlen(s_preview_trace_graph) > 0) && (WinType(s_preview_trace_graph) == 1))
905 KillWindow $s_preview_trace_graph
909 if (wavedims(data) == 2)
911 ModifyGraph /w=$s_profiles_graph /z wbRGB=(48640,56832,60160)
912 graphname = s_profiles_graph
913 elseif (wavedims(data) == 1)
914 duplicate /o data, preview_trace
915 if (!ParamIsDefault(xdata))
916 duplicate /o xdata, preview_trace_x
918 duplicate /o data, preview_trace_x
920 setscale d 0, 0, WaveUnits(data, 0), preview_trace_x
923 ModifyGraph /w=$s_preview_trace_graph wbRGB=(48640,56832,60160)
924 graphname = s_preview_trace_graph
929 string title = "Preview " + s_preview_file
930 if (strlen(s_preview_source) > 0)
931 title = title + " (" + s_preview_source[0,31] + ")"
933 dowindow /f/t $graphname, title
943 display /n=pearl_explorer_1d /k=1 ytrace vs xtrace as "Preview"
944 string graphname = s_name
945 ModifyGraph /w=$graphname rgb[0]=(0,0,0)
946 ModifyGraph /w=$graphname grid=2
947 ModifyGraph /w=$graphname mirror=1
948 ModifyGraph /w=$graphname minor=1
949 ModifyGraph /w=$graphname axThick=0.5
950 ModifyGraph /w=$graphname gridRGB=(52224,52224,52224)
951 ModifyGraph /w=$graphname gridHair=0
952 ModifyGraph /w=$graphname tick=0
953 ModifyGraph /w=$graphname btLen=4
956 string labels = note(ytrace)
958 lab = StringByKey("AxisLabelX", labels, "=", "\r")
962 Label /w=$graphname bottom lab + " (\\U)"
963 lab = StringByKey("AxisLabelD", labels, "=", "\r")
967 Label /w=$graphname left lab + " (\\U)"
975 dfref saveDF = GetDataFolderDFR()
976 setdatafolder $package_path
980 variable nn = numpnts(wSelectedFiles)
982 for (ii = 0; ii < nn; ii += 1)
983 if (wSelectedFiles[ii])
984 if (ParamIsDefault(options))
1000 dfref saveDF = GetDataFolderDFR()
1005 if (ParamIsDefault(options))
1012 if (ParamIsDefault(options))
1028 setdatafolder saveDF
1034 string mode = StringByKey("mode", options, ":", ";")
1035 string reduction_func = StringByKey("reduction_func", options, ":", ";")
1037 string modes = "load_reduced"
1040 if (strlen(mode) == 0)
1041 mode = StringFromList(0, modes, ";")
1043 if (strlen(reduction_func) == 0)
1044 reduction_func = StringFromList(0, reduction_functions, ";")
1047 prompt mode, "Mode", popup, modes
1048 prompt reduction_func, "Reduction Function", popup, reduction_functions
1049 doprompt "HDF5 Loading Options", mode, reduction_func
1052 options = ReplaceStringByKey("mode", options, mode, ":", ";")
1053 options = ReplaceStringByKey("reduction_func", options, reduction_func, ":", ";")
1080 string prompt_name = "prompt_" + func_name
1081 if (exists(prompt_name) == 6)
1083 return prompt_func(func_param)
1094 dfref saveDF = GetDataFolderDFR()
1096 string loaded_filename = ""
1098 if (ParamIsDefault(options))
1101 if (strlen(options) == 0)
1103 options = pref_options
1106 pref_options = options
1113 string mode = StringByKey("mode", options, ":", ";")
1116 case "load_reduced":
1117 string reduction_func = StringByKey("reduction_func", options, ":", ";")
1118 svar pref_params = $(
package_path + "s_reduction_params")
1119 string reduction_params = pref_params
1121 pref_params = reduction_params
1122 print reduction_func, reduction_params
1123 psh5_load_reduced (nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
1125 loaded_filename = s_filepath
1132 if (strlen(loaded_filename) > 0)
1133 setdatafolder $("root:" + nickname)
1134 dataDF = GetDataFolderDFR()
1138 setdatafolder saveDF
1146 dfref saveDF = GetDataFolderDFR()
1148 string loaded_filename = ""
1150 if (ParamIsDefault(options))
1153 if (strlen(options) == 0)
1155 options = pref_options
1158 pref_options = options
1165 string mode = StringByKey("mode", options, ":", ";")
1168 case "load_reduced":
1169 string reduction_func = StringByKey("reduction_func", options, ":", ";")
1170 svar pref_params = $(
package_path + "s_reduction_params")
1171 string reduction_params = pref_params
1173 pref_params = reduction_params
1174 print reduction_func, reduction_params
1175 loaded_filename =
adh5_load_reduced (nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
1182 if (strlen(loaded_filename) > 0)
1183 setdatafolder $("root:" + nickname)
1184 dataDF = GetDataFolderDFR()
1188 setdatafolder saveDF
1196 dfref saveDF = GetDataFolderDFR()
1199 if (ParamIsDefault(options))
1204 newdatafolder /s/o $("root:" + nickname)
1205 dfref dataDF = GetDataFolderDFR()
1212 LoadWave /t/p=pearl_explorer_filepath/q filename
1213 svar waves = s_wavenames
1214 dfref actDF = GetDataFolderDFR()
1219 if (!DataFolderRefsEqual(actDF, dataDF))
1222 setdatafolder dataDF
1223 if (ItemsInList(WaveList("*", ";", ""), ";") == 0)
1224 killdatafolder /z dataDF
1228 setdatafolder saveDF
1239 dfref saveDF = GetDataFolderDFR()
1242 #if exists("MFR_OpenResultFile") 1244 string datasets =
"" 1246 if (strlen(datasets) > 0)
1247 string /g pearl_explorer_import =
"load_mtrx_file" 1248 string s1 = StringFromList(0, datasets)
1250 dataDF = GetWavesDataFolderDFR(w1)
1254 setdatafolder saveDF
1274 if (ParamIsDefault(ignoredate))
1277 if (ParamIsDefault(unique))
1281 string basename = ParseFilePath(3, filename,
":" , 0, 0)
1282 string extension = ParseFilePath(4, filename, ":", 0, 0)
1286 if (strsearch(basename, "X03DA_PC", 0, 2) >= 0)
1287 autosource = "sscan"
1288 basename = ReplaceString("_", basename, "-")
1290 elseif (strsearch(basename, "otf", 0, 2) >= 0)
1293 if (ParamIsDefault(sourcename))
1294 sourcename = autosource
1297 variable nparts = ItemsInList(basename, "-")
1299 string datepart = StringFromList(nparts - 2, basename, "-")
1300 string indexpart = StringFromList(nparts - 1, basename, "-")
1302 sprintf nickname, "%s_%s", sourcename, indexpart
1304 sprintf nickname, "%s_%s_%s", sourcename, datepart, indexpart
1310 if (unique && CheckName(nickname, 11))
1311 nickname = UniqueName(nickname + "_", 11, 0)
1318 PauseUpdate; Silent 1
1319 NewPanel /K=1 /W=(800,0,1530,444) as "PEARL Data Explorer"
1320 ModifyPanel cbRGB=(48640,56832,60160)
1322 GroupBox gb_filepath,pos={8,4},size={224,52},title=
"file system folder" 1323 TitleBox tb_filepath,pos={20,24},size={174,20},frame=2
1324 TitleBox tb_filepath,variable=root:packages:pearl_explorer:s_filepath,fixedSize=1
1326 Button b_browse_filepath,fColor=(65280,48896,32768)
1328 GroupBox gb_prefs,pos={240,4},size={58,52},title=
"prefs" ,help={
"explorer package preferences" }
1330 Button b_save_prefs,help={
"save preferences of the data explorer package (data file path, attributes filter)" }
1331 Button b_save_prefs,fColor=(65280,48896,32768)
1333 Button b_load_prefs,help={
"load preferences of the data explorer package" }
1334 Button b_load_prefs,fColor=(65280,48896,32768)
1336 GroupBox gb_filelist,pos={8,64},size={224,372},title=
"data files" 1338 ListBox lb_files,listWave=root:packages:pearl_explorer:wtFiles
1339 ListBox lb_files,selWave=root:packages:pearl_explorer:wSelectedFiles,row= 11,mode= 4
1340 TitleBox tb_file_info,pos={20,300},size={198,78},frame=2,fixedSize=1
1341 TitleBox tb_file_info,variable= root:packages:pearl_explorer:s_file_info
1344 Button b_update_filelist,fColor=(65280,48896,32768)
1345 CheckBox cb_file_preview,pos={84,390},size={60,20},title=
"preview" 1346 CheckBox cb_file_preview,help={
"enable/disable automatic preview window when selecting a data file" }
1347 CheckBox cb_file_preview,value=1
1349 Button b_file_prev,help={
"previous file" }
1350 Button b_file_prev,fColor=(65280,48896,32768)
1352 Button b_file_next,help={
"next file" }
1353 Button b_file_next,fColor=(65280,48896,32768)
1356 Button b_load_files,help={
"load the complete contents from the selected files" }
1357 Button b_load_files,fColor=(65280,48896,32768)
1359 Button b_load_files_opt,help={
"load data from the selected files with options (reduced dimensions)" }
1360 Button b_load_files_opt,fColor=(65280,48896,32768)
1363 GroupBox gb_datasets,pos={240,64},size={224,372},title=
"datasets" 1365 ListBox lb_datasets,listWave=root:packages:pearl_explorer:wtDatasets
1366 ListBox lb_datasets,selWave=root:packages:pearl_explorer:wSelectedDatasets,mode= 1
1367 ListBox lb_datasets,selRow= -1
1370 Button b_update_datasets,help={
"update the list of datasets" }
1371 Button b_update_datasets,fColor=(65280,48896,32768)
1372 CheckBox cb_dataset_preview,pos={316,390},size={60,20},title=
"preview" 1373 CheckBox cb_dataset_preview,help={
"enable/disable automatic preview window when selecting a dataset" }
1374 CheckBox cb_dataset_preview,value=0
1376 Button b_dataset_prev,help={
"goto previous dataset" }
1377 Button b_dataset_prev,fColor=(65280,48896,32768)
1379 Button b_dataset_next,help={
"goto next dataset" }
1380 Button b_dataset_next,fColor=(65280,48896,32768)
1383 Button b_dataset_folder,help={
"set the current data folder of the selected dataset" }
1384 Button b_dataset_folder,fColor=(65280,48896,32768)
1386 Button b_dataset_display,help={
"display the selected dataset in its own window" }
1387 Button b_dataset_display,fColor=(65280,48896,32768)
1389 GroupBox gb_preview,pos={472,4},size={250,52},title=
"preview" 1390 TitleBox tb_preview_file,pos={484,24},size={226,20},frame=2
1391 TitleBox tb_preview_file,variable=root:packages:pearl_explorer:s_preview_file,fixedSize=1
1393 GroupBox gb_attributes,pos={472,64},size={250,372},title=
"attributes" 1395 Button b_attr_notebook,help={
"show attribute list in a notebook" }
1396 Button b_attr_notebook,fColor=(65280,48896,32768)
1398 String fldrSav0= GetDataFolder(1)
1399 SetDataFolder root:packages:pearl_explorer:
1400 Edit/W=(484,84,710,384)/HOST=# attr_names,attr_values
1401 ModifyTable format(Point)=1,width(Point)=0,width(attr_names)=103,width(attr_values)=103
1402 ModifyTable statsArea=85
1403 SetDataFolder fldrSav0
1405 SetActiveSubwindow ##
1409 STRUCT WMButtonAction &ba
1411 switch( ba.eventCode )
1422 static function bp_save_prefs(ba) : ButtonControl
1423 STRUCT WMButtonAction &ba
1425 switch( ba.eventCode )
1436 static function bp_browse_filepath(ba) : ButtonControl
1437 STRUCT WMButtonAction &ba
1439 dfref saveDF = GetDataFolderDFR()
1441 switch( ba.eventCode )
1443 PathInfo /S pearl_explorer_filepath
1444 NewPath /M=
"select data file folder" /O/Z pearl_explorer_filepath
1446 PathInfo /S pearl_explorer_filepath
1456 setdatafolder saveDF
1460 static function bp_update_filelist(ba) : ButtonControl
1461 STRUCT WMButtonAction &ba
1463 switch( ba.eventCode )
1474 static function bp_load_files(ba) : ButtonControl
1475 STRUCT WMButtonAction &ba
1477 switch( ba.eventCode )
1488 static function bp_load_files_opt(ba) : ButtonControl
1489 STRUCT WMButtonAction &ba
1491 switch( ba.eventCode )
1502 static function bp_file_next(ba) : ButtonControl
1503 STRUCT WMButtonAction &ba
1505 dfref saveDF = GetDataFolderDFR()
1507 switch( ba.eventCode )
1509 setdatafolder $package_path
1512 FindValue /i=1 wSelectedFiles
1514 if (v_value >= numpnts(wtFiles))
1515 v_value = min(numpnts(wtFiles) - 1, 0)
1517 wSelectedFiles = p == v_value
1519 variable ifile = v_value
1530 setdatafolder saveDF
1534 static function bp_file_prev(ba) : ButtonControl
1535 STRUCT WMButtonAction &ba
1537 dfref saveDF = GetDataFolderDFR()
1539 switch( ba.eventCode )
1541 setdatafolder $package_path
1544 FindValue /i=1 wSelectedFiles
1547 v_value = numpnts(wtFiles) - 1
1549 wSelectedFiles = p == v_value
1551 variable ifile = v_value
1562 setdatafolder saveDF
1567 STRUCT WMListboxAction &lba
1569 Variable row = lba.row
1570 Variable col = lba.col
1571 WAVE/T/Z listWave = lba.listWave
1572 WAVE/Z selWave = lba.selWave
1574 switch( lba.eventCode )
1601 static function bp_update_datasets(ba) : ButtonControl
1602 STRUCT WMButtonAction &ba
1604 switch( ba.eventCode )
1615 static function bp_dataset_folder(ba) : ButtonControl
1616 STRUCT WMButtonAction &ba
1618 switch( ba.eventCode )
1622 setdatafolder $package_path
1624 string dataset = wtDatasets[v_value]
1626 sprintf cmd,
"setdatafolder root:%s" , PossiblyQuoteName(dataset)
1628 cmd =
"setdatafolder :scan1" 1630 sprintf cmd,
"setdatafolder %s" , GetDataFolder(1)
1641 static function bp_dataset_display(ba) : ButtonControl
1642 STRUCT WMButtonAction &ba
1644 switch( ba.eventCode )
1648 setdatafolder $package_path
1650 string dataset = wtDatasets[v_value]
1661 static function bp_dataset_next(ba) : ButtonControl
1662 STRUCT WMButtonAction &ba
1664 switch( ba.eventCode )
1667 wave /t wtDatasets = $(s_datafolder + s_value)
1669 if (v_value >= numpnts(wtDatasets))
1670 v_value = min(0, numpnts(wtDatasets) - 1)
1674 variable ids = v_value
1688 static function bp_dataset_prev(ba) : ButtonControl
1689 STRUCT WMButtonAction &ba
1691 switch( ba.eventCode )
1694 wave /t wtDatasets = $(s_datafolder + s_value)
1697 v_value = max(-1, numpnts(wtDatasets) - 1)
1701 variable ids = v_value
1715 static function lbp_datasets(lba) : ListBoxControl
1716 STRUCT WMListboxAction &lba
1718 Variable row = lba.row
1719 Variable col = lba.col
1720 WAVE/T/Z listWave = lba.listWave
1721 WAVE/Z selWave = lba.selWave
1723 switch( lba.eventCode )
1750 static function bp_attr_notebook(ba) : ButtonControl
1751 STRUCT WMButtonAction &ba
1753 dfref saveDF = GetDataFolderDFR()
1755 switch( ba.eventCode )
1757 setdatafolder $package_path
1759 wave /t /z attr_names
1760 wave /t /z attr_values
1761 if (WaveExists(attr_names))
1769 setdatafolder saveDF
static dfr load_mtrx_file(string filename, string options=defaultValue)
load a matrix (STM) data file
-
static const string package_path
-
string adh5_load_preview(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
load a single image from a HDF5 file created by the Area Detector software.
-
static variable update_datasets()
-
string psh5_load_reduced(string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue)
load and reduce the ScientaImage dataset of the first scan of a PShell data file. ...
-
static variable bp_browse_filepath(WMButtonAction *ba)
-
static variable preview_file(string filename)
-
variable prompt_default_process(string *param)
prototype for prompting for processing function parameters.
-
string adh5_load_info(string APathName, string AFileName)
load descriptive info from a HDF5 file created by the Area Detector software.
-
static variable bp_dataset_prev(WMButtonAction *ba)
-
static string display_preview_trace(wave xtrace, wave ytrace)
-
static variable bp_file_prev(WMButtonAction *ba)
-
variable ad_brick_slicer(wave data)
open a slicer panel for 3D data.
-
interface for writing ELOG entries with Igor graphs as attachment.
-
static variable lbp_datasets(WMListboxAction *lba)
-
static variable bp_load_files_opt(WMButtonAction *ba)
-
static variable load_selected_files(string options=defaultValue)
-
string PearlCleanupName(string name)
-
static variable bp_load_files(WMButtonAction *ba)
-
static variable preview_datafolder()
-
static variable bp_file_next(WMButtonAction *ba)
-
static variable lbp_filelist(WMListboxAction *lba)
-
static variable prompt_hdf_options(string *options)
-
static variable bp_update_datasets(WMButtonAction *ba)
-
static const string ks_filematch_pshell
-
static const string ks_filematch_adh5
-
static wave preview_mtrx_file(string filename)
load the preview of a Matrix STM file.
-
static variable init_package()
initialize the global variables of the data explorer.
-
static wave preview_pshell_file(string filename)
load the preview of a PShell HDF5 file.
-
static variable bp_dataset_folder(WMButtonAction *ba)
-
static variable preview_dataset(string datasetname)
-
static const string package_name
-
static variable update_filelist()
read a list of PEARL files from the file system
-
static dfr load_itx_file(string filename, string options=defaultValue)
-
string psh5_load_preview(string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue, string pref_scans=defaultValue, string pref_datasets=defaultValue)
load a preview image from a PShell data file.
-
static variable bp_attr_notebook(WMButtonAction *ba)
-
static variable load_file(string filename, string options=defaultValue)
-
preview and import panel for PEARL data
-
static variable bp_load_prefs(WMButtonAction *ba)
-
static variable preview_setscale_x(wave data, wave preview)
-
static variable bp_save_prefs(WMButtonAction *ba)
-
static dfr load_hdf_file(string filename, string options=defaultValue)
-
string ad_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
generate the name of a data folder based on a file name.
-
static wave preview_hdf_file(string filename)
load the preview of a PEARL HDF5 file.
-
static variable pearl_file_type(string filename)
check whether a file can be imported by this module.
-
static variable bp_dataset_display(WMButtonAction *ba)
-
static const string ks_filematch_itx
-
string adh5_load_complete(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
import everything from a HDF5 file created by the Area Detector software.
-
static variable bp_dataset_next(WMButtonAction *ba)
-
static variable extract_preview_image(wave data, wave preview)
-
string psh5_load_info(string APathName, string AFileName)
load descriptive info from a PShell data file.
-
string adh5_load_reduced(string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable load_data=defaultValue, variable load_attr=defaultValue, variable progress=defaultValue)
load and reduce a dataset from a HDF5 file created by the Area Detector software. ...
-
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
-
static variable bp_update_filelist(WMButtonAction *ba)
-
variable pearl_data_explorer()
-
string itx_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
-
string psh5_load_complete(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
load everything from a PShell data file.
-
static variable load_prefs()
-
variable prompt_func_params(string func_name, string *func_param)
-
static wave preview_itx_file(string filename)
load the preview of a general ITX file.
-
static variable display_dataset(string datasetname)
-
static dfr load_pshell_file(string filename, string options=defaultValue)
-
static variable save_prefs()
save persistent package data to the preferences file.
-
variable test_attributes_notebook()
-
static string show_preview_graph(wave data, wave xdata=defaultValue)
-
string mtrx_load_preview(string destName, string pathName, string fileName, string traces=defaultValue)
load a preview image from a Matrix data file.
-
string ad_display_slice(wave data)
display three-dimensional data by 2D slice.
-
static const string ks_filematch_mtrx
-
static variable attributes_notebook(wave attr_names, wave attr_values, string title)
-
string mtrx_load_file(string pathName, string fileName, string traces=defaultValue)
load all data from a Matrix data file.
-
static variable preview_attributes(dfref attr_folder, dfref dest_folder=defaultValue, wave attr_filter=defaultValue, variable include_datawaves=defaultValue, variable include_infowaves=defaultValue)
-
string adh5_list_reduction_funcs()
get a list of functions which can be used as reduction functions.
-
static variable notebook_add_attributes(string notebook_name, wave attr_filter, wave attr_names, wave attr_values)
-
threadsafe wave ad_extract_slab(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue)
2D cut through 3D dataset, integrate in normal dimension
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.36
+
4 #pragma ModuleName = PearlDataExplorer
+
+
6 #include <HierarchicalListWidget> ,
version >= 1.14
+
7 #include
"pearl-area-import"
+
8 #include "pearl-area-profiles"
+
9 #include "pearl-area-display"
+
10 #include "pearl-compat"
+
11 #include "pearl-pshell-import"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
54 WMHL_AddColumns(
"PearlDataExplorer" ,
"lb_contents" , 1)
+
+
+
+
+
+
+
+
62 dfref save_df = GetDataFolderDFR()
+
+
64 newdatafolder /o/s packages
+
65 newdatafolder /o/s $package_name
+
66 if (exists("v_InitPanelDone") == 2)
+
+
+
+
+
+
72 make /o/n=0/i wSelectedFiles,wSelectedDatasets
+
73 make /o/n=0/t wtDatasets
+
74 make /o/n=0/t wtPositioners,wtDetectors
+
75 make /o/n=0/i wSelectedPositioners,wSelectedDetectors
+
+
77 make /o/n=(1,1) preview_image
+
78 make /o/n=0 preview_trace
+
79 make /o/n=0/t attr_names, attr_values, attr_filter, attr_filter_summary
+
+
+
82 string /g s_filepath = ""
+
83 string /g s_hdf_options = ""
+
84 string /g s_reduction_params = ""
+
85 string /g s_preview_pvs = ""
+
+
87 s_preview_pvs = "*OP:CURRENT*;*Stats*Total*;*KEITHLEY*READOUT;*CADC*"
+
+
89 redimension /n=26 attr_filter_summary
+
90 attr_filter_summary[0] = "MonoEnergy"
+
91 attr_filter_summary[1] = "MonoGrating"
+
92 attr_filter_summary[2] = "ExitSlit"
+
93 attr_filter_summary[3] = "FrontendHSize"
+
94 attr_filter_summary[4] = "FrontendVSize"
+
95 attr_filter_summary[5] = "ManipulatorPhi"
+
96 attr_filter_summary[6] = "ManipulatorTheta"
+
97 attr_filter_summary[7] = "ManipulatorTilt"
+
98 attr_filter_summary[8] = "ManipulatorX"
+
99 attr_filter_summary[9] = "ManipulatorY"
+
100 attr_filter_summary[10] = "ManipulatorZ"
+
101 attr_filter_summary[11] = "PassEnergy"
+
102 attr_filter_summary[12] = "LensMode"
+
103 attr_filter_summary[13] = "ScientaDwellTime"
+
104 attr_filter_summary[14] = "ScientaCenterEnergy"
+
105 attr_filter_summary[15] = "ScientaChannelBegin"
+
106 attr_filter_summary[16] = "ScientaChannelEnd"
+
107 attr_filter_summary[17] = "ScientaSliceBegin"
+
108 attr_filter_summary[18] = "ScientaSliceEnd"
+
109 attr_filter_summary[19] = "ScientaNumChannels"
+
110 attr_filter_summary[20] = "StepSize"
+
111 attr_filter_summary[21] = "ScientaNumSlices"
+
112 attr_filter_summary[22] = "ManipulatorTempA"
+
113 attr_filter_summary[23] = "ManipulatorTempB"
+
114 attr_filter_summary[24] = "RefCurrent"
+
115 attr_filter_summary[25] = "SampleCurrent"
+
+
+
118 string /g s_short_filepath = ""
+
119 string /g s_selected_file = ""
+
120 string /g s_selected_dataset = ""
+
121 string /g s_preview_file = ""
+
122 string /g s_preview_source = ""
+
123 string /g s_profiles_graph = ""
+
124 string /g s_preview_trace_graph = ""
+
125 string /g s_preview_graph = ""
+
126 string /g s_file_info = ""
+
127 string /g s_result = ""
+
+
129 variable/g v_InitPanelDone = 1
+
+
131 SetDataFolder save_df
+
+
+
+
140 dfref save_df = GetDataFolderDFR()
+
141 dfref df = $package_path
+
142 if (DataFolderRefStatus(df) == 1)
+
143 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
+
+
145 NewPath/O/C/Q tempPackagePrefsPath, fullPath
+
146 fullPath += ":preferences.pxp"
+
+
148 string objects = "attr_filter;attr_filter_summary;s_filepath;s_hdf_options;s_reduction_params;s_preview_pvs"
+
149 SaveData /O /Q /J=objects fullPath
+
150 KillPath/Z tempPackagePrefsPath
+
+
152 SetDataFolder save_df
+
+
+
+
+
+
158 dfref save_df = GetDataFolderDFR()
+
+
+
+
162 NewDataFolder /O/S packages
+
163 NewDataFolder /O/S $package_name
+
164 dfref package_df = GetDataFolderDFR()
+
165 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
+
+
+
168 GetFileFolderInfo /Q /Z fullPath
+
+
170 fullPath += ":preferences.pxp"
+
171 GetFileFolderInfo /Q /Z fullPath
+
+
173 LoadData /O /R /Q fullPath
+
+
+
+
+
+
179 svar /sdfr=package_df filepath = s_filepath
+
180 NewPath /O/Z pearl_explorer_filepath, filepath
+
+
+
+
+
185 SetDataFolder save_df
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
219 PathInfo /S pearl_explorer_filepath
+
+
+
+
+
+
+
+
232 dfref save_df = GetDataFolderDFR()
+
+
+
+
236 wave wSelectedFiles = $(
package_path + "wSelectedFiles")
+
+
+
239 PathInfo pearl_explorer_filepath
+
+
241 all_files = IndexedFile(pearl_explorer_filepath, -1, "????")
+
242 nn = ItemsInList(all_files)
+
+
+
+
+
+
248 make /n=(nn) /t /free wtAllFiles
+
249 wtAllFiles = StringFromList(p, all_files)
+
+
251 Sort /A /R wtFiles, wtFiles
+
+
253 redimension /n=(numpnts(wtFiles)) wSelectedFiles
+
+
+
256 setdatafolder save_df
+
+
+
+
+
+
+
+
276 dfref save_df = GetDataFolderDFR()
+
277 dfref package_df = $package_path
+
+
+
+
+
+
+
+
+
+
287 result = result >= 3 ? 0 : -2
+
+
+
+
291 dfref file_df = package_df:file_info
+
292 KillDataFolder /z file_df
+
+
+
+
296 setdatafolder save_df
+
+
+
+
+
+
+
304 dfref save_df = GetDataFolderDFR()
+
305 dfref temp_df = NewFreeDataFolder()
+
+
307 load_file (filename, options="mode:load_diags", dest_df=temp_df, quiet=1)
+
308 svar /sdfr=temp_df /z s_loaded_datasets
+
+
+
311 if (SVAR_Exists(s_loaded_datasets) && (strlen(s_loaded_datasets) >= 4))
+
+
+
+
+
+
+
+
319 if (DataFolderRefStatus(attr_df))
+
+
321 wave /t /sdfr=temp_df /z attr_names
+
322 wave /t /sdfr=temp_df /z attr_values
+
323 if (WaveExists(attr_names) && WaveExists(attr_values))
+
+
+
+
+
328 setdatafolder save_df
+
+
+
347 static function
extract_attributes (attr_df, [dest_df, attr_filter, include_datawaves, include_infowaves])
+
+
+
+
351 variable include_datawaves
+
352 variable include_infowaves
+
+
354 dfref save_df = GetDataFolderDFR()
+
355 dfref package_df = $package_path
+
+
357 if (ParamIsDefault(dest_df))
+
358 dest_df = GetDataFolderDFR()
+
+
360 if (ParamIsDefault(attr_filter) || !WaveExists(attr_filter))
+
361 wave /t /sdfr=package_df /z attr_filter
+
+
363 if (ParamIsDefault(include_datawaves))
+
364 include_datawaves = 1
+
+
366 if (ParamIsDefault(include_infowaves))
+
367 include_infowaves = 1
+
+
+
370 setdatafolder dest_df
+
371 wave /t /z attr_names, attr_values
+
372 if (!WaveExists(attr_names) || !WaveExists(attr_values))
+
373 make /n=(1) /o /t attr_names, attr_values
+
+
+
+
+
378 setdatafolder attr_df
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
394 if (WaveExists(IN) && include_infowaves)
+
+
+
+
+
399 if (include_datawaves)
+
400 string waves = WaveList("*", ";", "")
+
401 string exceptions = "ID;IN;IU;IV"
+
402 waves = RemoveFromList(exceptions, waves)
+
403 nw = ItemsInList(waves, ";")
+
+
+
+
+
408 if (WaveExists(attr_filter) && (numpnts(attr_filter) >= 1))
+
409 nattr = numpnts(attr_filter)
+
410 redimension /n=(nattr) attr_names
+
411 attr_names = attr_filter
+
+
+
414 redimension /n=(ninfo) attr_names
+
415 attr_names = SelectString(strlen(ID[p]) >= 0, IN[p], ID[p])
+
+
+
+
+
420 redimension /n=(nattr) attr_names
+
421 for (iw = 0; iw < nw; iw +=1 )
+
422 sw = StringFromList(iw, waves, ";")
+
423 ss = StringByKey("PV", note($sw), "=", "\r")
+
424 FindValue /text=sw attr_names
+
425 if ((v_value < 0) && (strlen(ss) >= 0))
+
426 attr_names[iattr] = sw
+
+
+
+
+
+
432 redimension /n=(nattr) attr_names, attr_values
+
433 sort attr_names, attr_names
+
+
+
436 for (iattr = 0; iattr < nattr; iattr += 1)
+
437 sw = attr_names[iattr]
+
+
+
440 FindValue /text=sw ID
+
+
442 attr_values[iattr] = IV[v_value]
+
+
444 FindValue /text=sw IN
+
+
446 attr_values[iattr] = IV[v_value]
+
+
+
+
+
+
452 switch (WaveType($sw, 1))
+
+
+
455 if (WaveExists(w) && (numpnts(w) >= 1))
+
456 sprintf ss, "%g", w[0]
+
457 attr_values[iattr] = ss
+
+
+
+
+
462 if (WaveExists(wt) && (numpnts(wt) >= 1))
+
463 attr_values[iattr] = wt[0]
+
+
+
+
+
+
+
470 setdatafolder save_df
+
+
+
+
474 dfref df = GetDataFolderDFR()
+
475 wave /t /sdfr=df attr_names
+
476 wave /t /sdfr=df attr_values
+
+
+
+
+
+
+
+
+
485 dfref save_df = GetDataFolderDFR()
+
486 setdatafolder $package_path
+
487 wave /t/z attr_filter, attr_filter_summary
+
+
+
490 if (WinType(name) == 5)
+
491 Notebook $name selection={startOfFile, endOfFile}
+
492 Notebook $name text=
""
+
+
494 NewNotebook /F=1 /K=1 /N=$name as title
+
495 GetWindow $name wsize
+
496 v_right = v_left + 260
+
497 v_bottom = v_top + 360
+
498 MoveWindow /W=$name v_left, v_top, v_right, v_bottom
+
499 Notebook $name tabs={2*72}
+
+
+
+
503 if (WaveExists(attr_filter_summary) && (numpnts(attr_filter_summary) >= 1))
+
504 notebook $name fStyle=1, text=
"Summary\r\r"
+
505 notebook $name fStyle=0
+
+
507 notebook $name text=
"\r"
+
+
+
+
511 notebook $name fStyle=1, text=
"All Attributes\r\r"
+
512 notebook $name fStyle=0
+
+
514 notebook $name selection={startOfFile,startOfFile}, findText={
"" ,1}
+
+
516 setdatafolder save_df
+
+
+
+
+
521 wave /t /z attr_filter
+
+
+
+
525 variable nw = numpnts(attr_names)
+
+
+
+
+
530 variable do_filter = WaveExists(attr_filter)
+
+
532 for (iw = 0; iw < nw; iw += 1)
+
+
+
535 FindValue /text=sw attr_filter
+
+
+
+
+
540 sprintf ss,
"%s\t%s\r" , attr_names[iw], attr_values[iw]
+
541 notebook $notebook_name text=ss
+
+
+
+
+
+
+
+
+
+
573 if (ParamIsDefault(filename))
+
574 svar /sdfr=file_df /z loaded_file=s_filepath
+
575 if (svar_Exists(loaded_file))
+
576 filename = loaded_file
+
+
+
+
+
+
582 if (ParamIsDefault(graphname))
+
+
+
+
+
+
588 if (exists(
"PearlElog#set_panel_attributes" ) == 6)
+
589 sprintf cmd,
"PearlElog#set_panel_attributes(\"\", \"File=%s\")" , ParseFilePath(0, filename,
":" , 1, 0)
+
+
591 if ((strlen(graphname) > 0) && (WinType(graphname) == 1))
+
592 sprintf cmd, "
PearlElog #set_panel_graphs(\"\", \"%s\")", graphname
+
+
+
595 svar /sdfr=file_df /z authors
+
596 if (svar_Exists(authors))
+
597 if (strlen(authors)>=1)
+
598 sprintf cmd,
"PearlElog#set_panel_attributes(\"\", \"author=%s\")" , authors
+
+
+
+
602 svar /sdfr=file_df /z pgroup
+
603 if (svar_Exists(pgroup))
+
604 if (strlen(pgroup)>=1)
+
605 sprintf cmd,
"PearlElog#set_panel_attributes(\"\", \"p-group=%s\")" , pgroup
+
+
+
+
609 svar /sdfr=file_df /z proposal
+
610 if (svar_Exists(proposal))
+
611 if (strlen(proposal)>=1)
+
612 sprintf cmd,
"PearlElog#set_panel_attributes(\"\", \"project=%s\")" , proposal
+
+
+
+
616 svar /sdfr=file_df /z proposer
+
617 svar /sdfr=file_df /z sample
+
618 if (svar_Exists(sample))
+
619 if (strlen(sample)>=1)
+
620 sprintf cmd,
"PearlElog#set_panel_attributes(\"\", \"sample=%s\")" , sample
+
+
+
+
+
+
+
+
+
+
+
+
632 dfref save_df = GetDataFolderDFR()
+
633 dfref preview_df = $package_path
+
+
635 killStrings /z authors, pgroup, proposal, proposer, sample
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
652 if (WaveExists(image))
+
+
+
+
656 setdatafolder save_df
+
+
+
+
+
+
+
674 dfref save_df = GetDataFolderDFR()
+
+
676 setdatafolder $package_path
+
677 dfref preview_df = GetDataFolderDFR()
+
+
679 svar s_preview_source
+
+
681 if (! svar_exists(s_file_info))
+
682 string /g s_file_info
+
+
+
685 dfref temp_df = NewFreeDataFolder()
+
686 dfref file_df =
psh5_preview ("pearl_explorer_filepath", filename, dest_df=temp_df)
+
687 svar /z /sdfr=temp_df dataname=s_preview_wave
+
+
689 s_preview_file = filename
+
690 s_preview_source = ""
+
+
692 wave /z /sdfr=temp_df data = $dataname
+
693 if (waveexists(data))
+
694 duplicate /o data, preview_df:preview_image
+
+
696 print "no data found in file " + filename
+
+
+
+
+
701 setdatafolder save_df
+
702 wave /z /sdfr=preview_df preview_image
+
+
+
+
+
+
+
720 dfref save_df = GetDataFolderDFR()
+
721 setdatafolder $package_path
+
+
723 svar s_preview_source
+
+
725 s_preview_file = filename
+
726 s_preview_source = ""
+
727 wave /z preview_image
+
+
+
730 if (! svar_exists(s_file_info))
+
731 string /g s_file_info
+
+
733 if (strlen(s_preview_file) > 0)
+
+
+
+
+
+
739 setdatafolder save_df
+
+
+
+
+
+
+
765 dfref save_df = GetDataFolderDFR()
+
766 setdatafolder $package_path
+
+
768 svar s_preview_source
+
+
+
771 dfref data_df = newfreedatafolder()
+
772 setdatafolder data_df
+
773 LoadWave /t/p=pearl_explorer_filepath/q filename
+
774 s_preview_file = s_filename
+
775 s_preview_source = ""
+
+
+
+
779 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
+
791 switch (WaveDims(data))
+
+
793 redimension /n=(numpnts(data)) preview
+
+
+
+
797 redimension /n=(dimsize(data, 0), dimsize(data, 1)) preview
+
+
+
+
801 redimension /n=(dimsize(data, 0), dimsize(data, 1)) preview
+
802 z1 = floor(DimSize(data, 2) / 2)
+
+
804 wave slab =
ad_extract_slab (data, nan, nan, nan, nan, z1, z2, "", pscale=1)
+
+
+
+
+
+
+
811 switch (WaveDims(data))
+
+
+
+
815 setscale /p y dimoffset(data, 1), dimdelta(data, 1), waveunits(data, 1), preview
+
+
817 setscale /p x dimoffset(data, 0), dimdelta(data, 0), waveunits(data, 0), preview
+
818 setscale d 0, 0, waveunits(data, -1), preview
+
+
+
+
+
827 dfref save_df = GetDataFolderDFR()
+
+
829 setdatafolder $package_path
+
+
831 svar s_preview_source
+
+
+
+
835 setdatafolder save_df
+
+
+
+
+
840 string d_names = WaveList("*", ";", "DP:1")
+
841 variable nw = ItemsInList(d_names, ";")
+
842 variable npv = ItemsInList(s_preview_pvs, ";")
+
+
844 string wname, wnote, pv_name, pv_match
+
845 for (iw = 0; iw < nw; iw += 1)
+
846 wname = StringFromList(iw, d_names, ";")
+
+
848 pv_name = StringByKey("PV", wnote, "=", "\r")
+
+
850 for (ipv = 0; ipv < npv; ipv += 1)
+
851 pv_match = StringFromList(ipv, s_preview_pvs)
+
852 if (StringMatch(pv_name, pv_match))
+
+
854 s_preview_source = pv_name
+
+
+
+
+
+
+
+
+
863 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
+
+
+
876 if ((DimOffset(preview, 0) == 0) && (DimDelta(preview, 0) == 1))
+
877 string xname = StringByKey("Axis1", note(data), "=", "\r")
+
878 wave /z xwave = $xname
+
879 if (WaveExists(xwave))
+
+
881 variable monotonic = 0
+
882 duplicate /free xwave, xdiff
+
883 differentiate /p xwave /D=xdiff
+
884 duplicate /free xdiff, xflag
+
+
886 monotonic = sum(xflag) > numpnts(xwave) * 0.9
+
+
888 monotonic = monotonic || (sum(xflag) > numpnts(xwave) * 0.9)
+
+
890 setscale /i x xwave[0], xwave[numpnts(xwave)-1], waveunits(xwave, -1), preview
+
+
+
+
+
+
+
+
+
+
901 dfref save_df = GetDataFolderDFR()
+
+
+
904 SetDataFolder data_df
+
905 string data_name = StringFromList(ItemsInList(dataset, "/") - 1, dataset, "/")
+
906 wave /z data=$data_name
+
+
908 if (WaveExists(data))
+
909 switch(WaveDims(data))
+
+
+
+
+
+
+
+
+
+
+
+
921 setdatafolder save_df
+
+
+
+
+
+
+
+
+
930 dfref save_df = GetDataFolderDFR()
+
931 setdatafolder $package_path
+
+
933 svar s_profiles_graph
+
+
935 svar s_preview_source
+
936 svar s_preview_trace_graph
+
+
+
939 if ((strlen(s_profiles_graph) > 0) && (WinType(s_profiles_graph) == 1))
+
940 KillWindow $s_profiles_graph
+
+
942 if ((strlen(s_preview_trace_graph) > 0) && (WinType(s_preview_trace_graph) == 1))
+
943 KillWindow $s_preview_trace_graph
+
+
+
+
947 if (wavedims(data) == 2)
+
+
949 ModifyGraph /w=$s_profiles_graph /z wbRGB=(48640,56832,60160)
+
950 graphname = s_profiles_graph
+
951 elseif (wavedims(data) == 1)
+
952 duplicate /o data, preview_trace
+
953 if (!ParamIsDefault(xdata))
+
954 duplicate /o xdata, preview_trace_x
+
+
956 duplicate /o data, preview_trace_x
+
+
958 setscale d 0, 0, WaveUnits(data, 0), preview_trace_x
+
+
+
961 ModifyGraph /w=$s_preview_trace_graph wbRGB=(48640,56832,60160)
+
962 graphname = s_preview_trace_graph
+
+
+
+
+
967 string title = "Preview " + s_preview_file
+
968 if (strlen(s_preview_source) > 0)
+
969 title = title + " (" + s_preview_source[0,31] + ")"
+
+
971 dowindow /f/t $graphname, title
+
972 s_preview_graph = graphname
+
+
974 setdatafolder save_df
+
+
+
+
+
+
+
+
982 if (WaveExists(xtrace))
+
983 display /n=pearl_explorer_1d /k=1 ytrace vs xtrace as "Preview"
+
+
985 display /n=pearl_explorer_1d /k=1 ytrace as "Preview"
+
+
+
988 string graphname = s_name
+
989 ModifyGraph /w=$graphname rgb[0]=(0,0,0)
+
990 ModifyGraph /w=$graphname grid=2
+
991 ModifyGraph /w=$graphname mirror=1
+
992 ModifyGraph /w=$graphname minor=1
+
993 ModifyGraph /w=$graphname axThick=0.5
+
994 ModifyGraph /w=$graphname gridRGB=(52224,52224,52224)
+
995 ModifyGraph /w=$graphname gridHair=0
+
996 ModifyGraph /w=$graphname tick=0
+
997 ModifyGraph /w=$graphname btLen=4
+
+
+
1000 string labels = note(ytrace)
+
+
1002 lab = StringByKey("AxisLabelX", labels, "=", "\r")
+
+
+
+
1006 Label /w=$graphname bottom lab + " (\\U)"
+
1007 lab = StringByKey("Dataset", labels, "=", "\r")
+
+
+
+
1011 Label /w=$graphname left lab + " (\\U)"
+
+
+
+
+
+
+
+
+
+
1028 dfref save_df = GetDataFolderDFR()
+
1029 setdatafolder $package_path
+
+
+
+
1033 variable nn = numpnts(wSelectedFiles)
+
+
1035 for (ii = 0; ii < nn; ii += 1)
+
1036 if (wSelectedFiles[ii])
+
1037 setdatafolder save_df
+
1038 if (ParamIsDefault(options))
+
+
+
+
+
+
+
+
+
1064 static function
load_file (filename, [options, dest_df, quiet])
+
+
+
+
+
+
1070 if (ParamIsDefault(options))
+
+
+
+
+
+
+
+
+
+
1080 load_hdf_file (filename, options=options, dest_df=dest_df, quiet=quiet)
+
+
+
+
+
+
+
+
+
+
+
+
+
1093 string mode = StringByKey("mode", options, ":", ";")
+
1094 string reduction_func = StringByKey("reduction_func", options, ":", ";")
+
+
1096 string modes = "load_scan;load_region;load_dataset;load_diags;load_complete;"
+
+
+
+
1100 if (strlen(mode) == 0)
+
1101 mode = StringFromList(0, modes, ";")
+
+
1103 if (strlen(reduction_func) == 0)
+
1104 reduction_func = StringFromList(0, reduction_funcs, ";")
+
+
+
1107 prompt mode, "Mode", popup, modes
+
1108 prompt reduction_func, "Reduction Function", popup, reduction_funcs
+
1109 doprompt "HDF5 Loading Options", mode, reduction_func
+
+
+
1112 options = ReplaceStringByKey("mode", options, mode, ":", ";")
+
1113 options = ReplaceStringByKey("reduction_func", options, reduction_func, ":", ";")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1140 string prompt_name = "prompt_" + func_name
+
1141 if (exists(prompt_name) == 6)
+
+
1143 return prompt_func(func_param)
+
+
+
+
+
+
+
+
+
+
+
+
+
1194 dfref save_df = GetDataFolderDFR()
+
+
+
1197 svar pref_params = $(
package_path + "s_reduction_params")
+
1198 string path = "pearl_explorer_filepath"
+
+
1200 if (ParamIsDefault(options))
+
1201 options = pref_options
+
+
+
1204 if (strlen(options) == 0)
+
+
1206 pref_options = options
+
+
+
+
+
+
1212 string reduction_func = StringByKey("reduction_func", options, ":", ";")
+
1213 string reduction_params = pref_params
+
1214 variable max_rank = 2
+
+
1216 if (exists(reduction_func) == 6)
+
+
+
1219 pref_params = reduction_params
+
+
+
+
+
+
1225 string mode = StringByKey("mode", options, ":", ";")
+
1226 string selected_datasets = WMHL_SelectedObjectsList("
PearlDataExplorer ", "lb_contents")
+
+
+
+
+
+
1232 print mode, filename
+
1233 if (strlen(reduction_func))
+
1234 print reduction_func, reduction_params
+
+
+
+
+
1239 case "load_complete":
+
+
1241 dfref file_df =
psh5_load (path, filename, "", "", "*", classes=dsc, reduction_func=reduction_func, reduction_params=reduction_params, dest_df=dest_df)
+
+
+
1244 if (ItemsInList(selected_scans, ";") == 0)
+
+
1246 print "no scan selected - defaulting to scan 1."
+
+
1248 selected_scans = "/scan1;"
+
+
+
1251 dfref file_df =
psh5_load (path, filename, selected_scans, "", "", classes=dsc, dest_df=dest_df)
+
+
+
1254 if (ItemsInList(selected_scans, ";") == 0)
+
+
1256 print "no scan selected - defaulting to scan 1."
+
+
1258 selected_scans = "/scan1;"
+
+
+
1261 dfref file_df =
psh5_load (path, filename, selected_scans, "", "", classes=dsc, max_rank=max_rank, reduction_func=reduction_func, reduction_params=reduction_params, dest_df=dest_df)
+
+
+
1264 if (ItemsInList(selected_regions, ";") == 0)
+
+
1266 print "no region selected - defaulting to scan 1/region 1."
+
+
1268 selected_regions = "/scan1/region1;"
+
+
+
1271 dfref file_df =
psh5_load (path, filename, "", selected_regions, "", classes=dsc, max_rank=max_rank, reduction_func=reduction_func, reduction_params=reduction_params, dest_df=dest_df)
+
+
1273 case "load_dataset":
+
1274 if (ItemsInList(selected_datasets, ";") > 0)
+
+
1276 dfref file_df =
psh5_load (path, filename, "", "", selected_datasets, classes=dsc, reduction_func=reduction_func, reduction_params=reduction_params, dest_df=dest_df)
+
+
+
1279 DoAlert /T="PShell Import" 0, "Please select the datasets to load."
+
+
+
+
+
+
1285 if (DataFolderRefStatus(file_df))
+
1286 setdatafolder file_df
+
+
+
1289 print "data loaded to", GetDataFolder(1)
+
+
+
1292 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
+
+
1304 dfref save_df = GetDataFolderDFR()
+
+
1306 string loaded_filename = ""
+
+
1308 if (ParamIsDefault(dest_df) || !DataFolderRefStatus(dest_df))
+
+
+
1311 DoAlert /T="
load_hdf_file " 0, "optional argument dest_df not supported."
+
+
+
+
1315 if (ParamIsDefault(options))
+
+
+
1318 if (strlen(options) == 0)
+
+
1320 options = pref_options
+
+
+
1323 pref_options = options
+
+
+
+
+
+
+
1330 string mode = StringByKey("mode", options, ":", ";")
+
+
+
1333 case "load_reduced":
+
1334 string reduction_func = StringByKey("reduction_func", options, ":", ";")
+
1335 svar pref_params = $(
package_path + "s_reduction_params")
+
1336 string reduction_params = pref_params
+
+
1338 pref_params = reduction_params
+
1339 print reduction_func, reduction_params
+
1340 loaded_filename =
adh5_load_reduced (nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
+
+
+
+
+
+
+
1347 if (strlen(loaded_filename) > 0)
+
1348 setdatafolder $("root:" + nickname)
+
1349 data_df = GetDataFolderDFR()
+
+
+
1352 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
+
+
1364 dfref save_df = GetDataFolderDFR()
+
+
+
1367 if (ParamIsDefault(options))
+
+
+
+
1371 variable own_data_df = 0
+
1372 if (ParamIsDefault(dest_df) || !DataFolderRefStatus(dest_df))
+
+
1374 newdatafolder /s/o $("root:" + nickname)
+
+
+
1377 setdatafolder dest_df
+
+
1379 dfref data_df = GetDataFolderDFR()
+
+
+
+
+
+
+
1386 LoadWave /t/p=pearl_explorer_filepath/q filename
+
1387 svar waves = s_wavenames
+
1388 dfref act_df = GetDataFolderDFR()
+
+
+
+
+
1393 if (!DataFolderRefsEqual(act_df, data_df) && own_data_df)
+
+
+
1396 setdatafolder data_df
+
1397 if (ItemsInList(WaveList("*", ";", ""), ";") == 0)
+
1398 killdatafolder /z data_df
+
+
+
+
1402 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
1433 if (ParamIsDefault(ignoredate))
+
+
+
1436 if (ParamIsDefault(unique))
+
+
+
+
1440 string basename = ParseFilePath(3, filename, ":", 0, 0)
+
1441 string extension = ParseFilePath(4, filename, ":", 0, 0)
+
+
+
+
1445 if (strsearch(basename, "X03DA_PC", 0, 2) >= 0)
+
1446 autosource = "sscan"
+
1447 basename = ReplaceString("_", basename, "-")
+
+
1449 elseif (strsearch(basename, "otf", 0, 2) >= 0)
+
+
+
1452 if (ParamIsDefault(sourcename))
+
1453 sourcename = autosource
+
+
+
1456 variable nparts = ItemsInList(basename, "-")
+
+
1458 string datepart = StringFromList(nparts - 2, basename, "-")
+
1459 string indexpart = StringFromList(nparts - 1, basename, "-")
+
+
1461 sprintf nickname, "%s_%s", sourcename, indexpart
+
+
1463 sprintf nickname, "%s_%s_%s", sourcename, datepart, indexpart
+
+
+
+
+
+
1469 if (unique && CheckName(nickname, 11))
+
1470 nickname = UniqueName(nickname + "_", 11, 0)
+
+
+
+
+
+
+
+
+
1479 PauseUpdate; Silent 1
+
1480 NewPanel /K=1 /W=(510,45,1190,539) as "PEARL Data Explorer"
+
1481 ModifyPanel cbRGB=(48640,56832,60160)
+
1482 GroupBox g_data_reduction,pos={355.00,370.00},size={306.00,49.00},title=
"data reduction"
+
1483 GroupBox g_data_reduction,help={
"data reduction of 3D ScientaImage" }
+
1484 GroupBox gb_filepath,pos={8.00,4.00},size={328.00,48.00},title=
"file system folder"
+
1485 TitleBox tb_filepath,pos={20.00,28.00},size={279.00,21.00},frame=0
+
1486 TitleBox tb_filepath,variable= root:packages:pearl_explorer:s_short_filepath,fixedSize=1
+
+
1488 Button b_browse_filepath,fColor=(65280,48896,32768)
+
1489 GroupBox gb_prefs,pos={8.00,351.00},size={65.00,131.00},title=
"prefs"
+
1490 GroupBox gb_prefs,help={
"explorer package preferences" }
+
+
1492 Button b_save_prefs,help={
"save preferences of the data explorer package (data file path, attributes filter)" }
+
1493 Button b_save_prefs,fColor=(65280,48896,32768)
+
+
1495 Button b_load_prefs,help={
"load preferences of the data explorer package" }
+
1496 Button b_load_prefs,fColor=(65280,48896,32768)
+
1497 GroupBox gb_filelist,pos={8.00,55.00},size={328.00,293.00},title=
"data files"
+
+
1499 ListBox lb_files,listWave=root:packages:pearl_explorer:wtFiles
+
1500 ListBox lb_files,selWave=root:packages:pearl_explorer:wSelectedFiles,mode= 4
+
+
1502 Button b_update_filelist,fColor=(65280,48896,32768)
+
1503 CheckBox cb_file_preview,pos={78.00,318.00},size={59.00,14.00},title=
"preview"
+
1504 CheckBox cb_file_preview,help={
"enable/disable automatic preview window when selecting a data file" }
+
1505 CheckBox cb_file_preview,value= 0
+
+
1507 Button b_file_prev,help={
"previous file" },fColor=(65280,48896,32768)
+
+
1509 Button b_file_next,help={
"next file" },fColor=(65280,48896,32768)
+
+
1511 Button b_goto_dataset,help={
"change the current data folder ot where the selected dataset could be located" }
+
1512 Button b_goto_dataset,fColor=(65280,48896,32768)
+
+
1514 Button b_display_dataset,help={
"display the selected dataset in its own window" }
+
1515 Button b_display_dataset,fColor=(65280,48896,32768)
+
+
1517 Button b_load_complete,help={
"load all datasets of the selected file." }
+
1518 Button b_load_complete,userdata=
"mode:load_complete;"
+
1519 Button b_load_complete,fColor=(65280,48896,32768)
+
1520 TitleBox tb_selected_file,pos={360.00,28.00},size={309.00,22.00},frame=0
+
1521 TitleBox tb_selected_file,variable= root:packages:pearl_explorer:s_selected_file,fixedSize=1
+
1522 GroupBox gb_contents,pos={346.00,55.00},size={327.00,294.00},title=
"datasets"
+
+
1524 Button b_attr_notebook,help={
"show a summary of attributes in a notebook window" }
+
1525 Button b_attr_notebook,fColor=(65280,48896,32768)
+
1526 ListBox lb_contents,pos={355.00,84.00},size={305.00,222.00}
+
1527 ListBox lb_contents,keySelectCol= 1
+
1528 GroupBox gb_selected_file,pos={346.00,4.00},size={328.00,48.00},title=
"selected file"
+
+
1530 Button b_load_region,help={
"load the selected region" }
+
1531 Button b_load_region,userdata=
"mode:load_region;" ,fColor=(65280,48896,32768)
+
+
1533 PopupMenu popup_reduction,help={
"data reduction of 3d ScientaImage. note: the list may contain unsuitable functions. check the code or documentation!" }
+
1534 PopupMenu popup_reduction,mode=1,popvalue=
"None" ,value= #
"PearlDataExplorer#pm_reduction_values()"
+
1535 GroupBox group_import,pos={346.00,351.00},size={326.00,131.00},title=
"import"
+
+
1537 Button b_load_scan,help={
"load the selected scan" },userdata=
"mode:load_scan;"
+
1538 Button b_load_scan,fColor=(65280,48896,32768)
+
+
1540 Button b_load_diags,help={
"load diagnostics of selected scans" },userdata=
"mode:load_diags;"
+
1541 Button b_load_diags,fColor=(65280,48896,32768)
+
+
1543 Button b_load_dataset,help={
"load the selected datasets" }
+
1544 Button b_load_dataset,userdata=
"mode:load_dataset;" ,fColor=(65280,48896,32768)
+
+
1546 Button b_reduction_params,help={
"set data reduction parameters" }
+
1547 Button b_reduction_params,fColor=(65280,48896,32768)
+
1548 GroupBox g_fileinfo,pos={85.00,351.00},size={251.00,131.00},title=
"file info"
+
+
1550 Button b_elog,help={
"send file metadata to ELOG panel (does not submit to ELOG)" }
+
1551 Button b_elog,fColor=(65280,48896,32768)
+
1552 ToolsGrid grid=(0,28.35,5)
+
+
+
+
1558 dfref package_df = $package_path
+
1559 svar /z /sdfr=package_df hl_contents_datasets
+
1560 wave /z /sdfr=package_df wSelectedFiles
+
+
1562 variable file_selected = 0
+
1563 if (WaveExists(wSelectedFiles))
+
1564 file_selected = sum(wSelectedFiles)
+
+
+
1567 string selected_datasets = WMHL_SelectedObjectsList("
PearlDataExplorer ", "lb_contents")
+
1568 variable scan_selected = strsearch(selected_datasets, "scan", 0, 2) == 0
+
1569 variable region_selected = strsearch(selected_datasets, "region", 0, 2) >= 0
+
+
1571 variable dataset_selected = 0
+
1572 variable nds = ItemsInList(selected_datasets, ";")
+
+
+
1575 if (svar_exists(hl_contents_datasets))
+
1576 for (ids = 0; ids < nds; ids += 1)
+
1577 ds = "/" + StringFromList(ids, selected_datasets, ";")
+
1578 if (NumType(NumberByKey(ds, hl_contents_datasets, ":", ";")) == 0)
+
1579 dataset_selected = 1
+
+
+
+
+
+
+
+
+
1588 dis = file_selected ? 0 : 2
+
+
+
1591 dis = file_selected && scan_selected ? 0 : 2
+
+
+
1594 dis = file_selected && (strlen(WinList("*ElogPanel*", ";", "WIN:64")) > 1) ? 0 : 2
+
+
1596 dis = scan_selected ? 0 : 2
+
+
1598 dis = region_selected ? 0 : 2
+
+
1600 dis = dataset_selected ? 0 : 2
+
+
+
1603 dis = file_selected && (nds > 0) ? 0 : 2
+
+
+
+
1607 if ((cmpstr(S_Value, "None") != 0) && (exists(S_Value) == 6))
+
+
+
+
+
+
+
+
+
+
+
+
1619 STRUCT WMButtonAction &ba
+
+
1621 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
+
1634 STRUCT WMButtonAction &ba
+
+
1636 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1655 string path = long_path
+
1656 variable ellipsis = 0
+
+
1658 if (strlen(path) > max_len)
+
1659 path = RemoveListItem(1, path, ":")
+
+
+
+
+
+
+
+
1667 path = AddListItem("
", path, ":", 1)
+
+
+
+
+
+
+
1674 STRUCT WMButtonAction &ba
+
+
1676 dfref save_df = GetDataFolderDFR()
+
+
1678 switch( ba.eventCode )
+
+
1680 PathInfo /S pearl_explorer_filepath
+
1681 NewPath /M="select data file folder" /O/Z pearl_explorer_filepath
+
+
+
+
+
+
+
+
+
+
+
1692 setdatafolder save_df
+
+
+
+
+
1697 STRUCT WMButtonAction &ba
+
+
1699 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1715 reduction_funcs = AddListItem("None", reduction_funcs, ";", 0)
+
1716 return reduction_funcs
+
+
+
+
1720 STRUCT WMPopupAction &pa
+
+
1722 switch( pa.eventCode )
+
+
1724 Variable popNum = pa.popNum
+
1725 String popStr = pa.popStr
+
+
+
+
+
+
+
+
+
+
+
1736 STRUCT WMButtonAction &ba
+
+
1738 switch( ba.eventCode )
+
+
+
1741 if ((cmpstr(S_Value, "None") != 0) && (exists(S_Value) == 6))
+
1742 svar pref_params = $(
package_path + "s_reduction_params")
+
1743 string reduction_func = S_Value
+
1744 string reduction_params = pref_params
+
+
1746 pref_params = reduction_params
+
+
+
+
+
+
+
+
+
+
+
+
1758 STRUCT WMButtonAction &ba
+
+
1760 switch( ba.eventCode )
+
+
+
+
1764 string options=ba.userData
+
+
+
+
1768 if ((cmpstr(S_Value, "None") != 0) && (exists(S_Value) == 6))
+
1769 options = ReplaceStringByKey("reduction_func", options, S_Value, ":", ";")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1795 dfref save_df = GetDataFolderDFR()
+
1796 setdatafolder $package_path
+
1797 svar s_selected_file
+
1798 s_selected_file = file
+
+
+
+
+
+
+
1805 setdatafolder save_df
+
+
+
+
+
1810 STRUCT WMButtonAction &ba
+
+
1812 dfref save_df = GetDataFolderDFR()
+
+
1814 switch( ba.eventCode )
+
+
1816 setdatafolder $package_path
+
+
+
1819 FindValue /i=1 wSelectedFiles
+
+
1821 if (v_value >= numpnts(wtFiles))
+
1822 v_value = min(numpnts(wtFiles) - 1, 0)
+
+
1824 wSelectedFiles = p == v_value
+
+
1826 variable ifile = v_value
+
+
+
+
+
+
+
+
+
+
1836 setdatafolder save_df
+
+
+
+
+
1841 STRUCT WMButtonAction &ba
+
+
1843 dfref save_df = GetDataFolderDFR()
+
+
1845 switch( ba.eventCode )
+
+
1847 setdatafolder $package_path
+
+
+
1850 FindValue /i=1 wSelectedFiles
+
+
+
1853 v_value = numpnts(wtFiles) - 1
+
+
1855 wSelectedFiles = p == v_value
+
+
1857 variable ifile = v_value
+
+
+
+
+
+
+
+
+
+
1867 setdatafolder save_df
+
+
+
+
+
1872 STRUCT WMListboxAction &lba
+
+
1874 dfref save_df = GetDataFolderDFR()
+
+
1876 Variable row = lba.row
+
1877 Variable col = lba.col
+
1878 WAVE/T/Z listWave = lba.listWave
+
1879 WAVE/Z selWave = lba.selWave
+
+
1881 switch( lba.eventCode )
+
+
+
+
1885 setdatafolder $package_path
+
+
+
1888 if (sum(wSelectedFiles) == 1)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1910 setdatafolder save_df
+
+
+
+
+
1915 STRUCT WMButtonAction &ba
+
+
1917 dfref save_df = GetDataFolderDFR()
+
+
1919 switch( ba.eventCode )
+
+
1921 setdatafolder $package_path
+
+
+
1924 variable nn = numpnts(wSelectedFiles)
+
+
1926 for (ii = 0; ii < nn; ii += 1)
+
1927 if (wSelectedFiles[ii])
+
+
+
+
+
+
+
+
+
+
1937 setdatafolder save_df
+
+
+
+
+
+
1943 dfref save_df = GetDataFolderDFR()
+
1944 setdatafolder $package_path
+
+
+
+
1948 setdatafolder save_df
+
+
+
+
+
+
1954 if (cmpstr(WMHL_GetItemForRowNumber("
PearlDataExplorer ", "lb_contents", 0), "<uninitialized>") != 0)
+
+
+
+
+
+
+
+
+
+
+
1969 dfref save_df = GetDataFolderDFR()
+
1970 setdatafolder $package_path
+
+
+
+
+
+
+
1977 string /g hl_contents_datasets = ""
+
+
1979 if (DataFolderRefStatus(file_df))
+
1980 svar /sdfr=file_df datasets = s_datasets
+
1981 svar /sdfr=file_df datatypes = s_datasets_datatypes
+
1982 svar /sdfr=file_df ranks = s_datasets_ranks
+
1983 svar /sdfr=file_df dimensions = s_datasets_dimensions
+
+
1985 nds = ItemsInList(datasets, ";")
+
1986 for (ids = 0; ids < nds; ids += 1)
+
1987 ds = StringFromList(ids, datasets, ";")
+
1988 extra = StringFromList(ids, dimensions, ";")
+
1989 hl_contents_datasets = ReplaceStringByKey(ds, hl_contents_datasets, extra, ":", ";")
+
+
+
+
+
+
+
1996 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
2006 dfref save_df = GetDataFolderDFR()
+
+
2008 if (!ParamIsDefault(dest_df))
+
2009 setdatafolder dest_df
+
+
2011 setdatafolder $package_path
+
2012 NewDataFolder /o /s file_info
+
+
+
2015 dfref file_df =
psh5_open_file (path_name, file_name, dest_df=GetDataFolderDFR())
+
2016 if (DataFolderRefStatus(file_df))
+
+
+
+
+
2021 setdatafolder save_df
+
+
+
+
+
+
+
+
2033 if (cmpstr(parent_path[0], "/") != 0)
+
2034 parent_path = "/" + parent_path
+
+
+
2037 variable nobj = ItemsInList(objects, ";")
+
+
+
+
+
+
2043 string child_path = ""
+
2044 string child_name = ""
+
2045 string child_names = ""
+
2046 string extra_data = ""
+
+
+
2049 for (iobj = 0; iobj < nobj; iobj += 1)
+
2050 obj = StringFromList(iobj, objects, ";")
+
+
2052 if (cmpstr(obj[0, strlen(parent_path)-1], parent_path) == 0)
+
2053 child_path = StringFromList(0, obj, ":")
+
2054 child_path = child_path[strlen(parent_path), strlen(child_path)-1]
+
2055 if (cmpstr(child_path[0], "/") == 0)
+
2056 child_path = child_path[1, strlen(child_path)-1]
+
+
2058 child_name = StringFromList(0, child_path, "/")
+
2059 nel = ItemsInList(child_path, "/")
+
2060 child_names = ReplaceNumberByKey(child_name, child_names, nel)
+
+
2062 extra = RemoveListItem(0, obj, ":")
+
2063 extra_data = ReplaceStringByKey(child_name, extra_data, extra)
+
+
+
+
+
+
+
+
2071 nobj = ItemsInList(child_names)
+
2072 for (iobj = 0; iobj < nobj; iobj += 1)
+
2073 obj = StringFromList(iobj, child_names)
+
2074 child_name = StringFromList(0, obj, ":")
+
2075 nel = NumberByKey(child_name, child_names)
+
2076 WMHL_AddObject("
PearlDataExplorer ", "lb_contents", parent_path[1, strlen(parent_path)], child_name, nel > 1)
+
+
2078 extra = StringByKey(child_name, extra_data)
+
2079 row = WMHL_GetRowNumberForItem("
PearlDataExplorer ", "lb_contents", parent_path[1, strlen(parent_path)] + "/" + child_name)
+
+
2081 WMHL_ExtraColumnData("
PearlDataExplorer ", "lb_contents", 0, row, StringFromList(0, extra, "|"), 0)
+
+
+
+
+
+
+
+
+
2090 dfref save_df = GetDataFolderDFR()
+
2091 setdatafolder $package_path
+
+
2093 svar hl_contents_datasets
+
2094 variable nds = ItemsInList(hl_contents_datasets, ";")
+
+
+
+
+
2099 for (ids = 0; ids < nds; ids += 1)
+
2100 sds = StringFromList(ids, hl_contents_datasets, ";")
+
2101 if (cmpstr(sds[0,4], "/scan", 0) == 0)
+
2102 scan = StringFromList(1, sds, "/")
+
2103 scans = ReplaceNumberByKey(scan, scans, 1)
+
+
+
+
2107 variable nscans = ItemsInList(scans)
+
+
2109 for (iscan = 0; iscan < nscans; iscan += 1)
+
2110 scan = StringFromList(iscan, scans)
+
2111 scan = StringFromList(0, scan, ":")
+
+
+
+
2115 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2130 String HostWindow, ListControlName, ContainerPath
+
+
2132 dfref save_df = GetDataFolderDFR()
+
2133 setdatafolder $package_path
+
2134 svar hl_contents_datasets
+
+
2136 setdatafolder save_df
+
+
+
+
2140 String HostWindow, ListControlName
+
+
+
+
2144 dfref save_df = GetDataFolderDFR()
+
2145 setdatafolder $package_path
+
+
+
+
+
+
+
+
+
+
+
+
2157 setdatafolder save_df
+
+
+
+
+
+
+
+
2179 dfref save_df = GetDataFolderDFR()
+
2180 setdatafolder $package_path
+
+
+
2183 string parent_folder
+
+
+
+
+
+
+
+
2191 path = "root:" + parent_folder
+
2192 if (DataFolderExists(path))
+
+
+
+
+
+
2198 variable nparts = ItemsInList(datapath, "/")
+
+
2200 for (ipart = 0; ipart < nparts; ipart += 1)
+
2201 folder = StringFromList(ipart, datapath, "/")
+
+
2203 if (DataFolderExists(path))
+
+
+
+
+
+
+
+
2211 if (DataFolderExists(parent_folder))
+
2212 setdatafolder $parent_folder
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2232 STRUCT WMButtonAction &ba
+
+
2234 switch( ba.eventCode )
+
+
2236 dfref save_df = GetDataFolderDFR()
+
2237 setdatafolder $package_path
+
2238 svar s_selected_file
+
2239 svar hl_contents_datasets
+
2240 string datapath = StringFromList(0, WMHL_SelectedObjectsList("
PearlDataExplorer ", "lb_contents"))
+
2241 if (strsearch(hl_contents_datasets, datapath, 0) != 0)
+
2242 datapath = datapath + "/"
+
+
+
+
2246 setdatafolder save_df
+
+
2248 msg = "Can't find data folder. Has the file been loaded?"
+
2249 DoAlert /T="Goto DF" 0, msg
+
+
+
+
+
+
+
+
+
+
+
+
2264 STRUCT WMButtonAction &ba
+
+
2266 switch( ba.eventCode )
+
+
2268 dfref save_df = GetDataFolderDFR()
+
2269 setdatafolder $package_path
+
2270 svar s_selected_file
+
2271 svar hl_contents_datasets
+
2272 string datapath = StringFromList(0, WMHL_SelectedObjectsList("
PearlDataExplorer ", "lb_contents"))
+
2273 if (strsearch(hl_contents_datasets, datapath, 0) < 0)
+
+
+
+
+
+
2279 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
2296 dfref save_df = GetDataFolderDFR()
+
+
2298 dfref preview_df = $package_path
+
2299 svar /z /sdfr=preview_df s_selected_file
+
2300 svar /z /sdfr=preview_df s_preview_file
+
2301 svar /z /sdfr=preview_df s_preview_graph
+
+
2303 if (!SVAR_Exists(s_selected_file) || (strlen(s_selected_file) < 1))
+
+
+
+
+
2308 variable result = -1
+
+
+
2311 dfref data_df = GetDataFolderDFR()
+
2312 svar /sdfr=data_df /z authors
+
2313 if (!svar_Exists(authors))
+
+
+
+
+
+
2319 dfref infoDF = preview_df:file_info
+
2320 if ((result != 0) && (DataFolderRefStatus(infoDF)))
+
2321 svar /z /sdfr=infoDF s_filepath
+
2322 if (SVAR_Exists(s_filepath) && (strsearch(s_filepath, s_selected_file, inf, 1) >= 0))
+
2323 dfref data_df = infoDF
+
+
+
+
+
+
2329 if ((result != 0) && (SVAR_Exists(s_preview_file) && (cmpstr(s_preview_file, s_selected_file) == 0)))
+
2330 dfref data_df = preview_df
+
+
+
+
+
2335 if (SVAR_Exists(s_preview_graph) && (WinType(s_preview_graph) == 1))
+
2336 graphname = s_preview_graph
+
+
+
+
+
+
+
+
2344 windowname = StringFromList(0, WinList("*ElogPanel*", ";", "WIN:64"), ";")
+
2345 DoWindow /F $windowname
+
+
+
2348 setdatafolder save_df
+
+
+
+
2352 STRUCT WMButtonAction &ba
+
+
2354 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
variable pearl_data_explorer()
show the pearl data explorer window
static variable save_prefs()
save persistent package data to the preferences file.
static variable bp_goto_dataset(WMButtonAction *ba)
"goto DF" button
string ps_fix_folder_name(string group_name)
convert HDF5 group name to data folder name and fix compatibility issues
static variable hlp_contents_selection(string HostWindow, string ListControlName, string SelectedItem, variable EventCode)
string adh5_list_reduction_funcs()
get a list of functions which can be used as reduction functions.
static string show_preview_graph(wave data, wave xdata=defaultValue)
string ad_display_slice(wave data)
display three-dimensional data by 2D slice.
static variable preview_datafolder()
preview data in the current data folder
const variable kDSCEssentialDiags
static variable update_controls()
update controls state
static const string ks_filematch_pshell
variable prompt_default_process(string *param)
prototype for prompting for processing function parameters.
static dfr get_pshell_info(string path_name, string file_name, dfref dest_df=defaultValue)
string adh5_load_preview(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
load a single image from a HDF5 file created by the Area Detector software.
static variable load_selected_files(string options=defaultValue)
load the selected files
string psh5_load_general_group(dfref file_df)
load organizational metadata from the general group.
static variable bp_elog(WMButtonAction *ba)
static variable update_filelist()
read a list of PEARL files from the file system
static variable create_attributes_notebook(wave attr_names, wave attr_values, string title)
static variable hl_default_selection()
string adh5_load_info(string APathName, string AFileName)
load descriptive info from a HDF5 file created by the Area Detector software.
static variable notebook_add_attributes(string notebook_name, wave attr_filter, wave attr_names, wave attr_values)
const variable kDSCMonitors
static variable pmp_reduction_func(WMPopupAction *pa)
static variable prompt_hdf_options(string *options)
static variable load_file(string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue)
load one file
static variable hl_contents_clear()
const variable kDSCPositioners
static const string ks_filematch_adh5
static variable bp_attr_notebook(WMButtonAction *ba)
static wave preview_pshell_file(string filename)
load the preview of a PShell HDF5 file.
static variable bp_load_prefs(WMButtonAction *ba)
static const string ks_filematch_itx
const variable kDSCScientaScaling
static variable bp_save_prefs(WMButtonAction *ba)
interface for writing ELOG entries with Igor graphs as attachment.
string psh5_extract_region_paths(string datasets)
trim dataset paths to the scan/region part
static variable selected_file(string file, variable do_preview)
actions after a file has been selected
static variable display_dataset(dfref file_df, string dataset)
displays the graph of a loaded dataset in its own window
static variable init_package()
static variable preview_setscale_x(wave data, wave preview)
static string shorten_filepath(string long_path, variable max_len)
shorten a file path for display
static variable bp_browse_filepath(WMButtonAction *ba)
static variable set_elog_attributes(dfref file_df, string filename=defaultValue, string graphname=defaultValue)
send general metadata to ELOG panel - if available
static variable lbp_filelist(WMListboxAction *lba)
static variable bp_display_dataset(WMButtonAction *ba)
"display dataset" button
static variable extract_attributes(dfref attr_df, dfref dest_df=defaultValue, wave attr_filter=defaultValue, variable include_datawaves=defaultValue, variable include_infowaves=defaultValue)
extract summary from attribute waves
static variable attributes_notebook(string filename)
load attributes
dfr psh5_dataset_to_folder(dfref parent_df, string datasetpath)
map dataset path to datafolder path
string ad_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
generate the name of a data folder based on a file name.
static dfr load_itx_file(string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue)
static variable goto_dataset_folder(string filename, string datapath)
open data folder corresponding to a file and data path
static variable get_file_info(string filename)
load the internal structure of a file
static dfr load_pshell_file(string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue)
load a pshell file
string adh5_load_complete(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
import everything from a HDF5 file created by the Area Detector software.
dfr ps_find_attr_folder(dfref scan_df)
find the attributes data folder
static variable hl_contents_update(dfref file_df)
populate the contents list box with the internal directory of a HDF5 file
string itx_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
suggest the name of a data folder based on an igor-text file name
static variable bp_reduction_params(WMButtonAction *ba)
static variable send_to_elog()
send file metadata to the ELOG panel
static variable bp_file_next(WMButtonAction *ba)
static variable hlp_setup()
threadsafe wave adh5_default_reduction(wave source, string *param)
function prototype for adh5_load_reduced_detector
threadsafe wave ad_extract_slab(wave dataset, variable x1, variable x2, variable y1, variable y2, variable z1, variable z2, string destname, variable noavg=defaultValue, variable pscale=defaultValue)
2D cut through 3D dataset, integrate in normal dimension
static wave preview_itx_file(string filename)
load the preview of a general ITX file.
static variable update_filepath()
update the file path after path change
const variable kDSCDetectors
dfr psh5_preview(string path_name, string file_name, dfref dest_df=defaultValue, string preview_datasets=defaultValue)
load preview
variable test_attributes_notebook()
static variable pearl_file_type(string filename)
check whether a file can be imported by this module.
variable psh5_close_file(dfref file_df)
close a HDF5 file opened by psh5_open_file.
string adh5_load_reduced(string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable load_data=defaultValue, variable load_attr=defaultValue, variable progress=defaultValue)
load and reduce a dataset from a HDF5 file created by the Area Detector software.
static string pm_reduction_values()
items for data reduction popup
string PearlCleanupName(string name)
static variable load_prefs()
variable prompt_func_params(string func_name, string *func_param)
dfr psh5_load(string path_name, string file_name, string scans, string regions, string datasets, variable classes=defaultValue, variable max_rank=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue, dfref dest_df=defaultValue)
main data loading function
static dfr load_hdf_file(string filename, string options=defaultValue, dfref dest_df=defaultValue, variable quiet=defaultValue)
static variable hlp_contents_open(string HostWindow, string ListControlName, string ContainerPath)
static variable bp_update_filelist(WMButtonAction *ba)
static variable extract_preview_image(wave data, wave preview)
extract a preview image from a wave of arbitrary dimension
static variable bp_file_prev(WMButtonAction *ba)
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
variable ad_brick_slicer(wave data)
open a slicer panel for 3D data.
static variable preview_file(string filename)
string psh5_extract_scan_paths(string datasets)
trim dataset paths to the scan part
dfr psh5_open_file(string path_name, string file_name, dfref dest_df=defaultValue)
open a HDF5 file created by the PShell data acquisition program and prepare the data folder.
static const string package_name
package name is used as data folder name
static string display_preview_trace(wave xtrace, wave ytrace)
static variable hl_expand_scans()
static variable bp_load_options(WMButtonAction *ba)
static variable hl_add_objects(string parent_path, string objects)
populate the contents list box with the given hierarchical paths
static const string package_path
static wave preview_hdf_file(string filename)
load the preview of a PEARL HDF5 file.
PEARL Procedures: pearl-elog.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -104,115 +106,115 @@ Namespaces
variable pearl_elog (string logbook) main function to initialize ELOG and to open an ELOG panel. More... main function to initialize ELOG and to open an ELOG panel. More... static variable IgorBeforeNewHook (string igorApplicationNameStr) save preferences and recent values before Igor opens a new experiment. More... save preferences and recent values before Igor opens a new experiment. More... static variable IgorQuitHook (string igorApplicationNameStr) save preferences and recent values before Igor quits. More... save preferences and recent values before Igor quits. More... static variable AfterFileOpenHook (variable refNum, string file, string pathName, string type, string creator, variable kind) initialize the package and reload preferences after an experiment is loaded. More... initialize the package and reload preferences after an experiment is loaded. More... static dfr get_elog_df (string name, variable category) get the package, logbook, or template datafolder. More... get the package, logbook, or template datafolder. More... static variable init_package (variable clean=defaultValue) initialize the package data folder. More... initialize the package data folder. More... variable elog_init_pearl_templates () setup PEARL template logbooks. More... setup PEARL template logbooks. More... static variable init_volatile_vars () initialize volatile variables. More... initialize volatile variables. More... variable elog_create_logbook (string name, string template=defaultValue) create a new logbook. More... create a new logbook. More... variable elog_config (string elog_path=defaultValue, string hostname=defaultValue, variable port=defaultValue, string subdir=defaultValue) set global module configuration parameters More... set global module configuration parameters More... variable elog_login (string logbook, string username, string password) set username and password for login to a logbook More... set username and password for login to a logbook More... variable elog_logout (string logbook) clear username and password of a logbook or all logbooks. More... clear username and password of a logbook or all logbooks. More... static variable save_prefs () save persistent package data to the preferences file. More... save persistent package data to the preferences file. More... static variable load_prefs () load persistent package data from the preferences file. More... load persistent package data from the preferences file. More... static string list_logbooks (variable templates=defaultValue) get a list of configured logbooks or templates. More... get a list of configured logbooks or templates. More... variable elog_validate_attributes (string logbook, string attributes) validate attributes More... validate attributes More... variable elog_create_entry (string logbook, string attributes, string message, variable encoding=defaultValue, string graphs=defaultValue, variable replyto=defaultValue) create a new entry in ELOG More... create a new entry in ELOG More... variable elog_add_attachment (string logbook, variable id, string graphs) add one or more graphs to an existing ELOG entry More... add one or more graphs to an existing ELOG entry More... static string prepare_command_line (string logbook) format the ELOG command and essential address arguments. More... format the ELOG command and essential address arguments. More... static string format_url (string logbook) format the URL for display to the user More... format the URL for display to the user More... static string prepare_graph_attachments (string graphs) prepare screenshots of graph windows for attachments More... prepare screenshots of graph windows for attachments More... static string get_timestamp (string sep) static string create_message_file (string message) save the message to a temporary text file More... save the message to a temporary text file More... static string create_graph_file (string graphname, variable fileindex) save a graph to a temporary graphics file More... save a graph to a temporary graphics file More... static string create_cmd_file (string cmd) write the command line to a file. More... write the command line to a file. More... static string get_log_path () static variable cleanup_temp_files () delete temporary files created by the ELOG module. More... delete temporary files created by the ELOG module. More... static variable parse_result () parse the result file from an elog invokation. More... parse the result file from an elog invokation. More... string elog_prompt_logbook () prompt to open or create a logbook More... prompt to open or create a logbook More... variable elog_prompt_login (string logbook) prompt the user for login to a logbook More... prompt the user for login to a logbook More... string PearlElogPanel (string logbook) open a new panel for submitting data to ELOG. More... open a new panel for submitting data to ELOG. More... static variable elog_panel_hook (WMWinHookStruct *s) static variable update_attach_items (string logbook) update the list of attachments More... update the list of attachments More... static variable move_attach_item (string logbook, variable item, variable distance) move an attachment item in the list of attachments More... move an attachment item in the list of attachments More... static variable bp_attach_updown (WMButtonAction *ba) button procedure for the attachment up and down buttons More... button procedure for the attachment up and down buttons More... static variable bp_submit (WMButtonAction *ba) button procedure for the Submit and Reply buttons More... button procedure for the Submit and Reply buttons More... static variable bp_attach_top (WMButtonAction *ba) select top graph window for attachment More... select top graph window for attachment More... static variable bp_attach_allnone (WMButtonAction *ba) select/deselect all graph windows for attachment More... select/deselect all graph windows for attachment More... static variable bp_attach (WMButtonAction *ba) static string get_default_panel_name () static string get_panel_attributes (string windowname) get a list of attributes from the fields of the ELOG panel. More... get a list of attributes from the fields of the ELOG panel. More... static string set_panel_attributes (string windowname, string attributes, variable clear=defaultValue) set the fields of the ELOG panel More... set the fields of the ELOG panel More... static string get_panel_message (string windowname) get the message field of the ELOG panel More... get the message field of the ELOG panel More... static string set_panel_message (string windowname, string message) set the message field of the ELOG panel More... set the message field of the ELOG panel More... static string get_panel_graphs (string windowname) get the names of the graphs selected for attachment More... get the names of the graphs selected for attachment More... static string set_panel_graphs (string windowname, string graphs) update selection of graphs for attachment More... update selection of graphs for attachment More...
attach any Igor graph to ELOG.
configurable logbook templates for logbooks that share the same configuration.
common server configurations available on the ELOG command line (hostname, port, SSL, username, password, sub-directory).
-not specific to the configuration at PEARL. PEARL code is concentrated in the elog_init_pearl_templates() function.
+not specific to the configuration at PEARL. PEARL code is concentrated in the elog_init_pearl_templates() function.
the configuration of the ELOG server and logbooks as well as the most recently used attributes are persisted in the preference file.
usage:
@@ -309,9 +311,9 @@ Variables
* [-n 0|1|2] Encoding: 0:ELcode,1:plain,2:HTML
* -m <textfile>] | <text>
* Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch Copyright 2013-17 Paul Scherrer Institut Copyright 2013-20 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-elog.ipf .
@@ -376,7 +378,7 @@ Variables
initialize the package and reload preferences after an experiment is loaded.
-Definition at line 143 of file pearl-elog.ipf .
+Definition at line 144 of file pearl-elog.ipf .
@@ -404,7 +406,7 @@ Variables
@@ -434,7 +436,7 @@ Variables
select/deselect all graph windows for attachment
-Definition at line 1614 of file pearl-elog.ipf .
+Definition at line 1615 of file pearl-elog.ipf .
@@ -464,7 +466,7 @@ Variables
select top graph window for attachment
-Definition at line 1598 of file pearl-elog.ipf .
+Definition at line 1599 of file pearl-elog.ipf .
@@ -494,7 +496,7 @@ Variables
button procedure for the attachment up and down buttons
-Definition at line 1519 of file pearl-elog.ipf .
+Definition at line 1520 of file pearl-elog.ipf .
@@ -522,7 +524,7 @@ Variables
@@ -550,7 +552,7 @@ Variables
@@ -578,7 +580,7 @@ Variables
@@ -606,7 +608,7 @@ Variables
@@ -636,7 +638,7 @@ Variables
button procedure for the Submit and Reply buttons
-Definition at line 1551 of file pearl-elog.ipf .
+Definition at line 1552 of file pearl-elog.ipf .
@@ -664,10 +666,10 @@ Variables
delete temporary files created by the ELOG module.
-
this deletes all temporary graph files that are referenced by the volatile temp_graph_files list. temp_graph_files is a semicolon-delimited string. items are added by create_graph_file() .
+
this deletes all temporary graph files that are referenced by the volatile temp_graph_files list. temp_graph_files is a semicolon-delimited string. items are added by create_graph_file() .
this function should be called before a new experiment is loaded or igor quits.
-
Definition at line 1115 of file pearl-elog.ipf .
+
Definition at line 1116 of file pearl-elog.ipf .
@@ -699,7 +701,7 @@ Variables
the command script changes the working directory to the Temporary directory. it also deletes a previous elog.log file.
Note somewhere the command line (even inside command files) is limited to 1024 bytes. for this reason all files should now be in the Temporary directory assigned by igor. Definition at line 1059 of file pearl-elog.ipf .
+Definition at line 1060 of file pearl-elog.ipf .
@@ -750,7 +752,7 @@ Variables
Returns (string) name of the created file. empty string if unsuccessful. Version 1.41 the return value has changed from full path to file name only due to the limited length of the command line (1024 bytes). Definition at line 1023 of file pearl-elog.ipf .
+Definition at line 1024 of file pearl-elog.ipf .
@@ -790,7 +792,7 @@ Variables
Returns (string) name of the created file. empty string if unsuccessful. Version 1.41 the return value has changed from full path to file name only due to the limited length of the command line (1024 bytes). Definition at line 982 of file pearl-elog.ipf .
+Definition at line 983 of file pearl-elog.ipf .
@@ -837,7 +839,7 @@ Variables
Warning this will delete all existing attachments of the entry! Definition at line 792 of file pearl-elog.ipf .
+Definition at line 793 of file pearl-elog.ipf .
@@ -881,7 +883,7 @@ Variables
set global module configuration parameters
-Definition at line 473 of file pearl-elog.ipf .
+Definition at line 474 of file pearl-elog.ipf .
@@ -956,7 +958,7 @@ Variables
-Definition at line 685 of file pearl-elog.ipf .
+Definition at line 686 of file pearl-elog.ipf .
@@ -996,7 +998,7 @@ Variables
-Definition at line 414 of file pearl-elog.ipf .
+Definition at line 415 of file pearl-elog.ipf .
@@ -1019,7 +1021,7 @@ Variables
template logbooks for PEARL.
-Definition at line 262 of file pearl-elog.ipf .
+Definition at line 263 of file pearl-elog.ipf .
@@ -1057,7 +1059,7 @@ Variables
set username and password for login to a logbook
the username and password are stored (in plain text) in global strings under the selected logbook folder. this is necessary for sending data to the ELOG server.
-call elog_logout() to clear the password variables and to avoid unintended use of your credentials.
+call elog_logout() to clear the password variables and to avoid unintended use of your credentials.
Warning igor does not have a built-in mechanism to protect passwords. user names and passwords are stored in plain text in the data folder tree. as such they are saved to experiment files and preferences. Parameters
@@ -1144,7 +1146,7 @@ Variables
prompt to open or create a logbook
-Definition at line 1184 of file pearl-elog.ipf .
+Definition at line 1185 of file pearl-elog.ipf .
@@ -1166,7 +1168,7 @@ Variables
prompt the user for login to a logbook
-Definition at line 1214 of file pearl-elog.ipf .
+Definition at line 1215 of file pearl-elog.ipf .
@@ -1200,7 +1202,7 @@ Variables
Returns 0 if all required attributes are present and enumerated items are correct. non-zero if a violation is detected. Todo: function currently not implemented, always returns 0 Definition at line 653 of file pearl-elog.ipf .
+Definition at line 654 of file pearl-elog.ipf .
@@ -1236,7 +1238,7 @@ Variables
Definition at line 902 of file pearl-elog.ipf .
+Definition at line 903 of file pearl-elog.ipf .
@@ -1263,7 +1265,7 @@ Variables
@@ -1317,7 +1319,7 @@ Variables
Returns data folder reference Definition at line 170 of file pearl-elog.ipf .
+Definition at line 171 of file pearl-elog.ipf .
@@ -1344,7 +1346,7 @@ Variables
@@ -1381,7 +1383,7 @@ Variables
Returns list of attributes to in the format "key1=value1;key2=value2". Definition at line 1760 of file pearl-elog.ipf .
+Definition at line 1761 of file pearl-elog.ipf .
@@ -1418,7 +1420,7 @@ Variables
Returns a semicolon-separated list, or the empty string if the selection is not valid. Definition at line 1926 of file pearl-elog.ipf .
+Definition at line 1927 of file pearl-elog.ipf .
@@ -1455,7 +1457,7 @@ Variables
Returns message text Definition at line 1880 of file pearl-elog.ipf .
+Definition at line 1881 of file pearl-elog.ipf .
@@ -1483,7 +1485,7 @@ Variables
@@ -1513,7 +1515,7 @@ Variables
save preferences and recent values before Igor opens a new experiment.
-Definition at line 127 of file pearl-elog.ipf .
+Definition at line 128 of file pearl-elog.ipf .
@@ -1543,7 +1545,7 @@ Variables
save preferences and recent values before Igor quits.
-Definition at line 135 of file pearl-elog.ipf .
+Definition at line 136 of file pearl-elog.ipf .
@@ -1584,7 +1586,7 @@ Variables
-Definition at line 217 of file pearl-elog.ipf .
+Definition at line 218 of file pearl-elog.ipf .
@@ -1613,9 +1615,9 @@ Variables
initialize volatile variables.
create and initialize all volatile variables for the configured notebooks. values of existing variables are not changed.
-this function must be called after new logbooks have been configured, specifically by elog_create_logbook() and load_prefs() .
+this function must be called after new logbooks have been configured, specifically by elog_create_logbook() and load_prefs() .
-Definition at line 340 of file pearl-elog.ipf .
+Definition at line 341 of file pearl-elog.ipf .
@@ -1653,7 +1655,7 @@ Variables
Returns semicolon-separated list of logbooks Definition at line 618 of file pearl-elog.ipf .
+Definition at line 619 of file pearl-elog.ipf .
@@ -1683,7 +1685,7 @@ Variables
load persistent package data from the preferences file.
the preferences file is an Igor packed experiment file in a special preferences folder
-Definition at line 584 of file pearl-elog.ipf .
+Definition at line 585 of file pearl-elog.ipf .
@@ -1729,7 +1731,7 @@ Variables
move an attachment item in the list of attachments
-Definition at line 1495 of file pearl-elog.ipf .
+Definition at line 1496 of file pearl-elog.ipf .
@@ -1759,7 +1761,7 @@ Variables
parse the result file from an elog invokation.
Returns the ID of the generated message, or a value <= 0 if an error occurred. Definition at line 1141 of file pearl-elog.ipf .
+Definition at line 1142 of file pearl-elog.ipf .
@@ -1783,12 +1785,12 @@ Variables
this function takes care of all necessary initialization, configuration, and preferences. if a panel exists, it will be moved to the front.
Parameters
- logbook name of the logbook if empty, the user is prompted to select or create a logbook by elog_prompt_logbook() . logbook name of the logbook if empty, the user is prompted to select or create a logbook by elog_prompt_logbook() .
Definition at line 97 of file pearl-elog.ipf .
+Definition at line 98 of file pearl-elog.ipf .
@@ -1809,7 +1811,7 @@ Variables
open a new panel for submitting data to ELOG.
-
this function creates only the panel but not the necessary data folders. call init_package() and load_prefs() once before creating panels.
+
this function creates only the panel but not the necessary data folders. call init_package() and load_prefs() once before creating panels.
Parameters
logbook name of the target logbook Definition at line 1241 of file pearl-elog.ipf .
+Definition at line 1242 of file pearl-elog.ipf .
@@ -1854,7 +1856,7 @@ Variables
-Definition at line 853 of file pearl-elog.ipf .
+Definition at line 854 of file pearl-elog.ipf .
@@ -1891,7 +1893,7 @@ Variables
-Definition at line 939 of file pearl-elog.ipf .
+Definition at line 940 of file pearl-elog.ipf .
@@ -1921,7 +1923,7 @@ Variables
save persistent package data to the preferences file.
saves everything under the persistent folder of the package.
-Definition at line 564 of file pearl-elog.ipf .
+Definition at line 565 of file pearl-elog.ipf .
@@ -1979,7 +1981,7 @@ Variables
-Definition at line 1807 of file pearl-elog.ipf .
+Definition at line 1808 of file pearl-elog.ipf .
@@ -2026,7 +2028,7 @@ Variables
-Definition at line 1966 of file pearl-elog.ipf .
+Definition at line 1967 of file pearl-elog.ipf .
@@ -2074,7 +2076,7 @@ Variables
Returns original message (unchanged) Definition at line 1906 of file pearl-elog.ipf .
+Definition at line 1907 of file pearl-elog.ipf .
@@ -2104,7 +2106,7 @@ Variables
update the list of attachments
-Definition at line 1434 of file pearl-elog.ipf .
+Definition at line 1435 of file pearl-elog.ipf .
@@ -2129,7 +2131,7 @@ Variables
@@ -2153,7 +2155,7 @@ Variables
@@ -2177,7 +2179,7 @@ Variables
@@ -2201,7 +2203,7 @@ Variables
@@ -2225,7 +2227,7 @@ Variables
@@ -2249,7 +2251,7 @@ Variables
@@ -2273,7 +2275,7 @@ Variables
@@ -2297,7 +2299,7 @@ Variables
@@ -2321,7 +2323,7 @@ Variables
@@ -2345,7 +2347,7 @@ Variables
@@ -2369,7 +2371,7 @@ Variables
@@ -2379,9 +2381,9 @@ Variables
diff --git a/doc/html/pearl-elog_8ipf_source.html b/doc/html/pearl-elog_8ipf_source.html
index 595137f..21d3993 100644
--- a/doc/html/pearl-elog_8ipf_source.html
+++ b/doc/html/pearl-elog_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-elog.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,77 +87,1714 @@ $(document).ready(function(){initNavTree('pearl-elog_8ipf_source.html','');});
pearl-elog.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 3 #pragma IgorVersion = 6.2 4 #pragma ModuleName = PearlElog 103 if (ItemsInList(templates) < 1)
108 if (strlen(logbook) == 0)
112 string win_name = logbook + "ElogPanel"
113 if (strlen(logbook) > 0)
114 if (strlen(WinList(win_name, ";", "")) > 0)
115 DoWindow /F $win_name
118 STRUCT WMWinHookStruct s
128 string igorApplicationNameStr
136 string igorApplicationNameStr
145 String file,pathName,type,creator
146 if( (kind >= 1) && (kind <= 2))
174 dfref df_package = $package_path
175 dfref df_persistent = df_package:persistent
176 dfref df_volatile = df_package:volatile
180 dfref df_parent = df_package
183 dfref df_parent = df_persistent
186 dfref df_parent = df_persistent:templates
189 dfref df_parent = df_volatile
192 Abort "
get_elog_df : undefined data folder category."
195 if ((strlen(name) > 0) && (category >= 1))
197 dfref df_logbooks = df_parent
199 dfref df_logbooks = df_parent:logbooks
201 dfref df_logbook = df_logbooks:$name
220 if (ParamIsDefault(clean))
224 dfref savedf = getdatafolderdfr()
226 if ((clean == 0) && (DataFolderRefStatus(df_root) == 1))
231 newdatafolder /o/s packages
232 newdatafolder /o/s $package_name
233 dfref df_package_root = getdatafolderdfr()
234 newdatafolder /o/s volatile
235 dfref df_volatile = getdatafolderdfr()
236 newdatafolder /o logbooks
237 setdatafolder df_package_root
238 newdatafolder /o/s persistent
239 dfref df_persistent = getdatafolderdfr()
240 newdatafolder /o logbooks
241 newdatafolder /o templates
244 setdatafolder df_persistent
245 string /g elog_path = "c:\\program files (x86)\\ELOG\\elog.exe"
246 string /g hostname = "localhost"
249 string /g subdir = ""
250 variable /g loglevel = 4
263 dfref savedf = getdatafolderdfr()
265 dfref df_root = get_elog_df("",
kdfRoot )
270 setdatafolder df_templates
271 newdatafolder /o/s Experiments
275 string /g attributes = "author;project;p-group;sample;source;task;technique;file;valid;"
278 string /g controls = "sv_author;sv_project;sv_pgroup;sv_sample;pm_source;pm_task;pm_technique;sv_file;cb_valid;"
280 string /g options = "source=sources;task=tasks;technique=techniques"
282 string /g required_attributes = "author;project;p-group;sample;source;task;technique;valid"
285 string /g sources = "Manual Entry;PShell;Scienta Data;SScan Data;Prosilica Data;OTF Data;Beamline Status;LEED Data;QMS Data;Matrix Data;Igor Pro;Other"
286 string /g tasks = "Measurement;Optimization;Analysis;Sample Preparation;Sample Storage;Comment;Development;Maintenance;Test;Other"
287 string /g techniques = "XPS;UPS;XPD;XAS;XMCD;PhD;ARUPS;STM;STS;LEED;AES;QMS;MBE;Sputter/Anneal;Test;Other"
290 setdatafolder df_templates
291 newdatafolder /o/s Calculations
295 string /g attributes = "author;project;p-group;sample;program;revision;machine;job;experiment;source path;result path;valid"
298 string /g controls = "sv_author;sv_project;sv_pgroup;sv_sample;pm_program;sv_revision;pm_machine;sv_job;sv_experiment;sv_sourcepath;sv_resultpath;cb_valid"
300 string /g options = "program=programs;machine=machines"
302 string /g required_attributes = "author;project;sample"
305 string /g programs = "PMSCO;EDAC;MSC;SSC;MUFPOT;DMSUP;Other"
306 string /g machines = "PC;VM;Ra;Merlin;llcx;Other"
309 setdatafolder df_templates
310 newdatafolder /o/s System
314 string /g attributes = "author;type;system;source;file"
317 string /g controls = "sv_author;pm_type;pm_system;pm_source;sv_file"
319 string /g options = "type=types;system=systems;source=sources"
321 string /g required_attributes = "author;type;system"
324 string /g types = "Installation;Repair;Maintenance;Test;Commissioning;Bakeout;Incident;Cool-down;Warm-up;Storage;Other"
325 string /g systems = "Vacuum;Control System;BL;XA;XP;SA;SP;T;LL;Monochromator;Carving;Scienta;STM;PC-Scienta;PC-Matrix;PC-Console;PC-Console-Win;PC-XP;EPS;LAC;Desiccator;Other"
326 string /g sources = "Manual Entry;PShell;Scienta Data;SScan Data;Prosilica Data;OTF Data;Beamline Status;LEED Data;QMS Data;Matrix Data;Igor Pro;Other"
341 dfref savedf = GetDataFolderDFR()
343 dfref df_volatile_root = get_elog_df("",
kdfVolatile )
344 dfref df_volatile_parent = df_volatile_root:logbooks
348 variable nlb = ItemsInList(logbooks)
351 SetDataFolder df_volatile_root
352 if (exists("temp_graph_files") != 2)
353 string /g temp_graph_files = ""
356 for (ilb = 0; ilb < nlb; ilb += 1)
357 logbook = StringFromList(ilb, logbooks)
359 SetDataFolder df_volatile_parent
360 if (DataFolderExists(logbook))
361 SetDataFolder $logbook
363 NewDataFolder /o/s $logbook
366 if (exists("username") != 2)
367 string /g username = ""
369 if (exists("password") != 2)
370 string /g password = ""
372 if (exists("msg_id") != 2)
373 variable /g msg_id = 0
375 if (exists("att_list") != 1)
376 make /n=(0,3) /t /o attach_list
377 make /n=(0,3) /i /o attach_sel
379 if (exists("url") != 2)
418 if (ParamIsDefault(template))
422 dfref savedf = getdatafolderdfr()
423 dfref df_root = get_elog_df("",
kdfRoot )
425 dfref df_persistent_parent = df_persistent_root:logbooks
426 dfref df_volatile_root = get_elog_df("",
kdfVolatile )
427 dfref df_volatile_parent = df_volatile_root:logbooks
429 setdatafolder df_persistent_parent
430 if (CheckName(name, 11) != 0)
432 Abort "invalid logbook name"
436 if (strlen(template) > 0)
439 if (DataFolderRefStatus(df_existing))
440 KillDataFolder /Z df_existing
442 DuplicateDataFolder df_template, df_persistent_parent:$name
444 NewDataFolder /o/s df_persistent_parent:$name
447 string /g logbook = name
450 string /g attributes = ""
453 string /g controls = ""
455 string /g options = ""
457 string /g required_attributes = ""
462 string /g recent = ""
463 string /g recent_message = ""
481 if (!ParamIsDefault(elog_path))
482 svar /sdfr=df g_elog_path = elog_path
483 g_elog_path = elog_path
485 if (!ParamIsDefault(hostname))
486 svar /sdfr=df g_hostname = hostname
487 g_hostname = hostname
489 if (!ParamIsDefault(port))
490 nvar /sdfr=df g_port = port
493 if (!ParamIsDefault(subdir))
494 svar /sdfr=df g_subdir = subdir
519 svar /sdfr=df g_username=username
520 svar /sdfr=df g_password=password
521 g_username = username
522 g_password = password
537 if (strlen(logbook) > 0)
538 svar /z /sdfr=df g_username=username
539 svar /z /sdfr=df g_password=password
540 if (svar_exists(g_username))
543 if (svar_exists(g_password))
547 dfref df2 = df:logbooks
548 variable nlb = CountObjectsDFR(df2, 4)
551 for (ilb = 0; ilb < nlb; ilb += 1)
552 slb = GetIndexedObjNameDFR(df2, 4, ilb)
565 dfref saveDF = GetDataFolderDFR()
568 if (DataFolderRefStatus(df) == 1)
569 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
571 NewPath/O/C/Q tempPackagePrefsPath, fullPath
572 fullPath += ":preferences.pxp"
574 SaveData /O /Q /R fullPath
575 KillPath/Z tempPackagePrefsPath
585 dfref saveDF = GetDataFolderDFR()
591 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
594 GetFileFolderInfo /Q /Z fullPath
596 fullPath += ":preferences.pxp"
597 GetFileFolderInfo /Q /Z fullPath
599 LoadData /O /R /Q fullPath
621 if (ParamIsDefault(templates))
627 dfref df_logbooks = df_persistent:templates
629 dfref df_logbooks = df_persistent:logbooks
633 variable nlb = CountObjectsDFR(df_logbooks, 4)
636 for (ilb = 0; ilb < nlb; ilb += 1)
637 slb = GetIndexedObjNameDFR(df_logbooks, 4, ilb)
639 logbooks = AddListItem(slb, logbooks)
643 return SortList(logbooks, ";", 16)
693 if (ParamIsDefault(encoding))
696 if (ParamIsDefault(graphs))
699 if (ParamIsDefault(replyto))
703 dfref savedf = getdatafolderdfr()
705 dfref df_volatile = get_elog_df(logbook,
kdfVolatile )
708 nvar /sdfr=df_volatile msg_id
709 nvar /sdfr=df_general loglevel
713 print "ELOG: failed to validate attributes."
719 if (strlen(cmd) == 0)
721 print "ELOG: failed to prepare command line."
727 cmd += " -r " + num2str(replyto)
729 cmd += " -n " + num2str(encoding)
731 variable nattr = ItemsInList(attributes, ";")
734 for (iattr = 0; (iattr < nattr) && (result == 0); iattr += 1)
735 sattr = StringFromList(iattr, attributes, ";")
736 if (strlen(StringFromList(1, sattr, "=")) > 0)
737 sattr = ReplaceString("%", sattr, "")
738 cmd += " -a \"" + sattr + "\""
744 cmd += " " + cmd_graphs
747 if ((result == 0) && (strlen(message) > 0))
749 if (strlen(messagefile) > 0)
750 cmd += " -m \"" + messagefile + "\""
756 if (strlen(cmd_file_path) > 0)
757 ExecuteScriptText cmd_file_path
762 print "ELOG: sent message " + num2str(
id )
766 print "ELOG: sending message failed."
775 print "ELOG: failed to create temporary message file."
797 dfref savedf = getdatafolderdfr()
799 dfref df_volatile = get_elog_df(logbook,
kdfVolatile )
802 nvar /sdfr=df_volatile msg_id
803 nvar /sdfr=df_general loglevel
806 if (strlen(cmd) == 0)
810 cmd += " -e " + num2str(
id )
814 if (strlen(cmd_graphs) == 0)
820 cmd += " " + cmd_graphs
823 if (strlen(cmd_file_path) > 0)
824 ExecuteScriptText cmd_file_path
829 print "ELOG: attached graphs to message " + num2str(
id )
833 print "ELOG: failed to attach graphs."
858 dfref df_volatile = get_elog_df(logbook,
kdfVolatile )
860 svar /sdfr=df_general elog_path
861 svar /sdfr=df_general hostname
862 nvar /sdfr=df_general port
863 nvar /sdfr=df_general ssl
864 svar /sdfr=df_general subdir
865 nvar /sdfr=df_general loglevel
866 svar /sdfr=df_volatile username
867 svar /sdfr=df_volatile password
870 cmd = "\"" + elog_path + "\""
874 cmd += " -h " + hostname
875 if ((nvar_exists(port)) && (port > 0))
876 cmd += " -p " + num2str(port)
878 if ((svar_exists(subdir)) && (strlen(subdir) > 0))
879 cmd += " -d " + subdir
881 cmd += " -l \"" + logbook + "\""
882 if ((nvar_exists(ssl)) && (ssl != 0))
886 if (svar_exists(username) && svar_exists(password) && (strlen(username) > 0) && (strlen(password) > 0))
887 cmd += " -u " + username + " " + password
907 svar /sdfr=df_general hostname
908 nvar /sdfr=df_general port
909 nvar /sdfr=df_general ssl
910 svar /sdfr=df_general subdir
913 if ((nvar_exists(ssl)) && (ssl != 0))
919 if ((nvar_exists(port)) && (port > 0))
920 cmd += ":" + num2str(port)
922 if ((svar_exists(subdir)) && (strlen(subdir) > 0))
943 variable ngraphs = ItemsInList(graphs, ";")
947 for (igraph = 0; igraph < ngraphs; igraph += 1)
948 sgraph = StringFromList(igraph, graphs, ";")
950 if (strlen(graph_path) > 0)
951 cmd += " -f \"" + graph_path + "\""
960 Variable now = DateTime
961 string dat = ReplaceString("-", Secs2Date(DateTime, -2), "")
962 string tim = ReplaceString(":", Secs2Time(DateTime, 3), "")
963 return dat + sep + tim
985 message = ReplaceString("%", message, "")
986 string path = SpecialDirPath("Temporary", 0, 1, 0)
987 variable len = strlen(path)
990 if (numtype(len) == 0)
991 filename = "elog_temp_message.txt"
1027 dfref df_volatile_root = get_elog_df("",
kdfVolatile )
1028 svar /sdfr=df_volatile_root temp_graph_files
1030 string path = SpecialDirPath("Temporary", 0, 1, 0)
1032 variable len = strlen(path)
1035 if (numtype(len) == 0)
1036 filename = "elog_" + ts + "_" + num2str(fileindex) + ".png"
1038 SavePICT /B=72 /E=-5 /M /O /W=(0,0,8,6) /WIN=$graphname /Z as path
1040 temp_graph_files = AddListItem(path, temp_graph_files, ";", inf)
1063 nvar /sdfr=df_general loglevel
1065 if (strlen(cmd) >= 1024)
1067 print "ELOG: command line too
long (add fewer attachments)."
1072 string work_path = SpecialDirPath("Temporary", 0, 1, 0)
1073 variable len = strlen(work_path)
1074 if (numtype(len) == 0)
1076 string cmd_path = work_path + "elog_temp_cmd.bat"
1082 cmdx = "cd \"" + work_path + "\"\r\n"
1084 cmdx = "del elog.log"
1085 fprintf f1, cmdx + "\r\n"
1096 string path = SpecialDirPath("Temporary", 0, 1, 0)
1097 variable len = strlen(path)
1098 if (numtype(len) == 0)
1116 dfref df_volatile_root = get_elog_df("",
kdfVolatile )
1117 if (DataFolderRefStatus(df_volatile_root))
1118 svar /sdfr=df_volatile_root /z temp_graph_files
1119 if (SVAR_Exists(temp_graph_files))
1120 variable nfi = ItemsInList(temp_graph_files)
1123 for (ifi = 0; ifi < nfi; ifi += 1)
1124 sfi = StringFromList(ifi, temp_graph_files)
1127 temp_graph_files = ""
1143 nvar /sdfr=df_general loglevel
1148 variable success = 0
1153 variable len = strlen(path)
1154 if (numtype(len) == 0)
1156 Open /R/Z f1 as path
1160 if (strlen(line) > 0)
1161 part1 = StringFromList(0, line, ",")
1162 part2 = ReplaceString(" ", StringFromList(1, line, ","), "")
1186 logbooks = AddListItem("(new)", logbooks)
1188 templates = AddListItem("(none)", templates)
1190 string logbook = StringFromList(0, logbooks)
1191 string template = StringFromList(0, logbooks)
1193 string username = ""
1194 string password = ""
1196 prompt logbook, "logbook", popup logbooks
1197 prompt template, "template", popup templates
1198 prompt name, "new logbook name"
1200 doprompt "select logbook", logbook, template, name
1202 if (cmpstr(logbook, "(new)") == 0)
1219 string username = ""
1220 string password = ""
1222 prompt logbook, "logbook", popup logbooks
1223 prompt username, "user name"
1224 prompt password, "password (blank to log out)"
1226 doprompt "log in to logbook", logbook, username, password
1244 dfref savedf = getdatafolderdfr()
1247 dfref df_volatile = get_elog_df(logbook,
kdfVolatile )
1249 string win_name = logbook + "ElogPanel"
1250 string win_title = "ELOG " + logbook
1252 NewPanel /K=1 /N=$win_name /W=(600,200,1200,700) as win_title
1254 ModifyPanel /w=$win_name cbRGB=(52224,52224,65280)
1256 svar /sdfr=df_persistent attributes
1257 svar /sdfr=df_persistent controls
1258 svar /sdfr=df_persistent options
1259 wave /t /sdfr=df_volatile attach_list
1260 wave /sdfr=df_volatile attach_sel
1261 svar /sdfr=df_volatile url
1264 variable nattr = ItemsInList(attributes, ";")
1268 string persistent_path = GetDataFolder(1, df_persistent)
1269 string volatile_path = GetDataFolder(1, df_volatile)
1271 string variable_path
1275 for (iattr = 0; iattr < nattr; iattr += 1)
1276 s_attr = StringFromList(iattr, attributes, ";")
1277 s_control = StringFromList(iattr, controls, ";")
1278 strswitch(s_control[0,1])
1280 SetVariable $s_control, win=$win_name, pos={0,ypos}, size={300,16}, bodyWidth=230
1281 SetVariable $s_control, win=$win_name, title=s_attr, value= _STR:
"" 1282 SetVariable $s_control, win=$win_name, userdata(attribute)=s_attr
1286 options_path = persistent_path + StringByKey(s_attr, options,
"=" ,
";" )
1287 PopupMenu $s_control, win=$win_name, pos={0,ypos}, size={300,21}, bodyWidth=230
1288 PopupMenu $s_control, win=$win_name, title=s_attr
1289 PopupMenu $s_control, win=$win_name, mode=1, popvalue=
"Test" , value= #options_path
1290 PopupMenu $s_control, win=$win_name, userdata(attribute)=s_attr
1294 CheckBox $s_control, win=$win_name, pos={70,ypos}, size={300,14}
1295 CheckBox $s_control, win=$win_name, title=s_attr, value= 1
1296 CheckBox $s_control, win=$win_name, userdata(attribute)=s_attr
1301 ypos = max(ypos, 80)
1303 TitleBox t_attach, win=$win_name, pos={308,5}, size={70,14}, title=
"Attachments" , frame=0
1304 height = ypos - 21 - 4
1305 ListBox lb_attach, win=$win_name, pos={308,21}, size={264,height}
1306 ListBox lb_attach, win=$win_name, listWave=attach_list
1307 ListBox lb_attach, win=$win_name, mode=1, selWave=attach_sel, selRow=-1
1308 ListBox lb_attach, win=$win_name, widths={20,160,80}
1309 ListBox lb_attach, win=$win_name, help={
"Choose graphs to attach to the message." }
1311 Button b_attach_top, win=$win_name, pos={420,2}, size={40,18}, title=
"top" 1312 Button b_attach_top, win=$win_name, fcolor=(56576,60928,47872)
1314 Button b_attach_top, win=$win_name, help={
"Select top graph for attachment." }
1315 Button b_attach_all, win=$win_name, pos={460,2}, size={40,18}, title=
"all" 1316 Button b_attach_all, win=$win_name, fcolor=(56576,60928,47872)
1318 Button b_attach_all, win=$win_name, help={
"Select all graphs for attachment." }
1319 Button b_attach_none, win=$win_name, pos={500,2}, size={40,18}, title=
"none" 1320 Button b_attach_none, win=$win_name, fcolor=(56576,60928,47872)
1322 Button b_attach_none, win=$win_name, help={
"Deselect all attachments." }
1323 Button b_save_graphs, win=$win_name, pos={540,2}, size={40,18}, title=
"save" 1324 Button b_save_graphs, win=$win_name, fcolor=(56576,60928,47872)
1326 Button b_save_graphs, win=$win_name, help={
"Save selected graphs as PNG bitmap files." }
1327 Button b_attach_up, win=$win_name, pos={576,20}, size={20,20}, title=
"\\W517" 1328 Button b_attach_up, win=$win_name, fcolor=(56576,60928,47872)
1330 Button b_attach_up, win=$win_name, help={
"Move selected graph up." }
1331 Button b_attach_dw, win=$win_name, pos={576,40}, size={20,20}, title=
"\\W523" 1332 Button b_attach_dw, win=$win_name, fcolor=(56576,60928,47872)
1334 Button b_attach_dw, win=$win_name, help={
"Move selected graph down." }
1337 Button b_submit,win=$win_name, pos={70,ypos},size={46,20},proc=
PearlElog #
bp_submit ,title=
"Submit" 1338 Button b_submit,win=$win_name, help={
"Submit form data to ELOG (new entry)." }
1339 Button b_submit,win=$win_name, fcolor=(56576,60928,47872)
1340 Button b_clear,win=$win_name, pos={120,ypos},size={46,20},proc=
PearlElog #
bp_clear ,title=
"Clear" 1341 Button b_clear,win=$win_name, help={
"Clear the form fields" }
1342 Button b_clear,win=$win_name, fcolor=(56576,60928,47872)
1345 variable_path = volatile_path +
"msg_id" 1346 SetVariable sv_id,win=$win_name, pos={51,ypos},size={119,16},bodyWidth=77
1347 SetVariable sv_id,win=$win_name, title=
"ID" ,value=$variable_path
1348 SetVariable sv_id,win=$win_name, help={
"ID of last submitted message, or message to attach or reply to." }
1350 TitleBox t_host, win=$win_name, pos={170,ypos+4}, size={112.00,14.00}, frame=0
1351 TitleBox t_host, win=$win_name, variable=url
1354 Button b_attach,win=$win_name, pos={170,ypos},size={48,20},proc=
PearlElog #
bp_attach ,title=
"Attach" 1355 Button b_attach,win=$win_name, help={
"Attach the selected graph to an existing ELOG entry (correct ID required)." }
1356 Button b_attach,win=$win_name, fcolor=(56576,60928,47872)
1357 Button b_reply,win=$win_name, pos={220,ypos},size={48,20},proc=
PearlElog #
bp_submit ,title=
"Reply" 1358 Button b_reply,win=$win_name, help={
"Submit form data to ELOG as a reply to an existing message (correct ID required)." }
1359 Button b_reply,win=$win_name, fcolor=(56576,60928,47872)
1360 Button b_login,win=$win_name, pos={550,ypos},size={46,20},proc=
PearlElog #
bp_login ,title=
"Login" 1361 Button b_login,win=$win_name, help={
"Enter user name and password." }
1362 Button b_login,win=$win_name, fcolor=(56576,60928,47872)
1363 Button b_logout,win=$win_name, pos={550,ypos},size={46,20},proc=
PearlElog #
bp_logout ,title=
"Logout" 1364 Button b_logout,win=$win_name, help={
"Clear user name and password." }
1365 Button b_logout,win=$win_name, fcolor=(56576,60928,47872), disable=3
1368 SetWindow $win_name, userdata(logbook)=logbook
1371 TitleBox t_message,win=$win_name, pos={10,ypos},size={58,16},fixedSize=1,frame=0,anchor=RT,title=
"Message" 1372 DefineGuide UGH0={FT,ypos},UGV0={FL,70},UGH1={FB,-52},UGV1={FR,-2}
1373 NewNotebook /F=0 /N=Message /OPTS=3 /W=(115,404,345,341)/FG=(UGV0,UGH0,UGV1,UGH1) /HOST=#
1374 Notebook kwTopWin, defaultTab=20, statusWidth=0, autoSave=0
1375 Notebook kwTopWin fSize=10, fStyle=0, textRGB=(0,0,0)
1376 RenameWindow #,Message
1377 string nb_name = win_name +
"#Message" 1378 SetActiveSubwindow ##
1381 svar /z /sdfr=df_persistent recent
1382 if (svar_exists(recent) && (strlen(recent) > 0))
1385 svar /z /sdfr=df_persistent recent_message
1386 if (svar_exists(recent_message) && (strlen(recent_message) > 0))
1389 Notebook $nb_name selection={startOfFile,startOfFile}, findText={
"" ,1}
1391 setdatafolder savedf
1396 STRUCT WMWinHookStruct &s
1398 Variable hookResult = 0
1402 string logbook = GetUserData(s.winName,
"" ,
"logbook" )
1403 if (strlen(logbook) > 0)
1405 svar /sdfr=df_volatile url
1412 variable b_top = s.winRect.bottom + 4
1413 Button b_submit,pos={70,b_top}
1414 Button b_clear,pos={120,b_top}
1415 TitleBox t_host, pos={170,b_top+4}
1417 Button b_attach,pos={170,b_top}
1418 Button b_reply,pos={220,b_top}
1419 Button b_login, pos={550,b_top}
1420 Button b_logout, pos={550,b_top}
1422 SetVariable sv_id,pos={51,b_top}
1437 dfref savedf = getdatafolderdfr()
1439 wave /t /sdfr=df_volatile attach_list
1440 wave /sdfr=df_volatile attach_sel
1442 if (!waveexists(attach_list))
1445 string names = WinList("*", ";", "WIN:1;VISIBLE:1")
1446 names = SortList(names, ";", 16)
1451 variable n = DimSize(attach_list, 0)
1453 for (i = n-1; i >= 0; i -= 1)
1454 s = attach_list[i][kAttachColName]
1455 if (WhichListItem(s, names) < 0)
1456 DeletePoints /M=0 i, 1, attach_list, attach_sel
1461 n = ItemsInList(names)
1462 for (i = 0; i < n; i += 1)
1463 s = StringFromList(i, names)
1464 FindValue /text=s /txop=4 /z attach_list
1466 k = DimSize(attach_list, 0)
1467 Redimension /n=(k+1,3) attach_list, attach_sel
1469 attach_list[k][kAttachColSel] = ""
1470 attach_list[k][kAttachColTitle] = ""
1471 attach_list[k][kAttachColName] = s
1472 attach_sel[k][kAttachColSel] = 32
1473 attach_sel[k][kAttachColTitle] = 0
1474 attach_sel[k][kAttachColName] = 0
1479 n = DimSize(attach_list, 0)
1480 for (i = n-1; i >= 0; i -= 1)
1481 s = attach_list[i][kAttachColName]
1482 getwindow /z $s, wtitle
1484 attach_list[i][kAttachColTitle] = s_value
1486 attach_list[i][kAttachColTitle] = s
1490 setdatafolder savedf
1500 dfref savedf = getdatafolderdfr()
1502 wave /t /sdfr=df_volatile attach_list
1503 wave /sdfr=df_volatile attach_sel
1504 variable n = DimSize(attach_list, 0)
1505 variable dest = item + distance
1507 if ((item >= 0) && (item < n) && (dest >= 0) && (dest < n))
1508 string name = attach_list[item][kAttachColName]
1509 variable sel = attach_sel[item][kAttachColSel]
1510 DeletePoints /M=0 item, 1, attach_list, attach_sel
1511 InsertPoints /M=0 dest, 1, attach_list, attach_sel
1512 attach_list[dest][kAttachColName] = name
1514 attach_sel[dest][kAttachColSel] = sel
1520 STRUCT WMButtonAction &ba
1522 switch( ba.eventCode )
1524 string logbook = GetUserData(ba.win, "", "logbook")
1525 ControlInfo /w=$ba.win lb_attach
1526 variable row = v_value
1527 dfref df = $s_datafolder
1528 wave /t /sdfr=df attach_list = $s_value
1529 if (cmpstr(ba.ctrlName, "b_attach_up") == 0)
1533 ListBox lb_attach, win=$ba.win, selRow=(row-1)
1537 if (row < DimSize(attach_list, 0) - 1)
1539 ListBox lb_attach, win=$ba.win, selRow=(row+1)
1551 static function bp_submit(ba) : ButtonControl
1552 STRUCT WMButtonAction &ba
1554 switch( ba.eventCode )
1556 string logbook = GetUserData(ba.win, "", "logbook")
1565 if (cmpstr(ba.ctrlName, "b_reply") == 0)
1567 ControlInfo /w=$ba.win sv_id
1576 result =
elog_create_entry (logbook, attributes, message, graphs=graphs, replyto=
id )
1579 svar /sdfr=df recent
1581 svar /sdfr=df recent_message
1582 recent_message = message
1584 abort "Submission failed. Error code " + num2str(result) + "."
1587 abort "Submission failed due to missing/invalid attribute."
1599 STRUCT WMButtonAction &ba
1601 switch( ba.eventCode )
1603 string graphs = WinName(0, 1, 1)
1615 STRUCT WMButtonAction &ba
1617 switch( ba.eventCode )
1619 string logbook = GetUserData(ba.win, "", "logbook")
1621 wave /sdfr=df_volatile attach_sel
1622 if (cmpstr(ba.ctrlName, "b_attach_all") == 0)
1623 attach_sel[][kAttachColSel] = attach_sel[p][kAttachColSel] | 16
1625 attach_sel[][kAttachColSel] = attach_sel[p][kAttachColSel] & ~16
1635 static function bp_attach(ba) : ButtonControl
1636 STRUCT WMButtonAction &ba
1638 switch( ba.eventCode )
1640 string logbook = GetUserData(ba.win, "", "logbook")
1645 ControlInfo /w=$ba.win sv_id
1649 DoAlert /T="ELOG" 1, "This operation will replace all existing attachments. Do you want to continue?"
1651 if ((
id > 0) && (v_flag == 1))
1655 abort "Submission failed. Error code " + num2str(result) + "."
1658 abort "Submission failed due to missing/invalid attribute."
1669 STRUCT WMButtonAction &ba
1671 switch( ba.eventCode )
1673 string logbook = GetUserData(ba.win, "", "logbook")
1675 variable ngraphs = ItemsInList(graphs, ";")
1680 for (igraph = 0; igraph < ngraphs; igraph += 1)
1681 sgraph = StringFromList(igraph, graphs, ";")
1683 if (strlen(graph_path) > 0)
1696 static function bp_clear(ba) : ButtonControl
1697 STRUCT WMButtonAction &ba
1699 switch( ba.eventCode )
1712 static function bp_login(ba) : ButtonControl
1713 STRUCT WMButtonAction &ba
1715 switch( ba.eventCode )
1717 string logbook = GetUserData(ba.win, "", "logbook")
1719 Button b_login, win=$ba.win, disable=3
1720 Button b_logout, win=$ba.win, disable=0
1730 static function bp_logout(ba) : ButtonControl
1731 STRUCT WMButtonAction &ba
1733 switch( ba.eventCode )
1735 string logbook = GetUserData(ba.win, "", "logbook")
1737 Button b_login, win=$ba.win, disable=0
1738 Button b_logout, win=$ba.win, disable=3
1749 windowname = StringFromList(0, WinList("*ElogPanel*", ";", "WIN:64"), ";")
1763 if (strlen(windowname) == 0)
1766 if (strlen(windowname) == 0)
1770 string controls = ControlNameList(windowname, ";")
1771 string attributes = ""
1775 variable nco = ItemsInList(controls, ";")
1776 for (ico = 0; ico < nco; ico += 1)
1777 control = StringFromList(ico, controls, ";")
1778 attribute = GetUserData(windowname, control, "attribute")
1779 if (strlen(attribute) > 0)
1780 ControlInfo /w=$windowname $control
1783 attributes = ReplaceNumberByKey(attribute, attributes, v_value, "=", ";")
1787 attributes = ReplaceStringByKey(attribute, attributes, s_value, "=", ";")
1812 if (strlen(windowname) == 0)
1815 if (strlen(windowname) == 0)
1818 if (ParamIsDefault(clear))
1824 string logbook = GetUserData(windowname, "", "logbook")
1826 string persistent_path = GetDataFolder(1, df_persistent)
1827 svar /sdfr=df_persistent options
1830 string controls = ControlNameList(windowname, ";")
1836 variable nco = ItemsInList(controls, ";")
1837 for (ico = 0; ico < nco; ico += 1)
1838 control = StringFromList(ico, controls, ";")
1839 attribute = GetUserData(windowname, control, "attribute")
1840 if (strlen(attribute))
1841 value = StringByKey(attribute, attributes, "=", ";")
1842 if (strlen(value) || clear)
1843 ControlInfo /w=$windowname $control
1846 numval = NumberByKey(attribute, attributes, "=", ";")
1847 if ((numtype(numval) != 0) && clear)
1850 if (numtype(numval) == 0)
1851 CheckBox $control, value=numval, win=$windowname
1855 options_path = persistent_path + StringByKey(attribute, options, "=", ";")
1856 svar values = $options_path
1857 numval = WhichListItem(value, values, ";") + 1
1859 PopupMenu $control, mode=numval, win=$windowname
1863 SetVariable /z $control, value= _STR:value, win=$windowname
1883 if (strlen(windowname) == 0)
1886 if (strlen(windowname) == 0)
1890 string nb = windowname + "
#Message" 1891 notebook $nb selection={startOfFile, endOfFile}
1892 getselection notebook, $nb, 2
1910 if (strlen(windowname) == 0)
1914 string nb = windowname + "
#Message" 1915 notebook $nb selection={startOfFile, endOfFile},text=message
1929 dfref savedf = getdatafolderdfr()
1930 if (strlen(windowname) == 0)
1933 if (strlen(windowname) == 0)
1937 string logbook = GetUserData(windowname, "", "logbook")
1939 wave /t /sdfr=df_volatile attach_list
1940 wave /sdfr=df_volatile attach_sel
1945 variable n = DimSize(attach_sel, 0)
1947 for (i = 0; i < n; i += 1)
1948 if (attach_sel[i][kAttachColSel] & 16)
1949 graphname = attach_list[i][kAttachColName]
1950 windows = WinList(graphname, ";", "WIN:1")
1951 if (ItemsInList(windows) == 1)
1952 graphs = AddListItem(graphname, graphs, ";", inf)
1970 if (strlen(windowname) == 0)
1973 if (strlen(windowname) == 0)
1977 string logbook = GetUserData(windowname, "", "logbook")
1980 wave /t /sdfr=df_volatile attach_list
1981 wave /sdfr=df_volatile attach_sel
1983 variable n = DimSize(attach_sel, 0)
1986 for (i = 0; i < n; i += 1)
1987 graphname = attach_list[i][kAttachColName]
1988 if (WhichListItem(graphname, graphs)>= 0)
1989 attach_sel[i][kAttachColSel] = 48
1991 attach_sel[i][kAttachColSel] = 32
variable elog_create_entry(string logbook, string attributes, string message, variable encoding=defaultValue, string graphs=defaultValue, variable replyto=defaultValue)
create a new entry in ELOG
-
static variable AfterFileOpenHook(variable refNum, string file, string pathName, string type, string creator, variable kind)
initialize the package and reload preferences after an experiment is loaded.
-
variable elog_add_attachment(string logbook, variable id, string graphs)
add one or more graphs to an existing ELOG entry
-
static const string package_path
-
static string get_panel_graphs(string windowname)
get the names of the graphs selected for attachment
-
static variable bp_attach_updown(WMButtonAction *ba)
button procedure for the attachment up and down buttons
-
static string create_message_file(string message)
save the message to a temporary text file
-
static variable parse_result()
parse the result file from an elog invokation.
-
variable elog_create_logbook(string name, string template=defaultValue)
create a new logbook.
-
static string set_panel_attributes(string windowname, string attributes, variable clear=defaultValue)
set the fields of the ELOG panel
-
static variable bp_logout(WMButtonAction *ba)
-
static string get_default_panel_name()
-
static variable elog_panel_hook(WMWinHookStruct *s)
-
variable elog_config(string elog_path=defaultValue, string hostname=defaultValue, variable port=defaultValue, string subdir=defaultValue)
set global module configuration parameters
-
interface for writing ELOG entries with Igor graphs as attachment.
-
static variable IgorBeforeNewHook(string igorApplicationNameStr)
save preferences and recent values before Igor opens a new experiment.
-
static string set_panel_graphs(string windowname, string graphs)
update selection of graphs for attachment
-
variable elog_init_pearl_templates()
setup PEARL template logbooks.
-
static string create_graph_file(string graphname, variable fileindex)
save a graph to a temporary graphics file
-
static const variable kAttachColName
-
static variable bp_clear(WMButtonAction *ba)
-
variable elog_login(string logbook, string username, string password)
set username and password for login to a logbook
-
static variable bp_attach_top(WMButtonAction *ba)
select top graph window for attachment
-
static const variable kAttachColSel
-
string PearlElogPanel(string logbook)
open a new panel for submitting data to ELOG.
-
variable elog_validate_attributes(string logbook, string attributes)
validate attributes
-
static string prepare_graph_attachments(string graphs)
prepare screenshots of graph windows for attachments
-
static string list_logbooks(variable templates=defaultValue)
get a list of configured logbooks or templates.
-
static variable bp_attach(WMButtonAction *ba)
-
static variable move_attach_item(string logbook, variable item, variable distance)
move an attachment item in the list of attachments
-
static dfr get_elog_df(string name, variable category)
get the package, logbook, or template datafolder.
-
string elog_prompt_logbook()
prompt to open or create a logbook
-
static variable bp_save_graphs(WMButtonAction *ba)
-
static variable update_attach_items(string logbook)
update the list of attachments
-
static variable bp_login(WMButtonAction *ba)
-
static const variable kdfVolatile
-
static const variable kdfTemplates
-
static string prepare_command_line(string logbook)
format the ELOG command and essential address arguments.
-
static variable cleanup_temp_files()
delete temporary files created by the ELOG module.
-
static string get_log_path()
-
static const variable kAttachColTitle
-
static const string elog_parse_id
-
static string get_panel_message(string windowname)
get the message field of the ELOG panel
-
static string create_cmd_file(string cmd)
write the command line to a file.
-
static variable init_volatile_vars()
initialize volatile variables.
-
static variable load_prefs()
load persistent package data from the preferences file.
-
static const variable kdfPersistent
-
static variable init_package(variable clean=defaultValue)
initialize the package data folder.
-
static variable save_prefs()
save persistent package data to the preferences file.
-
static const variable kdfRoot
-
variable elog_prompt_login(string logbook)
prompt the user for login to a logbook
-
static string set_panel_message(string windowname, string message)
set the message field of the ELOG panel
-
static variable IgorQuitHook(string igorApplicationNameStr)
save preferences and recent values before Igor quits.
-
static variable bp_submit(WMButtonAction *ba)
button procedure for the Submit and Reply buttons
-
static variable bp_attach_allnone(WMButtonAction *ba)
select/deselect all graph windows for attachment
-
static string get_panel_attributes(string windowname)
get a list of attributes from the fields of the ELOG panel.
-
static const string elog_success_msg
-
static string get_timestamp(string sep)
-
variable elog_logout(string logbook)
clear username and password of a logbook or all logbooks.
-
variable pearl_elog(string logbook)
main function to initialize ELOG and to open an ELOG panel.
-
static string format_url(string logbook)
format the URL for display to the user
-
static const string package_name
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
+
4 #pragma IgorVersion = 6.36
+
5 #pragma ModuleName = PearlElog
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
104 if (ItemsInList(templates) < 1)
+
+
+
+
+
109 if (strlen(logbook) == 0)
+
+
+
+
113 string win_name = logbook + "ElogPanel"
+
114 if (strlen(logbook) > 0)
+
115 if (strlen(WinList(win_name, ";", "")) > 0)
+
116 DoWindow /F $win_name
+
+
+
119 STRUCT WMWinHookStruct s
+
+
+
+
+
+
+
+
+
129 string igorApplicationNameStr
+
+
+
+
+
+
+
137 string igorApplicationNameStr
+
+
+
+
+
+
+
+
146 String file,pathName,type,creator
+
147 if( (kind >= 1) && (kind <= 2))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
175 dfref df_package = $package_path
+
176 dfref df_persistent = df_package:persistent
+
177 dfref df_volatile = df_package:volatile
+
+
+
+
181 dfref df_parent = df_package
+
+
+
184 dfref df_parent = df_persistent
+
+
+
187 dfref df_parent = df_persistent:templates
+
+
+
190 dfref df_parent = df_volatile
+
+
+
193 Abort "
get_elog_df : undefined data folder category."
+
+
+
196 if ((strlen(name) > 0) && (category >= 1))
+
+
198 dfref df_logbooks = df_parent
+
+
200 dfref df_logbooks = df_parent:logbooks
+
+
202 dfref df_logbook = df_logbooks:$name
+
+
+
+
+
+
+
+
+
+
221 if (ParamIsDefault(clean))
+
+
+
+
225 dfref savedf = getdatafolderdfr()
+
+
227 if ((clean == 0) && (DataFolderRefStatus(df_root) == 1))
+
+
+
+
+
232 newdatafolder /o/s packages
+
233 newdatafolder /o/s $package_name
+
234 dfref df_package_root = getdatafolderdfr()
+
235 newdatafolder /o/s volatile
+
236 dfref df_volatile = getdatafolderdfr()
+
237 newdatafolder /o logbooks
+
238 setdatafolder df_package_root
+
239 newdatafolder /o/s persistent
+
240 dfref df_persistent = getdatafolderdfr()
+
241 newdatafolder /o logbooks
+
242 newdatafolder /o templates
+
+
+
245 setdatafolder df_persistent
+
246 string /g elog_path = "c:\\program files (x86)\\ELOG\\elog.exe"
+
247 string /g hostname = "localhost"
+
+
+
250 string /g subdir = ""
+
251 variable /g loglevel = 4
+
+
+
+
+
+
+
264 dfref savedf = getdatafolderdfr()
+
+
+
+
+
+
+
271 setdatafolder df_templates
+
272 newdatafolder /o/s Experiments
+
+
+
+
276 string /g attributes = "author;project;p-group;sample;source;task;technique;file;valid;"
+
+
+
279 string /g controls = "sv_author;sv_project;sv_pgroup;sv_sample;pm_source;pm_task;pm_technique;sv_file;cb_valid;"
+
+
281 string /g options = "source=sources;task=tasks;technique=techniques"
+
+
283 string /g required_attributes = "author;project;sample;source;task;technique;valid"
+
+
+
286 string /g sources = "Manual Entry;PShell;Scienta Data;SScan Data;Prosilica Data;OTF Data;Beamline Status;LEED Data;QMS Data;Matrix Data;Igor Pro;Other"
+
287 string /g tasks = "Measurement;Optimization;Analysis;Sample Preparation;Sample Storage;Comment;Development;Maintenance;Test;Other"
+
288 string /g techniques = "XPS;UPS;XPD;XAS;XMCD;PhD;ARUPS;STM;STS;LEED;AES;QMS;MBE;Sputter/Anneal;Test;Other"
+
+
+
291 setdatafolder df_templates
+
292 newdatafolder /o/s Calculations
+
+
+
+
296 string /g attributes = "author;project;p-group;sample;program;revision;machine;job;experiment;source path;result path;valid"
+
+
+
299 string /g controls = "sv_author;sv_project;sv_pgroup;sv_sample;pm_program;sv_revision;pm_machine;sv_job;sv_experiment;sv_sourcepath;sv_resultpath;cb_valid"
+
+
301 string /g options = "program=programs;machine=machines"
+
+
303 string /g required_attributes = "author;project;sample"
+
+
+
306 string /g programs = "PMSCO;EDAC;MSC;SSC;MUFPOT;DMSUP;Other"
+
307 string /g machines = "PC;VM;Ra;Merlin;llcx;Other"
+
+
+
310 setdatafolder df_templates
+
311 newdatafolder /o/s System
+
+
+
+
315 string /g attributes = "author;type;system;source;file"
+
+
+
318 string /g controls = "sv_author;pm_type;pm_system;pm_source;sv_file"
+
+
320 string /g options = "type=types;system=systems;source=sources"
+
+
322 string /g required_attributes = "author;type;system"
+
+
+
325 string /g types = "Installation;Repair;Maintenance;Test;Commissioning;Bakeout;Incident;Cool-down;Warm-up;Storage;Other"
+
326 string /g systems = "Vacuum;Control System;BL;XA;XP;SA;SP;T;LL;Monochromator;Carving;Scienta;STM;PC-Scienta;PC-Matrix;PC-Console;PC-Console-Win;PC-XP;EPS;LAC;Desiccator;Other"
+
327 string /g sources = "Manual Entry;PShell;Scienta Data;SScan Data;Prosilica Data;OTF Data;Beamline Status;LEED Data;QMS Data;Matrix Data;Igor Pro;Other"
+
+
+
+
+
+
+
342 dfref savedf = GetDataFolderDFR()
+
+
+
345 dfref df_volatile_parent = df_volatile_root:logbooks
+
+
+
+
349 variable nlb = ItemsInList(logbooks)
+
+
+
352 SetDataFolder df_volatile_root
+
353 if (exists("temp_graph_files") != 2)
+
354 string /g temp_graph_files = ""
+
+
+
357 for (ilb = 0; ilb < nlb; ilb += 1)
+
358 logbook = StringFromList(ilb, logbooks)
+
+
360 SetDataFolder df_volatile_parent
+
361 if (DataFolderExists(logbook))
+
362 SetDataFolder $logbook
+
+
364 NewDataFolder /o/s $logbook
+
+
+
367 if (exists("username") != 2)
+
368 string /g username = ""
+
+
370 if (exists("password") != 2)
+
371 string /g password = ""
+
+
373 if (exists("msg_id") != 2)
+
374 variable /g msg_id = 0
+
+
376 if (exists("att_list") != 1)
+
377 make /n=(0,3) /t /o attach_list
+
378 make /n=(0,3) /i /o attach_sel
+
+
380 if (exists("url") != 2)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
419 if (ParamIsDefault(template))
+
+
+
+
423 dfref savedf = getdatafolderdfr()
+
+
+
426 dfref df_persistent_parent = df_persistent_root:logbooks
+
+
428 dfref df_volatile_parent = df_volatile_root:logbooks
+
+
430 setdatafolder df_persistent_parent
+
431 if (CheckName(name, 11) != 0)
+
+
433 Abort "invalid logbook name"
+
+
+
+
437 if (strlen(template) > 0)
+
+
+
440 if (DataFolderRefStatus(df_existing))
+
441 KillDataFolder /Z df_existing
+
+
443 DuplicateDataFolder df_template, df_persistent_parent:$name
+
+
445 NewDataFolder /o/s df_persistent_parent:$name
+
+
+
448 string /g logbook = name
+
+
+
451 string /g attributes = ""
+
+
+
454 string /g controls = ""
+
+
456 string /g options = ""
+
+
458 string /g required_attributes = ""
+
+
+
+
+
463 string /g recent = ""
+
464 string /g recent_message = ""
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
482 if (!ParamIsDefault(elog_path))
+
483 svar /sdfr=df g_elog_path = elog_path
+
484 g_elog_path = elog_path
+
+
486 if (!ParamIsDefault(hostname))
+
487 svar /sdfr=df g_hostname = hostname
+
488 g_hostname = hostname
+
+
490 if (!ParamIsDefault(port))
+
491 nvar /sdfr=df g_port = port
+
+
+
494 if (!ParamIsDefault(subdir))
+
495 svar /sdfr=df g_subdir = subdir
+
+
+
+
+
+
+
+
+
+
+
520 svar /sdfr=df g_username=username
+
521 svar /sdfr=df g_password=password
+
522 g_username = username
+
523 g_password = password
+
+
+
+
+
+
+
538 if (strlen(logbook) > 0)
+
539 svar /z /sdfr=df g_username=username
+
540 svar /z /sdfr=df g_password=password
+
541 if (svar_exists(g_username))
+
+
+
544 if (svar_exists(g_password))
+
+
+
+
548 dfref df2 = df:logbooks
+
549 variable nlb = CountObjectsDFR(df2, 4)
+
+
+
552 for (ilb = 0; ilb < nlb; ilb += 1)
+
553 slb = GetIndexedObjNameDFR(df2, 4, ilb)
+
+
+
+
+
+
+
+
+
566 dfref saveDF = GetDataFolderDFR()
+
+
+
569 if (DataFolderRefStatus(df) == 1)
+
570 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
+
+
572 NewPath/O/C/Q tempPackagePrefsPath, fullPath
+
573 fullPath += ":preferences.pxp"
+
+
575 SaveData /O /Q /R fullPath
+
576 KillPath/Z tempPackagePrefsPath
+
+
+
+
+
+
+
586 dfref saveDF = GetDataFolderDFR()
+
+
+
+
+
+
592 string fullPath = SpecialDirPath("Packages", 0, 0, 0)
+
+
+
595 GetFileFolderInfo /Q /Z fullPath
+
+
597 fullPath += ":preferences.pxp"
+
598 GetFileFolderInfo /Q /Z fullPath
+
+
600 LoadData /O /R /Q fullPath
+
+
+
+
+
+
+
+
+
+
+
+
+
622 if (ParamIsDefault(templates))
+
+
+
+
+
+
628 dfref df_logbooks = df_persistent:templates
+
+
630 dfref df_logbooks = df_persistent:logbooks
+
+
+
+
634 variable nlb = CountObjectsDFR(df_logbooks, 4)
+
+
+
637 for (ilb = 0; ilb < nlb; ilb += 1)
+
638 slb = GetIndexedObjNameDFR(df_logbooks, 4, ilb)
+
+
640 logbooks = AddListItem(slb, logbooks)
+
+
+
+
644 return SortList(logbooks, ";", 16)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
694 if (ParamIsDefault(encoding))
+
+
+
697 if (ParamIsDefault(graphs))
+
+
+
700 if (ParamIsDefault(replyto))
+
+
+
+
704 dfref savedf = getdatafolderdfr()
+
+
+
+
+
709 nvar /sdfr=df_volatile msg_id
+
710 nvar /sdfr=df_general loglevel
+
+
+
+
714 print "ELOG: failed to validate attributes."
+
+
+
+
+
+
720 if (strlen(cmd) == 0)
+
+
722 print "ELOG: failed to prepare command line."
+
+
+
+
+
+
728 cmd += " -r " + num2str(replyto)
+
+
730 cmd += " -n " + num2str(encoding)
+
+
732 variable nattr = ItemsInList(attributes, ";")
+
+
+
735 for (iattr = 0; (iattr < nattr) && (result == 0); iattr += 1)
+
736 sattr = StringFromList(iattr, attributes, ";")
+
737 if (strlen(StringFromList(1, sattr, "=")) > 0)
+
738 sattr = ReplaceString("%", sattr, "")
+
739 cmd += " -a \"" + sattr + "\""
+
+
+
+
+
+
745 cmd += " " + cmd_graphs
+
+
+
748 if ((result == 0) && (strlen(message) > 0))
+
+
750 if (strlen(messagefile) > 0)
+
751 cmd += " -m \"" + messagefile + "\""
+
+
+
+
+
+
757 if (strlen(cmd_file_path) > 0)
+
758 ExecuteScriptText cmd_file_path
+
+
+
+
+
763 print "ELOG: sent message " + num2str(
id )
+
+
+
+
767 print "ELOG: sending message failed."
+
+
+
+
+
+
+
+
+
776 print "ELOG: failed to create temporary message file."
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
798 dfref savedf = getdatafolderdfr()
+
+
+
+
+
803 nvar /sdfr=df_volatile msg_id
+
804 nvar /sdfr=df_general loglevel
+
+
+
807 if (strlen(cmd) == 0)
+
+
+
+
811 cmd += " -e " + num2str(
id )
+
+
+
+
815 if (strlen(cmd_graphs) == 0)
+
+
+
+
+
+
821 cmd += " " + cmd_graphs
+
+
+
824 if (strlen(cmd_file_path) > 0)
+
825 ExecuteScriptText cmd_file_path
+
+
+
+
+
830 print "ELOG: attached graphs to message " + num2str(
id )
+
+
+
+
834 print "ELOG: failed to attach graphs."
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
861 svar /sdfr=df_general elog_path
+
862 svar /sdfr=df_general hostname
+
863 nvar /sdfr=df_general port
+
864 nvar /sdfr=df_general ssl
+
865 svar /sdfr=df_general subdir
+
866 nvar /sdfr=df_general loglevel
+
867 svar /sdfr=df_volatile username
+
868 svar /sdfr=df_volatile password
+
+
+
871 cmd = "\"" + elog_path + "\""
+
+
+
+
875 cmd += " -h " + hostname
+
876 if ((nvar_exists(port)) && (port > 0))
+
877 cmd += " -p " + num2str(port)
+
+
879 if ((svar_exists(subdir)) && (strlen(subdir) > 0))
+
880 cmd += " -d " + subdir
+
+
882 cmd += " -l \"" + logbook + "\""
+
883 if ((nvar_exists(ssl)) && (ssl != 0))
+
+
+
+
887 if (svar_exists(username) && svar_exists(password) && (strlen(username) > 0) && (strlen(password) > 0))
+
888 cmd += " -u " + username + " " + password
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
908 svar /sdfr=df_general hostname
+
909 nvar /sdfr=df_general port
+
910 nvar /sdfr=df_general ssl
+
911 svar /sdfr=df_general subdir
+
+
+
914 if ((nvar_exists(ssl)) && (ssl != 0))
+
+
+
+
+
+
920 if ((nvar_exists(port)) && (port > 0))
+
921 cmd += ":" + num2str(port)
+
+
923 if ((svar_exists(subdir)) && (strlen(subdir) > 0))
+
+
+
+
+
+
+
+
+
+
+
+
944 variable ngraphs = ItemsInList(graphs, ";")
+
+
+
+
948 for (igraph = 0; igraph < ngraphs; igraph += 1)
+
949 sgraph = StringFromList(igraph, graphs, ";")
+
+
951 if (strlen(graph_path) > 0)
+
952 cmd += " -f \"" + graph_path + "\""
+
+
+
+
+
+
+
+
+
961 Variable now = DateTime
+
962 string dat = ReplaceString("-", Secs2Date(DateTime, -2), "")
+
963 string tim = ReplaceString(":", Secs2Time(DateTime, 3), "")
+
964 return dat + sep + tim
+
+
+
+
+
+
986 message = ReplaceString("%", message, "")
+
987 string path = SpecialDirPath("Temporary", 0, 1, 0)
+
988 variable len = strlen(path)
+
+
+
991 if (numtype(len) == 0)
+
992 filename = "elog_temp_message.txt"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1029 svar /sdfr=df_volatile_root temp_graph_files
+
+
1031 string path = SpecialDirPath("Temporary", 0, 1, 0)
+
+
1033 variable len = strlen(path)
+
+
+
1036 if (numtype(len) == 0)
+
1037 filename = "elog_" + ts + "_" + num2str(fileindex) + ".png"
+
+
1039 SavePICT /B=72 /E=-5 /M /O /W=(0,0,8,6) /WIN=$graphname /Z as path
+
+
1041 temp_graph_files = AddListItem(path, temp_graph_files, ";", inf)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1064 nvar /sdfr=df_general loglevel
+
+
1066 if (strlen(cmd) >= 1024)
+
+
1068 print "ELOG: command line too
long (add fewer attachments)."
+
+
+
+
+
1073 string work_path = SpecialDirPath("Temporary", 0, 1, 0)
+
1074 variable len = strlen(work_path)
+
1075 if (numtype(len) == 0)
+
+
1077 string cmd_path = work_path + "elog_temp_cmd.bat"
+
+
+
+
+
+
1083 cmdx = "cd \"" + work_path + "\"\r\n"
+
+
1085 cmdx = "del elog.log"
+
1086 fprintf f1, cmdx + "\r\n"
+
+
+
+
+
+
+
+
+
+
+
1097 string path = SpecialDirPath("Temporary", 0, 1, 0)
+
1098 variable len = strlen(path)
+
1099 if (numtype(len) == 0)
+
+
+
+
+
+
+
+
+
+
+
1118 if (DataFolderRefStatus(df_volatile_root))
+
1119 svar /sdfr=df_volatile_root /z temp_graph_files
+
1120 if (SVAR_Exists(temp_graph_files))
+
1121 variable nfi = ItemsInList(temp_graph_files)
+
+
+
1124 for (ifi = 0; ifi < nfi; ifi += 1)
+
1125 sfi = StringFromList(ifi, temp_graph_files)
+
+
+
1128 temp_graph_files = ""
+
+
+
+
+
+
+
+
+
+
+
1144 nvar /sdfr=df_general loglevel
+
+
+
+
+
1149 variable success = 0
+
+
+
+
+
1154 variable len = strlen(path)
+
1155 if (numtype(len) == 0)
+
+
1157 Open /R/Z f1 as path
+
+
+
+
1161 if (strlen(line) > 0)
+
1162 part1 = StringFromList(0, line, ",")
+
1163 part2 = ReplaceString(" ", StringFromList(1, line, ","), "")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1187 logbooks = AddListItem("(new)", logbooks)
+
+
1189 templates = AddListItem("(none)", templates)
+
+
1191 string logbook = StringFromList(0, logbooks)
+
1192 string template = StringFromList(0, logbooks)
+
+
1194 string username = ""
+
1195 string password = ""
+
+
1197 prompt logbook, "logbook", popup logbooks
+
1198 prompt template, "template", popup templates
+
1199 prompt name, "new logbook name"
+
+
1201 doprompt "select logbook", logbook, template, name
+
+
1203 if (cmpstr(logbook, "(new)") == 0)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1220 string username = ""
+
1221 string password = ""
+
+
1223 prompt logbook, "logbook", popup logbooks
+
1224 prompt username, "user name"
+
1225 prompt password, "password (blank to log out)"
+
+
1227 doprompt "log in to logbook", logbook, username, password
+
+
+
+
+
+
+
+
+
+
+
1245 dfref savedf = getdatafolderdfr()
+
+
+
+
+
1250 string win_name = logbook + "ElogPanel"
+
1251 string win_title = "ELOG " + logbook
+
+
1253 NewPanel /K=1 /N=$win_name /W=(600,200,1200,700) as win_title
+
+
1255 ModifyPanel /w=$win_name cbRGB=(52224,52224,65280)
+
+
1257 svar /sdfr=df_persistent attributes
+
1258 svar /sdfr=df_persistent controls
+
1259 svar /sdfr=df_persistent options
+
1260 wave /t /sdfr=df_volatile attach_list
+
1261 wave /sdfr=df_volatile attach_sel
+
1262 svar /sdfr=df_volatile url
+
+
+
1265 variable nattr = ItemsInList(attributes, ";")
+
+
+
+
1269 string persistent_path = GetDataFolder(1, df_persistent)
+
1270 string volatile_path = GetDataFolder(1, df_volatile)
+
+
1272 string variable_path
+
+
+
+
1276 for (iattr = 0; iattr < nattr; iattr += 1)
+
1277 s_attr = StringFromList(iattr, attributes, ";")
+
1278 s_control = StringFromList(iattr, controls, ";")
+
1279 strswitch(s_control[0,1])
+
+
1281 SetVariable $s_control, win=$win_name, pos={0,ypos}, size={300,16}, bodyWidth=230
+
1282 SetVariable $s_control, win=$win_name, title=s_attr, value= _STR:
""
+
1283 SetVariable $s_control, win=$win_name, userdata(attribute)=s_attr
+
+
+
+
1287 options_path = persistent_path + StringByKey(s_attr, options,
"=" ,
";" )
+
1288 PopupMenu $s_control, win=$win_name, pos={0,ypos}, size={300,21}, bodyWidth=230
+
1289 PopupMenu $s_control, win=$win_name, title=s_attr
+
1290 PopupMenu $s_control, win=$win_name, mode=1, popvalue=
"Test" , value= #options_path
+
1291 PopupMenu $s_control, win=$win_name, userdata(attribute)=s_attr
+
+
+
+
1295 CheckBox $s_control, win=$win_name, pos={70,ypos}, size={300,14}
+
1296 CheckBox $s_control, win=$win_name, title=s_attr, value= 1
+
1297 CheckBox $s_control, win=$win_name, userdata(attribute)=s_attr
+
+
+
+
+
1302 ypos = max(ypos, 80)
+
+
1304 TitleBox t_attach, win=$win_name, pos={308,5}, size={70,14}, title=
"Attachments" , frame=0
+
1305 height = ypos - 21 - 4
+
1306 ListBox lb_attach, win=$win_name, pos={308,21}, size={264,height}
+
1307 ListBox lb_attach, win=$win_name, listWave=attach_list
+
1308 ListBox lb_attach, win=$win_name, mode=1, selWave=attach_sel, selRow=-1
+
1309 ListBox lb_attach, win=$win_name, widths={20,160,80}
+
1310 ListBox lb_attach, win=$win_name, help={
"Choose graphs to attach to the message." }
+
+
1312 Button b_attach_top, win=$win_name, pos={420,2}, size={40,18}, title=
"top"
+
1313 Button b_attach_top, win=$win_name, fcolor=(56576,60928,47872)
+
+
1315 Button b_attach_top, win=$win_name, help={
"Select top graph for attachment." }
+
1316 Button b_attach_all, win=$win_name, pos={460,2}, size={40,18}, title=
"all"
+
1317 Button b_attach_all, win=$win_name, fcolor=(56576,60928,47872)
+
+
1319 Button b_attach_all, win=$win_name, help={
"Select all graphs for attachment." }
+
1320 Button b_attach_none, win=$win_name, pos={500,2}, size={40,18}, title=
"none"
+
1321 Button b_attach_none, win=$win_name, fcolor=(56576,60928,47872)
+
+
1323 Button b_attach_none, win=$win_name, help={
"Deselect all attachments." }
+
1324 Button b_save_graphs, win=$win_name, pos={540,2}, size={40,18}, title=
"save"
+
1325 Button b_save_graphs, win=$win_name, fcolor=(56576,60928,47872)
+
+
1327 Button b_save_graphs, win=$win_name, help={
"Save selected graphs as PNG bitmap files." }
+
1328 Button b_attach_up, win=$win_name, pos={576,20}, size={20,20}, title=
"\\W517"
+
1329 Button b_attach_up, win=$win_name, fcolor=(56576,60928,47872)
+
+
1331 Button b_attach_up, win=$win_name, help={
"Move selected graph up." }
+
1332 Button b_attach_dw, win=$win_name, pos={576,40}, size={20,20}, title=
"\\W523"
+
1333 Button b_attach_dw, win=$win_name, fcolor=(56576,60928,47872)
+
+
1335 Button b_attach_dw, win=$win_name, help={
"Move selected graph down." }
+
+
+
1338 Button b_submit,win=$win_name, pos={70,ypos},size={46,20},proc=
PearlElog #
bp_submit ,title=
"Submit"
+
1339 Button b_submit,win=$win_name, help={
"Submit form data to ELOG (new entry)." }
+
1340 Button b_submit,win=$win_name, fcolor=(56576,60928,47872)
+
1341 Button b_clear,win=$win_name, pos={120,ypos},size={46,20},proc=
PearlElog #
bp_clear ,title=
"Clear"
+
1342 Button b_clear,win=$win_name, help={
"Clear the form fields" }
+
1343 Button b_clear,win=$win_name, fcolor=(56576,60928,47872)
+
+
+
1346 variable_path = volatile_path +
"msg_id"
+
1347 SetVariable sv_id,win=$win_name, pos={51,ypos},size={119,16},bodyWidth=77
+
1348 SetVariable sv_id,win=$win_name, title=
"ID" ,value=$variable_path
+
1349 SetVariable sv_id,win=$win_name, help={
"ID of last submitted message, or message to attach or reply to." }
+
+
1351 TitleBox t_host, win=$win_name, pos={170,ypos+4}, size={112.00,14.00}, frame=0
+
1352 TitleBox t_host, win=$win_name, variable=url
+
+
+
1355 Button b_attach,win=$win_name, pos={170,ypos},size={48,20},proc=
PearlElog #
bp_attach ,title=
"Attach"
+
1356 Button b_attach,win=$win_name, help={
"Attach the selected graph to an existing ELOG entry (correct ID required)." }
+
1357 Button b_attach,win=$win_name, fcolor=(56576,60928,47872)
+
1358 Button b_reply,win=$win_name, pos={220,ypos},size={48,20},proc=
PearlElog #
bp_submit ,title=
"Reply"
+
1359 Button b_reply,win=$win_name, help={
"Submit form data to ELOG as a reply to an existing message (correct ID required)." }
+
1360 Button b_reply,win=$win_name, fcolor=(56576,60928,47872)
+
1361 Button b_login,win=$win_name, pos={550,ypos},size={46,20},proc=
PearlElog #
bp_login ,title=
"Login"
+
1362 Button b_login,win=$win_name, help={
"Enter user name and password." }
+
1363 Button b_login,win=$win_name, fcolor=(56576,60928,47872)
+
1364 Button b_logout,win=$win_name, pos={550,ypos},size={46,20},proc=
PearlElog #
bp_logout ,title=
"Logout"
+
1365 Button b_logout,win=$win_name, help={
"Clear user name and password." }
+
1366 Button b_logout,win=$win_name, fcolor=(56576,60928,47872), disable=3
+
+
+
1369 SetWindow $win_name, userdata(logbook)=logbook
+
+
+
1372 TitleBox t_message,win=$win_name, pos={10,ypos},size={58,16},fixedSize=1,frame=0,anchor=RT,title=
"Message"
+
1373 DefineGuide UGH0={FT,ypos},UGV0={FL,70},UGH1={FB,-52},UGV1={FR,-2}
+
1374 NewNotebook /F=0 /N=Message /OPTS=3 /W=(115,404,345,341)/FG=(UGV0,UGH0,UGV1,UGH1) /HOST=#
+
1375 Notebook kwTopWin, defaultTab=20, statusWidth=0, autoSave=0
+
1376 Notebook kwTopWin fSize=10, fStyle=0, textRGB=(0,0,0)
+
1377 RenameWindow #,Message
+
1378 string nb_name = win_name +
"#Message"
+
1379 SetActiveSubwindow ##
+
+
+
1382 svar /z /sdfr=df_persistent recent
+
1383 if (svar_exists(recent) && (strlen(recent) > 0))
+
+
+
1386 svar /z /sdfr=df_persistent recent_message
+
1387 if (svar_exists(recent_message) && (strlen(recent_message) > 0))
+
+
+
1390 Notebook $nb_name selection={startOfFile,startOfFile}, findText={
"" ,1}
+
+
1392 setdatafolder savedf
+
+
+
+
+
1397 STRUCT WMWinHookStruct &s
+
+
1399 Variable hookResult = 0
+
+
+
+
1403 string logbook = GetUserData(s.winName,
"" ,
"logbook" )
+
1404 if (strlen(logbook) > 0)
+
+
1406 svar /sdfr=df_volatile url
+
+
+
+
+
+
+
1413 variable b_top = s.winRect.bottom + 4
+
1414 Button b_submit,pos={70,b_top}
+
1415 Button b_clear,pos={120,b_top}
+
1416 TitleBox t_host, pos={170,b_top+4}
+
+
1418 Button b_attach,pos={170,b_top}
+
1419 Button b_reply,pos={220,b_top}
+
1420 Button b_login, pos={550,b_top}
+
1421 Button b_logout, pos={550,b_top}
+
+
1423 SetVariable sv_id,pos={51,b_top}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1438 dfref savedf = getdatafolderdfr()
+
+
1440 wave /t /sdfr=df_volatile attach_list
+
1441 wave /sdfr=df_volatile attach_sel
+
+
1443 if (!waveexists(attach_list))
+
+
+
1446 string names = WinList("*", ";", "WIN:1;VISIBLE:1")
+
1447 names = SortList(names, ";", 16)
+
+
+
+
+
1452 variable n = DimSize(attach_list, 0)
+
+
1454 for (i = n-1; i >= 0; i -= 1)
+
+
1456 if (WhichListItem(s, names) < 0)
+
1457 DeletePoints /M=0 i, 1, attach_list, attach_sel
+
+
+
+
+
1462 n = ItemsInList(names)
+
1463 for (i = 0; i < n; i += 1)
+
1464 s = StringFromList(i, names)
+
1465 FindValue /text=s /txop=4 /z attach_list
+
+
1467 k = DimSize(attach_list, 0)
+
1468 Redimension /n=(k+1,3) attach_list, attach_sel
+
+
+
+
+
+
+
+
+
+
+
+
1480 n = DimSize(attach_list, 0)
+
1481 for (i = n-1; i >= 0; i -= 1)
+
+
1483 getwindow /z $s, wtitle
+
+
+
+
+
+
+
+
1491 setdatafolder savedf
+
+
+
+
+
+
+
+
+
1501 dfref savedf = getdatafolderdfr()
+
+
1503 wave /t /sdfr=df_volatile attach_list
+
1504 wave /sdfr=df_volatile attach_sel
+
1505 variable n = DimSize(attach_list, 0)
+
1506 variable dest = item + distance
+
+
1508 if ((item >= 0) && (item < n) && (dest >= 0) && (dest < n))
+
+
+
1511 DeletePoints /M=0 item, 1, attach_list, attach_sel
+
1512 InsertPoints /M=0 dest, 1, attach_list, attach_sel
+
+
+
+
+
+
+
+
1521 STRUCT WMButtonAction &ba
+
+
1523 switch( ba.eventCode )
+
+
1525 string logbook = GetUserData(ba.win, "", "logbook")
+
1526 ControlInfo /w=$ba.win lb_attach
+
1527 variable row = v_value
+
1528 dfref df = $s_datafolder
+
1529 wave /t /sdfr=df attach_list = $s_value
+
1530 if (cmpstr(ba.ctrlName, "b_attach_up") == 0)
+
+
+
+
1534 ListBox lb_attach, win=$ba.win, selRow=(row-1)
+
+
+
+
1538 if (row < DimSize(attach_list, 0) - 1)
+
+
1540 ListBox lb_attach, win=$ba.win, selRow=(row+1)
+
+
+
+
+
+
+
+
+
+
+
+
1553 STRUCT WMButtonAction &ba
+
+
1555 switch( ba.eventCode )
+
+
1557 string logbook = GetUserData(ba.win, "", "logbook")
+
+
+
+
+
+
+
+
+
1566 if (cmpstr(ba.ctrlName, "b_reply") == 0)
+
+
1568 ControlInfo /w=$ba.win sv_id
+
+
+
+
+
+
+
+
+
1577 result =
elog_create_entry (logbook, attributes, message, graphs=graphs, replyto=
id )
+
+
+
1580 svar /sdfr=df recent
+
+
1582 svar /sdfr=df recent_message
+
1583 recent_message = message
+
+
1585 abort "Submission failed. Error code " + num2str(result) + "."
+
+
+
1588 abort "Submission failed due to missing/invalid attribute."
+
+
+
+
+
+
+
+
+
+
+
1600 STRUCT WMButtonAction &ba
+
+
1602 switch( ba.eventCode )
+
+
1604 string graphs = WinName(0, 1, 1)
+
+
+
+
+
+
+
+
+
+
+
1616 STRUCT WMButtonAction &ba
+
+
1618 switch( ba.eventCode )
+
+
1620 string logbook = GetUserData(ba.win, "", "logbook")
+
+
1622 wave /sdfr=df_volatile attach_sel
+
1623 if (cmpstr(ba.ctrlName, "b_attach_all") == 0)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1637 STRUCT WMButtonAction &ba
+
+
1639 switch( ba.eventCode )
+
+
1641 string logbook = GetUserData(ba.win, "", "logbook")
+
+
+
+
+
1646 ControlInfo /w=$ba.win sv_id
+
+
+
+
1650 DoAlert /T="ELOG" 1, "This operation will replace all existing attachments. Do you want to continue?"
+
+
1652 if ((
id > 0) && (v_flag == 1))
+
+
+
+
1656 abort "Submission failed. Error code " + num2str(result) + "."
+
+
+
1659 abort "Submission failed due to missing/invalid attribute."
+
+
+
+
+
+
+
+
+
+
+
1670 STRUCT WMButtonAction &ba
+
+
1672 switch( ba.eventCode )
+
+
1674 string logbook = GetUserData(ba.win, "", "logbook")
+
+
1676 variable ngraphs = ItemsInList(graphs, ";")
+
+
+
+
+
1681 for (igraph = 0; igraph < ngraphs; igraph += 1)
+
1682 sgraph = StringFromList(igraph, graphs, ";")
+
+
1684 if (strlen(graph_path) > 0)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1698 STRUCT WMButtonAction &ba
+
+
1700 switch( ba.eventCode )
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1714 STRUCT WMButtonAction &ba
+
+
1716 switch( ba.eventCode )
+
+
1718 string logbook = GetUserData(ba.win, "", "logbook")
+
+
1720 Button b_login, win=$ba.win, disable=3
+
1721 Button b_logout, win=$ba.win, disable=0
+
+
+
+
+
+
+
+
+
+
+
1732 STRUCT WMButtonAction &ba
+
+
1734 switch( ba.eventCode )
+
+
1736 string logbook = GetUserData(ba.win, "", "logbook")
+
+
1738 Button b_login, win=$ba.win, disable=0
+
1739 Button b_logout, win=$ba.win, disable=3
+
+
+
+
+
+
+
+
+
+
+
1750 windowname = StringFromList(0, WinList("*ElogPanel*", ";", "WIN:64"), ";")
+
+
+
+
+
+
+
1764 if (strlen(windowname) == 0)
+
+
+
1767 if (strlen(windowname) == 0)
+
+
+
+
1771 string controls = ControlNameList(windowname, ";")
+
1772 string attributes = ""
+
+
+
+
1776 variable nco = ItemsInList(controls, ";")
+
1777 for (ico = 0; ico < nco; ico += 1)
+
1778 control = StringFromList(ico, controls, ";")
+
1779 attribute = GetUserData(windowname, control, "attribute")
+
1780 if (strlen(attribute) > 0)
+
1781 ControlInfo /w=$windowname $control
+
+
+
1784 attributes = ReplaceNumberByKey(attribute, attributes, v_value, "=", ";")
+
+
+
+
1788 attributes = ReplaceStringByKey(attribute, attributes, s_value, "=", ";")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1813 if (strlen(windowname) == 0)
+
+
+
1816 if (strlen(windowname) == 0)
+
+
+
1819 if (ParamIsDefault(clear))
+
+
+
+
+
+
1825 string logbook = GetUserData(windowname, "", "logbook")
+
+
1827 string persistent_path = GetDataFolder(1, df_persistent)
+
1828 svar /sdfr=df_persistent options
+
+
+
1831 string controls = ControlNameList(windowname, ";")
+
+
+
+
+
+
1837 variable nco = ItemsInList(controls, ";")
+
1838 for (ico = 0; ico < nco; ico += 1)
+
1839 control = StringFromList(ico, controls, ";")
+
1840 attribute = GetUserData(windowname, control, "attribute")
+
1841 if (strlen(attribute))
+
1842 value = StringByKey(attribute, attributes, "=", ";")
+
1843 if (strlen(value) || clear)
+
1844 ControlInfo /w=$windowname $control
+
+
+
1847 numval = NumberByKey(attribute, attributes, "=", ";")
+
1848 if ((numtype(numval) != 0) && clear)
+
+
+
1851 if (numtype(numval) == 0)
+
1852 CheckBox $control, value=numval, win=$windowname
+
+
+
+
1856 options_path = persistent_path + StringByKey(attribute, options, "=", ";")
+
1857 svar values = $options_path
+
1858 numval = WhichListItem(value, values, ";") + 1
+
+
1860 PopupMenu $control, mode=numval, win=$windowname
+
+
+
+
1864 SetVariable /z $control, value= _STR:value, win=$windowname
+
+
+
+
+
+
+
+
+
+
+
+
+
1884 if (strlen(windowname) == 0)
+
+
+
1887 if (strlen(windowname) == 0)
+
+
+
+
1891 string nb = windowname + "
#Message"
+
1892 notebook $nb selection={startOfFile, endOfFile}
+
1893 getselection notebook, $nb, 2
+
+
+
+
+
+
+
+
+
1911 if (strlen(windowname) == 0)
+
+
+
+
1915 string nb = windowname + "
#Message"
+
1916 notebook $nb selection={startOfFile, endOfFile},text=message
+
+
+
+
+
+
+
+
1930 dfref savedf = getdatafolderdfr()
+
1931 if (strlen(windowname) == 0)
+
+
+
1934 if (strlen(windowname) == 0)
+
+
+
+
1938 string logbook = GetUserData(windowname, "", "logbook")
+
+
1940 wave /t /sdfr=df_volatile attach_list
+
1941 wave /sdfr=df_volatile attach_sel
+
+
+
+
+
1946 variable n = DimSize(attach_sel, 0)
+
+
1948 for (i = 0; i < n; i += 1)
+
+
+
1951 windows = WinList(graphname, ";", "WIN:1")
+
1952 if (ItemsInList(windows) == 1)
+
1953 graphs = AddListItem(graphname, graphs, ";", inf)
+
+
+
+
+
+
+
+
+
+
+
+
1971 if (strlen(windowname) == 0)
+
+
+
1974 if (strlen(windowname) == 0)
+
+
+
+
1978 string logbook = GetUserData(windowname, "", "logbook")
+
+
+
1981 wave /t /sdfr=df_volatile attach_list
+
1982 wave /sdfr=df_volatile attach_sel
+
+
1984 variable n = DimSize(attach_sel, 0)
+
+
+
1987 for (i = 0; i < n; i += 1)
+
+
1989 if (WhichListItem(graphname, graphs)>= 0)
+
+
+
+
+
+
static variable IgorQuitHook(string igorApplicationNameStr)
save preferences and recent values before Igor quits.
static variable bp_login(WMButtonAction *ba)
static string get_log_path()
variable elog_login(string logbook, string username, string password)
set username and password for login to a logbook
static const variable kdfTemplates
static string list_logbooks(variable templates=defaultValue)
get a list of configured logbooks or templates.
static string get_panel_graphs(string windowname)
get the names of the graphs selected for attachment
static const string package_path
static variable bp_attach_top(WMButtonAction *ba)
select top graph window for attachment
static string create_graph_file(string graphname, variable fileindex)
save a graph to a temporary graphics file
static variable bp_attach(WMButtonAction *ba)
static variable bp_logout(WMButtonAction *ba)
static const variable kAttachColTitle
variable elog_init_pearl_templates()
setup PEARL template logbooks.
variable elog_add_attachment(string logbook, variable id, string graphs)
add one or more graphs to an existing ELOG entry
string PearlElogPanel(string logbook)
open a new panel for submitting data to ELOG.
static variable move_attach_item(string logbook, variable item, variable distance)
move an attachment item in the list of attachments
variable pearl_elog(string logbook)
main function to initialize ELOG and to open an ELOG panel.
static variable bp_clear(WMButtonAction *ba)
static variable elog_panel_hook(WMWinHookStruct *s)
interface for writing ELOG entries with Igor graphs as attachment.
static string get_panel_attributes(string windowname)
get a list of attributes from the fields of the ELOG panel.
static string get_timestamp(string sep)
static const string elog_success_msg
static variable bp_attach_updown(WMButtonAction *ba)
button procedure for the attachment up and down buttons
string elog_prompt_logbook()
prompt to open or create a logbook
static string set_panel_message(string windowname, string message)
set the message field of the ELOG panel
static const variable kdfPersistent
variable elog_create_entry(string logbook, string attributes, string message, variable encoding=defaultValue, string graphs=defaultValue, variable replyto=defaultValue)
create a new entry in ELOG
static string create_cmd_file(string cmd)
write the command line to a file.
static string create_message_file(string message)
save the message to a temporary text file
static variable bp_attach_allnone(WMButtonAction *ba)
select/deselect all graph windows for attachment
static const string package_name
static string prepare_graph_attachments(string graphs)
prepare screenshots of graph windows for attachments
static variable IgorBeforeNewHook(string igorApplicationNameStr)
save preferences and recent values before Igor opens a new experiment.
static const string elog_parse_id
static dfr get_elog_df(string name, variable category)
get the package, logbook, or template datafolder.
static variable parse_result()
parse the result file from an elog invokation.
variable elog_config(string elog_path=defaultValue, string hostname=defaultValue, variable port=defaultValue, string subdir=defaultValue)
set global module configuration parameters
variable elog_create_logbook(string name, string template=defaultValue)
create a new logbook.
static string prepare_command_line(string logbook)
format the ELOG command and essential address arguments.
static string set_panel_graphs(string windowname, string graphs)
update selection of graphs for attachment
variable elog_prompt_login(string logbook)
prompt the user for login to a logbook
static variable cleanup_temp_files()
delete temporary files created by the ELOG module.
static variable save_prefs()
save persistent package data to the preferences file.
static variable update_attach_items(string logbook)
update the list of attachments
static const variable kdfVolatile
static const variable kAttachColSel
static variable bp_save_graphs(WMButtonAction *ba)
static string get_panel_message(string windowname)
get the message field of the ELOG panel
variable elog_logout(string logbook)
clear username and password of a logbook or all logbooks.
static variable init_volatile_vars()
initialize volatile variables.
static string format_url(string logbook)
format the URL for display to the user
static const variable kAttachColName
static variable bp_submit(WMButtonAction *ba)
button procedure for the Submit and Reply buttons
static const variable kdfRoot
variable elog_validate_attributes(string logbook, string attributes)
validate attributes
static variable load_prefs()
load persistent package data from the preferences file.
static string get_default_panel_name()
static variable AfterFileOpenHook(variable refNum, string file, string pathName, string type, string creator, variable kind)
initialize the package and reload preferences after an experiment is loaded.
static variable init_package(variable clean=defaultValue)
initialize the package data folder.
static string set_panel_attributes(string windowname, string attributes, variable clear=defaultValue)
set the fields of the ELOG panel
PEARL Procedures: pearl-fitfuncs.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -110,23 +112,29 @@ Namespaces
threadsafe variable MultiGaussLinBG (wave w, variable x) multiple gaussian peaks on a linear background fit function. More... multiple gaussian peaks on a linear background fit function. More... threadsafe variable MultiGaussLinBG_AO (wave pw, wave yw, wave xw) multiple gaussian peaks on a linear background fit function (all at once). More... multiple gaussian peaks on a linear background fit function (all at once). More... threadsafe variable DoubletGaussLinBG_AO (wave pw, wave yw, wave xw) doublet gaussian peaks on a linear background fit function (all at once). More... doublet gaussian peaks on a linear background fit function (all at once). More... variable MultiVoigtLinBG (wave w, variable x) multiple voigt peaks on a linear background fit function. More... threadsafe variable DblDoubletGaussLinBG_AO (wave pw, wave yw, wave xw) two doublet gaussian peaks on a linear background fit function (all at once). More... threadsafe variable MultiVoigtLinBG (wave w, variable x) multiple voigt peaks on a linear background fit function. More... threadsafe variable MultiVoigtLinBG_AO (wave pw, wave yw, wave xw) multiple voigt peaks on a linear background fit function. More... threadsafe variable DoniachSunjic (variable x, variable amp, variable pos, variable sing, variable fwhm) Doniach-Sunjic line shape. More... Doniach-Sunjic line shape. More... variable MultiDoniachSunjicLinBG (wave w, variable x) multiple doniach-sunjic peaks on a linear background fit function. More... threadsafe variable MultiDoniachSunjicLinBG (wave w, variable x) multiple doniach-sunjic peaks on a linear background fit function. More... threadsafe variable ds1_bg (wave w, variable x) threadsafe variable ds2_bg (wave w, variable x)variable ShowComponents_Au4f_2p3 (wave coef_wave, wave fit_wave) variable FermiGaussConv (wave pw, wave yw, wave xw) convolution of Fermi-Dirac distribution and a Gaussian. More... convolution of Fermi-Dirac distribution and a Gaussian. More... variable ShirleyBG (wave w, wave bg, variable p1, variable p2) calculate the shirley background More... calculate the shirley background More... various fit functions for photoelectron spectroscopy.
this procedure contains various functions for curve fitting.
Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
-
Copyright 2013-18 Paul Scherrer Institut Copyright 2013-18 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-fitfuncs.ipf .
@@ -197,7 +205,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); ◆
+
+
+
+ threadsafe variable DblDoubletGaussLinBG_AO
+ (
+ wave
+ pw ,
+
+ wave
+ yw ,
+
+ wave
+ xw
+
+ )
+
+
+
+
+
two doublet gaussian peaks on a linear background fit function (all at once).
+
this fits four gaussian peaks. peak positions are specified by center, splitting and shift rather than individually. amplitudes are specified as absolute values for peaks 1 and 3, and relative values for peaks 2 and 4.
+
can be used if a spin-orbit doublet is split by a chemical shift which affects both spin-orbit peaks equally.
+
Note FWHM = width * 2 * sqrt(ln(2)) = width * 1.665
+
Parameters
+
+ pw shape parameters.
+pw[0] = constant coefficient of background
+pw[1] = linear coefficient of background
+pw[2] = amplitude of peak 1
+pw[3] = amplitude of peak 2
+pw[4] = amplitude of peak 3, relative to peak 1
+pw[5] = amplitude of peak 4, relative to peak 2
+pw[6] = position of peak 1
+pw[7] = splitting (distance between peaks 1 and 3)
+pw[8] = shift (distance between peaks 1 and 2)
+pw[9] = width of peaks 1 and 3
+pw[10] = width of peaks 2 and 4
+
+ yw y (dependent) values. xw x (independent) independent values.
+
+
+
+
Definition at line 157 of file pearl-fitfuncs.ipf .
Definition at line 174 of file pearl-fitfuncs.ipf .
+Definition at line 253 of file pearl-fitfuncs.ipf .
@@ -384,7 +454,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 117 of file pearl-fitfuncs.ipf .
+Definition at line 118 of file pearl-fitfuncs.ipf .
@@ -492,7 +562,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); pw[5] = gaussian width = FWHM / 1.66511
-Definition at line 851 of file pearl-fitfuncs.ipf .
+Definition at line 930 of file pearl-fitfuncs.ipf .
@@ -670,18 +740,18 @@ Licensed under the Apache License, Version 2.0 (the "License"); ◆ ◆
- variable MultiDoniachSunjicLinBG
+ threadsafe variable MultiDoniachSunjicLinBG
(
wave
w , Definition at line 201 of file pearl-fitfuncs.ipf .
+Definition at line 280 of file pearl-fitfuncs.ipf .
@@ -764,7 +834,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 44 of file pearl-fitfuncs.ipf .
+Definition at line 45 of file pearl-fitfuncs.ipf .
@@ -819,18 +889,18 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 79 of file pearl-fitfuncs.ipf .
+Definition at line 80 of file pearl-fitfuncs.ipf .
-◆ ◆
- variable MultiVoigtLinBG
+ threadsafe variable MultiVoigtLinBG
(
wave
w , Definition at line 144 of file pearl-fitfuncs.ipf .
+Definition at line 190 of file pearl-fitfuncs.ipf .
+
+
+
+◆
+
+
+
+ threadsafe variable MultiVoigtLinBG_AO
+ (
+ wave
+ pw ,
+
+ wave
+ yw ,
+
+ wave
+ xw
+
+ )
+
+
+
+
+
multiple voigt peaks on a linear background fit function.
+
this is the all-at-once version of MultiVoigtLinBG . it runs slightly faster compared to the point-by-point function.
+
Parameters
+
+ pw shape parameters. the length of the wave defines the number of peaks.
+pw[0] = constant coefficient of background
+pw[1] = linear coefficient of background
+pw[2 + (i-1) * 4] = amplitude of peak i
+pw[3 + (i-1) * 4] = position of peak i
+pw[4 + (i-1) * 4] = width of peak i
+pw[5 + (i-1) * 4] = shape of peak i
+
+ yw y (dependent) values. xw x (independent) independent values.
+
+
+
+
Definition at line 224 of file pearl-fitfuncs.ipf .
calculate the shirley background
-Definition at line 901 of file pearl-fitfuncs.ipf .
+Definition at line 980 of file pearl-fitfuncs.ipf .
@@ -940,7 +1065,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
@@ -970,7 +1095,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
@@ -980,9 +1105,9 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-fitfuncs.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,37 +87,863 @@ $(document).ready(function(){initNavTree('pearl-fitfuncs_8ipf_source.html','');}
pearl-fitfuncs.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.2 3 #pragma ModuleName = PearlFitFuncs 5 #include "mm-physconst" 48 variable np = numpnts(w)
51 variable v = w[0] + x * w[1]
52 for (ip = 2; ip < np; ip += 3)
53 v += w[ip] * exp( -( (x - w[ip+1]) / w[ip+2] )^2 )
84 variable np = numpnts(pw)
87 yw = pw[0] + xw[p] * pw[1]
88 for (ip = 2; ip < np; ip += 3)
89 yw += pw[ip] * exp( -( (xw[p] - pw[ip+1]) / pw[ip+2] )^2 )
122 yw = pw[0] + xw[p] * pw[1]
123 yw += pw[2] * exp( -( (xw[p] - pw[4] - pw[5] /2) / pw[6] )^2 )
124 yw += pw[2] * pw[3] * exp( -( (xw[p] - pw[4] + pw[5] /2) / pw[6] / pw[7] )^2 )
148 variable np = numpnts(w)
151 variable v = w[0] + x * w[1]
152 for (ip = 2; ip < np; ip += 4)
153 v += w[ip] * VoigtFunc((x - w[ip+1]) / w[ip+2], w[ip+3])
182 nom = cos(pi * sing / 2 + (1 - sing) * atan((x - pos) / fwhm * 2))
183 denom = ((x - pos)^2 + fwhm^2 / 4)^((1 - sing) / 2)
185 return amp * nom / denom * fwhm / 2
205 variable np = numpnts(w)
208 variable v = w[0] + x * w[1]
209 for (ip = 2; ip < np; ip += 4)
217 threadsafe function
ds1_bg (w, x): FitFunc
240 threadsafe function
ds2_bg (w,x) : FitFunc
265 return w[0] + ds1 + ds2
297 Variable ds1, ds2, ds3, ds4
298 ds1=( w[1]*cos(pi*w[3]/2+(1-w[3])*atan((x-w[2])/w[4])))/(((x-w[2])^2+w[4]^2)^((1-w[3])/2))
299 ds2=( w[5]*cos(pi*w[7]/2+(1-w[7])*atan((x-w[6])/w[8])))/(((x-w[6])^2+w[8]^2)^((1-w[7])/2))
300 ds3=( w[9]*cos(pi*w[11]/2+(1-w[11])*atan((x-w[10])/w[12])))/(((x-w[10])^2+w[12]^2)^((1-w[11])/2))
301 ds4=( w[13]*cos(pi*w[15]/2+(1-w[15])*atan((x-w[14])/w[16])))/(((x-w[14])^2+w[16]^2)^((1-w[15])/2))
304 return w[0]+ds1+ds2+ds3+ds4
358 Variable ds1, ds2, ds3, ds4, ds5, ds6
359 ds1=( w[1]*cos(pi*w[3]/2+(1-w[3])*atan((x-w[2])/w[4])))/(((x-w[2])^2+w[4]^2)^((1-w[3])/2))
360 ds2=( w[5]*cos(pi*w[7]/2+(1-w[7])*atan((x-w[6])/w[8])))/(((x-w[6])^2+w[8]^2)^((1-w[7])/2))
361 ds3=( w[9]*cos(pi*w[11]/2+(1-w[11])*atan((x-w[10])/w[12])))/(((x-w[10])^2+w[12]^2)^((1-w[11])/2))
362 ds4=( w[13]*cos(pi*w[15]/2+(1-w[15])*atan((x-w[14])/w[16])))/(((x-w[14])^2+w[16]^2)^((1-w[15])/2))
363 ds5=( w[17]*cos(pi*w[19]/2+(1-w[19])*atan((x-w[18])/w[20])))/(((x-w[18])^2+w[20]^2)^((1-w[19])/2))
364 ds6=( w[21]*cos(pi*w[23]/2+(1-w[23])*atan((x-w[22])/w[24])))/(((x-w[22])^2+w[24]^2)^((1-w[23])/2))
366 return w[0]+ds1+ds2+ds3+ds4+ds5+ds6
380 variable oversampling
422 variable precision = s.precision
423 variable oversampling = s.oversampling
425 if (WaveExists(s.xdw))
428 wave broadening = s.broadening
429 wave convolution = s.convolution
431 make /n=0 /free xdw, model, broadening, convolution
432 redimension /d xdw, model, broadening, convolution
434 wave fs.model = model
435 wave fs.broadening = broadening
436 wave fs.convolution = convolution
440 differentiate /p xw /d=xdw
442 variable xd = wavemin(xdw) / oversampling
445 variable x0b = pw[6] * precision
446 variable nb = 2 * floor(x0b / xd) + 1
449 variable x0m = max(abs(wavemax(xw) - pw[1]), abs(wavemin(xw) - pw[1])) + x0b
450 variable nm = 2 * floor(x0m / xd) + 1
451 nb = min(nb, nm * 10)
454 redimension /n=(nb) broadening
455 redimension /n=(nm) model
456 setscale/i x -x0b, x0b, "", broadening
457 setscale/i x -x0m, x0m, "", model
459 broadening = exp( - (x / pw[6])^2 * 4 * ln(2))
460 variable nrm = area(broadening)
466 Convolve /a broadening, model
467 variable scale = pw[0] / wavemax(model)
472 x0m = xd * (nm - 1) / 2
473 setscale/i x -x0m, x0m, "", model
475 yw = model(xw[p] - pw[1]) + pw[7] + pw[8] * xw[p]
476 yw = numtype(yw) ? 0 : yw
512 dfref df = root:packages:pearl_fitfuncs:doniach_sunjic
513 if (DataFolderRefStatus(df) == 0)
514 newdatafolder root:packages:pearl_fitfuncs:doniach_sunjic
515 dfref df = root:packages:pearl_fitfuncs:doniach_sunjic
518 wave /z /sdfr=df fs.xdw = xdw
519 wave /z /sdfr=df fs.model = model
520 wave /z /sdfr=df fs.broadening = broadening
521 wave /z /sdfr=df fs.convolution = convolution
523 if (WaveExists(fs.xdw) == 0)
524 dfref savedf = GetDataFolderDFR()
526 make /n=0 /d xdw, model, broadening, convolution
528 wave fs.model = model
529 wave fs.broadening = broadening
530 wave fs.convolution = convolution
551 duplicate /free pw, fs.pw
552 duplicate /free yw, fs.xw
554 duplicate /free yw, fs.yw
576 duplicate /free pw, fs.pw
578 duplicate /free xw, fs.xw
580 duplicate /free yw, fs.xw
583 duplicate /free yw, fs.yw
585 variable v_chisq = nan
586 variable V_FitMaxIters = 100
587 make /n=1 /t /free constraints = {
"K0 >= 0" ,
"K2 > 0" ,
"K2 < 10" ,
"K3 >= 0" ,
"K3 < 1" ,
"K4 >= -10" ,
"K4 <= 10" ,
"K5 >= 0" ,
"K5 <= 1" ,
"K6 >= 0" ,
"K6 < 10" }
589 FuncFit /NTHR=1
DoniachSunjicBroadS , pw, yw /X=xw /D /STRC=fs /C=constraints /NWOK /I=1 /W=ww
618 variable np = numpnts(w)
630 variable vc1, vc2, vc3, vc4
631 vc2 = 2 * sqrt(ln(2)) / w[ip0-1]
632 for (ip = ip0; ip < np; ip += 3)
633 vc1 = w[ip] / sqrt(pi) * vc2
635 vc4 = vc2 * w[ip+2] / 2
636 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
660 variable bg = w[0] + w[1] * x
667 vc2 = 2 * sqrt(ln(2)) / w[2]
670 vc1 = w[3] / sqrt(pi) * vc2
673 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
676 vc1 = w[3] / sqrt(pi) * vc2 * w[9]
679 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
682 vc1 = w[6] / sqrt(pi) * vc2
685 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
688 vc1 = w[6] / sqrt(pi) * vc2 * w[9]
691 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
701 duplicate /free coef_wave, coef1, coef2
703 coef2[3] *= coef_wave[9]
704 coef2[4] += coef_wave[10]
705 coef2[6] *= coef_wave[9]
706 coef2[7] += coef_wave[10]
709 string s_fit_wave = NameOfWave(fit_wave)
710 string s_fit_p1 = s_fit_wave +
"_p1" 711 string s_fit_p2 = s_fit_wave +
"_p2" 712 duplicate /o fit_wave, $(s_fit_p1) /wave=fit_p1
713 duplicate /o fit_wave, $(s_fit_p2) /wave=fit_p2
718 string traces = TraceNameList(
"" ,
";" , 1)
719 if ((WhichListItem(s_fit_wave, traces,
";" ) >= 0) && (WhichListItem(s_fit_p1, traces,
";" ) < 0))
720 appendtograph fit_p1, fit_p2
721 ModifyGraph lstyle($s_fit_p1)=2
722 ModifyGraph lstyle($s_fit_p2)=2
723 ModifyGraph rgb($s_fit_p1)=(0,0,65280)
724 ModifyGraph rgb($s_fit_p2)=(0,0,65280)
747 variable bg = w[0] + w[1] * x
754 vc2 = 2 * sqrt(ln(2)) / w[2]
757 vc1 = w[3] / sqrt(pi) * vc2
760 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
763 vc1 = w[3] / sqrt(pi) * vc2 * w[9]
766 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
769 vc1 = w[3] / sqrt(pi) * vc2 * w[11]
772 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
775 vc1 = w[6] / sqrt(pi) * vc2
778 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
781 vc1 = w[6] / sqrt(pi) * vc2 * w[9]
784 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
787 vc1 = w[6] / sqrt(pi) * vc2 * w[11]
790 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
800 duplicate /free coef_wave, coef1, coef2, coef3
804 coef2[3] *= coef_wave[9]
805 coef2[4] += coef_wave[10]
806 coef2[6] *= coef_wave[9]
807 coef2[7] += coef_wave[10]
811 coef3[3] *= coef_wave[11]
812 coef3[4] += coef_wave[12]
813 coef3[6] *= coef_wave[11]
814 coef3[7] += coef_wave[12]
818 string s_fit_wave = NameOfWave(fit_wave)
819 string s_fit_p1 = s_fit_wave +
"_p1" 820 string s_fit_p2 = s_fit_wave +
"_p2" 821 string s_fit_p3 = s_fit_wave +
"_p3" 822 duplicate /o fit_wave, $(s_fit_p1) /wave=fit_p1
823 duplicate /o fit_wave, $(s_fit_p2) /wave=fit_p2
824 duplicate /o fit_wave, $(s_fit_p3) /wave=fit_p3
830 string traces = TraceNameList(
"" ,
";" , 1)
831 if ((WhichListItem(s_fit_wave, traces,
";" ) >= 0) && (WhichListItem(s_fit_p1, traces,
";" ) < 0))
832 appendtograph fit_p1, fit_p2, fit_p3
833 ModifyGraph lstyle($s_fit_p1)=2
834 ModifyGraph lstyle($s_fit_p2)=2
835 ModifyGraph lstyle($s_fit_p3)=2
836 ModifyGraph rgb($s_fit_p1)=(0,0,65280)
837 ModifyGraph rgb($s_fit_p2)=(0,0,65280)
838 ModifyGraph rgb($s_fit_p3)=(0,0,65280)
855 variable precision_g = 5
856 variable oversampling = 4
859 duplicate /free xw, xdw
860 differentiate /p xw /d=xdw
862 variable xd = wavemin(xdw) / oversampling
865 variable x0g = abs(pw[5]) * precision_g
866 variable ng = 2 * floor(x0g / xd) + 1
869 variable emax = wavemax(xw)
870 variable emin = wavemin(xw)
871 variable x0f = max(abs(emax - pw[3]), abs(emin - pw[3])) + x0g
872 variable ne = 2 * floor(x0f / xd) + 1
875 make /d /n=(ng) /free gausswave
876 make /d /n=(ne) /free fermiwave
877 setscale/i x -x0g, x0g,
"" , gausswave
878 setscale/i x -x0f, x0f,
"" , fermiwave
880 gausswave = exp( - (x / pw[5] )^2 )
881 fermiwave = 1 / (exp( x / (kBoltzmann * pw[4])) + 1.0 )
884 duplicate /free fermiwave, resultwave
885 Convolve /a gausswave, resultwave
886 variable rmax = wavemax(resultwave)
890 ng = numpnts(resultwave)
891 x0g = xd * (ng - 1) / 2
892 setscale/i x -x0g, x0g,
"" , resultwave
894 yw = pw[2] * resultwave(xw[p] - pw[3]) + pw[0] + pw[1] * xw[p]
907 integrate /meth=1 w /d=bg
909 variable bg1 = bg[p1]
910 variable bg2 = bg[p2]
threadsafe variable MultiGaussLinBG(wave w, variable x)
multiple gaussian peaks on a linear background fit function.
-
threadsafe variable DoubletGaussLinBG_AO(wave pw, wave yw, wave xw)
doublet gaussian peaks on a linear background fit function (all at once).
-
variable DoniachSunjicBroad(wave pw, wave yw, wave xw)
-
threadsafe variable MultiGaussLinBG_AO(wave pw, wave yw, wave xw)
multiple gaussian peaks on a linear background fit function (all at once).
-
variable ds4_bg(wave w, variable x)
-
-
variable FermiGaussConv(wave pw, wave yw, wave xw)
convolution of Fermi-Dirac distribution and a Gaussian.
-
threadsafe variable DoniachSunjicBroadS(DoniachSunjicStruct *s)
-
threadsafe variable DoniachSunjic(variable x, variable amp, variable pos, variable sing, variable fwhm)
Doniach-Sunjic line shape.
-
variable Au4f(wave w, variable x)
-
variable Au4f_2p3(wave w, variable x)
-
variable Au4f_2p2(wave w, variable x)
-
variable ShowComponents_Au4f_2p2(wave coef_wave, wave fit_wave)
-
variable Calc_DoniachSunjicBroad(wave pw, wave yw)
-
variable ShowComponents_Au4f_2p3(wave coef_wave, wave fit_wave)
-
variable Fit_DoniachSunjicBroad(wave pw, wave yw, wave xw, wave ww)
-
threadsafe variable ds2_bg(wave w, variable x)
-
variable ds6_bg(wave w, variable x)
-
variable ShirleyBG(wave w, wave bg, variable p1, variable p2)
calculate the shirley background
-
variable MultiDoniachSunjicLinBG(wave w, variable x)
multiple doniach-sunjic peaks on a linear background fit function.
-
threadsafe variable ds1_bg(wave w, variable x)
-
variable MultiVoigtLinBG(wave w, variable x)
multiple voigt peaks on a linear background fit function.
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.2
+
4 #pragma ModuleName = PearlFitFuncs
+
+
6 #include "mm-physconst"
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49 variable np = numpnts(w)
+
+
+
52 variable v = w[0] + x * w[1]
+
53 for (ip = 2; ip < np; ip += 3)
+
54 v += w[ip] * exp( -( (x - w[ip+1]) / w[ip+2] )^2 )
+
+
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+
85 variable np = numpnts(pw)
+
+
+
88 yw = pw[0] + xw[p] * pw[1]
+
89 for (ip = 2; ip < np; ip += 3)
+
90 yw += pw[ip] * exp( -( (xw[p] - pw[ip+1]) / pw[ip+2] )^2 )
+
+
+
+
+
+
+
+
+
123 yw = pw[0] + xw[p] * pw[1]
+
124 yw += pw[2] * exp( -( (xw[p] - pw[4] - pw[5] /2) / pw[6] )^2 )
+
125 yw += pw[2] * pw[3] * exp( -( (xw[p] - pw[4] + pw[5] /2) / pw[6] / pw[7] )^2 )
+
+
+
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162 yw = pw[0] + xw[p] * pw[1]
+
+
164 yw += pw[2] * exp( -( (xw[p] - pw[6]) / pw[9] )^2 )
+
+
166 yw += pw[3] * exp( -( (xw[p] - pw[6] - pw[8]) / pw[10] )^2 )
+
+
168 yw += pw[2] * pw[4] * exp( -( (xw[p] - pw[6] - pw[7]) / pw[9] )^2 )
+
+
170 yw += pw[3] * pw[5] * exp( -( (xw[p] - pw[6] - pw[7] - pw[8]) / pw[10] )^2 )
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194 variable np = numpnts(w)
+
+
+
197 variable v = w[0] + x * w[1]
+
198 for (ip = 2; ip < np; ip += 4)
+
199 v += w[ip] * VoigtFunc((x - w[ip+1]) / w[ip+2], w[ip+3])
+
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+
229 variable np = numpnts(pw)
+
+
+
232 yw = pw[0] + xw[p] * pw[1]
+
233 for (ip = 2; ip < np; ip += 4)
+
234 yw += pw[ip] * VoigtFunc((xw[p] - pw[ip+1]) / pw[ip+2], pw[ip+3])
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261 nom = cos(pi * sing / 2 + (1 - sing) * atan((x - pos) / fwhm * 2))
+
262 denom = ((x - pos)^2 + fwhm^2 / 4)^((1 - sing) / 2)
+
+
264 return amp * nom / denom * fwhm / 2
+
+
+
+
+
+
+
284 variable np = numpnts(w)
+
+
+
287 variable v = w[0] + x * w[1]
+
288 for (ip = 2; ip < np; ip += 4)
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296 threadsafe function
ds1_bg (w, x): FitFunc
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319 threadsafe function
ds2_bg (w,x) : FitFunc
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344 return w[0] + ds1 + ds2
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376 Variable ds1, ds2, ds3, ds4
+
377 ds1=( w[1]*cos(pi*w[3]/2+(1-w[3])*atan((x-w[2])/w[4])))/(((x-w[2])^2+w[4]^2)^((1-w[3])/2))
+
378 ds2=( w[5]*cos(pi*w[7]/2+(1-w[7])*atan((x-w[6])/w[8])))/(((x-w[6])^2+w[8]^2)^((1-w[7])/2))
+
379 ds3=( w[9]*cos(pi*w[11]/2+(1-w[11])*atan((x-w[10])/w[12])))/(((x-w[10])^2+w[12]^2)^((1-w[11])/2))
+
380 ds4=( w[13]*cos(pi*w[15]/2+(1-w[15])*atan((x-w[14])/w[16])))/(((x-w[14])^2+w[16]^2)^((1-w[15])/2))
+
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383 return w[0]+ds1+ds2+ds3+ds4
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437 Variable ds1, ds2, ds3, ds4, ds5, ds6
+
438 ds1=( w[1]*cos(pi*w[3]/2+(1-w[3])*atan((x-w[2])/w[4])))/(((x-w[2])^2+w[4]^2)^((1-w[3])/2))
+
439 ds2=( w[5]*cos(pi*w[7]/2+(1-w[7])*atan((x-w[6])/w[8])))/(((x-w[6])^2+w[8]^2)^((1-w[7])/2))
+
440 ds3=( w[9]*cos(pi*w[11]/2+(1-w[11])*atan((x-w[10])/w[12])))/(((x-w[10])^2+w[12]^2)^((1-w[11])/2))
+
441 ds4=( w[13]*cos(pi*w[15]/2+(1-w[15])*atan((x-w[14])/w[16])))/(((x-w[14])^2+w[16]^2)^((1-w[15])/2))
+
442 ds5=( w[17]*cos(pi*w[19]/2+(1-w[19])*atan((x-w[18])/w[20])))/(((x-w[18])^2+w[20]^2)^((1-w[19])/2))
+
443 ds6=( w[21]*cos(pi*w[23]/2+(1-w[23])*atan((x-w[22])/w[24])))/(((x-w[22])^2+w[24]^2)^((1-w[23])/2))
+
+
445 return w[0]+ds1+ds2+ds3+ds4+ds5+ds6
+
+
+
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+
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+
+
459 variable oversampling
+
+
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501 variable precision = s.precision
+
502 variable oversampling = s.oversampling
+
+
504 if (WaveExists(s.xdw))
+
+
+
507 wave broadening = s.broadening
+
508 wave convolution = s.convolution
+
+
510 make /n=0 /free xdw, model, broadening, convolution
+
511 redimension /d xdw, model, broadening, convolution
+
+
513 wave fs.model = model
+
514 wave fs.broadening = broadening
+
515 wave fs.convolution = convolution
+
+
+
+
519 differentiate /p xw /d=xdw
+
+
521 variable xd = wavemin(xdw) / oversampling
+
+
+
524 variable x0b = pw[6] * precision
+
525 variable nb = 2 * floor(x0b / xd) + 1
+
+
+
528 variable x0m = max(abs(wavemax(xw) - pw[1]), abs(wavemin(xw) - pw[1])) + x0b
+
529 variable nm = 2 * floor(x0m / xd) + 1
+
530 nb = min(nb, nm * 10)
+
+
+
533 redimension /n=(nb) broadening
+
534 redimension /n=(nm) model
+
535 setscale/i x -x0b, x0b, "", broadening
+
536 setscale/i x -x0m, x0m, "", model
+
+
538 broadening = exp( - (x / pw[6])^2 * 4 * ln(2))
+
539 variable nrm = area(broadening)
+
+
+
+
+
+
545 Convolve /a broadening, model
+
546 variable scale = pw[0] / wavemax(model)
+
+
+
+
+
551 x0m = xd * (nm - 1) / 2
+
552 setscale/i x -x0m, x0m, "", model
+
+
554 yw = model(xw[p] - pw[1]) + pw[7] + pw[8] * xw[p]
+
555 yw = numtype(yw) ? 0 : yw
+
+
+
+
+
+
+
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+
591 dfref df = root:packages:pearl_fitfuncs:doniach_sunjic
+
592 if (DataFolderRefStatus(df) == 0)
+
593 newdatafolder root:packages:pearl_fitfuncs:doniach_sunjic
+
594 dfref df = root:packages:pearl_fitfuncs:doniach_sunjic
+
+
+
597 wave /z /sdfr=df fs.xdw = xdw
+
598 wave /z /sdfr=df fs.model = model
+
599 wave /z /sdfr=df fs.broadening = broadening
+
600 wave /z /sdfr=df fs.convolution = convolution
+
+
602 if (WaveExists(fs.xdw) == 0)
+
603 dfref savedf = GetDataFolderDFR()
+
+
605 make /n=0 /d xdw, model, broadening, convolution
+
+
607 wave fs.model = model
+
608 wave fs.broadening = broadening
+
609 wave fs.convolution = convolution
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
630 duplicate /free pw, fs.pw
+
631 duplicate /free yw, fs.xw
+
+
633 duplicate /free yw, fs.yw
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+
+
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+
+
655 duplicate /free pw, fs.pw
+
+
657 duplicate /free xw, fs.xw
+
+
659 duplicate /free yw, fs.xw
+
+
+
662 duplicate /free yw, fs.yw
+
+
664 variable v_chisq = nan
+
665 variable V_FitMaxIters = 100
+
666 make /n=1 /t /free constraints = {
"K0 >= 0" ,
"K2 > 0" ,
"K2 < 10" ,
"K3 >= 0" ,
"K3 < 1" ,
"K4 >= -10" ,
"K4 <= 10" ,
"K5 >= 0" ,
"K5 <= 1" ,
"K6 >= 0" ,
"K6 < 10" }
+
+
668 FuncFit /NTHR=1
DoniachSunjicBroadS , pw, yw /X=xw /D /STRC=fs /C=constraints /NWOK /I=1 /W=ww
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
697 variable np = numpnts(w)
+
+
+
+
+
+
+
+
+
+
+
+
709 variable vc1, vc2, vc3, vc4
+
710 vc2 = 2 * sqrt(ln(2)) / w[ip0-1]
+
711 for (ip = ip0; ip < np; ip += 3)
+
712 vc1 = w[ip] / sqrt(pi) * vc2
+
+
714 vc4 = vc2 * w[ip+2] / 2
+
715 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
739 variable bg = w[0] + w[1] * x
+
+
+
+
+
+
+
746 vc2 = 2 * sqrt(ln(2)) / w[2]
+
+
+
749 vc1 = w[3] / sqrt(pi) * vc2
+
+
+
752 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
755 vc1 = w[3] / sqrt(pi) * vc2 * w[9]
+
+
+
758 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
761 vc1 = w[6] / sqrt(pi) * vc2
+
+
+
764 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
767 vc1 = w[6] / sqrt(pi) * vc2 * w[9]
+
+
+
770 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
+
+
+
+
+
+
+
780 duplicate /free coef_wave, coef1, coef2
+
+
782 coef2[3] *= coef_wave[9]
+
783 coef2[4] += coef_wave[10]
+
784 coef2[6] *= coef_wave[9]
+
785 coef2[7] += coef_wave[10]
+
+
+
788 string s_fit_wave = NameOfWave(fit_wave)
+
789 string s_fit_p1 = s_fit_wave +
"_p1"
+
790 string s_fit_p2 = s_fit_wave +
"_p2"
+
791 duplicate /o fit_wave, $(s_fit_p1) /wave=fit_p1
+
792 duplicate /o fit_wave, $(s_fit_p2) /wave=fit_p2
+
+
+
+
+
797 string traces = TraceNameList(
"" ,
";" , 1)
+
798 if ((WhichListItem(s_fit_wave, traces,
";" ) >= 0) && (WhichListItem(s_fit_p1, traces,
";" ) < 0))
+
799 appendtograph fit_p1, fit_p2
+
800 ModifyGraph lstyle($s_fit_p1)=2
+
801 ModifyGraph lstyle($s_fit_p2)=2
+
802 ModifyGraph rgb($s_fit_p1)=(0,0,65280)
+
803 ModifyGraph rgb($s_fit_p2)=(0,0,65280)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
826 variable bg = w[0] + w[1] * x
+
+
+
+
+
+
+
833 vc2 = 2 * sqrt(ln(2)) / w[2]
+
+
+
836 vc1 = w[3] / sqrt(pi) * vc2
+
+
+
839 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
842 vc1 = w[3] / sqrt(pi) * vc2 * w[9]
+
+
+
845 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
848 vc1 = w[3] / sqrt(pi) * vc2 * w[11]
+
+
+
851 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
854 vc1 = w[6] / sqrt(pi) * vc2
+
+
+
857 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
860 vc1 = w[6] / sqrt(pi) * vc2 * w[9]
+
+
+
863 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
866 vc1 = w[6] / sqrt(pi) * vc2 * w[11]
+
+
+
869 v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
+
+
+
+
+
+
+
+
+
+
879 duplicate /free coef_wave, coef1, coef2, coef3
+
+
+
+
883 coef2[3] *= coef_wave[9]
+
884 coef2[4] += coef_wave[10]
+
885 coef2[6] *= coef_wave[9]
+
886 coef2[7] += coef_wave[10]
+
+
+
+
890 coef3[3] *= coef_wave[11]
+
891 coef3[4] += coef_wave[12]
+
892 coef3[6] *= coef_wave[11]
+
893 coef3[7] += coef_wave[12]
+
+
+
+
897 string s_fit_wave = NameOfWave(fit_wave)
+
898 string s_fit_p1 = s_fit_wave +
"_p1"
+
899 string s_fit_p2 = s_fit_wave +
"_p2"
+
900 string s_fit_p3 = s_fit_wave +
"_p3"
+
901 duplicate /o fit_wave, $(s_fit_p1) /wave=fit_p1
+
902 duplicate /o fit_wave, $(s_fit_p2) /wave=fit_p2
+
903 duplicate /o fit_wave, $(s_fit_p3) /wave=fit_p3
+
+
+
+
+
+
909 string traces = TraceNameList(
"" ,
";" , 1)
+
910 if ((WhichListItem(s_fit_wave, traces,
";" ) >= 0) && (WhichListItem(s_fit_p1, traces,
";" ) < 0))
+
911 appendtograph fit_p1, fit_p2, fit_p3
+
912 ModifyGraph lstyle($s_fit_p1)=2
+
913 ModifyGraph lstyle($s_fit_p2)=2
+
914 ModifyGraph lstyle($s_fit_p3)=2
+
915 ModifyGraph rgb($s_fit_p1)=(0,0,65280)
+
916 ModifyGraph rgb($s_fit_p2)=(0,0,65280)
+
917 ModifyGraph rgb($s_fit_p3)=(0,0,65280)
+
+
+
+
+
+
+
+
934 variable precision_g = 5
+
935 variable oversampling = 4
+
+
+
938 duplicate /free xw, xdw
+
939 differentiate /p xw /d=xdw
+
+
941 variable xd = wavemin(xdw) / oversampling
+
+
+
944 variable x0g = abs(pw[5]) * precision_g
+
945 variable ng = 2 * floor(x0g / xd) + 1
+
+
+
948 variable emax = wavemax(xw)
+
949 variable emin = wavemin(xw)
+
950 variable x0f = max(abs(emax - pw[3]), abs(emin - pw[3])) + x0g
+
951 variable ne = 2 * floor(x0f / xd) + 1
+
+
+
954 make /d /n=(ng) /free gausswave
+
955 make /d /n=(ne) /free fermiwave
+
956 setscale/i x -x0g, x0g,
"" , gausswave
+
957 setscale/i x -x0f, x0f,
"" , fermiwave
+
+
959 gausswave = exp( - (x / pw[5] )^2 )
+
960 fermiwave = 1 / (exp( x / (kBoltzmann * pw[4])) + 1.0 )
+
+
+
963 duplicate /free fermiwave, resultwave
+
964 Convolve /a gausswave, resultwave
+
965 variable rmax = wavemax(resultwave)
+
+
+
+
969 ng = numpnts(resultwave)
+
970 x0g = xd * (ng - 1) / 2
+
971 setscale/i x -x0g, x0g,
"" , resultwave
+
+
973 yw = pw[2] * resultwave(xw[p] - pw[3]) + pw[0] + pw[1] * xw[p]
+
+
+
+
+
+
+
+
+
+
986 integrate /meth=1 w /d=bg
+
+
988 variable bg1 = bg[p1]
+
989 variable bg2 = bg[p2]
+
+
+
+
+
threadsafe variable DoniachSunjicBroadS(DoniachSunjicStruct *s)
variable DoniachSunjicBroad(wave pw, wave yw, wave xw)
threadsafe variable DblDoubletGaussLinBG_AO(wave pw, wave yw, wave xw)
two doublet gaussian peaks on a linear background fit function (all at once).
variable Calc_DoniachSunjicBroad(wave pw, wave yw)
threadsafe variable MultiVoigtLinBG_AO(wave pw, wave yw, wave xw)
multiple voigt peaks on a linear background fit function.
threadsafe variable MultiGaussLinBG_AO(wave pw, wave yw, wave xw)
multiple gaussian peaks on a linear background fit function (all at once).
threadsafe variable DoubletGaussLinBG_AO(wave pw, wave yw, wave xw)
doublet gaussian peaks on a linear background fit function (all at once).
threadsafe variable MultiVoigtLinBG(wave w, variable x)
multiple voigt peaks on a linear background fit function.
threadsafe variable ds2_bg(wave w, variable x)
variable ShowComponents_Au4f_2p3(wave coef_wave, wave fit_wave)
variable Fit_DoniachSunjicBroad(wave pw, wave yw, wave xw, wave ww)
variable Au4f_2p3(wave w, variable x)
variable ds6_bg(wave w, variable x)
variable Au4f(wave w, variable x)
variable Au4f_2p2(wave w, variable x)
variable ShowComponents_Au4f_2p2(wave coef_wave, wave fit_wave)
threadsafe variable ds1_bg(wave w, variable x)
variable ShirleyBG(wave w, wave bg, variable p1, variable p2)
calculate the shirley background
variable ds4_bg(wave w, variable x)
threadsafe variable MultiDoniachSunjicLinBG(wave w, variable x)
multiple doniach-sunjic peaks on a linear background fit function.
threadsafe variable DoniachSunjic(variable x, variable amp, variable pos, variable sing, variable fwhm)
Doniach-Sunjic line shape.
threadsafe variable MultiGaussLinBG(wave w, variable x)
multiple gaussian peaks on a linear background fit function.
variable FermiGaussConv(wave pw, wave yw, wave xw)
convolution of Fermi-Dirac distribution and a Gaussian.
PEARL Procedures: pearl-gui-tools.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -132,7 +134,7 @@ Functions
@@ -151,7 +153,7 @@ Functions
@@ -187,7 +189,7 @@ Functions
@@ -197,9 +199,9 @@ Functions
diff --git a/doc/html/pearl-gui-tools_8ipf_source.html b/doc/html/pearl-gui-tools_8ipf_source.html
index e64b1ca..6a429b6 100644
--- a/doc/html/pearl-gui-tools_8ipf_source.html
+++ b/doc/html/pearl-gui-tools_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-gui-tools.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,18 +87,71 @@ $(document).ready(function(){initNavTree('pearl-gui-tools_8ipf_source.html','');
pearl-gui-tools.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlGuiTools 23 NewPanel /K=1 /N=ProgressPanel /W=(200,200,402,260) as title
24 TitleBox t_message,pos={2,2},size={189,13},title=message
25 TitleBox t_message,frame=0
26 ValDisplay vd_progress,pos={2,20},size={198,13}
27 ValDisplay vd_progress,limits={0,progress_max,0},barmisc={0,0},mode= 3,value= _NUM:0
28 Button b_abort,pos={74,38},size={50,20},title=
"Abort" 29 DoUpdate /W=ProgressPanel /E=1
38 if (!ParamIsDefault(message))
39 TitleBox t_message,title=message,win=ProgressPanel
41 if (ParamIsDefault(progress_max))
42 ValDisplay vd_progress,value=_NUM:progress,win=ProgressPanel
44 ValDisplay vd_progress,limits={0,progress_max,0},value=_NUM:progress,win=ProgressPanel
46 DoUpdate /W=ProgressPanel
51 KillWindow ProgressPanel
-
-
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.1
+
4 #pragma ModuleName = PearlGuiTools
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
24 NewPanel /K=1 /N=ProgressPanel /W=(200,200,402,260) as title
+
25 TitleBox t_message,pos={2,2},size={189,13},title=message
+
26 TitleBox t_message,frame=0
+
27 ValDisplay vd_progress,pos={2,20},size={198,13}
+
28 ValDisplay vd_progress,limits={0,progress_max,0},barmisc={0,0},mode= 3,value= _NUM:0
+
29 Button b_abort,pos={74,38},size={50,20},title=
"Abort"
+
30 DoUpdate /W=ProgressPanel /E=1
+
+
+
+
+
+
+
+
+
39 if (!ParamIsDefault(message))
+
40 TitleBox t_message,title=message,win=ProgressPanel
+
+
42 if (ParamIsDefault(progress_max))
+
43 ValDisplay vd_progress,value=_NUM:progress,win=ProgressPanel
+
+
45 ValDisplay vd_progress,limits={0,progress_max,0},value=_NUM:progress,win=ProgressPanel
+
+
47 DoUpdate /W=ProgressPanel
+
+
+
+
+
52 KillWindow ProgressPanel
+
PEARL Procedures: pearl-matrix-import.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -111,62 +113,62 @@ Namespaces
static variable init_package () initialize the package data folder. More... initialize the package data folder. More... static variable check_package_folder () check that the package data folder exists More... check that the package data folder exists More... static variable AfterFileOpenHook (variable refNum, string file, string pathName, string type, string creator, variable kind) initialize the package and reload preferences after an experiment is loaded. More... initialize the package and reload preferences after an experiment is loaded. More... static variable BeforeFileOpenHook (variable refNum, string fileName, string path, string type, string creator, variable kind) open a matrix file that was dropped into Igor. More... open a matrix file that was dropped into Igor. More... string matrix_format_elog_message (wave metadata) generate elog message from bricklet metadata More... generate elog message from bricklet metadata More... variable matrix_preview_2d (wave data, wave metadata) static wave preview_matrix_file (string filename) load the preview of a Matrix data file More... load the preview of a Matrix data file More... static variable initStruct (errorCode *errorCode ) from matrixfilereader help More... from matrixfilereader help More... variable mtrx_load_all () load all data from a Matrix data file. More... load all data from a Matrix data file. More... variable mtrx_parse_filename (string fileName, string *resultFile, variable *runCycle, variable *scanCycle, string *channel) parse matrix file names More... parse matrix file names More... string mtrx_split_filename (string fileName, string *prefix, string *datepart, string *timepart) split a matrix filename and return the first three parts More... split a matrix filename and return the first three parts More... dfr mtrx_create_folder (string fileName, dfref df_base=defaultValue) create or look up a data folder based on a matrix file name. More... create or look up a data folder based on a matrix file name. More... dfr mtrx_get_cycle_folder (dfref df_base=defaultValue, variable runCycle=defaultValue, variable scanCycle=defaultValue) create a data folder for bricklet data. More... create a data folder for bricklet data. More... variable mtrx_file_brickletID (string resultFile, variable runCycle, variable scanCycle, string channel) find out bricklet ID of a file More... find out bricklet ID of a file More... variable mtrx_open_file (string pathName, string fileNameOrPath) open a matrix result or data file More... open a matrix result or data file More... string mtrx_load_preview (string destName, string pathName, string fileName, string traces=defaultValue) load a preview image from a Matrix data file. More... load a preview image from a Matrix data file. More... string mtrx_load_file (string pathName, string fileName, string traces=defaultValue) load all data from a Matrix data file. More... load all data from a Matrix data file. More... variable mtrx_scale_dataset (wave data) string mtrx_load_info (string APathName, string AFileName) load descriptive info from a Matrix data file. More... load descriptive info from a Matrix data file. More... variable subtract_line_bg (wave img) remove linear background line-by-line More... remove linear background line-by-line More...
the matrix file import requires the matrix file reader XOP by thomas braun (http://www.igorexchange.com/project/matrixFileReader ) which in turn requires an installation of vernissage by omicron nanotechnology.
Warning EXPERIMENTAL the matrix import module and its interface may change radically in future revisions! Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch Copyright 2016 Paul Scherrer Institut Copyright 2016 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-matrix-import.ipf .
@@ -250,7 +252,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); initialize the package and reload preferences after an experiment is loaded.
-Definition at line 85 of file pearl-matrix-import.ipf .
+Definition at line 86 of file pearl-matrix-import.ipf .
@@ -315,7 +317,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); open a matrix file that was dropped into Igor.
preliminary implementation. this should rather load the entire file and display a preview. graph windows should be reused by subsequent loads. also decide on a data saving location.
-Definition at line 102 of file pearl-matrix-import.ipf .
+Definition at line 103 of file pearl-matrix-import.ipf .
@@ -345,7 +347,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); check that the package data folder exists
initialize the package if the folder does not exist.
-Definition at line 72 of file pearl-matrix-import.ipf .
+Definition at line 73 of file pearl-matrix-import.ipf .
@@ -374,7 +376,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); initialize the package data folder.
-Definition at line 45 of file pearl-matrix-import.ipf .
+Definition at line 46 of file pearl-matrix-import.ipf .
@@ -404,7 +406,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); from matrixfilereader help
-Definition at line 212 of file pearl-matrix-import.ipf .
+Definition at line 213 of file pearl-matrix-import.ipf .
@@ -432,7 +434,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
Definition at line 120 of file pearl-matrix-import.ipf .
+Definition at line 121 of file pearl-matrix-import.ipf .
@@ -462,7 +464,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
@@ -504,7 +506,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns reference of the newly created or existing data folder. Definition at line 360 of file pearl-matrix-import.ipf .
+Definition at line 361 of file pearl-matrix-import.ipf .
@@ -559,7 +561,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns bricklet ID, or -1 if an error occurred. Definition at line 461 of file pearl-matrix-import.ipf .
+Definition at line 462 of file pearl-matrix-import.ipf .
@@ -608,7 +610,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns reference of the newly created or existing data folder. Definition at line 405 of file pearl-matrix-import.ipf .
+Definition at line 406 of file pearl-matrix-import.ipf .
@@ -629,7 +631,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); load all data from a Matrix data file.
-Definition at line 231 of file pearl-matrix-import.ipf .
+Definition at line 232 of file pearl-matrix-import.ipf .
@@ -677,7 +679,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns semicolon-separated list of loaded waves including partial path from current data folder. Definition at line 767 of file pearl-matrix-import.ipf .
+Definition at line 768 of file pearl-matrix-import.ipf .
@@ -723,7 +725,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns newline terminated string. Definition at line 863 of file pearl-matrix-import.ipf .
+Definition at line 864 of file pearl-matrix-import.ipf .
@@ -778,7 +780,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns semicolon-separated list of loaded waves including partial path from current data folder. Definition at line 682 of file pearl-matrix-import.ipf .
+Definition at line 683 of file pearl-matrix-import.ipf .
@@ -829,7 +831,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 545 of file pearl-matrix-import.ipf .
+Definition at line 546 of file pearl-matrix-import.ipf .
@@ -896,7 +898,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); result data files look like: default_2015Apr20-124353_STM-STM_AtomManipulation–136_1.Aux1(V)_mtrx, default_2015Apr20-124353_STM-STM_AtomManipulation–136_1.I(V)_mtrx, default_2015Apr20-124353_STM-STM_AtomManipulation–14_1.I_mtrx, default_2015Apr20-124353_STM-STM_AtomManipulation–14_1.Z_mtrx, etc. the function returns all results as described in the parameter list.
-Definition at line 294 of file pearl-matrix-import.ipf .
+Definition at line 295 of file pearl-matrix-import.ipf .
@@ -916,7 +918,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
@@ -961,7 +963,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
split a matrix filename and return the first three parts
we assume that the second (third) part contains the date (time). the parts are separated by dash or underscore.
-Definition at line 332 of file pearl-matrix-import.ipf .
+Definition at line 333 of file pearl-matrix-import.ipf .
@@ -1000,7 +1002,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
Returns wave reference of the preview image Definition at line 170 of file pearl-matrix-import.ipf .
+Definition at line 171 of file pearl-matrix-import.ipf .
@@ -1022,7 +1024,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
remove linear background line-by-line
-Definition at line 886 of file pearl-matrix-import.ipf .
+Definition at line 887 of file pearl-matrix-import.ipf .
@@ -1047,7 +1049,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
@@ -1071,7 +1073,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
@@ -1095,7 +1097,7 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
@@ -1105,9 +1107,9 @@ result file names look like: default_2015Apr20-124353_STM-STM_AtomManipulation_0
diff --git a/doc/html/pearl-matrix-import_8ipf_source.html b/doc/html/pearl-matrix-import_8ipf_source.html
index 2025116..2459cfc 100644
--- a/doc/html/pearl-matrix-import_8ipf_source.html
+++ b/doc/html/pearl-matrix-import_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-matrix-import.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,36 +87,700 @@ $(document).ready(function(){initNavTree('pearl-matrix-import_8ipf_source.html',
pearl-matrix-import.ipf
-
Go to the documentation of this file. 3 #pragma IgorVersion = 6.36 4 #pragma ModuleName = PearlMatrixImport 38 static strconstant
package_path =
"root:packages:pearl_matrix_import:" 47 dfref savedf = getdatafolderdfr()
50 newdatafolder /o/s packages
51 newdatafolder /o/s $package_name
53 variable /g loglevel = 3
54 string /g dataFilePath = ""
55 string /g resultFilePath = ""
56 variable /g runCycle = 0
57 variable /g scanCycle = 0
58 string /g channelName = ""
59 variable /g brickletID = 0
60 variable /g V_MatrixFileReaderOverwrite = 1
61 variable /g V_MatrixFileReaderFolder = 0
62 variable /g V_MatrixFileReaderDouble = 0
74 if (DataFolderRefStatus(df_pack))
75 svar /sdfr=df_pack /z resultFilePath
76 if (!svar_exists(resultFilePath))
87 String file,pathName,type,creator
88 if( (kind >= 1) && (kind <= 2))
104 String fileName,path,type,creator
106 Variable handledOpen = 0
109 newdatafolder /o /s matrix
125 variable nkeys = dimsize(metadata, 0)
128 message_keys = "resultFileName;sampleName;channelName;"
129 message_keys += "XYScanner.Points.value;XYScanner.Raster_Time.value;XYScanner.Raster_Time.unit;XYScanner.Width.value;XYScanner.Width.unit;XYScanner.Height.value;XYScanner.Height.unit;"
130 message_keys += "GapVoltageControl.Voltage.value;GapVoltageControl.Voltage.unit;"
131 message_keys += "Regulator.Loop_Gain_1_I.value;Regulator.Loop_Gain_1_I.unit;Regulator.Setpoint_1.value;Regulator.Setpoint_1.unit;"
132 message_keys += "Spectroscopy.Device_1_Start.value;Spectroscopy.Device_1_Start.unit;Spectroscopy.Spectroscopy_Mode.value;"
136 for (ikey = 0; ikey < nkeys; ikey += 1)
137 key = metadata[ikey][0]
138 value = metadata[ikey][1]
139 if (WhichListItem(key, message_keys) >= 0)
140 message += key + " = " + value + "\r"
151 ModifyImage data ctab= {*,*,Mud,0}
152 ModifyGraph margin(left)=30,margin(bottom)=30,margin(top)=5,margin(right)=5,height={Plan,1,left,bottom}
155 ModifyGraph axThick=0.5
173 dfref saveDF = GetDataFolderDFR()
174 setdatafolder $package_path
176 svar s_preview_source
178 s_preview_file = filename
179 s_preview_source = ""
180 wave /z preview_image
183 if (! svar_exists(s_file_info))
184 string /g s_file_info
186 if (strlen(s_preview_file) > 0)
200 int32 ALREADY_FILE_OPEN
201 int32 EMPTY_RESULTFILE
202 int32 FILE_NOT_READABLE
203 int32 NO_NEW_BRICKLETS
204 int32 WRONG_PARAMETER
205 int32 INTERNAL_ERROR_CONVERTING_DATA
222 errorCode .INTERNAL_ERROR_CONVERTING_DATA=10064
236 #if exists("MFR_OpenResultFile") 239 MFR_GetXOPErrorMessage
245 MFR_GetXOPErrorMessage
249 MFR_GetBrickletMetaData
251 MFR_GetXOPErrorMessage
301 variable fileType = 0
310 string extension =
"" 312 if (StringMatch(fileName,
"*.mtrx" ))
313 regexp =
"(.+)_([[:digit:]]+)\.(.+)" 314 SplitString /E=regexp fileName, resultFile, index1, extension
317 regexp =
"(.+)--([[:digit:]]+)_([[:digit:]]+)\.((.+)_mtrx)" 318 SplitString /E=regexp fileName, resultFile, index1, index2, extension, channel
320 runCycle = str2num(index1)
321 scanCycle = str2num(index2)
339 regexp =
"([[:alpha:][:digit:]]+)[-_]([[:alpha:][:digit:]]+)[-_]([[:alpha:][:digit:]]+)[-_].+" 340 SplitString /E=regexp fileName, prefix, datepart, timepart
364 if (ParamIsDefault(df_base))
365 df_base = GetDataFolderDFR()
374 folderName = "mtrx_" + datepart + "_" + timepart
375 folderName = CleanupName(folderName, 0)
377 dfref df_save = GetDataFolderDFR()
379 newdatafolder /o /s $foldername
380 dfref df = GetDataFolderDFR()
382 setdatafolder df_save
410 dfref df_save = GetDataFolderDFR()
412 if (ParamIsDefault(df_base))
413 df_base = GetDataFolderDFR()
415 if (ParamIsDefault(runCycle))
416 nvar /sdfr=df_pack defRunCycle = runCycle
417 runCycle = defRunCycle
419 if (ParamIsDefault(scanCycle))
420 nvar /sdfr=df_pack defScanCycle = scanCycle
421 scanCycle = defScanCycle
425 if ((runCycle >= 1) && (scanCycle >= 1))
426 sprintf dfname, "r%us%u", runCycle, scanCycle
427 setdatafolder df_base
429 if (DataFolderRefStatus(df) == 0)
430 newdatafolder $dfname
437 setdatafolder df_save
467 dfref df_overview = NewFreeDataFolder()
472 string resultFileName
473 #if exists("MFR_OpenResultFile") 477 sprintf resultFileName, "%s_%04u.mtrx
", resultFile, link 478 MFR_OpenResultFile /K resultFileName 479 if(V_flag != errorCode.SUCCESS) 482 MFR_CreateOverviewTable /DEST=df_overview 483 // dimension labels are: brickletID, scanCycleCount, runCycleCount, sequenceID, dimension, channelName 484 wave /t /sdfr=df_overview overviewTable 485 make /n=(dimsize(overviewTable, 0)) /i /u /free runcycles, scancycles, ids, match 486 make /n=(dimsize(overviewTable, 0)) /t /free channels 487 ids = str2num(overviewtable[p][%brickletID]) 489 runcycles = str2num(overviewtable[p][%runCycleCount]) 494 scancycles = str2num(overviewtable[p][%scanCycleCount]) 496 scancycles = scancycle 498 if (strlen(channel) > 0) 499 channels = overviewTable[p][%channelName] 503 Extract /FREE ids, match_ids, (scancycles == scanCycle) && (runcycles == runCycle) && (cmpstr(channels, channel) == 0) 504 if (numpnts(match_ids) > 0) 545 function mtrx_open_file(pathName, fileNameOrPath) 547 string fileNameOrPath 549 check_package_folder() 550 dfref df_save = GetDataFolderDFR() 551 dfref df_pack = $(package_path) 552 svar /sdfr=df_pack dataFilePath 553 svar /sdfr=df_pack resultFilePath 554 nvar /sdfr=df_pack runCycle 555 nvar /sdfr=df_pack scanCycle 556 svar /sdfr=df_pack channelName 557 nvar /sdfr=df_pack brickletID 559 string loc_resultFileName 560 string loc_resultFilePath 561 variable loc_runCycle 562 variable loc_scanCycle 563 string loc_channelName 565 // make sure we have a valid and complete file path 566 GetFileFolderInfo /P=$pathName /Q /Z=2 fileNameOrPath 568 if ((v_flag == 0) && (v_isFile)) 574 // get base file name 579 fileName = ParseFilePath(0, filePath, " :
", 1, 0) 580 fileDir = ParseFilePath(1, filePath, " :
", 1, 0) 581 fileType = mtrx_parse_filename(fileName, baseFileName, loc_runCycle, loc_scanCycle, loc_channelName) 586 variable using_cache = 0 588 struct errorCode errorCode 589 initStruct(errorCode) 591 sprintf loc_resultFileName, " %s_%04u.mtrx
", baseFileName, link 592 loc_resultFilePath = fileDir + loc_resultFileName 593 #if exists(" MFR_OpenResultFile
") 594 if ((strlen(resultFilePath) == 0) || (cmpstr(loc_resultFilePath, resultFilePath) != 0)) 595 MFR_OpenResultFile /K loc_resultFilePath 596 if(V_flag != errorCode.SUCCESS) 597 MFR_GetXOPErrorMessage 601 resultFilePath = loc_resultFilePath 603 dataFilePath = filePath 611 MFR_CreateOverviewTable /DEST=df_pack 612 if(V_flag != errorCode.SUCCESS) 613 MFR_GetXOPErrorMessage 622 print " matrixfilereader.xop not installed
" 626 // dimension labels are: brickletID, scanCycleCount, runCycleCount, sequenceID, dimension, channelName 627 wave /t /sdfr=df_pack overviewTable 628 make /n=(dimsize(overviewTable, 0)) /i /u /o df_pack:runCycles, df_pack:scanCycles, df_pack:ids 629 make /n=(dimsize(overviewTable, 0)) /t /o df_pack:channels 630 wave /sdfr=df_pack ids, runCycles, scanCycles 631 wave /t /sdfr=df_pack channels 632 ids = str2num(overviewtable[p][%brickletID]) 633 runCycles = str2num(overviewtable[p][%runCycleCount]) 634 scanCycles = str2num(overviewtable[p][%scanCycleCount]) 635 channels = overviewTable[p][%channelName] 638 // if a data file is opened, make sure we found the right result file 639 if ((loc_runCycle > 0) && (loc_scanCycle > 0)) 640 Extract /FREE ids, match_ids, (runCycles == loc_runCycle) && (scanCycles == loc_scanCycle) && (cmpstr(channels, loc_channelName) == 0) 641 if (numpnts(match_ids) > 0) 643 runCycle = loc_runCycle 644 scanCycle = loc_scanCycle 645 channelName = loc_channelName 682 function /s mtrx_load_preview(destName, pathName, fileName, [traces]) 688 if (ParamIsDefault(traces)) 689 traces = " *Up;*Down;*ReUp;*ReDown;
" 692 dfref df_save = GetDataFolderDFR() 694 string datanames = " " 695 string datapaths = " " 696 variable filestatus = mtrx_open_file(pathName, fileName) 701 dfref df_pack = $(package_path) 702 svar /sdfr=df_pack dataFilePath 703 svar /sdfr=df_pack resultFilePath 704 nvar /sdfr=df_pack runCycle 705 nvar /sdfr=df_pack scanCycle 706 svar /sdfr=df_pack channelName 707 nvar /sdfr=df_pack brickletID 709 #if exists(" MFR_OpenResultFile
") 710 dfref df_data = df_save 711 variable /g df_data:V_MatrixFileReaderOverwrite = 1 712 variable /g df_data:V_MatrixFileReaderFolder = 0 713 variable /g df_data:V_MatrixFileReaderDouble = 0 714 struct errorCode errorCode 715 initStruct(errorCode) 716 MFR_GetBrickletData /N=destName /R=(brickletID) /S=2 /DEST=df_data 717 if(V_flag == errorCode.SUCCESS) 718 datanames = S_waveNames 720 variable n = ItemsInList(datanames) 722 s = StringFromList(0, datanames) 724 mtrx_scale_dataset(data) 725 if (WaveDims(data) == 2) 726 subtract_line_bg(data) 728 datapaths = AddListItem(GetWavesDataFolder(data, 4), datapaths, " ;
", inf) 729 for (i = 1; i < n; i += 1) 730 s = StringFromList(i, datanames) 734 MFR_GetXOPErrorMessage 736 //MFR_GetBrickletMetaData /N=ANickName /R=(brickletID) // /DEST=dfref 738 print " matrixfilereader.xop not installed
" 741 setdatafolder df_save 767 function /s mtrx_load_file(pathName, fileName, [traces]) 772 if (ParamIsDefault(traces)) 773 traces = " *Up;*Down;*ReUp;*ReDown;
" 776 dfref df_save = GetDataFolderDFR() 778 string datanames = " " 779 string datapaths = " " 780 variable filestatus = mtrx_open_file(pathName, fileName) 785 dfref df_pack = $(package_path) 786 svar /sdfr=df_pack dataFilePath 787 svar /sdfr=df_pack resultFilePath 788 nvar /sdfr=df_pack runCycle 789 nvar /sdfr=df_pack scanCycle 790 svar /sdfr=df_pack channelName 791 nvar /sdfr=df_pack brickletID 793 #if exists(" MFR_OpenResultFile
") 794 string resultFileName = ParseFilePath(0, resultFilePath, " :
", 1, 0) 795 dfref df_result = mtrx_create_folder(resultFileName, df_base=df_save) 796 dfref df_data = mtrx_get_cycle_folder(df_base = df_result) 797 variable /g df_data:V_MatrixFileReaderOverwrite = 1 798 variable /g df_data:V_MatrixFileReaderFolder = 0 799 variable /g df_data:V_MatrixFileReaderDouble = 0 801 struct errorCode errorCode 802 initStruct(errorCode) 804 name = CleanupName(channelName, 0) 805 MFR_GetBrickletData /N=name /R=(brickletID) /DEST=df_data 806 if(V_flag == errorCode.SUCCESS) 807 datanames = S_waveNames 809 variable n = ItemsInList(datanames) 811 for (i = 0; i < n; i += 1) 812 s = StringFromList(i, datanames) 813 wave /sdfr=df_data data = $s 814 mtrx_scale_dataset(data) 815 datapaths = AddListItem(GetWavesDataFolder(data, 4), datapaths, " ;
", inf) 818 MFR_GetXOPErrorMessage 820 //MFR_GetBrickletMetaData /N=ANickName /R=(brickletID) // /DEST=dfref 822 print " matrixfilereader.xop not installed
" 825 setdatafolder df_save 829 function mtrx_scale_dataset(data) 832 dfref df_pack = $(package_path) 833 nvar /sdfr=df_pack runCycle 834 nvar /sdfr=df_pack scanCycle 835 svar /sdfr=df_pack channelName 836 nvar /sdfr=df_pack brickletID 838 string scanDir = StringFromList(2, NameOfWave(data), " _
") 839 if (WaveDims(data) == 2) 840 Note data, " AxisLabelX=X
" 841 Note data, " AxisLabelY=Y
" 843 Note data, " AxisLabelD=
" + channelName 845 sprintf title, " %u-%u %s %s
", runCycle, scanCycle, channelName, scanDir 846 Note data, " Dataset=
" + title 863 function /s mtrx_load_info(APathName, AFileName) 867 dfref saveDF = GetDataFolderDFR() 868 dfref fileDF = NewFreeDataFolder() 886 function subtract_line_bg(img) 889 variable nx = dimsize(img, 0) 890 variable ny = dimsize(img, 1) 892 make /n=(nx) /free line, fit 893 for (iy = 0; iy < ny; iy += 1) 895 if (numtype(sum(line)) == 0) 896 CurveFit /N /Q /NTHR=0 line line /D=fit 897 img[][iy] = line[p] - fit[p] static const string package_path
-
dfr mtrx_create_folder(string fileName, dfref df_base=defaultValue)
create or look up a data folder based on a matrix file name.
-
variable mtrx_file_brickletID(string resultFile, variable runCycle, variable scanCycle, string channel)
find out bricklet ID of a file
-
static variable initStruct(errorCode *errorCode)
from matrixfilereader help
-
string mtrx_split_filename(string fileName, string *prefix, string *datepart, string *timepart)
split a matrix filename and return the first three parts
-
variable matrix_preview_2d(wave data, wave metadata)
-
static wave preview_matrix_file(string filename)
load the preview of a Matrix data file
-
string mtrx_load_info(string APathName, string AFileName)
load descriptive info from a Matrix data file.
-
string matrix_format_elog_message(wave metadata)
generate elog message from bricklet metadata
-
from matrixfilereader help
-
variable mtrx_load_all()
load all data from a Matrix data file.
-
-
static const string ks_filematch_mtrx
-
static variable AfterFileOpenHook(variable refNum, string file, string pathName, string type, string creator, variable kind)
initialize the package and reload preferences after an experiment is loaded.
-
dfr mtrx_get_cycle_folder(dfref df_base=defaultValue, variable runCycle=defaultValue, variable scanCycle=defaultValue)
create a data folder for bricklet data.
-
static variable init_package()
initialize the package data folder.
-
variable mtrx_parse_filename(string fileName, string *resultFile, variable *runCycle, variable *scanCycle, string *channel)
parse matrix file names
-
string mtrx_load_preview(string destName, string pathName, string fileName, string traces=defaultValue)
load a preview image from a Matrix data file.
-
static variable BeforeFileOpenHook(variable refNum, string fileName, string path, string type, string creator, variable kind)
open a matrix file that was dropped into Igor.
-
static const string package_name
-
static variable check_package_folder()
check that the package data folder exists
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
+
+
4 #pragma IgorVersion = 6.36
+
5 #pragma ModuleName = PearlMatrixImport
+
+
+
+
+
+
+
+
+
+
+
+
+
39 static strconstant
package_path =
"root:packages:pearl_matrix_import:"
+
+
+
+
+
+
48 dfref savedf = getdatafolderdfr()
+
+
+
51 newdatafolder /o/s packages
+
52 newdatafolder /o/s $package_name
+
+
54 variable /g loglevel = 3
+
55 string /g dataFilePath = ""
+
56 string /g resultFilePath = ""
+
57 variable /g runCycle = 0
+
58 variable /g scanCycle = 0
+
59 string /g channelName = ""
+
60 variable /g brickletID = 0
+
61 variable /g V_MatrixFileReaderOverwrite = 1
+
62 variable /g V_MatrixFileReaderFolder = 0
+
63 variable /g V_MatrixFileReaderDouble = 0
+
+
+
+
+
+
+
+
75 if (DataFolderRefStatus(df_pack))
+
76 svar /sdfr=df_pack /z resultFilePath
+
77 if (!svar_exists(resultFilePath))
+
+
+
+
+
+
+
+
+
+
88 String file,pathName,type,creator
+
89 if( (kind >= 1) && (kind <= 2))
+
+
+
+
+
+
+
+
+
105 String fileName,path,type,creator
+
+
107 Variable handledOpen = 0
+
+
+
110 newdatafolder /o /s matrix
+
+
+
+
+
+
+
+
+
+
+
+
126 variable nkeys = dimsize(metadata, 0)
+
+
+
129 message_keys = "resultFileName;sampleName;channelName;"
+
130 message_keys += "XYScanner.Points.value;XYScanner.Raster_Time.value;XYScanner.Raster_Time.unit;XYScanner.Width.value;XYScanner.Width.unit;XYScanner.Height.value;XYScanner.Height.unit;"
+
131 message_keys += "GapVoltageControl.Voltage.value;GapVoltageControl.Voltage.unit;"
+
132 message_keys += "Regulator.Loop_Gain_1_I.value;Regulator.Loop_Gain_1_I.unit;Regulator.Setpoint_1.value;Regulator.Setpoint_1.unit;"
+
133 message_keys += "Spectroscopy.Device_1_Start.value;Spectroscopy.Device_1_Start.unit;Spectroscopy.Spectroscopy_Mode.value;"
+
+
+
+
137 for (ikey = 0; ikey < nkeys; ikey += 1)
+
138 key = metadata[ikey][0]
+
139 value = metadata[ikey][1]
+
140 if (WhichListItem(key, message_keys) >= 0)
+
141 message += key + " = " + value + "\r"
+
+
+
+
+
+
+
+
+
+
+
152 ModifyImage data ctab= {*,*,Mud,0}
+
153 ModifyGraph margin(left)=30,margin(bottom)=30,margin(top)=5,margin(right)=5,height={Plan,1,left,bottom}
+
+
+
156 ModifyGraph axThick=0.5
+
+
+
+
+
+
+
+
174 dfref saveDF = GetDataFolderDFR()
+
175 setdatafolder $package_path
+
+
177 svar s_preview_source
+
+
179 s_preview_file = filename
+
180 s_preview_source = ""
+
181 wave /z preview_image
+
+
+
184 if (! svar_exists(s_file_info))
+
185 string /g s_file_info
+
+
187 if (strlen(s_preview_file) > 0)
+
+
+
+
+
+
+
+
+
+
+
+
+
201 int32 ALREADY_FILE_OPEN
+
202 int32 EMPTY_RESULTFILE
+
203 int32 FILE_NOT_READABLE
+
204 int32 NO_NEW_BRICKLETS
+
205 int32 WRONG_PARAMETER
+
206 int32 INTERNAL_ERROR_CONVERTING_DATA
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
223 errorCode .INTERNAL_ERROR_CONVERTING_DATA=10064
+
+
+
+
+
+
+
+
+
+
+
+
237 #if exists("MFR_OpenResultFile")
+
+
+
240 MFR_GetXOPErrorMessage
+
+
+
+
+
+
246 MFR_GetXOPErrorMessage
+
+
+
+
250 MFR_GetBrickletMetaData
+
+
252 MFR_GetXOPErrorMessage
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
302 variable fileType = 0
+
+
+
+
+
+
+
+
+
311 string extension =
""
+
+
313 if (StringMatch(fileName,
"*.mtrx" ))
+
314 regexp =
"(.+)_([[:digit:]]+)\.(.+)"
+
315 SplitString /E=regexp fileName, resultFile, index1, extension
+
+
+
318 regexp =
"(.+)--([[:digit:]]+)_([[:digit:]]+)\.((.+)_mtrx)"
+
319 SplitString /E=regexp fileName, resultFile, index1, index2, extension, channel
+
+
321 runCycle = str2num(index1)
+
322 scanCycle = str2num(index2)
+
+
+
+
+
+
+
+
+
+
+
+
+
340 regexp =
"([[:alpha:][:digit:]]+)[-_]([[:alpha:][:digit:]]+)[-_]([[:alpha:][:digit:]]+)[-_].+"
+
341 SplitString /E=regexp fileName, prefix, datepart, timepart
+
+
+
+
+
+
+
+
365 if (ParamIsDefault(df_base))
+
366 df_base = GetDataFolderDFR()
+
+
+
+
+
+
+
+
+
375 folderName = "mtrx_" + datepart + "_" + timepart
+
376 folderName = CleanupName(folderName, 0)
+
+
378 dfref df_save = GetDataFolderDFR()
+
+
380 newdatafolder /o /s $foldername
+
381 dfref df = GetDataFolderDFR()
+
+
383 setdatafolder df_save
+
+
+
+
+
+
+
+
+
411 dfref df_save = GetDataFolderDFR()
+
+
413 if (ParamIsDefault(df_base))
+
414 df_base = GetDataFolderDFR()
+
+
416 if (ParamIsDefault(runCycle))
+
417 nvar /sdfr=df_pack defRunCycle = runCycle
+
418 runCycle = defRunCycle
+
+
420 if (ParamIsDefault(scanCycle))
+
421 nvar /sdfr=df_pack defScanCycle = scanCycle
+
422 scanCycle = defScanCycle
+
+
+
+
426 if ((runCycle >= 1) && (scanCycle >= 1))
+
427 sprintf dfname, "r%us%u", runCycle, scanCycle
+
428 setdatafolder df_base
+
+
430 if (DataFolderRefStatus(df) == 0)
+
431 newdatafolder $dfname
+
+
+
+
+
+
+
438 setdatafolder df_save
+
+
+
+
+
+
+
+
+
+
468 dfref df_overview = NewFreeDataFolder()
+
+
+
+
+
473 string resultFileName
+
474 #if exists("MFR_OpenResultFile")
+
+
+
+
478 sprintf resultFileName, "%s_%04u.mtrx
", resultFile, link
+
479 MFR_OpenResultFile /K resultFileName
+
480 if(V_flag != errorCode.SUCCESS)
+
+
+
483 MFR_CreateOverviewTable /DEST=df_overview
+
484 // dimension labels are: brickletID, scanCycleCount, runCycleCount, sequenceID, dimension, channelName
+
485 wave /t /sdfr=df_overview overviewTable
+
486 make /n=(dimsize(overviewTable, 0)) /i /u /free runcycles, scancycles, ids, match
+
487 make /n=(dimsize(overviewTable, 0)) /t /free channels
+
488 ids = str2num(overviewtable[p][%brickletID])
+
+
490 runcycles = str2num(overviewtable[p][%runCycleCount])
+
+
+
+
+
495 scancycles = str2num(overviewtable[p][%scanCycleCount])
+
+
497 scancycles = scancycle
+
+
499 if (strlen(channel) > 0)
+
500 channels = overviewTable[p][%channelName]
+
+
+
+
504 Extract /FREE ids, match_ids, (scancycles == scanCycle) && (runcycles == runCycle) && (cmpstr(channels, channel) == 0)
+
505 if (numpnts(match_ids) > 0)
+
+
+
+
+
+
+
+
+
+
546 function mtrx_open_file(pathName, fileNameOrPath)
+
+
548 string fileNameOrPath
+
+
550 check_package_folder()
+
551 dfref df_save = GetDataFolderDFR()
+
552 dfref df_pack = $(package_path)
+
553 svar /sdfr=df_pack dataFilePath
+
554 svar /sdfr=df_pack resultFilePath
+
555 nvar /sdfr=df_pack runCycle
+
556 nvar /sdfr=df_pack scanCycle
+
557 svar /sdfr=df_pack channelName
+
558 nvar /sdfr=df_pack brickletID
+
+
560 string loc_resultFileName
+
561 string loc_resultFilePath
+
562 variable loc_runCycle
+
563 variable loc_scanCycle
+
564 string loc_channelName
+
+
566 // make sure we have a valid and complete file path
+
567 GetFileFolderInfo /P=$pathName /Q /Z=2 fileNameOrPath
+
+
569 if ((v_flag == 0) && (v_isFile))
+
+
+
+
+
+
575 // get base file name
+
+
+
+
+
580 fileName = ParseFilePath(0, filePath, " :
", 1, 0)
+
581 fileDir = ParseFilePath(1, filePath, " :
", 1, 0)
+
582 fileType = mtrx_parse_filename(fileName, baseFileName, loc_runCycle, loc_scanCycle, loc_channelName)
+
+
+
+
+
587 variable using_cache = 0
+
+
589 struct errorCode errorCode
+
590 initStruct(errorCode)
+
+
592 sprintf loc_resultFileName, " %s_%04u.mtrx
", baseFileName, link
+
593 loc_resultFilePath = fileDir + loc_resultFileName
+
594 #if exists(" MFR_OpenResultFile
")
+
595 if ((strlen(resultFilePath) == 0) || (cmpstr(loc_resultFilePath, resultFilePath) != 0))
+
596 MFR_OpenResultFile /K loc_resultFilePath
+
597 if(V_flag != errorCode.SUCCESS)
+
598 MFR_GetXOPErrorMessage
+
+
+
+
602 resultFilePath = loc_resultFilePath
+
+
604 dataFilePath = filePath
+
+
+
+
+
+
+
+
612 MFR_CreateOverviewTable /DEST=df_pack
+
613 if(V_flag != errorCode.SUCCESS)
+
614 MFR_GetXOPErrorMessage
+
+
+
+
+
+
+
+
+
623 print " matrixfilereader.xop not installed
"
+
+
+
+
627 // dimension labels are: brickletID, scanCycleCount, runCycleCount, sequenceID, dimension, channelName
+
628 wave /t /sdfr=df_pack overviewTable
+
629 make /n=(dimsize(overviewTable, 0)) /i /u /o df_pack:runCycles, df_pack:scanCycles, df_pack:ids
+
630 make /n=(dimsize(overviewTable, 0)) /t /o df_pack:channels
+
631 wave /sdfr=df_pack ids, runCycles, scanCycles
+
632 wave /t /sdfr=df_pack channels
+
633 ids = str2num(overviewtable[p][%brickletID])
+
634 runCycles = str2num(overviewtable[p][%runCycleCount])
+
635 scanCycles = str2num(overviewtable[p][%scanCycleCount])
+
636 channels = overviewTable[p][%channelName]
+
+
+
639 // if a data file is opened, make sure we found the right result file
+
640 if ((loc_runCycle > 0) && (loc_scanCycle > 0))
+
641 Extract /FREE ids, match_ids, (runCycles == loc_runCycle) && (scanCycles == loc_scanCycle) && (cmpstr(channels, loc_channelName) == 0)
+
642 if (numpnts(match_ids) > 0)
+
+
644 runCycle = loc_runCycle
+
645 scanCycle = loc_scanCycle
+
646 channelName = loc_channelName
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
683 function /s mtrx_load_preview(destName, pathName, fileName, [traces])
+
+
+
+
+
+
689 if (ParamIsDefault(traces))
+
690 traces = " *Up;*Down;*ReUp;*ReDown;
"
+
+
+
693 dfref df_save = GetDataFolderDFR()
+
+
695 string datanames = " "
+
696 string datapaths = " "
+
697 variable filestatus = mtrx_open_file(pathName, fileName)
+
+
+
+
+
702 dfref df_pack = $(package_path)
+
703 svar /sdfr=df_pack dataFilePath
+
704 svar /sdfr=df_pack resultFilePath
+
705 nvar /sdfr=df_pack runCycle
+
706 nvar /sdfr=df_pack scanCycle
+
707 svar /sdfr=df_pack channelName
+
708 nvar /sdfr=df_pack brickletID
+
+
710 #if exists(" MFR_OpenResultFile
")
+
711 dfref df_data = df_save
+
712 variable /g df_data:V_MatrixFileReaderOverwrite = 1
+
713 variable /g df_data:V_MatrixFileReaderFolder = 0
+
714 variable /g df_data:V_MatrixFileReaderDouble = 0
+
715 struct errorCode errorCode
+
716 initStruct(errorCode)
+
717 MFR_GetBrickletData /N=destName /R=(brickletID) /S=2 /DEST=df_data
+
718 if(V_flag == errorCode.SUCCESS)
+
719 datanames = S_waveNames
+
+
721 variable n = ItemsInList(datanames)
+
+
723 s = StringFromList(0, datanames)
+
+
725 mtrx_scale_dataset(data)
+
726 if (WaveDims(data) == 2)
+
727 subtract_line_bg(data)
+
+
729 datapaths = AddListItem(GetWavesDataFolder(data, 4), datapaths, " ;
", inf)
+
730 for (i = 1; i < n; i += 1)
+
731 s = StringFromList(i, datanames)
+
+
+
+
735 MFR_GetXOPErrorMessage
+
+
737 //MFR_GetBrickletMetaData /N=ANickName /R=(brickletID) // /DEST=dfref
+
+
739 print " matrixfilereader.xop not installed
"
+
+
+
742 setdatafolder df_save
+
+
+
+
768 function /s mtrx_load_file(pathName, fileName, [traces])
+
+
+
+
+
773 if (ParamIsDefault(traces))
+
774 traces = " *Up;*Down;*ReUp;*ReDown;
"
+
+
+
777 dfref df_save = GetDataFolderDFR()
+
+
779 string datanames = " "
+
780 string datapaths = " "
+
781 variable filestatus = mtrx_open_file(pathName, fileName)
+
+
+
+
+
786 dfref df_pack = $(package_path)
+
787 svar /sdfr=df_pack dataFilePath
+
788 svar /sdfr=df_pack resultFilePath
+
789 nvar /sdfr=df_pack runCycle
+
790 nvar /sdfr=df_pack scanCycle
+
791 svar /sdfr=df_pack channelName
+
792 nvar /sdfr=df_pack brickletID
+
+
794 #if exists(" MFR_OpenResultFile
")
+
795 string resultFileName = ParseFilePath(0, resultFilePath, " :
", 1, 0)
+
796 dfref df_result = mtrx_create_folder(resultFileName, df_base=df_save)
+
797 dfref df_data = mtrx_get_cycle_folder(df_base = df_result)
+
798 variable /g df_data:V_MatrixFileReaderOverwrite = 1
+
799 variable /g df_data:V_MatrixFileReaderFolder = 0
+
800 variable /g df_data:V_MatrixFileReaderDouble = 0
+
+
802 struct errorCode errorCode
+
803 initStruct(errorCode)
+
+
805 name = CleanupName(channelName, 0)
+
806 MFR_GetBrickletData /N=name /R=(brickletID) /DEST=df_data
+
807 if(V_flag == errorCode.SUCCESS)
+
808 datanames = S_waveNames
+
+
810 variable n = ItemsInList(datanames)
+
+
812 for (i = 0; i < n; i += 1)
+
813 s = StringFromList(i, datanames)
+
814 wave /sdfr=df_data data = $s
+
815 mtrx_scale_dataset(data)
+
816 datapaths = AddListItem(GetWavesDataFolder(data, 4), datapaths, " ;
", inf)
+
+
+
819 MFR_GetXOPErrorMessage
+
+
821 //MFR_GetBrickletMetaData /N=ANickName /R=(brickletID) // /DEST=dfref
+
+
823 print " matrixfilereader.xop not installed
"
+
+
+
826 setdatafolder df_save
+
+
+
+
830 function mtrx_scale_dataset(data)
+
+
+
833 dfref df_pack = $(package_path)
+
834 nvar /sdfr=df_pack runCycle
+
835 nvar /sdfr=df_pack scanCycle
+
836 svar /sdfr=df_pack channelName
+
837 nvar /sdfr=df_pack brickletID
+
+
839 string scanDir = StringFromList(2, NameOfWave(data), " _
")
+
840 if (WaveDims(data) == 2)
+
841 Note data, " AxisLabelX=X
"
+
842 Note data, " AxisLabelY=Y
"
+
+
844 Note data, " AxisLabelD=
" + channelName
+
+
846 sprintf title, " %u-%u %s %s
", runCycle, scanCycle, channelName, scanDir
+
847 Note data, " Dataset=
" + title
+
+
+
864 function /s mtrx_load_info(APathName, AFileName)
+
+
+
+
868 dfref saveDF = GetDataFolderDFR()
+
869 dfref fileDF = NewFreeDataFolder()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
887 function subtract_line_bg(img)
+
+
+
890 variable nx = dimsize(img, 0)
+
891 variable ny = dimsize(img, 1)
+
+
893 make /n=(nx) /free line, fit
+
894 for (iy = 0; iy < ny; iy += 1)
+
+
896 if (numtype(sum(line)) == 0)
+
897 CurveFit /N /Q /NTHR=0 line line /D=fit
+
898 img[][iy] = line[p] - fit[p]
+
+
+
static const string package_path
static const string package_name
variable mtrx_load_all()
load all data from a Matrix data file.
variable mtrx_file_brickletID(string resultFile, variable runCycle, variable scanCycle, string channel)
find out bricklet ID of a file
variable matrix_preview_2d(wave data, wave metadata)
variable mtrx_parse_filename(string fileName, string *resultFile, variable *runCycle, variable *scanCycle, string *channel)
parse matrix file names
dfr mtrx_get_cycle_folder(dfref df_base=defaultValue, variable runCycle=defaultValue, variable scanCycle=defaultValue)
create a data folder for bricklet data.
static variable BeforeFileOpenHook(variable refNum, string fileName, string path, string type, string creator, variable kind)
open a matrix file that was dropped into Igor.
static const string ks_filematch_mtrx
static variable AfterFileOpenHook(variable refNum, string file, string pathName, string type, string creator, variable kind)
initialize the package and reload preferences after an experiment is loaded.
string mtrx_load_info(string APathName, string AFileName)
load descriptive info from a Matrix data file.
string matrix_format_elog_message(wave metadata)
generate elog message from bricklet metadata
dfr mtrx_create_folder(string fileName, dfref df_base=defaultValue)
create or look up a data folder based on a matrix file name.
static wave preview_matrix_file(string filename)
load the preview of a Matrix data file
from matrixfilereader help
static variable initStruct(errorCode *errorCode)
from matrixfilereader help
static variable check_package_folder()
check that the package data folder exists
string mtrx_load_preview(string destName, string pathName, string fileName, string traces=defaultValue)
load a preview image from a Matrix data file.
static variable init_package()
initialize the package data folder.
string mtrx_split_filename(string fileName, string *prefix, string *datepart, string *timepart)
split a matrix filename and return the first three parts
PEARL Procedures: pearl-menu.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -93,7 +95,7 @@ $(document).ready(function(){initNavTree('pearl-menu_8ipf.html','');});
string PearlMenuEnableFunc (string funcname)
-
check whether a function name exists More...
+
check whether a function name exists More... variable LoadPearlOptics ()
@@ -108,16 +110,16 @@ Functions
variable DisplayGizmoSlicer () variable PearlLiveDisplay (string epicsname, string nickname, string wbRGB) area detector live display More... area detector live display More... variable PearlCameraDisplay (string epicsname, string nickname, string wbRGB) area detector surveillance camera display More... area detector surveillance camera display More... variable PearlAnglescanTracker (string epicsname, string wbRGB) display the angle scan tracker window More... display the angle scan tracker window More... variable PearlSampleTracker (variable action) display the sample tracker window More... display the sample tracker window More... Definition at line 242 of file pearl-menu.ipf .
+Definition at line 243 of file pearl-menu.ipf .
@@ -317,7 +319,7 @@ Functions
-Definition at line 218 of file pearl-menu.ipf .
+Definition at line 219 of file pearl-menu.ipf .
@@ -354,7 +356,7 @@ Functions
area detector live display
-
display an area detector channel in an ad_display_profiles() window.
+
display an area detector channel in an ad_display_profiles() window.
Parameters
epicsname base name of the detector, e.g. X03DA-SCIENTA: image1: and cam1: are appended by the function. see ad_connect(). Definition at line 185 of file pearl-menu.ipf .
+Definition at line 186 of file pearl-menu.ipf .
@@ -387,7 +389,7 @@ Functions
check whether a function name exists
return a prefix which disables the menu item if the function does not exist
-Definition at line 89 of file pearl-menu.ipf .
+Definition at line 90 of file pearl-menu.ipf .
@@ -416,7 +418,7 @@ Functions
-Definition at line 261 of file pearl-menu.ipf .
+Definition at line 262 of file pearl-menu.ipf .
@@ -426,9 +428,9 @@ Functions
diff --git a/doc/html/pearl-menu_8ipf_source.html b/doc/html/pearl-menu_8ipf_source.html
index 491133a..69dee94 100644
--- a/doc/html/pearl-menu_8ipf_source.html
+++ b/doc/html/pearl-menu_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-menu.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,37 +87,255 @@ $(document).ready(function(){initNavTree('pearl-menu_8ipf_source.html','');});
pearl-menu.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=1 // Use modern global access method. 2 #pragma ModuleName = PearlMenu 20 help = {
"Data explorer panel with file import and preview" ,
"Requires ARPES package and HDF5 XOP" }
22 help = {
"Import area detector HDF5 data file" ,
"Requires ARPES package and HDF5 XOP" }
25 submenu
"On-the-Fly Data" 27 help = {
"Renames otf_xxxxxx_yyyyyy_zzzz data folders to otf_yyyyyy (removing date and suffix)" ,
"Requires Optics package" }
29 help = {
"Copies data from all otf_* folders into otf_batch folder" ,
"Requires Optics package" }
30 PearlMenuEnableFunc (
"PearlOpticsPreviewPanel" ) +
"OTF Preview" , /Q, PearlOpticsPreviewPanel()
31 help = {
"Opens a preview panel for OTF data in otf_* folders" ,
"Requires Optics package" }
34 submenu
"Scienta Analyser" 36 help = {
"Display preview panel with latest image from Scienta" ,
"Requires ARPES package and EPICS XOP" }
38 help = {
"Preview of acquired angle scan data and current detection angles." ,
"Requires ARPES package and EPICS XOP" }
40 help = {
"Live tracking and adjustment of sample position." ,
"Requires ARPES package and EPICS XOP" }
45 help = {
"Display preview panel with latest image from Scienta" ,
"Requires ARPES package and EPICS XOP" }
47 help = {
"Display live panel of the exit slit camera" ,
"Requires ARPES package and EPICS XOP" }
52 help = {
"Profiles display of 2D data" ,
"Requires ARPES package" }
54 help = {
"Slice and profiles display of 3D data" ,
"Requires ARPES package" }
56 help = {
"Gizmo display of 3D data" ,
"Requires ARPES package" }
61 help = {
"Data processing of two-pi angle scans" ,
"Requires ARPES package" }
66 help = {
"Open an ELOG panel to send entries to an ELOG logbook" }
69 submenu
"Sample Preparation" 71 help = {
"Sample annealing ramp generator" }
76 help = {
"Data processing and analysis for ARPES experiments" }
78 help = {
"Process control for sample preparation" }
80 help = {
"Data processing and analysis for beamline commissioning" }
91 if (exists(funcname) >= 3)
99 execute /p/q/z "INSERTINCLUDE \"pearl-optics\""
100 execute /p/q/z "COMPILEPROCEDURES "
101 execute /p/q/z "BuildMenu \"PEARL\""
105 execute /p/q/z "INSERTINCLUDE \"pearl-arpes\""
106 execute /p/q/z "COMPILEPROCEDURES "
107 execute /p/q/z "BuildMenu \"PEARL\""
111 execute /p/q/z "INSERTINCLUDE \"pearl-preparation\""
112 execute /p/q/z "COMPILEPROCEDURES "
113 execute /p/q/z "BuildMenu \"PEARL\""
117 dfref dfBefore = GetDataFolderDFR()
118 Execute /q/z "CreateBrowser prompt=\"Select 2D wave\", showWaves=1, showVars=0, showStrs=0"
119 dfref dfAfter = GetDataFolderDFR()
120 SetDataFolder dfBefore
122 SVAR list = S_BrowserList
125 if ((flag != 0) && (ItemsInList(list) >= 1))
126 string brickname = StringFromList(0, list)
134 dfref dfBefore = GetDataFolderDFR()
135 Execute /q/z "CreateBrowser prompt=\"Select 3D wave\", showWaves=1, showVars=0, showStrs=0"
136 dfref dfAfter = GetDataFolderDFR()
137 SetDataFolder dfBefore
139 SVAR list = S_BrowserList
142 if ((flag != 0) && (ItemsInList(list) >= 1))
143 string brickname = StringFromList(0, list)
153 dfref dfBefore = GetDataFolderDFR()
154 Execute /q/z "CreateBrowser prompt=\"Select 3D wave\", showWaves=1, showVars=0, showStrs=0"
155 dfref dfAfter = GetDataFolderDFR()
156 SetDataFolder dfBefore
158 SVAR list = S_BrowserList
161 if ((flag != 0) && (ItemsInList(list) >= 1))
162 string brickname = StringFromList(0, list)
191 sprintf cmd, "ad_connect(\"%s\", \"%s\")", epicsname, nickname
197 sprintf cmd, "ModifyGraph wbRGB=%s", wbRGB
199 sprintf cmd, "add_roi_controls()"
224 sprintf cmd, "ad_connect(\"%s\", \"%s\")", epicsname, nickname
226 sprintf cmd, "display; appendimage root:pearl_epics:%s:image", nickname
228 sprintf cmd, "ModifyGraph wbRGB=%s", wbRGB
230 cmd = "ModifyGraph height={Plan,1,left,bottom}
" 242 function PearlAnglescanTracker(epicsname, wbRGB) 249 sprintf cmd, " ModifyGraph wbRGB=%s
", wbRGB 261 function PearlSampleTracker(action) 264 sprintf cmd, " sample_tracker(%u)
", action
-
-
variable ad_load_dialog(string APathName)
load area detector data files selected in a file dialog window
-
variable ad_brick_slicer(wave data)
open a slicer panel for 3D data.
-
variable ast_setup()
set up data structures, display graph, and try to connect to analyser.
-
-
-
-
-
-
-
-
variable otf_gather_batch(string ywavematch, string xwavematch, string destfolder)
-
variable asp_show_panel()
create the angle scan processing panel
-
variable otf_rename_folders(string pattern, variable unique_index=defaultValue, string new_suffix=defaultValue, string match_str=defaultValue)
-
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
-
variable pearl_data_explorer()
-
-
string ad_display_slice(wave data)
display three-dimensional data by 2D slice.
-
variable pearl_elog(string logbook)
main function to initialize ELOG and to open an ELOG panel.
-
string ad_display_brick(wave data)
open a new "gizmo" window with three-dimensional data.
-
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=1 // Use modern global access method.
+
3 #pragma ModuleName = PearlMenu
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
21 help = {
"Data explorer panel with file import and preview" ,
"Requires ARPES package and HDF5 XOP" }
+
+
23 help = {
"Import area detector HDF5 data file" ,
"Requires ARPES package and HDF5 XOP" }
+
+
+
26 submenu
"On-the-Fly Data"
+
+
28 help = {
"Renames otf_xxxxxx_yyyyyy_zzzz data folders to otf_yyyyyy (removing date and suffix)" ,
"Requires Optics package" }
+
+
30 help = {
"Copies data from all otf_* folders into otf_batch folder" ,
"Requires Optics package" }
+
31 PearlMenuEnableFunc (
"PearlOpticsPreviewPanel" ) +
"OTF Preview" , /Q, PearlOpticsPreviewPanel()
+
32 help = {
"Opens a preview panel for OTF data in otf_* folders" ,
"Requires Optics package" }
+
+
+
35 submenu
"Scienta Analyser"
+
+
37 help = {
"Display preview panel with latest image from Scienta" ,
"Requires ARPES package and EPICS XOP" }
+
+
39 help = {
"Preview of acquired angle scan data and current detection angles." ,
"Requires ARPES package and EPICS XOP" }
+
+
41 help = {
"Live tracking and adjustment of sample position." ,
"Requires ARPES package and EPICS XOP" }
+
+
+
+
+
46 help = {
"Display preview panel with latest image from Scienta" ,
"Requires ARPES package and EPICS XOP" }
+
+
48 help = {
"Display live panel of the exit slit camera" ,
"Requires ARPES package and EPICS XOP" }
+
+
+
+
+
53 help = {
"Profiles display of 2D data" ,
"Requires ARPES package" }
+
+
55 help = {
"Slice and profiles display of 3D data" ,
"Requires ARPES package" }
+
+
57 help = {
"Gizmo display of 3D data" ,
"Requires ARPES package" }
+
+
+
+
+
62 help = {
"Data processing of two-pi angle scans" ,
"Requires ARPES package" }
+
+
+
+
+
67 help = {
"Open an ELOG panel to send entries to an ELOG logbook" }
+
+
+
70 submenu
"Sample Preparation"
+
+
72 help = {
"Sample annealing ramp generator" }
+
+
+
+
+
77 help = {
"Data processing and analysis for ARPES experiments" }
+
+
79 help = {
"Process control for sample preparation" }
+
+
81 help = {
"Data processing and analysis for beamline commissioning" }
+
+
+
+
+
+
92 if (exists(funcname) >= 3)
+
+
+
+
+
+
+
+
100 execute /p/q/z "INSERTINCLUDE \"pearl-optics\""
+
101 execute /p/q/z "COMPILEPROCEDURES "
+
102 execute /p/q/z "BuildMenu \"PEARL\""
+
+
+
+
106 execute /p/q/z "INSERTINCLUDE \"pearl-arpes\""
+
107 execute /p/q/z "COMPILEPROCEDURES "
+
108 execute /p/q/z "BuildMenu \"PEARL\""
+
+
+
+
112 execute /p/q/z "INSERTINCLUDE \"pearl-preparation\""
+
113 execute /p/q/z "COMPILEPROCEDURES "
+
114 execute /p/q/z "BuildMenu \"PEARL\""
+
+
+
+
118 dfref dfBefore = GetDataFolderDFR()
+
119 Execute /q/z "CreateBrowser prompt=\"Select 2D wave\", showWaves=1, showVars=0, showStrs=0"
+
120 dfref dfAfter = GetDataFolderDFR()
+
121 SetDataFolder dfBefore
+
+
123 SVAR list = S_BrowserList
+
+
+
126 if ((flag != 0) && (ItemsInList(list) >= 1))
+
127 string brickname = StringFromList(0, list)
+
+
+
+
+
+
+
+
135 dfref dfBefore = GetDataFolderDFR()
+
136 Execute /q/z "CreateBrowser prompt=\"Select 3D wave\", showWaves=1, showVars=0, showStrs=0"
+
137 dfref dfAfter = GetDataFolderDFR()
+
138 SetDataFolder dfBefore
+
+
140 SVAR list = S_BrowserList
+
+
+
143 if ((flag != 0) && (ItemsInList(list) >= 1))
+
144 string brickname = StringFromList(0, list)
+
+
+
+
+
+
+
+
+
+
154 dfref dfBefore = GetDataFolderDFR()
+
155 Execute /q/z "CreateBrowser prompt=\"Select 3D wave\", showWaves=1, showVars=0, showStrs=0"
+
156 dfref dfAfter = GetDataFolderDFR()
+
157 SetDataFolder dfBefore
+
+
159 SVAR list = S_BrowserList
+
+
+
162 if ((flag != 0) && (ItemsInList(list) >= 1))
+
163 string brickname = StringFromList(0, list)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
192 sprintf cmd, "ad_connect(\"%s\", \"%s\")", epicsname, nickname
+
+
+
+
+
+
198 sprintf cmd, "ModifyGraph wbRGB=%s", wbRGB
+
+
200 sprintf cmd, "add_roi_controls()"
+
+
+
+
+
+
+
+
+
+
225 sprintf cmd, "ad_connect(\"%s\", \"%s\")", epicsname, nickname
+
+
227 sprintf cmd, "display; appendimage root:pearl_epics:%s:image", nickname
+
+
229 sprintf cmd, "ModifyGraph wbRGB=%s", wbRGB
+
+
231 cmd = "ModifyGraph height={Plan,1,left,bottom}
"
+
+
+
+
243 function PearlAnglescanTracker(epicsname, wbRGB)
+
+
+
+
+
+
+
250 sprintf cmd, " ModifyGraph wbRGB=%s
", wbRGB
+
+
+
+
262 function PearlSampleTracker(action)
+
+
+
265 sprintf cmd, " sample_tracker(%u)
", action
+
+
+
variable pearl_data_explorer()
show the pearl data explorer window
string ad_display_slice(wave data)
display three-dimensional data by 2D slice.
variable otf_gather_batch(string ywavematch, string xwavematch, string destfolder)
variable ad_load_dialog(string APathName)
load area detector data files selected in a file dialog window
string ad_display_brick(wave data)
open a new "gizmo" window with three-dimensional data.
variable pearl_elog(string logbook)
main function to initialize ELOG and to open an ELOG panel.
variable asp_show_panel()
create the angle scan processing panel
variable ast_setup()
set up data structures, display graph, and try to connect to analyser.
string ad_display_profiles(wave image, string filter=defaultValue)
open a new profiles graph window.
variable ad_brick_slicer(wave data)
open a slicer panel for 3D data.
variable otf_rename_folders(string pattern, variable unique_index=defaultValue, string new_suffix=defaultValue, string match_str=defaultValue)
PEARL Procedures: pearl-otf-import.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -464,9 +466,9 @@ Functions
diff --git a/doc/html/pearl-otf-import_8ipf_source.html b/doc/html/pearl-otf-import_8ipf_source.html
index ac78ca0..d1bba61 100644
--- a/doc/html/pearl-otf-import_8ipf_source.html
+++ b/doc/html/pearl-otf-import_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-otf-import.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,26 +87,340 @@ $(document).ready(function(){initNavTree('pearl-otf-import_8ipf_source.html','')
pearl-otf-import.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=1 // Use modern global access method. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlOtfImport 39 if (strlen(pathname) <= 0)
41 pathname =
"otf_load_itx" 43 string filelist = IndexedFile($pathname, -1,
".itx" )
44 filelist = ListMatch(filelist, "otf*.itx", ";")
45 variable nfile = ItemsInList(filelist, ";")
47 for (ifile = 0; ifile < nfile; ifile += 1)
48 filename = StringFromList(ifile, filelist, ";")
62 if (strlen(pathname) <= 0)
66 string filelist = IndexedFile($pathname, -1, ".itx")
67 filelist = ListMatch(filelist, matchstr, ";")
68 variable nfile = ItemsInList(filelist, ";")
70 for (ifile = 0; ifile < nfile; ifile += 1)
71 filename = StringFromList(ifile, filelist, ";")
84 dfref savedf = GetDataFolderDFR()
87 newdatafolder /s/o otf_load_itx_temp
88 if (strlen(pathname) > 0)
89 LoadWave /O/P=$pathname/Q/T filename
91 LoadWave /O/Q/T filename
95 foldername = ParseFilePath(3, s_filename, "/", 0, 0)
96 foldername = foldername[0,16]
97 foldername = CleanupName(foldername, 0)
99 renamedatafolder root:otf_load_itx_temp, $foldername
100 printf "loaded otf data from file %s into folder %s\r", s_filename, foldername
119 string prefix, sdate, stime
122 src_folder = GetDataFolder(0, df)
123 sscanf src_folder, "%[^_]_%[0-9]_%[0-9]", prefix, sdate, stime
125 if (strlen(sdate) > 0)
128 if (strlen(stime) > 0)
131 dst_folder = StringByKey("destfolder", sdata)
133 src_name = StringByKey("xwavematch", sdata)
134 src_name = WaveList(src_name, "", "")
135 if (ItemsInList(src_name) >= 1)
136 src_name = StringFromList(0, src_name)
137 dst_name = dst_folder + src_name + df_id
139 duplicate $src_name, $dst_name
142 src_name = StringByKey("ywavematch", sdata)
143 src_name = WaveList(src_name, "", "")
144 if (ItemsInList(src_name) >= 1)
145 src_name = StringFromList(0, src_name)
146 dst_name = dst_folder + src_name + df_id
148 duplicate $src_name, $dst_name
159 return
gather_batch ("otf*", ywavematch, xwavematch, destfolder)
170 dfref savedf = GetDataFolderDFR()
171 newdatafolder /o/s $destfolder
172 destfolder = GetDataFolder(1)
174 string iteratordata = ""
175 iteratordata = ReplaceStringByKey("xwavematch", iteratordata, xwavematch)
176 iteratordata = ReplaceStringByKey("ywavematch", iteratordata, ywavematch)
177 iteratordata = ReplaceStringByKey("destfolder", iteratordata, destfolder)
190 string pattern = StringByKey("pattern", sdata)
191 variable unique_index = NumberByKey("unique_index", sdata)
192 string new_suffix = StringByKey("new_suffix", sdata)
196 string sprefix, sdate, stime, ssuffix
199 src_folder = GetDataFolder(0, df)
201 sscanf src_folder, "otf_%[0-9]_%[0-9]%s", sdate, stime, ssuffix
203 if ((strlen(sdate) == 0) || (strlen(stime) == 0))
208 if (cmpstr(pattern[0], "0") != 0)
209 dst_folder += "_" + sdate
211 if (cmpstr(pattern[1], "0") != 0)
212 dst_folder += "_" + stime
214 if (cmpstr(pattern[2], "0") != 0)
215 if (strlen(new_suffix) > 0)
216 ssuffix = "_" + new_suffix
218 dst_folder += ssuffix
221 if ((unique_index > 0) || (CheckName(dst_folder, 11) != 0))
222 dst_folder = UniqueName(dst_folder + "_", 11, unique_index)
226 print src_folder + " -> " + dst_folder
227 RenameDataFolder $src_folder, $dst_folder
237 variable unique_index
249 dfref savedf = GetDataFolderDFR()
251 if (ParamIsDefault(unique_index))
254 if (ParamIsDefault(new_suffix))
257 if (ParamIsDefault(match_str))
261 string iteratordata = ""
262 iteratordata = ReplaceStringByKey("pattern", iteratordata, pattern)
263 iteratordata = ReplaceNumberByKey("unique_index", iteratordata, unique_index)
264 iteratordata = ReplaceStringByKey("new_suffix", iteratordata, new_suffix)
277 wave ch1 = current_ch1
278 wave ch2 = current_ch2
279 wave pe = photonenergy
281 wave rc = ringcurrent
283 duplicate /o ch1, current_ch1_int
284 wave ch1i = current_ch1_int
285 duplicate /o ch2, current_ch2_int
286 wave ch2i = current_ch2_int
287 duplicate /o pe, photonenergy_int
288 wave pei = photonenergy_int
289 duplicate /o cff, cff_int
291 duplicate /o rc, ringcurrent_int
292 wave rci = ringcurrent_int
294 redimension /n=(npts) ch1i, ch2i, pei, cffi, rci
295 setscale /i x e1, e2, "eV", ch1i, ch2i, pei, cffi, rci
311 duplicate /free win, wtmp
312 smooth /b /e=3 smo, wtmp
313 wout = interp(x, wpe, wtmp)
variable otf_gather_iterator(dfref df, string *sdata)
-
-
variable otf_load_itx(string pathname, string filename)
-
variable otf_interp(variable e1, variable e2, variable npts, variable smo)
-
variable gather_batch(string foldermatch, string ywavematch, string xwavematch, string destfolder)
-
variable otf_load_itx_match(string pathname, string matchstr)
-
variable otf_gather_batch(string ywavematch, string xwavematch, string destfolder)
-
variable otf_rename_folders(string pattern, variable unique_index=defaultValue, string new_suffix=defaultValue, string match_str=defaultValue)
-
variable otf_rename_folders_iterator(dfref df, string *sdata)
-
variable otf_load_itx_all(string pathname)
-
variable otf_smo_int(wave win, wave wout, wave wpe, variable smo)
+
Go to the documentation of this file. 1 #pragma rtGlobals=1 // Use modern global access method.
+
2 #pragma IgorVersion = 6.1
+
3 #pragma ModuleName = PearlOtfImport
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
39 if (strlen(pathname) <= 0)
+
+
41 pathname =
"otf_load_itx"
+
+
43 string filelist = IndexedFile($pathname, -1,
".itx" )
+
44 filelist = ListMatch(filelist, "otf*.itx", ";")
+
45 variable nfile = ItemsInList(filelist, ";")
+
+
47 for (ifile = 0; ifile < nfile; ifile += 1)
+
48 filename = StringFromList(ifile, filelist, ";")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
62 if (strlen(pathname) <= 0)
+
+
+
+
66 string filelist = IndexedFile($pathname, -1, ".itx")
+
67 filelist = ListMatch(filelist, matchstr, ";")
+
68 variable nfile = ItemsInList(filelist, ";")
+
+
70 for (ifile = 0; ifile < nfile; ifile += 1)
+
71 filename = StringFromList(ifile, filelist, ";")
+
+
+
+
+
+
+
+
+
+
+
+
+
84 dfref savedf = GetDataFolderDFR()
+
+
+
87 newdatafolder /s/o otf_load_itx_temp
+
88 if (strlen(pathname) > 0)
+
89 LoadWave /O/P=$pathname/Q/T filename
+
+
91 LoadWave /O/Q/T filename
+
+
+
+
95 foldername = ParseFilePath(3, s_filename, "/", 0, 0)
+
96 foldername = foldername[0,16]
+
97 foldername = CleanupName(foldername, 0)
+
+
99 renamedatafolder root:otf_load_itx_temp, $foldername
+
100 printf "loaded otf data from file %s into folder %s\r", s_filename, foldername
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
119 string prefix, sdate, stime
+
+
+
122 src_folder = GetDataFolder(0, df)
+
123 sscanf src_folder, "%[^_]_%[0-9]_%[0-9]", prefix, sdate, stime
+
+
125 if (strlen(sdate) > 0)
+
+
+
128 if (strlen(stime) > 0)
+
+
+
131 dst_folder = StringByKey("destfolder", sdata)
+
+
133 src_name = StringByKey("xwavematch", sdata)
+
134 src_name = WaveList(src_name, "", "")
+
135 if (ItemsInList(src_name) >= 1)
+
136 src_name = StringFromList(0, src_name)
+
137 dst_name = dst_folder + src_name + df_id
+
+
139 duplicate $src_name, $dst_name
+
+
+
142 src_name = StringByKey("ywavematch", sdata)
+
143 src_name = WaveList(src_name, "", "")
+
144 if (ItemsInList(src_name) >= 1)
+
145 src_name = StringFromList(0, src_name)
+
146 dst_name = dst_folder + src_name + df_id
+
+
148 duplicate $src_name, $dst_name
+
+
+
+
+
+
+
+
+
+
+
159 return
gather_batch ("otf*", ywavematch, xwavematch, destfolder)
+
+
+
+
+
+
+
+
+
+
+
170 dfref savedf = GetDataFolderDFR()
+
171 newdatafolder /o/s $destfolder
+
172 destfolder = GetDataFolder(1)
+
+
174 string iteratordata = ""
+
175 iteratordata = ReplaceStringByKey("xwavematch", iteratordata, xwavematch)
+
176 iteratordata = ReplaceStringByKey("ywavematch", iteratordata, ywavematch)
+
177 iteratordata = ReplaceStringByKey("destfolder", iteratordata, destfolder)
+
+
+
+
+
+
+
+
+
+
+
+
+
190 string pattern = StringByKey("pattern", sdata)
+
191 variable unique_index = NumberByKey("unique_index", sdata)
+
192 string new_suffix = StringByKey("new_suffix", sdata)
+
+
+
+
196 string sprefix, sdate, stime, ssuffix
+
+
+
199 src_folder = GetDataFolder(0, df)
+
+
201 sscanf src_folder, "otf_%[0-9]_%[0-9]%s", sdate, stime, ssuffix
+
+
203 if ((strlen(sdate) == 0) || (strlen(stime) == 0))
+
+
+
+
+
208 if (cmpstr(pattern[0], "0") != 0)
+
209 dst_folder += "_" + sdate
+
+
211 if (cmpstr(pattern[1], "0") != 0)
+
212 dst_folder += "_" + stime
+
+
214 if (cmpstr(pattern[2], "0") != 0)
+
215 if (strlen(new_suffix) > 0)
+
216 ssuffix = "_" + new_suffix
+
+
218 dst_folder += ssuffix
+
+
+
221 if ((unique_index > 0) || (CheckName(dst_folder, 11) != 0))
+
222 dst_folder = UniqueName(dst_folder + "_", 11, unique_index)
+
+
+
+
226 print src_folder + " -> " + dst_folder
+
227 RenameDataFolder $src_folder, $dst_folder
+
+
+
+
+
+
+
+
+
+
237 variable unique_index
+
+
+
+
+
+
+
+
+
+
+
+
249 dfref savedf = GetDataFolderDFR()
+
+
251 if (ParamIsDefault(unique_index))
+
+
+
254 if (ParamIsDefault(new_suffix))
+
+
+
257 if (ParamIsDefault(match_str))
+
+
+
+
261 string iteratordata = ""
+
262 iteratordata = ReplaceStringByKey("pattern", iteratordata, pattern)
+
263 iteratordata = ReplaceNumberByKey("unique_index", iteratordata, unique_index)
+
264 iteratordata = ReplaceStringByKey("new_suffix", iteratordata, new_suffix)
+
+
+
+
+
+
+
+
+
+
+
+
+
277 wave ch1 = current_ch1
+
278 wave ch2 = current_ch2
+
279 wave pe = photonenergy
+
+
281 wave rc = ringcurrent
+
+
283 duplicate /o ch1, current_ch1_int
+
284 wave ch1i = current_ch1_int
+
285 duplicate /o ch2, current_ch2_int
+
286 wave ch2i = current_ch2_int
+
287 duplicate /o pe, photonenergy_int
+
288 wave pei = photonenergy_int
+
289 duplicate /o cff, cff_int
+
+
291 duplicate /o rc, ringcurrent_int
+
292 wave rci = ringcurrent_int
+
+
294 redimension /n=(npts) ch1i, ch2i, pei, cffi, rci
+
295 setscale /i x e1, e2, "eV", ch1i, ch2i, pei, cffi, rci
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
311 duplicate /free win, wtmp
+
312 smooth /b /e=3 smo, wtmp
+
313 wout = interp(x, wpe, wtmp)
+
variable gather_batch(string foldermatch, string ywavematch, string xwavematch, string destfolder)
variable otf_gather_batch(string ywavematch, string xwavematch, string destfolder)
variable otf_rename_folders_iterator(dfref df, string *sdata)
variable otf_gather_iterator(dfref df, string *sdata)
variable otf_load_itx_all(string pathname)
variable otf_interp(variable e1, variable e2, variable npts, variable smo)
variable otf_smo_int(wave win, wave wout, wave wpe, variable smo)
variable otf_load_itx_match(string pathname, string matchstr)
variable otf_load_itx(string pathname, string filename)
variable otf_rename_folders(string pattern, variable unique_index=defaultValue, string new_suffix=defaultValue, string match_str=defaultValue)
PEARL Procedures: pearl-pmsco-import.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -103,25 +105,146 @@ Namespaces
string pmsco_save_scan (string pathname, string filename, string energy, string theta, string phi, string alpha, string intensity, string sigma, dfref sdfr=defaultValue) save waves in a PMSCO scan data file. More... save waves in a PMSCO scan data file. More... static string save_scan_helper (string destname, string value, wave template, dfref destdfr, string wavenames) helper function for save_pmsco_scan() More... helper function for save_pmsco_scan() More... string load_pmsco_scan (string pathname, string filename, variable is_modulation=defaultValue, variable quiet=defaultValue) load a PMSCO scan file into the current data folder. More... string load_pmsco_result (string pathname, string filename, variable quiet=defaultValue) load a PMSCO result file into the current data folder. More... string pmsco_load_xyz (string pathname, string filename) load an xyz cluster file More... load an xyz cluster file More... data import/export procedures for multiple scattering calculations.
Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
-
Copyright 2018 Paul Scherrer Institut Copyright 2018 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-pmsco-import.ipf .
◆
+
+
+
+ string load_pmsco_result
+ (
+ string
+ pathname ,
+
+ string
+ filename ,
+
+ variable
+ quiet = defaultValue
+
+ )
+
+
+
+
+
load a PMSCO result file into the current data folder.
+
result files have the extension dat or tasks.dat. this will overwrite existing waves. the function loads all columns.
+
Parameters
+
+ pathname name of a symbolic path filename file name quiet (optional)
+0 (default) print the file name and wave names to the history.
+1 do not print messages to the history.
+
+
+
+
+
+
Definition at line 286 of file pearl-pmsco-import.ipf .
+
+
+
◆
+
+
+
+ string load_pmsco_scan
+ (
+ string
+ pathname ,
+
+ string
+ filename ,
+
+ variable
+ is_modulation = defaultValue,
+
+ variable
+ quiet = defaultValue
+
+ )
+
+
+
+
+
load a PMSCO scan file into the current data folder.
+
the function loads all columns from the file. the waves are named with two-letter names according to the file extension. existing waves are overwritten.
+
the file extension must be etpais or a subset of it, e.g., etpi. the wave names will be en (energy), th (theta), ph (phi), al (alpha), in (intensity) or mo (modulation), and si (sigma).
+
Parameters
+
+ pathname name of igor symbolic path to destination folder. prompt user if empty. filename requested file name. prompt user if empty. the extension must be a string of characters indicating the data of each column. it must be "etpais" or any substring of it, and the columns must be ordered accordingly. if the name contains .modf, the intensity wave is named as mo rather than in. this behaviour can be overridden by the is_modulation flag. is_modulation select whether the intensity column is named mo rather than in.
+0 (default) decide based on existens of .modf in the file name.
+> 0 use mo regardless of file name.
+< 0 use in regardless of file name.
+
+ quiet (optional)
+0 (default) print the file name and wave names to the history.
+1 do not print messages to the history.
+
+
+
+
+
+
Definition at line 207 of file pearl-pmsco-import.ipf .
+
+
+
◆ Definition at line 188 of file pearl-pmsco-import.ipf .
+Definition at line 320 of file pearl-pmsco-import.ipf .
@@ -269,7 +392,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns file name Definition at line 88 of file pearl-pmsco-import.ipf .
+Definition at line 89 of file pearl-pmsco-import.ipf .
@@ -327,7 +450,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); helper function for save_pmsco_scan()
-Definition at line 126 of file pearl-pmsco-import.ipf .
+Definition at line 127 of file pearl-pmsco-import.ipf .
@@ -337,9 +460,9 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-pmsco-import.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,18 +87,224 @@ $(document).ready(function(){initNavTree('pearl-pmsco-import_8ipf_source.html','
pearl-pmsco-import.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.2 3 #pragma ModuleName = PearlPmscoImport 88 function /s
pmsco_save_scan (pathname, filename, energy, theta, phi, alpha, intensity, sigma, [sdfr])
102 dfref savedf = GetDataFolderDFR()
103 dfref tempdf = NewFreeDataFolder()
105 if (ParamIsDefault(sdfr))
109 wave w_intensity = $intensity
110 string wavenames = ""
112 wavenames =
save_scan_helper ("w_energy", energy, w_intensity, tempdf, wavenames)
113 wavenames =
save_scan_helper ("w_theta", theta, w_intensity, tempdf, wavenames)
115 wavenames =
save_scan_helper ("w_alpha", alpha, w_intensity, tempdf, wavenames)
116 wavenames =
save_scan_helper ("w_intensity", intensity, w_intensity, tempdf, wavenames)
117 wavenames =
save_scan_helper ("w_sigma", sigma, w_intensity, tempdf, wavenames)
120 save /b /g /m="\n" /p=$pathname wavenames as filename
134 if (strlen(value) > 0)
135 if (exists(value) == 1)
136 duplicate $value, destdfr:$destname
137 wave /sdfr=destdfr w=$destname
139 duplicate template, destdfr:$destname
140 wave /sdfr=destdfr w=$destname
141 variable numval = str2num(value)
143 if (numtype(numval) == 0)
149 w = DimOffset(template, 0) + DimDelta(template, 0) * p
152 w = DimOffset(template, 1) + DimDelta(template, 1) * q
155 w = DimOffset(template, 2) + DimDelta(template, 2) * r
158 w = DimOffset(template, 3) + DimDelta(template, 3) * s
162 sprintf msg, "invalid %s argument", StringFromList(1, destname, "_")
167 wavenames = AddListItem(destname, wavenames, ";", inf)
168 variable npts = DimSize(w, 0) * max(DimSize(w, 1), 1) * max(DimSize(w, 2), 1) * max(DimSize(w, 3), 1)
169 Redimension /n=(npts) w
192 string cis = "N=at;N=xx;N=yy;N=zz;"
193 LoadWave /A /B=cis /J /K=0 /L={0, 2, 0, 0, 0} /V={
" " ,
" " , 0, 0} /O /P=$pathname filename
195 at = unpadstring(at, 32)
string pmsco_save_scan(string pathname, string filename, string energy, string theta, string phi, string alpha, string intensity, string sigma, dfref sdfr=defaultValue)
save waves in a PMSCO scan data file.
-
static string save_scan_helper(string destname, string value, wave template, dfref destdfr, string wavenames)
helper function for save_pmsco_scan()
-
string pmsco_load_xyz(string pathname, string filename)
load an xyz cluster file
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.2
+
4 #pragma ModuleName = PearlPmscoImport
+
+
+
+
+
+
+
+
+
+
+
+
+
+
89 function /s
pmsco_save_scan (pathname, filename, energy, theta, phi, alpha, intensity, sigma, [sdfr])
+
+
+
+
+
+
+
+
+
+
+
+
+
+
103 dfref savedf = GetDataFolderDFR()
+
104 dfref tempdf = NewFreeDataFolder()
+
+
106 if (ParamIsDefault(sdfr))
+
+
+
+
110 wave w_intensity = $intensity
+
111 string wavenames = ""
+
+
113 wavenames =
save_scan_helper ("w_energy", energy, w_intensity, tempdf, wavenames)
+
114 wavenames =
save_scan_helper ("w_theta", theta, w_intensity, tempdf, wavenames)
+
+
116 wavenames =
save_scan_helper ("w_alpha", alpha, w_intensity, tempdf, wavenames)
+
117 wavenames =
save_scan_helper ("w_intensity", intensity, w_intensity, tempdf, wavenames)
+
118 wavenames =
save_scan_helper ("w_sigma", sigma, w_intensity, tempdf, wavenames)
+
+
+
121 save /b /g /m="\n" /p=$pathname wavenames as filename
+
+
+
+
+
+
+
+
+
+
+
+
135 if (strlen(value) > 0)
+
136 if (exists(value) == 1)
+
137 duplicate $value, destdfr:$destname
+
138 wave /sdfr=destdfr w=$destname
+
+
140 duplicate template, destdfr:$destname
+
141 wave /sdfr=destdfr w=$destname
+
142 variable numval = str2num(value)
+
+
144 if (numtype(numval) == 0)
+
+
+
+
+
+
150 w = DimOffset(template, 0) + DimDelta(template, 0) * p
+
+
+
153 w = DimOffset(template, 1) + DimDelta(template, 1) * q
+
+
+
156 w = DimOffset(template, 2) + DimDelta(template, 2) * r
+
+
+
159 w = DimOffset(template, 3) + DimDelta(template, 3) * s
+
+
+
+
163 sprintf msg, "invalid %s argument", StringFromList(1, destname, "_")
+
+
+
+
+
168 wavenames = AddListItem(destname, wavenames, ";", inf)
+
169 variable npts = DimSize(w, 0) * max(DimSize(w, 1), 1) * max(DimSize(w, 2), 1) * max(DimSize(w, 3), 1)
+
170 Redimension /n=(npts) w
+
+
+
+
+
+
+
+
+
+
+
210 variable is_modulation
+
+
+
213 if (ParamIsDefault(quiet))
+
+
+
+
217 loadwave /p=$pathname /a /g /o /q filename
+
+
219 if (ParamIsDefault(is_modulation))
+
220 is_modulation = StringMatch(s_filename, "*.modf.*")
+
+
222 is_modulation = is_modulation > 0
+
+
+
+
+
+
228 fileext = StringFromList(ItemsInList(s_filename, ".") - 1, s_filename, ".")
+
229 variable nw = ItemsInList(s_wavenames)
+
+
+
232 for (iw = 0; iw < nw; iw += 1)
+
233 sw1 = StringFromlist(iw, s_wavenames)
+
234 strswitch(fileext[iw])
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
258 duplicate /o $sw1, $sw2
+
+
260 waves = AddListItem(sw2, waves, ",", inf)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
291 if (ParamIsDefault(quiet))
+
+
+
+
+
296 loadwave /p=$pathname /a /w /g /o /q filename
+
+
298 loadwave /p=$pathname /a /w /g /o filename
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
324 string cis = "N=at;N=xx;N=yy;N=zz;"
+
325 LoadWave /A /B=cis /J /K=0 /L={0, 2, 0, 0, 0} /V={
" " ,
" " , 0, 0} /O /P=$pathname filename
+
+
327 at = unpadstring(at, 32)
+
static string save_scan_helper(string destname, string value, wave template, dfref destdfr, string wavenames)
helper function for save_pmsco_scan()
string load_pmsco_result(string pathname, string filename, variable quiet=defaultValue)
load a PMSCO result file into the current data folder.
string pmsco_save_scan(string pathname, string filename, string energy, string theta, string phi, string alpha, string intensity, string sigma, dfref sdfr=defaultValue)
save waves in a PMSCO scan data file.
string load_pmsco_scan(string pathname, string filename, variable is_modulation=defaultValue, variable quiet=defaultValue)
load a PMSCO scan file into the current data folder.
string pmsco_load_xyz(string pathname, string filename)
load an xyz cluster file
PEARL Procedures: pearl-polar-coordinates.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -154,7 +156,7 @@ Functions
@@ -184,7 +186,7 @@ Functions
@@ -238,7 +240,7 @@ Functions
@@ -268,7 +270,7 @@ Functions
@@ -310,7 +312,7 @@ Functions
@@ -320,9 +322,9 @@ Functions
diff --git a/doc/html/pearl-polar-coordinates_8ipf_source.html b/doc/html/pearl-polar-coordinates_8ipf_source.html
index 4a80f72..90d2379 100644
--- a/doc/html/pearl-polar-coordinates_8ipf_source.html
+++ b/doc/html/pearl-polar-coordinates_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-polar-coordinates.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,20 +87,106 @@ $(document).ready(function(){initNavTree('pearl-polar-coordinates_8ipf_source.ht
pearl-polar-coordinates.ipf
-
Go to the documentation of this file. 3 #pragma IgorVersion = 6.1 4 #pragma ModuleName = PearlPolarCoordinates 13 variable &radius, &theta, &phi
15 radius = sqrt(xx^2 + yy^2 + zz^2)
18 theta = acos(zz / radius) * 180 / pi
24 phi = atan(yy / xx) * 180 / pi
26 phi = atan(yy / xx) * 180 / pi + 180
42 out[0][] = sqrt(in[0][q]^2 + in[1][q]^2 + in[2][q]^2)
43 out[1][] = acos(in[2][q] / out[0][q]) * 180 / pi
44 out[2][] = atan(in[1][q] / in[0][q]) * 180 / pi + 180 * (in[0][q] < 0)
45 out[2][] = numtype(out[2][q]) == 0 ? out[2][q] : 90 + 180 * (in[1][q] < 0)
50 variable radius, theta, phi
51 variable &xx, &yy, &zz
53 xx = radius * sin(theta * pi / 180) * cos(phi * pi / 180)
54 yy = radius * sin(theta * pi / 180) * sin(phi * pi / 180)
55 zz = radius * cos(theta * pi / 180)
64 out[0][] = in[0][q] * sin(in[1][q] * pi / 180) * cos(in[2][q] * pi / 180)
65 out[1][] = in[0][q] * sin(in[1][q] * pi / 180) * sin(in[2][q] * pi / 180)
66 out[2][] = in[0][q] * cos(in[1][q] * pi / 180)
71 variable polar1, azim1
73 variable polar2, azim2
76 variable xx1, yy1, zz1
77 variable xx2, yy2, zz2
80 polar2cart(1, polar2, azim2, xx2, yy2, zz2)
83 vv = (xx1 * xx2 + yy1 * yy2 + zz1 * zz2) / sqrt(xx1^2 + yy1^2 + zz1^2) / sqrt(xx2^2 + yy2^2 + zz2^2)
84 return acos(vv) * 180 / pi
variable polar2cart_wave(wave in, wave out)
-
variable cart2polar(variable xx, variable yy, variable zz, variable *radius, variable *theta, variable *phi)
-
variable cart2polar_wave(wave in, wave out)
-
variable polar_distance(variable polar1, variable azim1, variable polar2, variable azim2)
-
variable polar2cart(variable radius, variable theta, variable phi, variable *xx, variable *yy, variable *zz)
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
+
+
4 #pragma IgorVersion = 6.1
+
5 #pragma ModuleName = PearlPolarCoordinates
+
+
+
+
+
+
+
+
+
14 variable &radius, &theta, &phi
+
+
16 radius = sqrt(xx^2 + yy^2 + zz^2)
+
+
+
19 theta = acos(zz / radius) * 180 / pi
+
+
+
+
+
+
25 phi = atan(yy / xx) * 180 / pi
+
+
27 phi = atan(yy / xx) * 180 / pi + 180
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
43 out[0][] = sqrt(in[0][q]^2 + in[1][q]^2 + in[2][q]^2)
+
44 out[1][] = acos(in[2][q] / out[0][q]) * 180 / pi
+
45 out[2][] = atan(in[1][q] / in[0][q]) * 180 / pi + 180 * (in[0][q] < 0)
+
46 out[2][] = numtype(out[2][q]) == 0 ? out[2][q] : 90 + 180 * (in[1][q] < 0)
+
+
+
+
+
51 variable radius, theta, phi
+
52 variable &xx, &yy, &zz
+
+
54 xx = radius * sin(theta * pi / 180) * cos(phi * pi / 180)
+
55 yy = radius * sin(theta * pi / 180) * sin(phi * pi / 180)
+
56 zz = radius * cos(theta * pi / 180)
+
+
+
+
+
+
+
+
+
65 out[0][] = in[0][q] * sin(in[1][q] * pi / 180) * cos(in[2][q] * pi / 180)
+
66 out[1][] = in[0][q] * sin(in[1][q] * pi / 180) * sin(in[2][q] * pi / 180)
+
67 out[2][] = in[0][q] * cos(in[1][q] * pi / 180)
+
+
+
+
+
72 variable polar1, azim1
+
+
74 variable polar2, azim2
+
+
+
77 variable xx1, yy1, zz1
+
78 variable xx2, yy2, zz2
+
+
+
+
+
+
84 vv = (xx1 * xx2 + yy1 * yy2 + zz1 * zz2) / sqrt(xx1^2 + yy1^2 + zz1^2) / sqrt(xx2^2 + yy2^2 + zz2^2)
+
85 return acos(vv) * 180 / pi
+
variable polar2cart(variable radius, variable theta, variable phi, variable *xx, variable *yy, variable *zz)
variable cart2polar(variable xx, variable yy, variable zz, variable *radius, variable *theta, variable *phi)
variable cart2polar_wave(wave in, wave out)
variable polar_distance(variable polar1, variable azim1, variable polar2, variable azim2)
variable polar2cart_wave(wave in, wave out)
PEARL Procedures: pearl-pshell-import.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -107,227 +109,217 @@ Namespaces
variable psh5_open_file (string ANickName, string APathName, string AFileName) open a HDF5 file created by the PShell data acquisition program and prepare the data folder. More... variable psh5_close_file (variable fileID) close a HDF5 file opened by psh5_open_file. More... string psh5_load_complete (string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue) load everything from a PShell data file. More... string psh5_load_preview (string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue, string pref_scans=defaultValue, string pref_datasets=defaultValue) load a preview image from a PShell data file. More... string psh5_load_scan_complete (variable fileID, string scanpath, variable load_data=defaultValue, variable load_attr=defaultValue) load all data of a selected scan from a PShell data file. More... string psh5_list_scans (variable fileID) list scan groups of a PShell data file. More... string psh5_list_scan_datasets (variable fileID, string scanpath, variable include_regions=defaultValue) list datasets of a PShell scan group. More... string psh5_list_scan_regions (variable fileID, string scanpath) list regions of a PShell scan group. More... string psh5_load_scan_data (variable fileID, string scanpath) load all datasets of a PShell scan group. More... string psh5_load_scan_attrs (variable fileID, string scanpath, variable attr_sets=defaultValue) load attributes of a PShell scan group. More... string psh5_load_scan_meta (variable fileID, string scanpath) load metadata of a PShell scan group. More... string psh5_load_dataset (variable fileID, string scanpath, string datasetname, variable set_scale=defaultValue) load a dataset from an open PShell HDF5 file. More... static string select_dataset (string file_datasets, string pref_datasets) select the preferred dataset from a list of available datasets. More... string psh5_load_scan_preview (variable fileID, string scanpath, variable set_scale=defaultValue, string pref_datasets=defaultValue) load a preview dataset from an open PShell HDF5 file. More... string psh5_load_scan_section (variable fileID, string scanpath, variable dim, variable set_scale=defaultValue, string pref_datasets=defaultValue) load a longitudinal section of a scan from an open PShell HDF5 file. More... variable psh5_load_dataset_meta (variable fileID, string datapath, string datasetname, wave datawave) load metadata of a PShell dataset. More... string psh5_load_dataset_slabs (variable fileID, string datapath, string datasetname, variable progress=defaultValue) load a dataset slab-wise from the open PShell HDF5 file. More... string psh5_load_dataset_slab (variable fileID, string datapath, string datasetname, variable dim2start, variable dim2count, variable dim3start, variable dim3count) load a single image from the open PShell data file. More... variable ps_set_dimlabels (wave data) set dimension labels according to the axis type More... variable ps_set_dimlabels2 (wave data, string name) set dimension labels according to the axis type More... static dfr find_scan_folder (dfref dataDF) find the scan folder More... static dfr find_attr_folder (dfref dataDF) find the attributes data folder More... variable ps_scale_datasets () set the dimension scales of loaded PShell Scienta datasets according to attributes. More... variable ps_scale_dataset (wave data) set the dimension scales of a loaded PShell Scienta dataset according to attributes. More... static wave find_scale_wave (string name, dfref dataDF, dfref scanDF, dfref attrDF) variable ps_detect_scale (wave ax, wave lo, wave hi, wave un) detect the dimension scales from attributes. More... variable ps_scale_dataset_2 (wave data, wave ax, wave lo, wave hi, wave un) set the dimension scales of a dataset. More... string psh5_load_reduced (string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue) load and reduce the ScientaImage dataset of the first scan of a PShell data file. More... string psh5_load_dataset_reduced (variable fileID, string scanpath, string datasetname, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue) load a reduced dataset from the open PShell HDF5 file. More... static threadsafe variable reduce_slab_worker (funcref reduction_func) static threadsafe wave reduce_slab_image (wave slabdata, wave image, funcref reduction_func, string reduction_param) string psh5_load_info (string APathName, string AFileName) load descriptive info from a PShell data file. More... string psh5_load_scan_info (variable fileID, string scanpath) load descriptive info from a PShell scan. More... dfr psh5_load (string path_name, string file_name, string scans, string regions, string datasets, variable classes=defaultValue, variable max_rank=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue, dfref dest_df=defaultValue) main data loading function More... dfr psh5_preview (string path_name, string file_name, dfref dest_df=defaultValue, string preview_datasets=defaultValue) load preview More... dfr psh5_open_file (string path_name, string file_name, dfref dest_df=defaultValue) open a HDF5 file created by the PShell data acquisition program and prepare the data folder. More... variable psh5_close_file (dfref file_df) close a HDF5 file opened by psh5_open_file. More... static string twave2list (wave wt, string sep) convert text wave to list. More... convert text wave to list. More... static string wave2list (wave w, string format, string sep) convert numeric wave to list. More... convert numeric wave to list. More... string psh5_list_scans (variable file_id) list scan groups of a PShell data file. More... string psh5_list_all_datasets (variable file_id) list all datasets in a file More... variable[string datatypes, string ranks, string dimensions] psh5_list_dataset_info (string variable, string file_id, variable string, sds datasets) list data types and dimensions of datasets More... string psh5_filter_datasets_rank (string datasets, string ranks, variable min_rank, variable max_rank) filter datasets by rank More... static string unique_strings (string list) remove duplicate items from list More... string psh5_extract_scan_paths (string datasets) trim dataset paths to the scan part More... string psh5_extract_region_paths (string datasets) trim dataset paths to the scan/region part More... string psh5_match_dataset_classes (string datasets, variable classes, string positioners=defaultValue, string detectors=defaultValue) filter a list of datasets by classification More... dfr psh5_create_folders (string datasetpath) create all data folders along a dataset path More... dfr psh5_dataset_to_folder (dfref parent_df, string datasetpath) map dataset path to datafolder path More... string ps_fix_folder_name (string group_name) convert HDF5 group name to data folder name and fix compatibility issues More... string psh5_load_datasets (dfref file_df, string datasets, variable create_folders=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue) load multiple datasets from open file More... string psh5_load_dataset (dfref file_df, string datasetpath, variable create_folders=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue) load a dataset from an open PShell HDF5 file. More... string psh5_load_dataset_slabs (dfref file_df, string datasetpath, variable create_folders=defaultValue, variable progress=defaultValue) load a dataset slab-wise from the open PShell HDF5 file. More... string psh5_load_dataset_reduced (dfref file_df, string datasetpath, funcref reduction_func, string reduction_params, variable create_folders=defaultValue, variable progress=defaultValue, variable nthreads=defaultValue) load a dataset with reduced dimensionality More... static threadsafe variable reduce_slab_worker (funcref reduction_func) static threadsafe wave reduce_slab_image (wave slabdata, wave image, funcref reduction_func, string reduction_params) string psh5_load_general_group (dfref file_df) load organizational metadata from the general group. More... string psh_load_general_string (dfref file_df, string name) load a string from the general group. More... variable psh5_load_dataset_meta (dfref file_df, string datasetpath, wave datawave) load metadata of a PShell dataset. More... string psh5_load_scan_meta (dfref file_df, string scanpath) load metadata of a PShell scan group. More... variable ps_set_dimlabels (wave data) set dimension labels according to the axis type More... variable ps_set_dimlabels2 (wave data, string name) set dimension labels according to the axis type More... dfr ps_find_scan_folder (dfref data_df) find the scan folder of current data More... dfr ps_find_attr_folder (dfref scan_df) find the attributes data folder More... wave ps_find_scale_wave (string name, dfref df1, dfref df2, dfref df3) find a wave in scan and attr data folders More... variable ps_detect_scale (dfref data_df, wave ax, wave lo, wave hi, wave un) detect the dimension scales from attributes. More... variable ps_scale_dataset_2 (wave data, wave ax, wave lo, wave hi, wave un) set the dimension scales of a dataset. More... variable ps_scale_datasets (dfref scan_df) set the dimension scales of loaded PShell Scienta datasets according to attributes. More... variable ps_scale_dataset (wave data) set the dimension scales of a loaded PShell Scienta dataset according to attributes. More... string kill_matching_waves (dfref dfr, string pattern, variable recurse, string killed=defaultValue) kill any waves matching a pattern in the experiment More...
const string kEnergyDimLabel = "energy" Dimension label for the energy dispersive dimension of multi-dimensional datasets. More... Dimension label for the energy dispersive dimension of multi-dimensional datasets. More... const string kAngleDimLabel = "angle" Dimension label for the angle dispersive dimension of multi-dimensional datasets. More... Dimension label for the angle dispersive dimension of multi-dimensional datasets. More... const string kScanDimLabel = "scan" Dimension label for the scan dimension of multi-dimensional datasets. More... Dimension label for the scan dimension of multi-dimensional datasets. More... const string kDataDimLabel = "data" Dimension label for the data dimension. More... Dimension label for the data dimension. More... const string kPreviewDatasets = "ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent;" List of preferred datasets to load for preview. More... const string kPreviewDatasets = "ImageEnergyDistribution;ScientaSpectrum;ScientaImage;Counts;SampleCurrent;" List of preferred datasets to load for preview. More... const string kScientaScalingDatasets = "LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;" List of datasets that must be loaded to determine the axis scaling of a Scienta image. More... const string kScientaScalingDatasets = "LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;Eph;" List of datasets that must be loaded to determine the axis scaling of a Scienta image. More... const string kEssentialDiagnostics = "ManipulatorX;ManipulatorY;ManipulatorZ;ManipulatorTheta;ManipulatorTilt;ManipulatorPhi;MonoEnergy;" List of diagnostic datasets that are normally loaded with a scan. More... const string kTransposedDatasets = "ScientaImage;" List of datasets that should be transposed upon loading. More... List of datasets that must be transposed upon loading. More... const variable kDetectorSensitivity = 1 multiply scienta detector intensity by this value to get actual counts. More... const variable kDSCPositioners = 0x0001 const variable kDSCDetectors = 0x0002 const variable kDSCScientaScaling = 0x0004 const variable kDSCPreview = 0x0008 const variable kDSCEssentialDiags = 0x0010 const variable kDSCAttrs = 0x0020 const variable kDSCDiags = 0x0040 const variable kDSCSnaps = 0x0080 const variable kDSCMeta = 0x0100 const variable kDSCMonitors = 0x0200 const variable kDSCRegions = 0x0400 const variable kDSCOther = 0x8000 const variable kDSCAll = 0xffff
import data from PShell
-
HDF5 file import from the PShell data acquisition program. the main import functions are:
+
HDF5 file import from the PShell data acquisition program.
+
the module provides two main entry functions:
-
the following helper functions are also needed:
-
+
Version up to igor 8, this module requires the HDF5 XOP which must be enabled manually. as of igor 9 and later, HDF5 is built in.
+
+in version 2.0, the interface has changed significantly. Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
-
Copyright 2013-18 Paul Scherrer Institut Copyright 2013-22 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-pshell-import.ipf .
◆ ◆
-
-
-
- static dfr find_attr_folder
+ string kill_matching_waves
(
dfref
- dataDF )
- dfr ,
-
-
-
-static
-
-
-
-
-◆
-
-
-
-
-
- static wave find_scale_wave
- (
+ string
- name , pattern ,
dfref
- dataDF , variable
+ recurse ,
dfref
- scanDF ,
-
- dfref
- attrDF string
+ killed = defaultValue
-
-
-static
-
-
-
Definition at line 1564 of file pearl-pshell-import.ipf .
+
kill any waves matching a pattern in the experiment
+
this may be used to kill big waves of original data before saving.
+
example: to kill all ScientaImage waves:
+
Definition at line 2554 of file pearl-pshell-import.ipf .
◆
-
-
-
-
-
-
- static dfr find_scan_folder
- (
- dfref
- dataDF )
-
-
-
-
-static
-
-
-
-
-
find the scan folder
-
the scan folder is the one that contains the :attr folder the data and scan folders may refer to the same folder.
-
-
Definition at line 1459 of file pearl-pshell-import.ipf .
-
-
-
◆ ◆
@@ -386,6 +346,12 @@ Licensed under the Apache License, Version 2.0 (the "License");
variable ps_detect_scale
(
+ dfref
+ data_df ,
+
+ wave
ax ,
@@ -416,15 +382,15 @@ Licensed under the Apache License, Version 2.0 (the "License");
detect the dimension scales from attributes.
-
the function checks the data , scan and attributes folders for scan parameters. the results are written to the provided waves. the function is normally called by ps_scale_datasets() but can also be used independently.
-
the current datafolder must be the data or the scan folder. the data folder contains the waves that are to be scaled. the scan folder contains the scan positions and the :attr folder.
+
the function checks the data , scan and attributes folders for scan parameters. the results are written to the provided waves. the function is normally called by ps_scale_datasets() but can also be used independently.
+
the data folder contains the waves that are to be scaled. the function looks for the scan positions and diagnostics as necessary. if the scaling data is not found, the scales are not changed. the kEssentialDiags flag can be used with psh5_load() to select the necessary datasets.
the provided waves are redimensioned by the function, and dimension labels are set. the scale parameters can then be extracted by keyword, e.g.,
lo[%energy] analyser energy dimension. lo[%angle] analyser angle dimension. lo[%scan] scan dimension. lo[%data] data dimension.
-
the function tries to read the following waves, in the data, scan, and attributes folders, where the first folder in the list takes precedence. it may fall back to more or less reasonable default values if no data is not found.
+the function tries to read the following waves, in the data, scan, and attributes/diagnostics folders, where the first folder in the list takes precedence. it may fall back to more or less reasonable default values if no data is not found.
LensMode ScientaChannelBegin ScientaChannelEnd
Parameters
+ data_df data folder which contains the waves to be scaled. this is usually the "scan" or "region" folder. ax text wave to receive the axis labels. lo wave to receive the lower limits. hi wave to receive the upper limits.
Returns the function results are written to the lo, hi, un, and ax waves. Version this function supports regions from version 1.03. check that you're in the correct data folder! Returns the function results are written to the lo, hi, un, and ax waves. Definition at line 1621 of file pearl-pshell-import.ipf .
+Definition at line 2225 of file pearl-pshell-import.ipf .
+
+
+
+◆
+
+
+
+ dfr ps_find_attr_folder
+ (
+ dfref
+ scan_df )
+
+
+
+
+
find the attributes data folder
+
the attributes folder contains diagnostic beamline data at each scan point. the folder can have one of several names due to different pshell versions: "attr", "attrs", or "diags" (from 2022 on). historically, the folder was named "attr" due to the area detector software.
+
assuming we are in the scan folder (where the ScanWritables, etc.) are, find the associated attributes folder.
+
+
Definition at line 2134 of file pearl-pshell-import.ipf .
+
+
+
◆
+
+
+
+ wave ps_find_scale_wave
+ (
+ string
+ name ,
+
+ dfref
+ df1 ,
+
+ dfref
+ df2 ,
+
+ dfref
+ df3
+
+ )
+
+
+
+
+
find a wave in scan and attr data folders
+
look up a wave by name in the given three data folders. return the first one found.
+
Parameters
+
+ df1 first data folder to check df2 second data folder to check df3 third data folder to check
+
+
+
Returns wave reference, empty reference if not found
+
+
Definition at line 2161 of file pearl-pshell-import.ipf .
+
+
+
◆
+
+
+
+ dfr ps_find_scan_folder
+ (
+ dfref
+ data_df )
+
+
+
+
+
find the scan folder of current data
+
assuming we are in the data folder (where the scan results, ScientaSpectrum, etc.) are, find the associated scan folder. this can either be the same (usually) or the parent folder (multi-region scans).
+
the scan folder is the one that contains the ScanWritables wave. the data and scan folders may refer to the same folder.
+
+
Definition at line 2111 of file pearl-pshell-import.ipf .
+
+
+
◆
+
+
+
+ string ps_fix_folder_name
+ (
+ string
+ group_name )
+
+
+
+
+
convert HDF5 group name to data folder name and fix compatibility issues
+
+
Definition at line 1065 of file pearl-pshell-import.ipf .
set the dimension scales of a loaded PShell Scienta dataset according to attributes.
the current datafolder must contain the :attr folder. the data wave can be in the current folder or a sub-folder.
-the dimension labels of the dataset waves must have been set correctly, e.g. by ps_set_dimlabels() . this is implicitly done by the high-level load functions.
-the function is useful if a single dataset is loaded and scaled. if multiple datasets are loaded, ps_scale_datasets() is slightly more efficient.
+the dimension labels of the dataset waves must have been set correctly, e.g. by ps_set_dimlabels() . this is implicitly done by the high-level load functions.
+the function is useful if a single dataset is loaded and scaled. if multiple datasets are loaded, ps_scale_datasets() is slightly more efficient.
Parameters
- data data wave to be scaled. dimension labels (index -1) must be set correctly, cf. ps_set_dimlabels() . data data wave to be scaled. dimension labels (index -1) must be set correctly, cf. ps_set_dimlabels() .
Version this function supports regions from version 1.03. Definition at line 1550 of file pearl-pshell-import.ipf .
+Definition at line 2528 of file pearl-pshell-import.ipf .
@@ -526,8 +616,8 @@ Licensed under the Apache License, Version 2.0 (the "License");
set the dimension scales of a dataset.
-
the function is normally called by ps_scale_datasets() but can also be used independently. the limits and units must be given as function arguments with proper dimension labels.
-
the provided limit and unit waves must have dimension labels matching the -1 index dimension labels of the data wave, such as set by the ps_detect_scale() function. the scale parameters are extracted by keyword, e.g.,
+the function is normally called by ps_scale_datasets() but can also be used independently. the limits and units must be given as function arguments with proper dimension labels.
+the provided limit and unit waves must have dimension labels matching the -1 index dimension labels of the data wave, such as set by the ps_detect_scale() function. the scale parameters are extracted by keyword, e.g.,
lo[%energy] analyser energy dimension. lo[%angle] analyser angle dimension. lo[%scan] scan dimension. Version this function supports regions from version 1.03. Definition at line 1781 of file pearl-pshell-import.ipf .
+Definition at line 2389 of file pearl-pshell-import.ipf .
-◆ ◆
@@ -559,7 +649,8 @@ Licensed under the Apache License, Version 2.0 (the "License");
variable ps_scale_datasets
(
- )
+ dfref
+ scan_df )
@@ -567,11 +658,16 @@ Licensed under the Apache License, Version 2.0 (the "License");
set the dimension scales of loaded PShell Scienta datasets according to attributes.
datasets listed in the ScanReadables waves are scaled according to the attribute waves in the data, scan, and attributes folders, whichever is found first.
-
the current datafolder must contain the ScanReadables wave and the :attr folder. the ScanReadables text wave contains names of the waves to scale. wave names can include a relative path to a sub-folder. the path separator is "/".
-
the dimension labels of the dataset waves must have been set correctly, e.g. by ps_set_dimlabels() . this is implicitly done by the high-level load functions.
-
Version this function supports regions from version 1.03. check that you're in the correct data folder!
+
the specified datafolder must contain the ScanReadables wave and the :attr folder. the ScanReadables text wave contains names of the waves to scale. wave names can include a relative path to a sub-folder. the path separator is "/".
+
the dimension labels of the dataset waves must have been set correctly, e.g. by ps_set_dimlabels() . this is implicitly done by the high-level load functions.
+
Parameters
+
+ scan_df scan data folder. must contain the ScanReadables wave.
+
+
-
Definition at line 1504 of file pearl-pshell-import.ipf .
+
Definition at line 2483 of file pearl-pshell-import.ipf .
@@ -607,7 +703,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Definition at line 1383 of file pearl-pshell-import.ipf .
+Definition at line 2031 of file pearl-pshell-import.ipf .
@@ -638,7 +734,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
set dimension labels according to the axis type
-
same as ps_set_dimlabels() except that the dimension labels are set according to a separate name argument instead of the wave name.
+
same as ps_set_dimlabels() except that the dimension labels are set according to a separate name argument instead of the wave name.
Parameters
data data wave as loaded from PShell file. Definition at line 1402 of file pearl-pshell-import.ipf .
+Definition at line 2050 of file pearl-pshell-import.ipf .
-◆ ◆
@@ -666,8 +762,8 @@ Licensed under the Apache License, Version 2.0 (the "License");
variable psh5_close_file
(
- variable
- fileID )
+ dfref
+ file_df )
@@ -675,40 +771,70 @@ Licensed under the Apache License, Version 2.0 (the "License"); close a HDF5 file opened by psh5_open_file.
this function just closes the HDF5 file. no change is made to the loaded data.
+the function requires the specified data folder to contain a variable named file_id that specifies the HDF5 file ID. the variable may also be in a parent folder. the variable is killed after the file has been closed. if the folder or variable can't be found, the function does nothing.
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . file_df data folder reference of open HDF5 file from psh5_open_file() . the reference may also point to a child folder, the function will look for a file_id variable in all parent folders.
Note on the command line, data folder references can be specified using the $-notation like $"foldername". the current folder is written as $":". Definition at line 140 of file pearl-pshell-import.ipf .
+Definition at line 509 of file pearl-pshell-import.ipf .
-◆ ◆
- string psh5_list_scan_datasets
+ dfr psh5_create_folders
(
- variable
- fileID , string
+ datasetpath )
+
+
+
+
+
create all data folders along a dataset path
+
if the path ends with a slash, the path is interpreted as a group path, and each part is mapped to a data folder. else, the last part of the path is the name of a dataset and will not produce a folder.
+
the path will always be interpreted as starting from the root, regardless whether it starts with a slash or not.
+
spaces are removed from folder names, and the names are cleaned up to produce simple names.
+
a string variable named "s_hdf5_group" is added to each created folder and contains the incremental path.
+
the first child folder is created in the current data folder. at the end, the lowest child folder is selected and returned as the function result.
+
Parameters
+
+ datasetpath hdf5 group path to dataset, e.g. "/scan 1/region 1/ScientaImage".
+
+
+
Returns data folder reference of the lowest child folder.
+
+
Definition at line 990 of file pearl-pshell-import.ipf .
+
+
+
+◆
+
+
+
+ dfr psh5_dataset_to_folder
+ (
+ dfref
+ parent_df ,
string
- scanpath ,
-
- variable
- include_regions = defaultValue datasetpath
-
list datasets of a PShell scan group.
-
the function returns a list of all datasets of the selected scan. this does not include datasets from the attributes sub-group.
-
Note in a future version, an option may be introduced to filter datasets by function (Readable and/or Writable ).
+
map dataset path to datafolder path
+
if the path ends with a slash, the path is interpreted as a group path, and each part maps to a data folder. if the last part of the path is the name of a dataset, it is discarded.
+
spaces are removed from folder names, and the names are cleaned up to produce simple names.
+
the path is interpreted as relative to the specified parent data folder. regardless whether it starts with a slash or not.
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". datasetpath hdf5 group path to dataset, e.g. "/scan 1/region 1/ScientaImage". parent_df parent data folder
-
Returns semicolon-separated list of dataset paths.
-
Version since version 1.03 this function returns paths relative to scanpath.
+
Returns data folder reference
-
Definition at line 440 of file pearl-pshell-import.ipf .
+
Definition at line 1034 of file pearl-pshell-import.ipf .
◆ ◆
- string psh5_list_scan_regions
+ string psh5_extract_region_paths
(
- variable
- fileID , string
+ datasets )
+
+
+
+
+
trim dataset paths to the scan/region part
+
return dataset paths stripped to the form /scan*/region*/.
+
the function matches each path for scan and region tokens in the first two path elements and strips off the remainder. if there are no region-based datasets, the function returns an empty string.
+
the function operates on a single path or a semicolon-separated list of paths. the items of the returned list are unique.
+
Parameters
+
+ datasets semicolon separated list of dataset paths
+
+
+
Returns list of scan/region paths (no duplicates)
+
+
Definition at line 853 of file pearl-pshell-import.ipf .
+
+
+
+◆
+
+
+
+ string psh5_extract_scan_paths
+ (
+ string
+ datasets )
+
+
+
+
+
trim dataset paths to the scan part
+
return dataset paths stripped to the form /scan*/.
+
the function matches each path for a scan token in the first path element and strips off the remaining path. if there are no scan-based datasets, the function returns an empty string.
+
the function operates on a single path or a semicolon-separated list of paths. the items of the returned list are unique.
+
Parameters
+
+ datasets semicolon separated list of dataset paths
+
+
+
Returns list of scan paths (no duplicates)
+
+
Definition at line 803 of file pearl-pshell-import.ipf .
+
+
+
◆
+
+
+
+ string psh5_filter_datasets_rank
+ (
+ string
+ datasets ,
string
- scanpath ranks ,
+
+ variable
+ min_rank ,
+
+ variable
+ max_rank
-
list regions of a PShell scan group.
-
the function returns a list of all region groups of the selected scan.
+
filter datasets by rank
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". datasets semicolon-separated list of datasets to be checked. ranks semicolon-separated list of ranks of each dataset.
-
Returns semicolon-separated list of datagroup paths.
+
Returns filtered dataset list.
-
Definition at line 481 of file pearl-pshell-import.ipf .
+
Definition at line 728 of file pearl-pshell-import.ipf .
◆ ◆
+
+
+
+ string psh5_list_all_datasets
+ (
+ variable
+ file_id )
+
+
+
+
+
list all datasets in a file
+
the function returns a list of all datasets in a file. each dataset is listed by its full path like, e.g., "/scan 1/region 1/dataset 1".
+
this function wraps a one-line HDF5 operation and is provided just to be more memorable.
+
Parameters
+
+
+
+
Returns semicolon-separated list of absolute dataset paths.
+
+
Definition at line 605 of file pearl-pshell-import.ipf .
+
+
+
◆
+
+
+
+ variable [string datatypes, string ranks, string dimensions] psh5_list_dataset_info
+ (
+ string
+ variable ,
+
+ string
+ file_id ,
+
+ variable
+ string ,
+
+ sds
+ datasets
+
+ )
+
+
+
+
+
list data types and dimensions of datasets
+
this function has multiple returns.
+
Parameters
+
+
+
+
Returns semicolon-separated list of (simplified) datatypes. datatypes are marked as "i" (integer), "f" (float), "s" (string) or "?" (unknown).
+
+semicolon-separated list of ranks (number of dimensions).
+
+semicolon-separated list of dimensions. each item is a comma-separated list of dimension sizes. items do not contain trailing commas.
+
filter a list of datasets by string matching
+
this function can be used to extract certain dataset paths from a list of all datasets in a file. the matching is insensitive to spaces and case.
+
examples match strings:
+"*‍/scan1/region1/*" match all datasets in scan 1, region 1"!*‍/diags/*" remove diagnostics from list
+
Parameters
+
+ datasets semicolon separated list of dataset paths match match string for igor's StringMatch function
+
+
+
Returns list of matching datasets
+
+
Definition at line 631 of file pearl-pshell-import.ipf .
+
+
+
◆
@@ -786,7 +1088,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
string psh5_list_scans
(
variable
-
fileID )
+
file_id )
@@ -796,51 +1098,81 @@ Licensed under the Apache License, Version 2.0 (the "License");
the function returns a list of all top-level groups whose name starts with "scan".
Parameters
Returns semicolon-separated list of group paths.
-
Definition at line 405 of file pearl-pshell-import.ipf .
+
Definition at line 574 of file pearl-pshell-import.ipf .
-◆ ◆
- string psh5_load_complete
+ dfr psh5_load
(
string
- ANickName , path_name ,
string
- APathName , file_name ,
string
- AFileName , scans ,
+
+ string
+ regions ,
+
+ string
+ datasets ,
variable
- load_data = defaultValue, classes = defaultValue,
variable
- load_attr = defaultValue max_rank = defaultValue,
+
+ string
+ reduction_func = defaultValue,
+
+ string
+ reduction_params = defaultValue,
+
+ dfref
+ dest_df = defaultValue
-
load everything from a PShell data file.
+
main data loading function
+
load the requested elements from the given file.
+
scans, regions and datasets are additive. wildcards can be used to select multiple or all datasets.
+
classes are subtractive: only datasets of specified classes are loaded. by default, only positioners, detectors, scaling and essential diagnostics are loaded.
+
essential diags, scaling, positioners related to requested detectors are always loaded
+
data reduction (if specified) applies to 3d data, see psh5_load_dataset_reduced() for details.
Parameters
- ANickName destination folder name (top level under root) APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed AFileName if empty a dialog box shows up load_data select whether datasets (positioners and detectors) are loaded.
-1 (default) load data.
-0 do not load data.
-
- load_attr select whether attributes (auxiliary device readbacks) are loaded. for proper wave scaling, the attributes must be loaded.
-1 (default) load attributes.
-0 do not load attributes.
-
- path_name igor symbolic path name. can be empty if the path is specified in file_name or a dialog box should be displayed file_name if empty a dialog box shows up dest_df destination folder reference. if dest_df is specified, data is loaded into this folder. else, a new folder derived from the file name is created under root: scans semicolon-separated list of scan paths to load. scan groups are at the top level, their name consists of "scan", an optional space and a number. all datasets in the group and sub-groups are considered for loading unless excluded by other arguments. if empty, no datasets are loaded based on their relation to a scan. names are matched by Igor's StringMatch function. the matching is insensitive to case and spaces. to load all scans, pass "/scan*". the leading slash before "scan" can be omitted. regions semicolon-separated list of region paths to load. region groups are children of scan groups, their name consists of "region", an optional space and a number. all datasets in the group and sub-groups are considered for loading unless excluded by other arguments. if empty, no datasets are loaded based on their relation to a region. names are matched by Igor's StringMatch function. the matching is insensitive to case and spaces. to load all regions of scan 1, pass "/scan1/region*". to load regions 1 of all scans, pass "/scan*‍/region1". the leading slash before "scan" can be omitted. datasets semicolon-separated list of dataset paths to load. this allows to load individual datasets. names are matched by Igor's StringMatch function against full dataset paths. to load all datasets named "SampleCurrent", pass "*‍/SampleCurrent". the matching is insensitive to case and spaces. additional datasets may be loaded for scaling. classes filter datasets (that were selected by the scans, regions and datasets arguments) by class. this allows, for example, to exclude the diagnostics. note that scaling datasets are always loaded. the value is a bit-wise switch, typically the arithmetic disjunction of kDSCXxxx constants. by default, only positioners, detectors, scaling and essential diagnostics are loaded. to completely load all datasets, specify kDSCAll. max_rank load only datasets with lower or equal rank.
-
Returns complete path of the loaded file if successful. empty string otherwise.
+Returns data folder reference of the file-level data folder. same as dest_df if specified.
global string s_filepath in new data folder contains the full file path on disk.
-global string s_scanpaths in new data folder contains a list of scan groups inside the file.
+global string s_loaded_datasets in new data folder contains a list of loaded datasets. the items are full group paths of the HDF5 file. dataset paths can be mapped to loaded data folders using the psh5_dataset_to_folder function.
-
Definition at line 170 of file pearl-pshell-import.ipf .
+
Definition at line 158 of file pearl-pshell-import.ipf .
-◆ ◆
@@ -888,26 +1222,32 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
string psh5_load_dataset
(
- variable
- fileID , dfref
+ file_df ,
string
- scanpath ,
-
- string
- datasetname , datasetpath ,
variable
- set_scale = defaultValue create_folders = defaultValue,
+
+ string
+ reduction_func = defaultValue,
+
+ string
+ reduction_params = defaultValue
load a dataset from an open PShell HDF5 file.
-
if the dataset has a maximum of two dimensions, the function loads it at once. if it has more than two dimension, the function calls psh5_load_dataset_slabs() to load the data slab by slab.
+
if the dataset has a maximum of two dimensions, the function loads it at once. if it has more than two dimension, the function calls psh5_load_dataset_slabs() to load the data slab by slab.
-
the dataset is loaded into the current data folder unless datasetname contains a region specifier. in the latter case, the dataset is loaded into sub-folder with the name of the region. the function returns from the original data folder.
+
the dataset is loaded into the current data folder or a tree based on the group path given in the datasetpath argument. the function returns from the original data folder.
+
only numeric and string data types are supported, string datasets must have rank 1.
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". datasetname name of the dataset. the name of the loaded wave is a cleaned up version of the dataset name. the name can include the region name as a relative path, e.g. "region1/ScientaSpectrum". in this case, the dataset is loaded into a sub-folder named "region1". set_scale by default, the function tries to set the wave scaling if the attributes have been loaded. if multiple datasets are loaded from a file, it is more efficient to set the scaling of all loaded datasets at the end by calling ps_scale_datasets() .
-1 (default) set the wave scaling.
-0 do not set the wave scaling.
-
- file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed. datasetpath group path and name of the dataset, e.g. "/scan 1/ScientaImage". HDF5 groups map to igor data folders below the current data folder, the wave is placed into the leaf folder. the names of groups and waves are cleaned up to produce simple names, in particular, spaces and other illegal characters are removed. create_folders if 1 (default), data folders according to the group path are created. if 0, the dataset is loaded into the current folder. reduction_func data reduction function. three-dimensional datasets can be reduced in dimensionality by on-the-fly data reduction. by default (or if empty string), no reduction is applied. see psh5_load_dataset_reduced() . reduction_params parameter string for the reduction function.
-
Returns name of loaded wave if successful. empty string otherwise.
-
Version this function supports regions as of version 1.03.
+
Returns semicolon-separated list of loaded wave names. multiple waves are loaded if the dataset has a compound data type. in that case the wave name is a concatenation of the dataset and field names (see HDF5LoadData).
-
Definition at line 706 of file pearl-pshell-import.ipf .
+
Definition at line 1176 of file pearl-pshell-import.ipf .
-◆ ◆
@@ -954,20 +1290,14 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
variable psh5_load_dataset_meta
(
- variable
- fileID , dfref
+ file_df ,
string
- datapath ,
-
- string
- datasetname , datasetpath ,
load metadata of a PShell dataset.
-
"metadata" are the HDF5 attributes attached to the scan dataset.
-
data is added to the wave note.
+
metadata are the HDF5 attributes attached to a dataset. they are mapped to "key=value" pairs and added to the wave note in separate lines. the following attributes are loaded. names and mappings are hard-coded.
+
+"Writable Dimension" -> "ScanDimension"
+"Writable Index" -> "WriteableIndex"
+"Readable Index" -> "ReadableIndex"
+
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . datapath path to the containing group in the HDF5 file. path separator is the slash "/". datasetname name of the dataset. may include relative path. file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed. datasetpath group path and name of the dataset. path separator is the slash "/". datawave metadata is added to the wave note of this wave.
Returns 0 if successful, non-zero if an error occurred.
-
Definition at line 1091 of file pearl-pshell-import.ipf .
+
Definition at line 1887 of file pearl-pshell-import.ipf .
-◆ ◆
@@ -1010,20 +1343,14 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
string psh5_load_dataset_reduced
(
- variable
- fileID , dfref
+ file_df ,
string
- scanpath ,
-
- string
- datasetname , datasetpath ,
string
- reduction_param , reduction_params ,
+
+ variable
+ create_folders = defaultValue,
-
load a reduced dataset from the open PShell HDF5 file.
-
the function loads the dataset image by image using the hyperslab option and applies a custom reduction function to each image. the results from the reduction function are written to the ReducedData1, ReducedData2, etc. waves. the raw data are discarded.
-
by default, the reduction function is called in separate threads to reduce the total loading time. (see the global variable psh5_perf_secs which reports the total run time of the function.) the effect varies depending on the balance between file loading (image size) and data processing (complexity of the reduction function). for debugging the reduction function, multi-threading can be disabled.
-
if the reduction function requires the image waves to be scaled properly, the attributes must have been loaded by psh5_load_scan_attrs() before. in this case, the scales of the result waves are also set by the function. otherwise, the results can also be scaled by ps_scale_dataset() later.
+
load a dataset with reduced dimensionality
+
the function loads the dataset image by image using the hyperslab option and applies a custom reduction function like numeric integration, curve fitting, etc. to each image. the results from the reduction function are written to the ReducedData1, ReducedData2, etc. waves. the raw data are discarded.
+
example reduction functions can be found in the PearlScientaPreprocess module. they must implement the adh5_default_reduction() interface.
+
by default, the reduction function is called in separate threads to reduce the total loading time. (psh5_load() reports the total run time in the global variable psh5_perf_secs.) the effect varies depending on the balance between file loading (image size) and data processing (complexity of the reduction function).
+
the function loads images (as hyperslabs) one by one and passes them to the reduction function. only a limited number of images are held in the queue at a time to limit memory use. for debugging the reduction function, multi-threading can be disabled (also remove threadsafe attributes from reduce_slab_image() and the reduction function!)
+
if the reduction function requires the image waves to be scaled properly, the attributes must have been loaded by psh5_load_scan_attrs() before. in this case, the scales of the result waves are also set by the function. otherwise, the results can also be scaled by ps_scale_dataset() later.
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed. scanpath path to scan group in the HDF5 file. datasetname name of the dataset. this must currently be "ScientaImage", other data is not supported. the name of the loaded wave is a cleaned up version of the dataset name. the name can include the region name as a relative path, e.g. "region1/ScientaImage". in this case, the dataset is loaded into a sub-folder named "region1". reduction_func custom data reduction function. this can be any user-defined function which has the same parameters as adh5_default_reduction . some reduction functions are predefined in the PearlScientaPreprocess module. reduction_param parameter string for the reduction function. reduction_params parameter string for the reduction function. create_folders if 1 (default), data folders according to the group path are created. if 0, the dataset is loaded into the current folder. progress progress window.
1 (default) show progress window
0 do not show progress window
@@ -1082,91 +1418,14 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
-
Returns semicolon-separated list of the loaded dataset ReducedData1, ReducedData2, etc. if successful. auxiliary waves, scan positions, attributes are loaded but not listed in the string. empty string if an error occurred. error messages are printed to the history.
-
Version this function supports regions as of version 1.03.
+
Returns semicolon-separated list of the loaded dataset ReducedData1, ReducedData2, etc. if successful. auxiliary waves, scan positions, attributes are loaded but not listed in the string. empty string if an error occurred. error messages are printed to the history.
-
Definition at line 2040 of file pearl-pshell-import.ipf .
+
Definition at line 1472 of file pearl-pshell-import.ipf .
◆
-
-
-
- string psh5_load_dataset_slab
- (
- variable
- fileID ,
-
- string
- datapath ,
-
- string
- datasetname ,
-
- variable
- dim2start ,
-
- variable
- dim2count ,
-
- variable
- dim3start ,
-
- variable
- dim3count
-
- )
-
-
-
-
-
load a single image from the open PShell data file.
-
the function can average over a region in the extra dimensions.
-
Parameters
-
- fileID ID of open HDF5 file from psh5_open_file() . datapath path to the containing group in the HDF5 file. path separator is the slash "/". dataset name of the dataset. also defines the name of the loaded wave. dim2start 2nd dimension coordinate of the first image set to 0 if dimension may not be present dim2count number of subsequent images to average set to 1 if dimension may not be present dim3start 3rd dimension coordinate of the first image set to 0 if dimension may not be present dim3count number of subsequent images to average set to 1 if dimension may not be present
-
-
-
Returns name of loaded wave if successful. empty string otherwise.
-
-
Definition at line 1284 of file pearl-pshell-import.ipf .
-
-
-
◆ ◆
@@ -1174,20 +1433,20 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
string psh5_load_dataset_slabs
(
+ dfref
+ file_df ,
+
+ string
+ datasetpath ,
+
+ variable
- fileID ,
-
- string
- datapath ,
-
- string
- datasetname , create_folders = defaultValue,
load a dataset slab-wise from the open PShell HDF5 file.
-
the function loads the dataset image by image using the hyperslab option.
+
the function loads the dataset image by image using the hyperslab option. the wave is loaded into the current data folder.
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . datapath path to the containing group in the HDF5 file. path separator is the slash "/". dataset name of the dataset. also defines the name of the loaded wave. file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed. datasetpath group path and name of the dataset. the dataset name defines the name of the loaded wave (after cleaning up). progress select whether a progress window is displayed during the process.
1 (default) show progress window.
0 do not show progress window.
create_folders if 1 (default), data folders according to the group path are created. if 0, the dataset is loaded into the current folder.
-
Returns name of loaded wave if successful. empty string otherwise.
+
Returns semicolon-separated list of loaded wave names. in the current version, the function returns zero or one wave, as it does not support compound types.
-
Definition at line 1148 of file pearl-pshell-import.ipf .
+
Definition at line 1289 of file pearl-pshell-import.ipf .
-◆ ◆
- string psh5_load_info
+ string psh5_load_datasets
(
- string
- APathName , dfref
+ file_df ,
string
- AFileName datasets ,
+
+ variable
+ create_folders = defaultValue,
+
+ string
+ reduction_func = defaultValue,
+
+ string
+ reduction_params = defaultValue
-
load descriptive info from a PShell data file.
-
the info string lists the following information for each scan contained in the file:
-path of the scan group inside the file.
-number of scan positions.
-dataset names of scan positioners.
-dataset names of detectors.
-
+
load multiple datasets from open file
Parameters
- APathName igor symbolic path name. can be empty if the path is specified in AFileName or a dialog box should be displayed AFileName if empty a dialog box shows up file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed. create_folders if 1 (default), data folders according to the group path are created. if 0, the dataset is loaded into the current folder. the latter option should be used with care because datasets with same names may be overwritten. reduction_func data reduction function. three-dimensional datasets can be reduced in dimensionality by on-the-fly data reduction. by default (or if empty string), no reduction is applied. see psh5_load_dataset_reduced() . reduction_params parameter string for the reduction function.
-
Returns newline terminated string.
+
Returns (string) semicolon-separated list of loaded datasets
-
Definition at line 2367 of file pearl-pshell-import.ipf .
+
Definition at line 1098 of file pearl-pshell-import.ipf .
-◆ ◆
- string psh5_load_preview
+ string psh5_load_general_group
(
- string
- APathName ,
-
- dfref
+ file_df )
string
- AFileName ,
-
- variable
- load_data = defaultValue,
-
- variable
- load_attr = defaultValue,
-
- string
- pref_scans = defaultValue,
-
- string
- pref_datasets = defaultValue
-
- )
-
-
load a preview image from a PShell data file.
-
the data wave is loaded into the current data folder. attributes are loaded into the attr subfolder. existing waves in attr are deleted.
+
load organizational metadata from the general group.
+
the general group contains the following datasets: authors, pgroup, proposal, proposer, sample.
+
data is loaded into the current data folder. all items are loaded into strings, authors is a comma-separated list. missing items default to empty strings.
Parameters
- APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed AFileName if empty a dialog box shows up load_data 1 (default): load data; 0: do not load data load_attr 1 (default): load attributes; 0: do not load attributes note: for correct scaling of the image, the attributes need to be loaded pref_scans semicolon-separated list of preferred scans. the items of the list are match strings for the Igor StringMatch function. the first matching scan (i.e. top-level HDF5 group with a matching name) is loaded from the file. if no match is found, the first scan is loaded. pref_datasets semicolon-separated list of preferred datasets. the items of the list are match strings for the Igor StringMatch function. the first matching dataset is loaded from the file. if no match is found, the first dataset listed in the file is loaded. file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed.
-
Returns name of loaded preview wave.
+
Returns semicolon-separated list of the objects.
-
Definition at line 251 of file pearl-pshell-import.ipf .
+
Definition at line 1803 of file pearl-pshell-import.ipf .
-◆
-
-
-
- string psh5_load_reduced
- (
- string
- ANickName ,
-
- string
- APathName ,
-
- string
- AFileName ,
-
- funcref
- reduction_func ,
-
- string
- reduction_param ,
-
- variable
- progress = defaultValue,
-
- variable
- nthreads = defaultValue
-
- )
-
-
-
-
-
load and reduce the ScientaImage dataset of the first scan of a PShell data file.
-
the resulting dataset is reduced in one image dimension by a user-defined reduction function, e.g. by region-of-interest integration, curve fitting, etc. cf. adh5_default_reduction for further details.
-
the function loads the dataset image by image using the hyperslab option and applies a custom reduction function to each image. the results from the reduction function are composed into one result wave. the raw data are discarded.
-
if the data is from the electron analyser driver and some special attributes are included, the function will set the scales of the image dimensions.
-
by default, the reduction function is called in separate threads to reduce the total loading time. (see the global variable psh5_perf_secs which reports the total run time of the function.) the effect varies depending on the balance between file loading (image size) and data processing (complexity of the reduction function). for debugging the reduction function, multi-threading can be disabled.
-
Parameters
-
- ANickName destination folder name (top level under root). APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed. AFileName if empty a dialog box shows up. reduction_func custom data reduction function. this can be any user-defined function which has the same parameters as adh5_default_reduction . some reduction functions are predefined in the PearlScientaPreprocess module. reduction_param parameter string for the reduction function. progress progress window.
-1 (default) show progress window
-0 do not show progress window
-
- nthreads
--1 (default) use as many threads as there are processor cores (in addition to main thread).
-0 use main thread only (for debugging and profiling).
->= 1 use a fixed number of (additional) threads.
-
-
-
-
-
Returns semicolon-separated list of the loaded dataset ReducedData1, ReducedData2, etc. if successful. auxiliary waves, scan positions, attributes are loaded but not listed in the string. empty string if an error occurred. error messages are printed to the history.
-
-global string s_filepath in new data folder contains the full file path on disk.
-
-global string s_scanpaths in new data folder contains a list of scan groups inside the file.
-
-
Definition at line 1911 of file pearl-pshell-import.ipf .
-
-
-
◆
-
-
-
- string psh5_load_scan_attrs
- (
- variable
- fileID ,
-
- string
- scanpath ,
-
- variable
- attr_sets = defaultValue
-
- )
-
-
-
-
-
load attributes of a PShell scan group.
-
"attributes" are the auxiliary data inside the attrs group. do not confuse with HDF5 attributes! HDF5 attributes are loaded by the psh5_load_scan_meta() function.
-
data is loaded into the current data folder. this should normally be the :attr folder inside the respective scan folder.
-
Parameters
-
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". attr_sets specify the attribute sets to be loaded. this value can be an arithmetic OR of the following constants. by default, all attributes are loaded.
-1 all datasets that are present in the file.
-2 datasets relevant for wave scaling of Scienta data.
-
-
-
-
-
Returns semicolon-separated list of the loaded waves.
-
-
Definition at line 554 of file pearl-pshell-import.ipf .
-
-
-
◆
-
-
-
- string psh5_load_scan_complete
- (
- variable
- fileID ,
-
- string
- scanpath ,
-
- variable
- load_data = defaultValue,
-
- variable
- load_attr = defaultValue
-
- )
-
-
-
-
-
load all data of a selected scan from a PShell data file.
-
data is loaded into the current data folder. attribute datasets are loaded into sub-folder attr. region datasets are loaded into region sub-folders. existing data, if present, is overwritten.
-
Parameters
-
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". load_data select whether datasets (positioners and detectors) are loaded.
-1 (default) load data.
-0 do not load data.
-
- load_attr select whether attributes (auxiliary device readbacks) are loaded. for proper wave scaling, the attributes must be loaded.
-1 (default) load attributes.
-0 do not load attributes.
-
-
-
-
-
Returns semicolon-separated list of the loaded data waves (excluding attributes).
-
-
Definition at line 361 of file pearl-pshell-import.ipf .
-
-
-
◆
-
-
-
- string psh5_load_scan_data
- (
- variable
- fileID ,
-
- string
- scanpath
-
- )
-
-
-
-
-
load all datasets of a PShell scan group.
-
data is loaded into the current data folder. region datasets are loaded into the respective region sub-folders.
-
this function does not scale the datasets. call ps_scale_datasets() separately.
-
Parameters
-
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1".
-
-
-
Returns semicolon-separated list of the loaded waves.
-
-
Definition at line 514 of file pearl-pshell-import.ipf .
-
-
-
◆
-
-
-
- string psh5_load_scan_info
- (
- variable
- fileID ,
-
- string
- scanpath
-
- )
-
-
-
-
-
load descriptive info from a PShell scan.
-
the info string contains up to three lines which are made up of the following information:
-number of scan positions.
-dataset names of scan positioners.
-dataset names of detectors (without region names).
-region names
-
-
Parameters
-
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to scan group in the HDF5 file.
-
-
-
Returns newline terminated string.
-
-
Definition at line 2414 of file pearl-pshell-import.ipf .
-
-
-
◆ ◆
@@ -1644,8 +1583,8 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
string psh5_load_scan_meta
(
- variable
- fileID , dfref
+ file_df ,
data is loaded into the current data folder.
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed. scanpath path to the scan group in the HDF5 file, e.g. "/scan 1".
Returns semicolon-separated list of the loaded waves. Definition at line 625 of file pearl-pshell-import.ipf .
+Definition at line 1954 of file pearl-pshell-import.ipf .
-◆ ◆
- string psh5_load_scan_preview
+ string psh5_match_dataset_classes
(
- variable
- fileID ,
-
- string
- scanpath , datasets ,
variable
- set_scale = defaultValue, classes ,
string
- pref_datasets = defaultValue positioners = defaultValue,
+
+ string
+ detectors = defaultValue
-
load a preview dataset from an open PShell HDF5 file.
-
if the dataset has a maximum of two dimensions, the function loads it at once. if it has more than two dimension, the function selects and loads one two-dimensional slab.
+
filter a list of datasets by classification
Parameters
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". set_scale by default, the function tries to set the wave scaling if the attributes have been loaded. if multiple datasets are loaded from a file, it is more efficient to set the scaling of all loaded datasets at the end by calling ps_scale_datasets() .
-1 (default) set the wave scaling.
-0 do not set the wave scaling.
-
- pref_datasets semicolon-separated list of preferred datasets. the items of the list are match strings for the Igor StringMatch function. the first matching dataset is loaded from the file. if no match is found, the first dataset listed in the file is loaded. if empty, a hard-coded default preference list is used. datasets semicolon separated list of dataset paths classes dataset classes. arithmetic OR of the kDSCXxxx constants.
-
Returns name of loaded wave if successful. empty string otherwise.
+
Returns list of scan/region paths (no duplicates)
-
Definition at line 840 of file pearl-pshell-import.ipf .
+
Definition at line 899 of file pearl-pshell-import.ipf .
-◆ ◆
- string psh5_load_scan_section
- (
- variable
- fileID ,
-
- string
- scanpath ,
-
- variable
- dim ,
-
- variable
- set_scale = defaultValue,
-
- string
- pref_datasets = defaultValue
-
- )
-
-
-
-
-
load a longitudinal section of a scan from an open PShell HDF5 file.
-
the dataset must have three dimensions.
-
Parameters
-
- fileID ID of open HDF5 file from psh5_open_file() . scanpath path to the scan group in the HDF5 file, e.g. "/scan 1". dim reserved, must be 0. set_scale by default, the function tries to set the wave scaling if the attributes have been loaded. if multiple datasets are loaded from a file, it is more efficient to set the scaling of all loaded datasets at the end by calling ps_scale_datasets() .
-1 (default) set the wave scaling.
-0 do not set the wave scaling.
-
- pref_datasets semicolon-separated list of preferred datasets. the items of the list are match strings for the Igor StringMatch function. the first matching dataset is loaded from the file. if no match is found, the first dataset listed in the file is loaded. if empty, a hard-coded default preference list is used.
-
-
-
Returns name of loaded wave if successful. empty string otherwise.
-
Warning EXPERIMENTAL: this function is under development.
-
-
Definition at line 953 of file pearl-pshell-import.ipf .
-
-
-
-◆
-
-
-
- variable psh5_open_file
+ dfr psh5_open_file
(
string
- ANickName , path_name ,
string
- APathName , file_name ,
string
- AFileName dfref
+ dest_df = defaultValue
open a HDF5 file created by the PShell data acquisition program and prepare the data folder.
-
the function opens a specified or interactively selected HDF5 file, creates a data folder $ANickName under root, and changes to the new data folder.
-
the file must be closed by psh5_close_file() after use.
+
the function opens a specified or interactively selected HDF5 file, and loads general information about the file including a list of contained datasets.
+
data can be loaded into an existing or new data folder under root.
+
the file must be closed by psh5_close_file() after use. the HDF5 file ID is stored in the global variable file_id until the file is closed.
Parameters
- ANickName destination folder name (top level under root). APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed AFileName if empty a dialog box shows up path_name igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed file_name if empty a dialog box shows up dest_df destination folder reference. if dest_df is specified, data is loaded into this folder. else, by default, a new folder derived from the file name is created in root:
-
Returns ID of open HDF5 file from HDF5OpenFile. zero if an error occurred.
+Returns the return value of the function is a data folder reference of the created data folder.
+
+global variable file_id contains ID number of open HDF5 file from HDF5OpenFile. zero if an error occurred.
global string s_filepath in new data folder contains the full file path on disk.
global string s_scanpaths in new data folder contains a list of scan groups inside the file. Definition at line 110 of file pearl-pshell-import.ipf .
+Definition at line 450 of file pearl-pshell-import.ipf .
-◆ ◆
+
+
+
+ dfr psh5_preview
+ (
+ string
+ path_name ,
+
+ string
+ file_name ,
+
+ dfref
+ dest_df = defaultValue,
+
+ string
+ preview_datasets = defaultValue
+
+ )
+
+
+
+
+
load preview
+
load information about the file structure and a preview dataset
+
+
Definition at line 345 of file pearl-pshell-import.ipf .
+
+
+
◆
+
+
+
+ string psh_load_general_string
+ (
+ dfref
+ file_df ,
+
+ string
+ name
+
+ )
+
+
+
+
+
load a string from the general group.
+
the general group contains the following datasets: authors, pgroup, proposal, proposer, sample.
+
data is loaded into a global string in the current data folder. arrays with multiple items are loaded into a comma-separated list. a missing item defaults to the empty string.
+
Parameters
+
+ file_df data folder reference of open HDF5 file from psh5_open_file() . if undefined, the current datafolder is assumed.
+
+
+
Returns comma-separated list of values.
+
+
Definition at line 1838 of file pearl-pshell-import.ipf .
+
+
+
◆
@@ -1897,7 +1851,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
string
- reduction_param reduction_params
◆
-
-
-
-
-
-
- static string select_dataset
- (
- string
- file_datasets ,
-
- string
- pref_datasets
-
- )
-
-
-
-
-static
-
-
-
-
-
select the preferred dataset from a list of available datasets.
-
Parameters
-
- file_datasets semicolon-separated list of datasets that are available in the file. the items may include a path separated by slashes "/". only the last component of the path is checked. pref_datasets semicolon-separated list of preferred datasets. the items of the list are match strings for the Igor StringMatch function. the first matching dataset is loaded from the file. if no match is found, the first file dataset is selected.
-
-
-
Returns selected dataset.
-
-
Definition at line 778 of file pearl-pshell-import.ipf .
+
Definition at line 1737 of file pearl-pshell-import.ipf .
convert text wave to list.
-Definition at line 2473 of file pearl-pshell-import.ipf .
+Definition at line 532 of file pearl-pshell-import.ipf .
+
+
+
+◆
+
+
+
+
+
+
+ static string unique_strings
+ (
+ string
+ list )
+
+
+
+
+static
+
+
+
+
+
remove duplicate items from list
+
Parameters
+
+ list semicolon-separated list of strings. strings can contain any printable character except the semicolon.
+
+
+
Returns list of strings with duplicates (second and further instances) removed. all remaining items retain the position of their first occurrence in the original list. the function uses Igor's FindDuplicates operation.
+
+
Definition at line 764 of file pearl-pshell-import.ipf .
convert numeric wave to list.
-Definition at line 2490 of file pearl-pshell-import.ipf .
+Definition at line 549 of file pearl-pshell-import.ipf .
@@ -2093,7 +2036,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
Dimension label for the angle dispersive dimension of multi-dimensional datasets.
-Definition at line 68 of file pearl-pshell-import.ipf .
+Definition at line 53 of file pearl-pshell-import.ipf .
@@ -2112,25 +2055,215 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
Dimension label for the data dimension.
This label may be used to store the parameters for the setscale d operation.
-Definition at line 75 of file pearl-pshell-import.ipf .
+Definition at line 60 of file pearl-pshell-import.ipf .
-◆ ◆
- const variable kDetectorSensitivity = 1
+ const variable kDSCAll = 0xffff
+
+◆
+
+
+
+ const variable kDSCAttrs = 0x0020
+
+
+
+
◆
+
+
+
+ const variable kDSCDetectors = 0x0002
+
+
+
+
◆
+
+
+
+ const variable kDSCDiags = 0x0040
+
+
+
+
◆
+
+
+
+ const variable kDSCEssentialDiags = 0x0010
+
+
+
+
◆
+
+
+
+ const variable kDSCMeta = 0x0100
+
+
+
+
◆
+
+
+
+ const variable kDSCMonitors = 0x0200
+
+
+
+
◆
+
+
+
+ const variable kDSCOther = 0x8000
+
+
+
+
◆
+
+
+
+ const variable kDSCPositioners = 0x0001
+
+
+
+
◆
+
+
+
+ const variable kDSCPreview = 0x0008
+
+
+
+
◆
+
+
+
+ const variable kDSCRegions = 0x0400
+
+
+
+
◆
+
+
+
+ const variable kDSCScientaScaling = 0x0004
+
+
+
+
◆
+
+
+
+ const variable kDSCSnaps = 0x0080
+
+
+
Dimension label for the energy dispersive dimension of multi-dimensional datasets.
-Definition at line 65 of file pearl-pshell-import.ipf .
+Definition at line 50 of file pearl-pshell-import.ipf .
+
+
+
+◆
+
+
+
+ const string kEssentialDiagnostics = "ManipulatorX;ManipulatorY;ManipulatorZ;ManipulatorTheta;ManipulatorTilt;ManipulatorPhi;MonoEnergy;"
+
+
+
+
+
List of diagnostic datasets that are normally loaded with a scan.
+
+
Definition at line 69 of file pearl-pshell-import.ipf .
- const string kPreviewDatasets = "ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent;"
+ const string kPreviewDatasets = "ImageEnergyDistribution;ScientaSpectrum;ScientaImage;Counts;SampleCurrent;"
@@ -2184,7 +2335,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
Dimension label for the scan dimension of multi-dimensional datasets.
-Definition at line 71 of file pearl-pshell-import.ipf .
+Definition at line 56 of file pearl-pshell-import.ipf .
@@ -2195,14 +2346,14 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
- const string kScientaScalingDatasets = "LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;"
+ const string kScientaScalingDatasets = "LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;Eph;"
@@ -2218,21 +2369,22 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
+string kill_matching_waves(dfref dfr, string pattern, variable recurse, string killed=defaultValue)
kill any waves matching a pattern in the experiment
PEARL Procedures: pearl-pshell-import.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,36 +87,1981 @@ $(document).ready(function(){initNavTree('pearl-pshell-import_8ipf_source.html',
pearl-pshell-import.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.36 3 #pragma ModuleName = PearlPShellImport 4 #include <HDF5 Browser> 5 #include "pearl-compat" 6 #include "pearl-gui-tools" 7 #include "pearl-area-import" 78 strconstant
kPreviewDatasets =
"ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent;" 116 newdatafolder /s /o $(
"root:" + ANickName)
117 dfref fileDF = GetDataFolderDFR()
120 HDF5OpenFile /P=$APathName /R fileID as AFileName
123 string /g s_scanpaths
124 s_filepath = s_path + s_filename
177 if (ParamIsDefault(load_data))
180 if (ParamIsDefault(load_attr))
184 dfref saveDF = GetDataFolderDFR()
188 variable /g psh5_perf_secs
189 timerRefNum = startMSTimer
193 dfref fileDF = GetDataFolderDFR()
196 AFileName = s_filepath
197 print "loading " + s_filepath + "\r"
200 variable ng = ItemsInList(s_scanpaths, ";")
204 for (ig = 0; ig < ng; ig += 1)
205 sg = StringFromList(ig, s_scanpaths, ";")
206 folder = ReplaceString("/", sg, "")
207 folder = ReplaceString(" ", folder, "")
210 newdatafolder /s /o $folder
219 psh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
251 function /s
psh5_load_preview (APathName, AFileName, [load_data, load_attr, pref_scans, pref_datasets])
259 if (ParamIsDefault(load_data))
262 if (ParamIsDefault(load_attr))
265 if (ParamIsDefault(pref_scans))
266 pref_scans = "*scan1*;"
268 if (ParamIsDefault(pref_datasets))
272 dfref saveDF = GetDataFolderDFR()
275 string scanpaths = ""
280 variable /g adh5_perf_secs
281 timerRefNum = startMSTimer
283 HDF5OpenFile /P=$APathName /R /Z fileID as AFileName
285 AFileName = s_path + s_filename
286 dfref fileDF = GetDataFolderDFR()
289 variable ng = ItemsInList(scanpaths)
292 variable np = ItemsInList(pref_scans)
297 for (ip = 0; ip < np; ip += 1)
298 for (ig = 0; ig < ng; ig += 1)
299 sg = StringFromList(ig, scanpaths)
300 sp = StringFromList(ip, pref_scans)
301 if (StringMatch(sg, sp))
313 sg = StringFromList(ig, scanpaths)
317 newdatafolder /o/s attr
325 print "no scans found in file " + AFileName
331 if (timerRefNum >= 0)
332 adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
367 if (ParamIsDefault(load_data))
370 if (ParamIsDefault(load_attr))
374 dfref saveDF = GetDataFolderDFR()
376 dfref dataDF = GetDataFolderDFR()
381 newdatafolder /s /o attr
388 if (load_data && load_attr)
408 HDF5ListGroup /F /TYPE=1 fileID, "/"
411 variable ng = ItemsInList(S_HDF5ListGroup, ";")
415 for (ig = 0; ig < ng; ig += 1)
416 sg = StringFromList(ig, S_HDF5ListGroup, ";")
417 if (cmpstr(sg[1,4], "scan") == 0)
418 scans = AddListItem(sg, scans, ";", inf)
443 variable include_regions
445 if (ParamIsDefault(include_regions))
450 HDF5ListGroup /TYPE=2 /Z fileID, scanpath
451 result = S_HDF5ListGroup
454 HDF5ListGroup /R /TYPE=2 /Z fileID, scanpath
455 variable n = ItemsInList(S_HDF5ListGroup)
458 string region_datasets
459 for (i = 0; i < n; i += 1)
460 ds = StringFromList(i, S_HDF5ListGroup)
461 if (StringMatch(ds, "region*
const string kEnergyDimLabel
Dimension label for the energy dispersive dimension of multi-dimensional datasets.
-
string psh5_load_scan_preview(variable fileID, string scanpath, variable set_scale=defaultValue, string pref_datasets=defaultValue)
load a preview dataset from an open PShell HDF5 file.
-
string psh5_load_scan_attrs(variable fileID, string scanpath, variable attr_sets=defaultValue)
load attributes of a PShell scan group.
-
const string kTransposedDatasets
List of datasets that should be transposed upon loading.
-
string psh5_load_scan_complete(variable fileID, string scanpath, variable load_data=defaultValue, variable load_attr=defaultValue)
load all data of a selected scan from a PShell data file.
-
const string kScanDimLabel
Dimension label for the scan dimension of multi-dimensional datasets.
-
string PearlCleanupName(string name)
-
const string kAngleDimLabel
Dimension label for the angle dispersive dimension of multi-dimensional datasets. ...
-
const string kDataDimLabel
Dimension label for the data dimension.
-
string psh5_load_preview(string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue, string pref_scans=defaultValue, string pref_datasets=defaultValue)
load a preview image from a PShell data file.
-
variable psh5_open_file(string ANickName, string APathName, string AFileName)
open a HDF5 file created by the PShell data acquisition program and prepare the data folder...
-
variable ps_scale_datasets()
set the dimension scales of loaded PShell Scienta datasets according to attributes.
-
string psh5_load_scan_meta(variable fileID, string scanpath)
load metadata of a PShell scan group.
-
const string kScientaScalingDatasets
List of datasets that must be loaded to determine the axis scaling of a Scienta image.
-
string psh5_list_scan_datasets(variable fileID, string scanpath, variable include_regions=defaultValue)
list datasets of a PShell scan group.
-
string psh5_load_scan_data(variable fileID, string scanpath)
load all datasets of a PShell scan group.
-
const variable kDetectorSensitivity
multiply scienta detector intensity by this value to get actual counts.
-
string psh5_load_complete(string ANickName, string APathName, string AFileName, variable load_data=defaultValue, variable load_attr=defaultValue)
load everything from a PShell data file.
-
string psh5_list_scans(variable fileID)
list scan groups of a PShell data file.
-
variable psh5_close_file(variable fileID)
close a HDF5 file opened by psh5_open_file.
-
const string kPreviewDatasets
List of preferred datasets to load for preview.
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 8.00
+
4 #pragma ModuleName = PearlPShellImport
+
+
6 #if IgorVersion() < 9.00
+
7 #include <HDF5 Browser>
+
+
9 #include "pearl-compat"
+
10 #include "pearl-gui-tools"
+
11 #include "pearl-area-import"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
63 strconstant
kPreviewDatasets =
"ImageEnergyDistribution;ScientaSpectrum;ScientaImage;Counts;SampleCurrent;"
+
+
66 strconstant
kScientaScalingDatasets =
"LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;Eph;"
+
+
69 strconstant
kEssentialDiagnostics =
"ManipulatorX;ManipulatorY;ManipulatorZ;ManipulatorTheta;ManipulatorTilt;ManipulatorPhi;MonoEnergy;"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
158 function /df
psh5_load (path_name, file_name, scans, regions, datasets, [classes, max_rank, reduction_func, reduction_params, dest_df])
+
+
+
+
+
+
+
+
166 string reduction_func
+
167 string reduction_params
+
+
+
170 dfref save_df = GetDataFolderDFR()
+
171 variable timerRefNum = startMSTimer
+
+
173 if (ParamIsDefault(classes) || (classes == 0))
+
+
+
+
+
178 if (ParamIsDefault(dest_df) || !DataFolderRefStatus(dest_df))
+
+
+
+
+
183 if (ParamIsDefault(reduction_func))
+
+
+
186 if (ParamIsDefault(reduction_params))
+
187 reduction_params = ""
+
+
+
190 if (DataFolderRefStatus(dest_df))
+
191 setdatafolder dest_df
+
+
+
+
195 svar /sdfr=dest_df file_datasets = s_datasets
+
+
+
198 string ranked_datasets = ""
+
199 if (ParamIsDefault(max_rank))
+
200 ranked_datasets = file_datasets
+
+
202 svar /sdfr=dest_df file_ranks = s_datasets_ranks
+
+
+
+
206 string matching_datasets = ""
+
207 string matching_essentials = ""
+
208 string scan_datasets = ""
+
209 string region_datasets = ""
+
210 string free_datasets = ""
+
211 string selected_datasets = ""
+
212 string essential_datasets = ""
+
+
+
+
+
+
+
219 n_items = ItemsInList(scans, ";")
+
220 for (i_item = 0; i_item < n_items; i_item += 1)
+
221 item = StringFromList(i_item, scans, ";")
+
222 if (cmpstr(item[0,3], "scan") == 0)
+
+
+
225 item = ReplaceString("
+
226 matching_datasets = psh5_match_datasets(ranked_datasets, item)
+
227 scan_datasets = scan_datasets + matching_datasets
+
+
+
+
231 n_items = ItemsInList(regions, ";")
+
232 for (i_item = 0; i_item < n_items; i_item += 1)
+
233 item = StringFromList(i_item, regions, ";")
+
234 if (cmpstr(item[0,3], "scan") == 0)
+
+
+
237 item = ReplaceString("
+
238 matching_datasets = psh5_match_datasets(ranked_datasets, item)
+
239 region_datasets = region_datasets + matching_datasets
+
+
+
+
243 n_items = ItemsInList(datasets, ";")
+
244 for (i_item = 0; i_item < n_items; i_item += 1)
+
245 item = StringFromList(i_item, datasets, ";")
+
246 if (cmpstr(item[0,3], "scan") == 0)
+
+
+
249 matching_datasets = psh5_match_datasets(ranked_datasets, item)
+
250 free_datasets = free_datasets + matching_datasets
+
+
+
253 selected_datasets = scan_datasets + region_datasets + free_datasets
+
+
255 string filtered_datasets = ""
+
256 string diag_datasets = ""
+
+
+
259 variable n_scans = ItemsInList(selected_scans)
+
+
+
+
263 variable n_regions = ItemsInList(selected_regions)
+
+
+
+
+
+
+
270 for (i_region = 0; i_region < n_regions; i_region += 1)
+
271 region = StringFromList(i_region, selected_regions, ";")
+
272 region_datasets = region_datasets + GrepList(file_datasets, "(?i)^" + region + "[[:alpha:]]+$")
+
+
+
+
+
277 for (i_scan = 0; i_scan < n_scans; i_scan += 1)
+
278 scan = StringFromList(i_scan, selected_scans, ";")
+
+
+
281 diag_datasets = psh5_match_datasets(file_datasets, scan + "*")
+
+
283 diag_datasets = diag_datasets + GrepList(file_datasets, "(?i)^" + scan + "[[:alpha:]]+$")
+
284 diag_datasets = diag_datasets + psh5_match_datasets(region_datasets, scan + "*")
+
+
+
287 setdatafolder dest_df
+
+
289 setdatafolder scan_df
+
+
291 wave /t /z ScanWritables
+
292 wave /t /z ScanReadables
+
293 if (WaveExists(ScanWritables))
+
+
+
+
+
298 if (WaveExists(ScanReadables))
+
+
+
+
+
+
+
+
+
+
308 if (strlen(matching_datasets) > 1)
+
309 essential_datasets =
psh5_match_dataset_classes (diag_datasets, essential_classes, positioners=positioners, detectors=detectors)
+
+
+
+
313 filtered_datasets = essential_datasets + filtered_datasets + matching_datasets
+
+
+
+
317 setdatafolder dest_df
+
318 string /g s_loaded_datasets = ""
+
319 s_loaded_datasets =
psh5_load_datasets (dest_df, filtered_datasets, reduction_func=reduction_func, reduction_params=reduction_params)
+
+
+
322 for (i_scan = 0; i_scan < n_scans; i_scan += 1)
+
323 scan = StringFromList(i_scan, selected_scans, ";")
+
+
+
+
+
+
+
330 if (timerRefNum >= 0)
+
331 setdatafolder dest_df
+
332 variable /g psh5_perf_secs
+
333 psh5_perf_secs = stopMSTimer(timerRefNum) / 1e6
+
+
+
+
337 setdatafolder save_df
+
+
+
+
345 function /df
psh5_preview (path_name, file_name, [dest_df, preview_datasets])
+
+
+
+
349 string preview_datasets
+
+
351 dfref save_df = GetDataFolderDFR()
+
+
353 if (ParamIsDefault(dest_df))
+
+
+
+
+
358 if (ParamIsDefault(preview_datasets))
+
+
+
+
+
363 if (DataFolderRefStatus(dest_df))
+
364 setdatafolder dest_df
+
+
+
+
368 svar /sdfr=dest_df file_datasets = s_datasets
+
369 svar /sdfr=dest_df file_datasets_ranks = s_datasets_ranks
+
370 string selected_datasets = ""
+
371 string essential_datasets = ""
+
372 string scan_datasets = ""
+
373 string filtered_datasets = ""
+
+
375 variable nds = ItemsInList(preview_datasets, ";")
+
+
+
378 for (ids = 0; ids < nds; ids += 1)
+
379 ds = StringFromList(ids, preview_datasets, ";")
+
+
381 selected_datasets = psh5_match_datasets(selected_datasets, "/scan*" + ds)
+
382 if (strlen(selected_datasets) > 1)
+
383 selected_datasets = StringFromList(0, selected_datasets, ";")
+
+
+
+
+
+
389 if (strlen(selected_datasets) > 1)
+
+
+
+
+
394 scan = StringFromList(0, selected_scans, ";")
+
395 scan_datasets = psh5_match_datasets(file_datasets, scan + "*")
+
+
+
398 wave /t /z ScanWritables
+
399 if (WaveExists(ScanWritables))
+
+
+
+
+
+
+
406 filtered_datasets = essential_datasets + selected_datasets
+
+
+
+
+
411 string /g s_preview_dataset = StringFromList(0, selected_datasets, ";")
+
412 string /g s_preview_wave = StringFromList(ItemsInList(s_preview_dataset, "/") - 1, s_preview_dataset, "/")
+
+
+
+
+
+
418 setdatafolder save_df
+
+
+
+
+
+
+
+
+
455 dfref save_df = GetDataFolderDFR()
+
+
+
458 HDF5OpenFile /P=$path_name /R fid as file_name
+
+
460 if (!ParamIsDefault(dest_df))
+
461 setdatafolder dest_df
+
+
+
+
465 newdatafolder /s /o $("root:" + dest_name)
+
+
467 dfref file_df = GetDataFolderDFR()
+
+
469 variable /g file_id = fid
+
+
471 string /g s_scanpaths
+
+
+
+
+
476 s_filepath = s_path + s_filename
+
+
+
+
480 string /g s_datasets_datatypes = datatypes
+
481 string /g s_datasets_ranks = ranks
+
482 string /g s_datasets_dimensions = dimensions
+
+
+
+
+
487 setdatafolder save_df
+
+
+
+
+
+
+
512 if (DataFolderRefStatus(file_df))
+
513 nvar /sdfr=file_df /z file_id
+
514 if (nvar_Exists(file_id))
+
515 HDF5CloseFile /z file_id
+
+
517 KillVariables /z file_id
+
+
519 dfref parent_df = $(GetDataFolder(1, file_df) + ":")
+
520 if (DataFolderRefStatus(parent_df))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
537 variable n = numpnts(wt)
+
+
539 for (i = 0; i < n; i += 1)
+
540 list = AddListItem(wt[i], list, sep, inf)
+
+
+
+
+
+
+
+
+
+
+
+
555 variable n = numpnts(w)
+
+
+
558 for (i = 0; i < n; i += 1)
+
559 sprintf s, format, w[i]
+
560 list = AddListItem(s, list, sep, inf)
+
+
+
+
+
+
+
+
+
577 HDF5ListGroup /F /TYPE=1 file_id, "/"
+
+
+
580 variable ng = ItemsInList(S_HDF5ListGroup, ";")
+
+
+
+
584 for (ig = 0; ig < ng; ig += 1)
+
585 sg = StringFromList(ig, S_HDF5ListGroup, ";")
+
586 if (cmpstr(sg[1,4], "scan") == 0)
+
587 scans = AddListItem(sg, scans, ";", inf)
+
+
+
+
+
+
+
+
+
+
608 HDF5ListGroup /F /R /TYPE=2 /Z file_id, "/"
+
+
610 return S_HDF5ListGroup
+
+
+
+
+
+
+
632 variable nds = ItemsInList(datasets, ";")
+
+
+
635 STRUCT HDF5DataInfo di
+
+
+
+
+
+
+
+
+
644 for (ids = 0; ids < nds; ids += 1)
+
645 sds = StringFromList(ids, datasets, ";")
+
646 err = HDF5DatasetInfo(file_id, sds, 0, di)
+
+
648 switch (di.datatype_class)
+
+
650 datatypes = AddListItem("i", datatypes, ";", ids)
+
+
+
653 datatypes = AddListItem("f", datatypes, ";", ids)
+
+
+
656 datatypes = AddListItem("s", datatypes, ";", ids)
+
+
+
659 datatypes = AddListItem("?", datatypes, ";", ids)
+
+
+
+
663 ranks = AddListItem(num2str(di.ndims), ranks, ";", ids)
+
+
+
666 for (idim = 0; idim < di.ndims; idim += 1)
+
667 sdims = AddListItem(num2str(di.dims[idim]), sdims, ",", idim)
+
+
669 if (strlen(sdims) > 1)
+
670 sdims = sdims[0, strlen(sdims)-2]
+
+
672 dimensions = AddListItem(sdims, dimensions, ";", ids)
+
+
+
+
+
692 function /s psh5_match_datasets(datasets, match)
+
+
+
+
+
+
698 string spaceless_datasets = ReplaceString(" ", datasets, "")
+
699 string spaceless_match = ReplaceString(" ", match, "")
+
+
+
702 variable seplen = strlen(sep)
+
703 variable nds = ItemsInList(spaceless_datasets, sep)
+
+
+
+
+
708 for (ids = 0; ids < nds; ids += 1)
+
709 ds = StringFromList(0, spaceless_datasets, sep, offset)
+
710 offset += strlen(ds) + seplen
+
711 if (StringMatch(ds, spaceless_match))
+
712 ds = StringFromList(ids, datasets, sep, 0)
+
713 result = AddListItem(ds, result, sep, inf)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
736 variable seplen = strlen(sep)
+
737 variable nds = ItemsInList(datasets, sep)
+
+
+
+
+
+
743 for (ids = 0; ids < nds; ids += 1)
+
744 ds = StringFromList(0, datasets, sep, offset)
+
745 offset += strlen(ds) + seplen
+
746 rank = str2num(StringFromList(ids, ranks, sep))
+
747 if ((rank >= min_rank) && (rank <= max_rank))
+
748 result = AddListItem(ds, result, sep, inf)
+
+
+
+
+
+
+
+
+
+
+
+
+
770 variable seplen = strlen(sep)
+
771 variable nn = ItemsInList(list, sep)
+
+
+
+
+
776 make /n=(nn) /t /free wt_in
+
777 for (ii = 0; ii < nn; ii += 1)
+
778 item = StringFromList(0, list, sep, offset)
+
779 offset += strlen(item) + seplen
+
+
+
+
783 FindDuplicates /Z /FREE /RT=wt_out wt_in
+
+
+
+
+
+
+
+
+
+
808 variable seplen = strlen(sep)
+
809 variable nds = ItemsInList(datasets, sep)
+
+
+
+
+
+
+
816 for (ids = 0; ids < nds; ids += 1)
+
817 ds = StringFromList(0, datasets, sep, offset)
+
818 offset += strlen(ds) + seplen
+
819 if (cmpstr(ds[0], "/") != 0)
+
+
+
+
823 scan = StringFromList(1, ds, "/")
+
824 if (StringMatch(scan, "scan*"))
+
825 item = "/" + scan + "/"
+
+
+
+
+
830 if ((strlen(item) > 0) && (WhichListItem(item, result, ";", 0, 0) < 0))
+
831 result = AddListItem(item, result, ";", inf)
+
+
+
+
+
+
+
+
+
+
+
+
858 variable seplen = strlen(sep)
+
859 variable nds = ItemsInList(datasets, sep)
+
+
+
+
+
+
+
+
867 for (ids = 0; ids < nds; ids += 1)
+
868 ds = StringFromList(0, datasets, sep, offset)
+
869 offset += strlen(ds) + seplen
+
870 if (cmpstr(ds[0], "/") != 0)
+
+
+
+
874 scan = StringFromList(1, ds, "/")
+
875 region = StringFromList(2, ds, "/")
+
876 if (StringMatch(scan, "scan*") && StringMatch(region, "region*"))
+
877 item = "/" + scan + "/" + region + "/"
+
+
+
+
+
882 if ((strlen(item) > 0) && (WhichListItem(item, result, ";", 0, 0) < 0))
+
883 result = AddListItem(item, result, ";", inf)
+
+
+
+
+
+
+
+
+
+
+
+
+
905 if (ParamIsDefault(positioners))
+
+
+
908 if (ParamIsDefault(detectors) || (strlen(detectors) == 0))
+
+
+
+
+
+
914 variable seplen = strlen(sep)
+
915 variable nds = ItemsInList(datasets, sep)
+
+
+
+
+
+
+
+
+
+
925 for (ids = 0; ids < nds; ids += 1)
+
926 ds = StringFromList(0, datasets, sep, offset)
+
927 offset += strlen(ds) + seplen
+
928 nparts = ItemsInList(ds, "/")
+
929 ds_parent = StringFromList(nparts - 2, ds, "/")
+
930 ds_name = StringFromList(nparts - 1, ds, "/")
+
931 if (cmpstr(ds[0,4], "/scan") == 0)
+
932 ds_scan_rel = RemoveListItem(0, ds[1, strlen(ds) - 1], "/")
+
+
+
+
+
+
938 if (strlen(ds_parent) > 0)
+
939 ds_class = ds_class | (cmpstr(ds_parent, "attr") == 0 ?
kDSCAttrs : 0)
+
940 ds_class = ds_class | (cmpstr(ds_parent, "attrs") == 0 ?
kDSCAttrs : 0)
+
941 ds_class = ds_class | (cmpstr(ds_parent, "diags") == 0 ?
kDSCDiags : 0)
+
942 ds_class = ds_class | (cmpstr(ds_parent, "snaps") == 0 ?
kDSCSnaps : 0)
+
943 ds_class = ds_class | (cmpstr(ds_parent, "meta") == 0 ?
kDSCMeta : 0)
+
944 ds_class = ds_class | (cmpstr(ds_parent, "monitors") == 0 ?
kDSCMonitors : 0)
+
945 ds_class = ds_class | (cmpstr(ds_parent[0,5], "region") == 0 ?
kDSCRegions : 0)
+
+
+
948 if (strlen(ds_name) > 0)
+
949 ds_class = ds_class | (WhichListItem(ds_scan_rel, positioners, sep, 0, 0) >= 0 ?
kDSCPositioners : 0)
+
950 ds_class = ds_class | (WhichListItem(ds_scan_rel, detectors, sep, 0, 0) >= 0 ?
kDSCDetectors : 0)
+
+
+
+
+
+
+
+
+
+
960 if (ds_class & classes)
+
961 result = AddListItem(ds, result, sep, inf)
+
+
+
+
+
+
+
+
+
+
993 if (cmpstr(datasetpath[0], "/") == 0)
+
994 datasetpath = datasetpath[1, strlen(datasetpath)-1]
+
+
996 if (cmpstr(datasetpath[strlen(datasetpath)-1], "/") == 0)
+
997 datasetpath += "dummy"
+
+
+
1000 variable nfolders = ItemsInList(datasetpath, "/") - 1
+
+
+
1003 string inc_path = "/"
+
+
1005 for (ifolder = 0; ifolder < nfolders; ifolder += 1)
+
1006 folder = StringFromList(ifolder, datasetpath, "/")
+
+
1008 NewDataFolder /o/s $folder
+
+
+
1011 string /g s_hdf5_group = inc_path
+
+
+
1014 return GetDataFolderDFR()
+
+
+
+
+
+
+
1038 if (cmpstr(datasetpath[0], "/") == 0)
+
1039 datasetpath = datasetpath[1, strlen(datasetpath)-1]
+
+
1041 if (cmpstr(datasetpath[strlen(datasetpath)-1], "/") == 0)
+
1042 datasetpath += "dummy"
+
+
+
1045 variable nfolders = ItemsInList(datasetpath, "/") - 1
+
+
+
1048 string inc_path = ""
+
+
1050 for (ifolder = 0; ifolder < nfolders; ifolder += 1)
+
1051 folder = StringFromList(ifolder, datasetpath, "/")
+
+
+
+
+
+
+
+
1059 dfref out_df = parent_df:$inc_path
+
+
+
+
+
+
+
+
1069 folder_name = ReplaceString(" ", group_name, "")
+
1070 if (cmpstr(folder_name, "attrs") == 0)
+
1071 folder_name = "attr"
+
+
+
+
+
+
+
+
+
+
+
+
1101 variable create_folders
+
1102 string reduction_func
+
1103 string reduction_params
+
+
1105 if (!DataFolderRefStatus(file_df))
+
1106 dfref file_df = GetDataFolderDFR()
+
+
1108 if (ParamIsDefault(create_folders))
+
+
+
1111 if (ParamIsDefault(reduction_func))
+
+
+
1114 if (ParamIsDefault(reduction_params))
+
1115 reduction_params = ""
+
+
+
1118 dfref save_df = GetdataFolderDFR()
+
+
+
1121 variable nds = ItemsInList(datasets, ";")
+
+
+
1124 string loaded_datasets = ""
+
1125 string loaded_waves = ""
+
+
1127 for (ids = 0; ids < nds; ids += 1)
+
1128 SetDataFolder file_df
+
1129 ds = StringFromList(ids, datasets, ";")
+
1130 loaded_waves =
psh5_load_dataset (file_df, ds, create_folders=create_folders, reduction_func=reduction_func, reduction_params=reduction_params)
+
1131 if (strlen(loaded_waves) > 1)
+
1132 loaded_datasets = loaded_datasets + ds + ";"
+
+
+
+
1136 setdatafolder save_df
+
1137 return loaded_datasets
+
+
+
1176 function /s
psh5_load_dataset (file_df, datasetpath, [create_folders, reduction_func, reduction_params])
+
+
+
1179 variable create_folders
+
1180 string reduction_func
+
1181 string reduction_params
+
+
1183 dfref base_df = GetDataFolderDFR()
+
1184 if (!DataFolderRefStatus(file_df))
+
1185 dfref file_df = GetDataFolderDFR()
+
+
1187 nvar /sdfr=file_df file_id
+
+
1189 if (ParamIsDefault(create_folders))
+
+
+
+
+
+
1195 if (ParamIsDefault(reduction_func))
+
+
+
1198 if (ParamIsDefault(reduction_params))
+
1199 reduction_params = ""
+
+
+
1202 STRUCT HDF5DataInfo di
+
1203 InitHDF5DataInfo(di)
+
1204 variable err = HDF5DatasetInfo(file_id, datasetpath, 0, di)
+
+
+
+
+
+
1210 variable numeric = 0
+
1211 variable compound = 0
+
+
1213 switch (di.datatype_class)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1236 string wave_names = ""
+
+
1238 string datasetname = StringFromList(ItemsInList(datasetpath, "/") - 1, datasetpath, "/")
+
+
1240 HDF5LoadData /O /Q /Z /TRAN=(transpose) file_id, datasetpath
+
1241 wave_names = S_waveNames
+
+
1243 if (exists(reduction_func) == 6)
+
+
+
+
+
+
+
1250 variable nw = ItemsInList(wave_names, ";")
+
+
+
1253 string loaded_waves = ""
+
1254 for (iw = 0; iw < nw; iw += 1)
+
1255 sw = StringFromList(iw, wave_names)
+
+
+
1258 loaded_waves = loaded_waves + sw + ";"
+
+
+
+
+
+
1264 setdatafolder base_df
+
+
+
+
+
+
+
1292 variable create_folders
+
+
+
1295 if (ParamIsDefault(create_folders))
+
+
+
1298 if (ParamIsDefault(progress))
+
+
+
+
1302 if (!DataFolderRefStatus(file_df))
+
1303 dfref file_df = GetDataFolderDFR()
+
+
1305 nvar /sdfr=file_df file_id
+
+
+
1308 string datawavename = StringFromList(ItemsInList(datasetpath, "/") - 1, datasetpath, "/")
+
+
+
+
+
+
1314 STRUCT HDF5DataInfo di
+
1315 InitHDF5DataInfo(di)
+
1316 variable err = HDF5DatasetInfo(file_id, datasetpath, 0, di)
+
+
1318 print "error accessing dataset", datasetpath
+
+
+
+
1322 print "error: rank of dataset < 2", datasetpath
+
+
1324 elseif (di.ndims < 3)
+
+
+
1327 if ((di.datatype_class != H5T_INTEGER) && (di.datatype_class != H5T_FLOAT))
+
1328 print "error: unsupported datatype", datasetpath
+
+
+
+
1332 variable idx, idy, idz, idt, izt
+
+
+
+
+
+
+
+
+
+
+
+
1344 variable nx, ny, nz, nt, nzt
+
+
+
+
+
1349 make /n=(nx,ny,nz,nt) /o $datawavename
+
1350 wave data = $datawavename
+
+
+
+
+
+
+
+
+
+
+
1361 HDF5MakeHyperslabWave("slab", max(di.ndims, 4))
+
+
+
+
+
+
1367 slab[idx][%Block] = nx
+
1368 slab[idy][%Block] = ny
+
+
+
1371 for (iz = 0; iz < nz; iz += 1)
+
1372 for (it = 0; it < nt; it += 1)
+
1373 slab[idz][%Start] = iz
+
1374 slab[idt][%Start] = it
+
1375 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata file_id, datasetpath
+
+
+
1378 data[][][iz][it] = slabdata[q][p][0][0]
+
+
1380 data[][][iz][it] = slabdata[p][q][0][0]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1401 killwaves /z slab, slabdata
+
+
+
1404 return NameOfWave(data) + ";"
+
+
+
+
+
+
+
+
+
+
+
+
+
1476 string reduction_params
+
1477 variable create_folders
+
+
+
+
1481 if (ParamIsDefault(create_folders))
+
+
+
1484 if (ParamIsDefault(progress))
+
+
+
1487 if (ParamIsDefault(nthreads))
+
+
+
+
1491 dfref base_df = GetDataFolderDFR()
+
1492 if (!DataFolderRefStatus(file_df))
+
1493 dfref file_df = GetDataFolderDFR()
+
+
1495 nvar /sdfr=file_df file_id
+
+
+
1498 string datawavename = StringFromList(ItemsInList(datasetpath, "/") - 1, datasetpath, "/")
+
1499 string wavenames = ""
+
+
+
+
+
+
1505 STRUCT HDF5DataInfo di
+
1506 InitHDF5DataInfo(di)
+
1507 variable err = HDF5DatasetInfo(file_id, datasetpath, 0, di)
+
+
1509 print "error accessing detector/data"
+
+
+
+
+
1514 print "error: rank of dataset < 2"
+
+
+
1517 elseif (di.ndims < 3)
+
+
+
+
1521 variable idx, idy, idz, idt
+
+
+
+
+
+
+
+
+
+
+
+
1533 variable nx, ny, nz, nt, nzt
+
+
+
+
+
+
+
+
+
+
+
1544 HDF5MakeHyperslabWave("slab", max(di.ndims, 4))
+
+
+
+
+
+
1550 slab[idx][%Block] = nx
+
1551 slab[idy][%Block] = ny
+
+
+
+
1555 nthreads = ThreadProcessorCount
+
+
+
1558 variable threadGroupID = ThreadGroupCreate(nthreads)
+
+
1560 for (ithread = 0; ithread < nthreads; ithread += 1)
+
+
+
+
1564 make /n=(nzt) /df /free processing_folders
+
+
+
+
+
+
+
+
1572 make /n=(nx,ny) /d /o $datawavename
+
1573 wave template = $datawavename
+
+
+
+
1577 variable iz, it, izt
+
+
1579 variable n_recvd = 0
+
+
+
+
+
+
1585 make /n=0 /free /wave result_waves
+
+
+
+
+
+
+
1592 if (n_sent < max(1, nthreads) * 10 + n_recvd)
+
+
+
+
1596 slab[idz][%Start] = iz
+
1597 slab[idt][%Start] = it
+
1598 dfname = "processing_" + num2str(n_sent)
+
1599 NewDataFolder /s $dfname
+
1600 HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata file_id, datasetpath
+
+
1602 duplicate template, image
+
1603 variable /g r_index = iz
+
1604 variable /g s_index = it
+
1605 string /g func_param = reduction_params
+
+
+
+
+
1610 ThreadGroupPutDF threadGroupID, :
+
+
+
1613 processing_folders[n_sent] = GetDataFolderDFR()
+
1614 make /n=1/d profile1, profile2
+
+
1616 wave /wave reduced_waves =
reduce_slab_image (slabdata, image, reduction_func, func_param)
+
1617 variable /g func_result = numpnts(reduced_waves)
+
+
1619 WaveClear slabdata, image, reduced_waves
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1633 tmo = min(100, tmo + 10)
+
+
+
+
+
+
1639 dfr = ThreadGroupGetDFR(threadGroupID, tmo)
+
+
1641 dfr = processing_folders[n_recvd]
+
1642 processing_folders[n_recvd] = $""
+
+
+
1645 if (DatafolderRefStatus(dfr) != 0)
+
+
1647 nvar rr = dfr:r_index
+
1648 nvar ss = dfr:s_index
+
1649 nvar func_result = dfr:func_result
+
+
1651 if (func_result < 1)
+
1652 print "error during data reduction."
+
+
+
+
+
+
1658 if (numpnts(result_waves) == 0)
+
1659 redimension /n=(func_result) result_waves
+
1660 for (iw = 0; iw < func_result; iw += 1)
+
1661 sw = "redw_" + num2str(iw)
+
1662 wave profile = dfr:$sw
+
1663 sw = "ReducedData" + num2str(iw+1)
+
1664 make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
+
+
1666 setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
+
1667 setdimlabel 1, -1, $kScanDimLabel, data
+
1668 note data, note(profile)
+
+
1670 setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
+
1671 setscale d 0, 0, waveunits(profile, -1), data
+
1672 result_waves[iw] = data
+
+
+
+
+
1677 for (iw = 0; iw < func_result; iw += 1)
+
1678 sw = "redw_" + num2str(iw)
+
1679 wave profile = dfr:$sw
+
1680 wave data = result_waves[iw]
+
1681 data[][rr][ss] = profile[p]
+
+
+
+
1685 KillDataFolder /Z dfr
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1700 while ((n_recvd < nzt) && (result == 0))
+
+
+
1703 killwaves /z slab, slabdata, template
+
+
+
1706 variable tstatus = ThreadGroupRelease(threadGroupID)
+
+
1708 print "error: thread did not terminate properly."
+
+
+
+
+
+
1714 nw = numpnts(result_waves)
+
+
1716 for (iw = 0; iw < nw; iw += 1)
+
1717 wave /z data = result_waves[iw]
+
1718 if (WaveExists(data))
+
+
1720 redimension /n=(-1, 0, 0) data
+
+
1722 redimension /n=(-1, nz, 0) data
+
+
1724 wavenames += nameofwave(data) + ";"
+
+
+
+
+
+
+
+
1732 setdatafolder base_df
+
+
+
+
+
+
+
+
+
+
1742 dfref dfr = ThreadGroupGetDFR(0, 1000)
+
1743 if (DataFolderRefStatus(dfr) == 0)
+
+
+
+
+
+
+
+
+
+
1753 wave slabdata = dfr:slabdata
+
1754 wave image = dfr:image
+
1755 svar func_param = dfr:func_param
+
1756 nvar rr = dfr:r_index
+
1757 nvar ss = dfr:s_index
+
+
+
1760 newdatafolder /s out_df
+
1761 variable /g r_index = rr
+
1762 variable /g s_index = ss
+
1763 wave /wave reduced_waves =
reduce_slab_image (slabdata, image, reduction_func, func_param)
+
1764 variable /g func_result = numpnts(reduced_waves)
+
+
+
+
1768 WaveClear slabdata, image, reduced_waves
+
1769 ThreadGroupPutDF 0, :
+
+
+
+
+
+
+
1776 threadsafe static function /wave
reduce_slab_image (slabdata, image, reduction_func, reduction_params)
+
+
+
+
1780 string reduction_params
+
+
1782 image = slabdata[q][p][0][0]
+
+
1784 return reduction_func(image, reduction_params)
+
+
+
+
+
+
+
+
1806 if (!DataFolderRefStatus(file_df))
+
1807 dfref file_df = GetDataFolderDFR()
+
+
1809 nvar /sdfr=file_df file_id
+
+
1811 string obj_names = "authors;pgroup;proposal;proposer;sample;"
+
1812 variable nn = ItemsInList(obj_names, ";")
+
+
+
+
1816 for (ii = 0; ii < nn; ii += 1)
+
1817 name = StringFromList(ii, obj_names, ";")
+
+
+
+
+
+
+
+
+
+
+
1842 if (!DataFolderRefStatus(file_df))
+
1843 dfref file_df = GetDataFolderDFR()
+
+
1845 nvar /sdfr=file_df file_id
+
+
1847 string path = "/general/" + name
+
1848 HDF5LoadData /O /Q /Z /N=wt_load_general /TYPE=1 file_id, path
+
+
+
1851 wave /t wt_load_general
+
1852 variable nn = numpnts(wt_load_general)
+
+
1854 for (ii = 0; ii < nn; ii += 1)
+
1855 values = AddListItem(wt_load_general[ii], values, ",", inf)
+
+
1857 killwaves /z wt_load_general
+
1858 if (strlen(values) >= 1)
+
1859 values = values[0,strlen(values)-2]
+
+
+
1862 string /g $name = values
+
+
+
+
+
+
+
+
+
1892 if (!DataFolderRefStatus(file_df))
+
1893 dfref file_df = GetDataFolderDFR()
+
+
1895 nvar /sdfr=file_df file_id
+
+
1897 dfref save_df = GetDataFolderDFR()
+
1898 SetDataFolder NewFreeDataFolder()
+
+
+
+
1902 HDF5LoadData /O /Q /Z /A="Writable Dimension" /N=WriteDim file_id, datasetpath
+
+
+
+
1906 sprintf wnote, "ScanDimension=%u", WriteDim[0]
+
1907 Note datawave, wnote
+
+
+
1910 HDF5LoadData /O /Q /Z /A="Writable Index" /N=WriteIndex file_id, datasetpath
+
+
+
1913 sprintf wnote, "WriteableIndex=%u", WriteIndex[0]
+
1914 Note datawave, wnote
+
+
+
1917 HDF5LoadData /O /Q /Z /A="Readable Index" /N=ReadIndex file_id, datasetpath
+
+
+
1920 sprintf wnote, "ReadableIndex=%u", ReadIndex[0]
+
1921 Note datawave, wnote
+
+
+
1924 setdatafolder save_df
+
+
+
+
+
+
+
+
1958 string wavenames = ""
+
+
1960 if (!DataFolderRefStatus(file_df))
+
1961 dfref file_df = GetDataFolderDFR()
+
+
1963 nvar /sdfr=file_df file_id
+
+
1965 HDF5LoadData /O /Q /Z /A="Dimensions" /N=ScanDimensions /TYPE=1 file_id, scanpath
+
+
1967 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
1969 make /n=1 /o ScanDimensions
+
+
1971 wavenames = AddListItem("ScanDimensions", wavenames, ";", inf)
+
+
1973 HDF5LoadData /O /Q /Z /A="Readables" /N=ScanReadables /TYPE=1 file_id, scanpath
+
+
1975 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
1977 make /n=1 /o /t ScanReadables
+
1978 ScanReadables[0] = "ScientaSpectrum"
+
1979 wavenames = AddListItem("ScanReadables", wavenames, ";", inf)
+
+
1981 HDF5LoadData /O /Q /Z /A="Writables" /N=ScanWritables /TYPE=1 file_id, scanpath
+
+
1983 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
+
1986 HDF5LoadData /O /Q /Z /A="PlotDomain" /N=ScanWritables /TYPE=1 file_id, scanpath
+
+
1988 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
+
1991 HDF5LoadData /O /Q /Z /A="Steps" /N=ScanSteps /TYPE=1 file_id, scanpath
+
+
1993 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
1995 wavenames = ReplaceString(";;", wavenames, ";")
+
+
+
1998 HDF5LoadData /O /Q /Z /A="Iterations" /N=ScanIterations /TYPE=1 file_id, scanpath
+
+
2000 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
2002 HDF5LoadData /O /Q /Z /A="Step Size" /N=ScanStepSize /TYPE=1 file_id, scanpath
+
+
2004 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
2006 HDF5LoadData /O /Q /Z /A="Step Time" /N=ScanStepTime /TYPE=1 file_id, scanpath
+
+
2008 wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2058 case "ScientaImage":
+
2059 setdimlabel 0, -1, $kEnergyDimLabel, data
+
2060 setdimlabel 1, -1, $kAngleDimLabel, data
+
2061 if (WaveDims(data) >= 3)
+
2062 setdimlabel 2, -1, $kScanDimLabel, data
+
+
+
+
2066 case "ImageAngleDistribution":
+
2067 case "ScientaAngleDistribution":
+
2068 if (WaveDims(data) >= 2)
+
2069 setdimlabel 0, -1, $kScanDimLabel, data
+
2070 setdimlabel 1, -1, $kAngleDimLabel, data
+
+
2072 setdimlabel 0, -1, $kAngleDimLabel, data
+
+
+
+
2076 case "ScientaSpectrum":
+
2077 case "ImageEnergyDistribution":
+
2078 case "ScientaEnergyDistribution":
+
2079 if (WaveDims(data) >= 2)
+
2080 setdimlabel 0, -1, $kScanDimLabel, data
+
2081 setdimlabel 1, -1, $kEnergyDimLabel, data
+
+
2083 setdimlabel 0, -1, $kEnergyDimLabel, data
+
+
+
+
+
2088 if (WaveDims(data) == 1)
+
2089 setdimlabel 0, -1, $kScanDimLabel, data
+
+
+
+
+
+
+
2096 dummy = GetRTError(1)
+
+
+
+
+
+
+
+
+
2114 wave /z /t /sdfr=data_df ScanWritables=::ScanWritables
+
2115 if (WaveExists(ScanWritables))
+
2116 string sdf = GetDataFolder(1, data_df)
+
2117 dfref parent_df = $(sdf + ":")
+
+
+
+
+
+
+
+
+
+
2137 dfref diags_df = data_df:diags
+
2138 dfref attrs_df = scan_df:attrs
+
2139 dfref attr_df = scan_df:attr
+
2140 if (DataFolderRefStatus(diags_df))
+
+
2142 elseif (DataFolderRefStatus(attrs_df))
+
+
2144 elseif (DataFolderRefStatus(attr_df))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2169 make /n=(ndf) /df /free dfs
+
2170 dfs[0] = {df1, df2, df3}
+
2171 for (idf = 0; idf < ndf; idf += 1)
+
2172 if (DataFolderRefStatus(dfs[idf]))
+
2173 wave /SDFR=dfs[idf] /Z w = $name
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2235 redimension /n=4 lo, hi, un, ax
+
2236 setdimlabel 0, 0, $kEnergyDimLabel, lo, hi, un, ax
+
2237 setdimlabel 0, 1, $kAngleDimLabel, lo, hi, un, ax
+
2238 setdimlabel 0, 2, $kScanDimLabel, lo, hi, un, ax
+
2239 setdimlabel 0, 3, $kDataDimLabel, lo, hi, un, ax
+
+
+
2242 lo[%$kEnergyDimLabel] = 0
+
2243 hi[%$kEnergyDimLabel] = 1
+
2244 un[%$kEnergyDimLabel] =
"eV"
+
2245 ax[%$kEnergyDimLabel] =
"Ekin"
+
+
2247 lo[%$kAngleDimLabel] = -1
+
2248 hi[%$kAngleDimLabel] = 1
+
2249 un[%$kAngleDimLabel] =
"arb."
+
2250 un[%$kAngleDimLabel] =
"slice"
+
+
2252 lo[%$kScanDimLabel] = 0
+
2253 hi[%$kScanDimLabel] = 1
+
2254 un[%$kScanDimLabel] =
"arb."
+
2255 ax[%$kScanDimLabel] =
"scan"
+
+
2257 lo[%$kDataDimLabel] = 0
+
2258 hi[%$kDataDimLabel] = 0
+
2259 un[%$kDataDimLabel] =
"arb."
+
2260 ax[%$kDataDimLabel] =
"value"
+
+
+
2263 wave /Z ChannelBegin =
ps_find_scale_wave (
"ScientaChannelBegin" , data_df, scan_df, attr_df)
+
2264 wave /Z ChannelEnd =
ps_find_scale_wave (
"ScientaChannelEnd" , data_df, scan_df, attr_df)
+
2265 wave /Z SliceBegin =
ps_find_scale_wave (
"ScientaSliceBegin" , data_df, scan_df, attr_df)
+
+
2267 wave /Z ScientaChannels =
ps_find_scale_wave (
"ScientaChannels" , data_df, scan_df, attr_df)
+
+
+
2270 if (waveexists(LensMode) && (numpnts(LensMode) >= 1))
+
2271 strswitch(LensMode[0])
+
+
2273 lo[%$kAngleDimLabel] = -45/2
+
2274 hi[%$kAngleDimLabel] = +45/2
+
2275 un[%$kAngleDimLabel] =
"°"
+
2276 ax[%$kAngleDimLabel] =
"angle"
+
+
+
2279 lo[%$kAngleDimLabel] = -60/2
+
2280 hi[%$kAngleDimLabel] = +60/2
+
2281 un[%$kAngleDimLabel] =
"°"
+
2282 ax[%$kAngleDimLabel] =
"angle"
+
+
2284 case "Transmission" :
+
2285 un[%$kAngleDimLabel] =
"arb."
+
2286 ax[%$kAngleDimLabel] =
"offset"
+
+
+
+
+
+
2292 if (waveexists(ChannelBegin) && waveexists(ChannelEnd) && (numpnts(ChannelBegin) >= 1) && (numpnts(ChannelEnd) >= 1))
+
2293 lo[%$kEnergyDimLabel] = ChannelBegin[0]
+
2294 hi[%$kEnergyDimLabel] = ChannelEnd[0]
+
2295 elseif (waveexists(ScientaChannels) && (numpnts(ScientaChannels) >= 1))
+
2296 lo[%$kEnergyDimLabel] = ScientaChannels[0]
+
2297 hi[%$kEnergyDimLabel] = ScientaChannels[numpnts(ScientaChannels)-1]
+
+
2299 if (waveexists(SliceBegin) && waveexists(SliceEnd) && (numpnts(SliceBegin) >= 1) && (numpnts(SliceEnd) >= 1))
+
2300 lo[%$kAngleDimLabel] = SliceBegin[0]
+
2301 hi[%$kAngleDimLabel] = SliceEnd[0]
+
+
+
2304 wave /z /t /SDFR=scan_df ScanWritables
+
2305 if (WaveExists(ScanWritables))
+
2306 wave /z /SDFR=scan_df scanner = $ScanWritables[0]
+
2307 if (!WaveExists(scanner))
+
2308 wave /z /SDFR=attr_df scanner = $ScanWritables[0]
+
+
2310 if (WaveExists(scanner) && (numpnts(scanner) >= 1))
+
2311 lo[%$kScanDimLabel] = scanner[0]
+
2312 hi[%$kScanDimLabel] = scanner[numpnts(scanner)-1]
+
2313 ax[%$kScanDimLabel] = NameOfWave(scanner)
+
2314 strswitch(NameOfWave(scanner))
+
+
2316 ax[%$kScanDimLabel] = "photon energy"
+
2317 un[%$kScanDimLabel] = "eV"
+
+
2319 case "ManipulatorX":
+
2320 case "ManipulatorY":
+
2321 case "ManipulatorZ":
+
+
+
2324 case "RefocusYTrans":
+
2325 case "RefocusZTrans":
+
+
2327 un[%$kScanDimLabel] = "mm"
+
+
+
2330 un[%$kScanDimLabel] = "µm"
+
+
2332 case "ManipulatorTheta":
+
2333 case "ManipulatorTilt":
+
2334 case "ManipulatorPhi":
+
2335 un[%$kScanDimLabel] = "°"
+
+
+
+
+
+
+
+
2343 un[%$kScanDimLabel] = "mrad"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2396 string snote = note(data)
+
+
2398 sdim = GetDimLabel(data, 0, -1)
+
+
2400 setscale /i x lo[%$sdim], hi[%$sdim], un[%$sdim], data
+
2401 snote = ReplaceStringByKey("AxisLabelX", snote, ax[%$sdim], "=", "\r")
+
+
+
2404 sdim = GetDimLabel(data, 1, -1)
+
+
2406 setscale /i y lo[%$sdim], hi[%$sdim], un[%$sdim], data
+
2407 snote = ReplaceStringByKey("AxisLabelY", snote, ax[%$sdim], "=", "\r")
+
+
+
2410 sdim = GetDimLabel(data, 2, -1)
+
+
2412 setscale /i z lo[%$sdim], hi[%$sdim], un[%$sdim], data
+
2413 snote = ReplaceStringByKey("AxisLabelZ", snote, ax[%$sdim], "=", "\r")
+
+
+
2416 string data_unit = un[%$kDataDimLabel]
+
2417 string data_label = ax[%$kDataDimLabel]
+
+
2419 variable def = (cmpstr(data_unit, "arb.") == 0) && (cmpstr(data_label, "value") == 0)
+
+
+
2422 s = StringByKey("AxisLabelD", snote, "=", "\r")
+
+
+
+
+
2427 s = StringByKey("AxisUnitD", snote, "=", "\r")
+
+
+
+
+
+
+
+
2435 strswitch(NameOfWave(data))
+
2436 case "ScientaImage":
+
2437 case "ImageAngleDistribution":
+
2438 case "ScientaAngleDistribution":
+
2439 case "ScientaSpectrum":
+
2440 case "ImageEnergyDistribution":
+
2441 case "ScientaEnergyDistribution":
+
+
2443 data_label = "intensity"
+
+
+
2446 case "SampleCurrent":
+
+
+
+
2450 data_label = "current"
+
+
+
2453 case "MachineCurrent":
+
+
2455 data_label = "current"
+
+
+
+
+
+
2461 setscale d 0, 0, data_unit, data
+
2462 snote = ReplaceStringByKey("AxisLabelD", snote, data_label, "=", "\r")
+
2463 snote = ReplaceStringByKey("AxisUnitD", snote, data_unit, "=", "\r")
+
2464 snote = ReplaceStringByKey("Dataset", snote, NameOfWave(data), "=", "\r")
+
+
+
+
+
+
+
2486 make /n=3 /free lo, hi
+
2487 make /n=3 /t /free ax, un
+
2488 wave /t /z /SDFR=scan_df ScanReadables
+
2489 if (WaveExists(ScanReadables))
+
+
2491 variable nsr = numpnts(ScanReadables)
+
+
+
+
2495 for (isr = 0; isr < nsr; isr += 1)
+
2496 ssr = ScanReadables[isr]
+
+
2498 if (!DataFolderRefStatus(data_df))
+
2499 dfref data_df = scan_df
+
+
2501 nel = ItemsInList(ssr, "/")
+
2502 sds = StringFromList(nel - 1, ssr, "/")
+
2503 wave /z /sdfr=data_df wsr=$sds
+
2504 if (WaveExists(wsr))
+
+
+
+
+
+
+
+
+
+
+
2531 dfref save_df = GetDataFolderDFR()
+
2532 dfref data_df = GetWavesDataFolderDFR(data)
+
+
2534 setdatafolder data_df
+
2535 make /n=3 /free lo, hi
+
2536 make /n=3 /t /free ax, un
+
+
+
2539 setdatafolder save_df
+
+
+
+
+
+
+
+
+
+
+
+
2560 if (ParamIsDefault(killed))
+
+
+
+
+
+
+
+
2568 Wave/Z w = WaveRefIndexedDFR(dfr, index)
+
+
+
+
+
+
2574 if (stringmatch(s, pattern))
+
+
2576 killed = AddListItem(s, killed, ";", Inf)
+
+
+
+
+
+
+
2583 Variable numChildDataFolders = CountObjectsDFR(dfr, 4)
+
+
2585 for(i=0; i<numChildDataFolders; i+=1)
+
2586 String childDFName = GetIndexedObjNameDFR(dfr, 4, i)
+
2587 DFREF childDFR = dfr:$childDFName
+
+
+
+
+
+
string psh5_load_dataset(dfref file_df, string datasetpath, variable create_folders=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue)
load a dataset from an open PShell HDF5 file.
string ps_fix_folder_name(string group_name)
convert HDF5 group name to data folder name and fix compatibility issues
static threadsafe variable reduce_slab_worker(funcref reduction_func)
string psh5_filter_datasets_rank(string datasets, string ranks, variable min_rank, variable max_rank)
filter datasets by rank
wave ps_find_scale_wave(string name, dfref df1, dfref df2, dfref df3)
find a wave in scan and attr data folders
const variable kDSCEssentialDiags
dfr psh5_create_folders(string datasetpath)
create all data folders along a dataset path
variable ps_set_dimlabels(wave data)
set dimension labels according to the axis type
variable ps_set_dimlabels2(wave data, string name)
set dimension labels according to the axis type
string psh5_load_general_group(dfref file_df)
load organizational metadata from the general group.
string psh_load_general_string(dfref file_df, string name)
load a string from the general group.
string psh5_load_dataset_slabs(dfref file_df, string datasetpath, variable create_folders=defaultValue, variable progress=defaultValue)
load a dataset slab-wise from the open PShell HDF5 file.
const string kScientaScalingDatasets
List of datasets that must be loaded to determine the axis scaling of a Scienta image.
const variable kDSCMonitors
string psh5_load_dataset_reduced(dfref file_df, string datasetpath, funcref reduction_func, string reduction_params, variable create_folders=defaultValue, variable progress=defaultValue, variable nthreads=defaultValue)
load a dataset with reduced dimensionality
const variable kDSCRegions
const variable kDSCPositioners
threadsafe variable adh5_get_result_waves(wave results, string result_prefix, variable start_index)
copy waves from wave reference wave into current data folder
const variable kDSCPreview
string psh5_load_scan_meta(dfref file_df, string scanpath)
load metadata of a PShell scan group.
static string twave2list(wave wt, string sep)
convert text wave to list.
const variable kDSCScientaScaling
variable psh5_load_dataset_meta(dfref file_df, string datasetpath, wave datawave)
load metadata of a PShell dataset.
variable ps_scale_dataset(wave data)
set the dimension scales of a loaded PShell Scienta dataset according to attributes.
string psh5_extract_region_paths(string datasets)
trim dataset paths to the scan/region part
const string kAngleDimLabel
Dimension label for the angle dispersive dimension of multi-dimensional datasets.
variable ps_scale_dataset_2(wave data, wave ax, wave lo, wave hi, wave un)
set the dimension scales of a dataset.
const string kTransposedDatasets
List of datasets that must be transposed upon loading.
dfr psh5_dataset_to_folder(dfref parent_df, string datasetpath)
map dataset path to datafolder path
string ad_suggest_foldername(string filename, variable ignoredate=defaultValue, string sourcename=defaultValue, variable unique=defaultValue)
generate the name of a data folder based on a file name.
const string kPreviewDatasets
List of preferred datasets to load for preview.
dfr ps_find_attr_folder(dfref scan_df)
find the attributes data folder
string psh5_list_all_datasets(variable file_id)
list all datasets in a file
string psh5_load_datasets(dfref file_df, string datasets, variable create_folders=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue)
load multiple datasets from open file
const string kEssentialDiagnostics
List of diagnostic datasets that are normally loaded with a scan.
const string kDataDimLabel
Dimension label for the data dimension.
static string wave2list(wave w, string format, string sep)
convert numeric wave to list.
threadsafe wave adh5_default_reduction(wave source, string *param)
function prototype for adh5_load_reduced_detector
const variable kDSCDetectors
dfr psh5_preview(string path_name, string file_name, dfref dest_df=defaultValue, string preview_datasets=defaultValue)
load preview
variable psh5_close_file(dfref file_df)
close a HDF5 file opened by psh5_open_file.
string psh5_list_scans(variable file_id)
list scan groups of a PShell data file.
string kill_matching_waves(dfref dfr, string pattern, variable recurse, string killed=defaultValue)
kill any waves matching a pattern in the experiment
string PearlCleanupName(string name)
static string unique_strings(string list)
remove duplicate items from list
variable ps_scale_datasets(dfref scan_df)
set the dimension scales of loaded PShell Scienta datasets according to attributes.
dfr psh5_load(string path_name, string file_name, string scans, string regions, string datasets, variable classes=defaultValue, variable max_rank=defaultValue, string reduction_func=defaultValue, string reduction_params=defaultValue, dfref dest_df=defaultValue)
main data loading function
const string kScanDimLabel
Dimension label for the scan dimension of multi-dimensional datasets.
string psh5_match_dataset_classes(string datasets, variable classes, string positioners=defaultValue, string detectors=defaultValue)
filter a list of datasets by classification
variable ps_detect_scale(dfref data_df, wave ax, wave lo, wave hi, wave un)
detect the dimension scales from attributes.
variable[string datatypes, string ranks, string dimensions] psh5_list_dataset_info(string variable, string file_id, variable string, sds datasets)
list data types and dimensions of datasets
const string kEnergyDimLabel
Dimension label for the energy dispersive dimension of multi-dimensional datasets.
string psh5_extract_scan_paths(string datasets)
trim dataset paths to the scan part
dfr psh5_open_file(string path_name, string file_name, dfref dest_df=defaultValue)
open a HDF5 file created by the PShell data acquisition program and prepare the data folder.
static threadsafe wave reduce_slab_image(wave slabdata, wave image, funcref reduction_func, string reduction_params)
dfr ps_find_scan_folder(dfref data_df)
find the scan folder of current data
PEARL Procedures: pearl-scienta-countrate.ipf File Reference
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- rev-distro-2.1.1-1-gf419e92-dirty
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count rate functions for Scienta detector images.
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#include "pearl-area-display"
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Go to the source code of this file.
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-variable ScientaLiveDisplay (string epicsname, string nickname, string wbRGB) open live display of most recent scienta measurement More... variable check_exposure_opt (wave image, wave outmask, variable dwelltime, dfref calc_df=defaultValue) optimized check exposure and calculate overexposure indicator mask More...
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count rate functions for Scienta detector images.
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this procedure contains functions for working with true count rates.
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Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
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Copyright 2019 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0
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-
Definition in file pearl-scienta-countrate.ipf .
-
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◆
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- variable check_exposure_opt
- (
- wave
- image ,
-
- wave
- outmask ,
-
- variable
- dwelltime ,
-
- dfref
- calc_df = defaultValue
-
- )
-
-
-
-
-
optimized check exposure and calculate overexposure indicator mask
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calculate the local count rate density and return a mask to indicate where the maximum count rate is exceeded. the raw image is filtered by FFT with a gaussian kernel.
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the raw image must have been acquired in fixed mode. slicing and dwell time are accounted for.
-
this function does the same as check_exposure() but keeps intermediate waves for time-optimized processing. moreover it is compatible with igor 6.
-
Parameters
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Definition at line 150 of file pearl-scienta-countrate.ipf .
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- variable ScientaLiveDisplay
- (
- string
- epicsname ,
-
- string
- nickname ,
-
- string
- wbRGB
-
- )
-
-
-
-
-
open live display of most recent scienta measurement
-
Parameters
-
- epicsname base name of the detector, e.g. X03DA-SCIENTA: image1: and cam1: are appended by the function. see ad_connect. nickname nick name under which this detector is referred to in Igor. must be a valid data folder name. see ad_connect. wbRGB window background color, e.g. "32768,49152,55296"
-
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Definition at line 43 of file pearl-scienta-countrate.ipf .
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PEARL Procedures: pearl-scienta-countrate.ipf Source File
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- rev-distro-2.1.1-1-gf419e92-dirty
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Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.35 3 #pragma ModuleName = PearlScientaCountrate 4 #include "pearl-area-display" 48 ad_connect(epicsname, nickname)
50 sprintf df_name,
"ad_display_profiles(root:pearl_epics:%s)" , nickname
52 wave /sdfr=df img = image
54 wbRGB = replacestring(
"(" , wbRGB,
"" )
55 wbRGB = replacestring(")", wbRGB, "")
56 variable rr = str2num(StringFromList(0, wbRGB, ","))
57 variable gg = str2num(StringFromList(1, wbRGB, ","))
58 variable bb = str2num(StringFromList(2, wbRGB, ","))
59 ModifyGraph /w=$graphname wbRGB=(rr,gg,bb)
64 #if igorVersion() >= 8 65 function check_exposure(image, outmask, dwelltime)
93 variable ybin = 902 / dimsize(image, 1)
94 variable thresh = 1e5 / 900 / 900
96 duplicate /free image, filt
97 setscale /p x -dimsize(image, 0)/2, 1, "", filt
98 setscale /p y -dimsize(image, 1)/2, 1, "", filt
99 variable wx = sqrt(500) / xbin
100 variable wy = sqrt(500) / ybin
101 filt = exp(-((x/wx)^2 + (y/wy)^2))
102 variable nfilt = sum(filt)
104 fft /free /dest=filt_fft filt
106 duplicate /free image, img
108 setscale /p x -dimsize(image, 0)/2, 1, "", img
109 setscale /p y -dimsize(image, 1)/2, 1, "", img
110 fft /free /dest=img_fft img
112 ifft /free /dest=img_ifft img_fft
113 imagetransform swap img_ifft
115 outmask = (img_ifft < thresh) * 64
157 variable ybin = 902 / dimsize(image, 1)
158 variable thresh = 1e5 / 900 / 900
160 dfref save_df = GetDataFolderDFR()
161 if (ParamIsDefault(calc_df))
162 dfref source_df = GetWavesDataFolderDFR(image)
164 dfref calc_df = source_df:$calc_df_name
166 NewDataFolder /o /s calc_df
169 wave /z /c co_filt_fft
171 wave /z /c co_img_fft
173 nvar /z co_img_size_x
174 nvar /z co_img_size_y
177 if (waveexists(co_filt))
178 cache = (dimsize(image, 0) == co_img_size_x) && (dimsize(image, 1) == co_img_size_y)
180 redimension /n=(dimsize(image, 0), dimsize(image, 1)) co_filt, co_filt_fft, co_img, co_img_fft, co_img_ifft
183 duplicate /o image, co_filt, co_img, co_img_ifft
184 make /n=(dimsize(image, 0), dimsize(image, 1)) /c co_filt_fft, co_img_fft
185 variable /g co_img_size_x
186 variable /g co_img_size_y
189 co_img_size_x = dimsize(image, 0)
190 co_img_size_y = dimsize(image, 1)
191 setscale /p x -co_img_size_x/2, 1, "", co_filt, co_filt_fft, co_img, co_img_fft, co_img_ifft
192 setscale /p y -co_img_size_y/2, 1, "", co_filt, co_filt_fft, co_img, co_img_fft, co_img_ifft
195 variable wx = sqrt(500) / xbin
196 variable wy = sqrt(500) / ybin
197 co_filt = exp(-((x/wx)^2 + (y/wy)^2))
198 variable nfilt = sum(co_filt)
200 fft /dest=co_filt_fft co_filt
204 fft /dest=co_img_fft co_img
205 co_img_fft *= co_filt_fft
206 ifft /dest=co_img_ifft co_img_fft
207 imagetransform swap co_img_ifft
209 redimension /n=(dimsize(co_img_ifft, 0), dimsize(co_img_ifft, 1)) outmask
210 outmask = (co_img_ifft < thresh) * 64
212 SetDataFolder save_df
variable check_exposure_opt(wave image, wave outmask, variable dwelltime, dfref calc_df=defaultValue)
optimized check exposure and calculate overexposure indicator mask
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string PearlCleanupName(string name)
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string ad_display(wave image)
open a new graph window with a 2D image.
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wave ad_add_overlay(wave image, string rgba=defaultValue)
add an overlay on top of the displayed image
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variable ScientaLiveDisplay(string epicsname, string nickname, string wbRGB)
open live display of most recent scienta measurement
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PEARL Procedures: pearl-scienta-preprocess.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
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preprocessing functions for Scienta detector images.
More...
#include "pearl-fitfuncs"#include "pearl-area-import"
Go to the source code of this file.
preprocessing functions for Scienta detector images.
this procedure contains functions for data reduction and instrument-specific normalization.
Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
-
Copyright 2013-18 Paul Scherrer Institut Copyright 2013-18 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-scienta-preprocess.ipf .
@@ -173,7 +178,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Note on profile graphs, the necessary cursors can be configured easily by calling the ad_profile_cursor_mode() function, e.g. ad_profiles_cursor_mode(root:packages:pearl_explorer:preview_image, 1). Definition at line 93 of file pearl-scienta-preprocess.ipf .
+Definition at line 95 of file pearl-scienta-preprocess.ipf .
Returns parameter string for linear background subtraction Definition at line 133 of file pearl-scienta-preprocess.ipf .
+Definition at line 135 of file pearl-scienta-preprocess.ipf .
@@ -267,7 +272,37 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns free wave containing references of the result waves. the number of waves is two times the number of peaks that are fit. the first npeaks waves contain the peak integrals, the second npeaks waves the corresponding error estimates. Definition at line 718 of file pearl-scienta-preprocess.ipf .
+Definition at line 720 of file pearl-scienta-preprocess.ipf .
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+ (
+ wave
+ source ,
+
+ string *
+ param
+
+ )
+
+
+
Returns free wave containing references of the two result waves. the first wave is the integral minus linear background. the second wave is the Poisson one-sigma error. Definition at line 260 of file pearl-scienta-preprocess.ipf .
+Definition at line 262 of file pearl-scienta-preprocess.ipf .
@@ -369,7 +404,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns free wave containing references of the two result waves. the first wave is the integral minus linear background. the second wave is the Poisson one-sigma error. Definition at line 413 of file pearl-scienta-preprocess.ipf .
+Definition at line 415 of file pearl-scienta-preprocess.ipf .
@@ -391,7 +426,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); prompt for the gauss4_reduction parameters
-Definition at line 626 of file pearl-scienta-preprocess.ipf .
+Definition at line 628 of file pearl-scienta-preprocess.ipf .
@@ -413,7 +448,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); prompt the user for integrate on linear background reduction parameters.
-Definition at line 35 of file pearl-scienta-preprocess.ipf .
+Definition at line 37 of file pearl-scienta-preprocess.ipf .
@@ -433,7 +468,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); linear background reduction function for incorrectly dimensioned scienta image
if the energy step size does not divide the energy range to an integer number, the scienta image is exported with the wrong array size. this can be fixed by redimensioning the array.
the current implementation works in the case where dimension 0 needs to be incremented. the function may be generalized to dimension 1 and/or decrementing by additional parameters. it is not known yet whether a generalization is needed or whether it can cover all cases.
-background subtraction and peak integration is the same as by the int_linbg_reduction() function.
+background subtraction and peak integration is the same as by the int_linbg_reduction() function.
Parameters
source source wave Scienta detector image, energy axis along X, angle axis along Y typical values (peak centered on detector, FWHM ~ 20 % of image) Lcrop=0.11;Hcrop=0.11;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.2
Returns free wave containing references of the two result waves. the first wave is the integral minus linear background. the second wave is the Poisson one-sigma error. Definition at line 572 of file pearl-scienta-preprocess.ipf .
+Definition at line 574 of file pearl-scienta-preprocess.ipf .
@@ -537,7 +572,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); apply the gauss4_reduction function to a single image
useful for testing or manual processing. to debug, (temporarily) remove the threadsafe attribute from the gauss2_reduction function.
-Definition at line 592 of file pearl-scienta-preprocess.ipf .
+Definition at line 594 of file pearl-scienta-preprocess.ipf .
@@ -547,9 +582,9 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-scienta-preprocess.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,31 +87,1319 @@ $(document).ready(function(){initNavTree('pearl-scienta-preprocess_8ipf_source.h
pearl-scienta-preprocess.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 2 #pragma IgorVersion = 6.1 3 #pragma ModuleName = PearlScientaPreprocess 4 #include "pearl-fitfuncs" 38 variable Lcrop = NumberByKey(
"Lcrop" , param,
"=" ,
";" )
39 variable Lsize = NumberByKey("Lsize", param, "=", ";")
40 variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
41 variable Hsize = NumberByKey("Hsize", param, "=", ";")
42 variable Cpos = NumberByKey("Cpos", param, "=", ";")
43 variable Csize = NumberByKey("Csize", param, "=", ";")
45 prompt Lcrop, "Lower cropping region"
46 prompt Hcrop, "Upper cropping region"
47 prompt Lsize, "Lower background region"
48 prompt Hsize, "Upper background region"
49 prompt Cpos, "Center position"
50 prompt Csize, "Center integration region"
54 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
55 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
56 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
57 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
58 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
59 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
95 svar /z global_params = root:packages:pearl_explorer:s_reduction_params
96 if (svar_exists(global_params))
140 make /n=(nc) /free positions
143 string imagename = ""
144 string tracename = ""
147 for (ic = 0; ic < nc; ic += 1)
148 sc = num2char(char2num("A") + ic)
149 wave /z wc = CsrWaveRef($sc, win)
150 info = CsrInfo($sc, win)
151 tracename = StringByKey("TNAME", info, ":", ";")
152 if (waveexists(wc) && (wavedims(wc) == 2))
153 if (!waveexists(image))
155 imagename = tracename
157 if (cmpstr(tracename, imagename) == 0)
158 positions[np] = pcsr($sc, win)
164 np = floor(np / 2) * 2
165 redimension /n=(np) positions
166 sort positions, positions
168 positions = p >= np / 2 ? positions + 1 : positions
169 positions = positions / dimsize(image, 0)
172 variable ip2 = np / 2
173 variable ip1 = ip2 - 1
177 Cpos = (positions[ip1] + positions[ip2]) / 2
178 Csize = positions[ip2] - positions[ip1]
191 Lsize = positions[ip1]
192 Hsize = 1 - positions[ip2]
195 Lsize = Cpos - Csize / 2
196 Hsize = 1 - (Cpos + Csize / 2)
205 Lcrop = positions[ip1]
206 Hcrop = 1 - positions[ip2]
209 if (dimsize(image, 0) >= 992)
214 Lsize = max(Lsize - Lcrop, 0)
215 Hsize = max(Hsize - Hcrop, 0)
218 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
219 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
220 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
221 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
222 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
223 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
264 variable nx = dimsize(source, 0)
265 variable ny = dimsize(source, 1)
268 variable lcrop = NumberByKey("Lcrop", param, "=", ";")
269 variable lsize = NumberByKey("Lsize", param, "=", ";")
270 variable hcrop = NumberByKey("Hcrop", param, "=", ";")
271 variable hsize = NumberByKey("Hsize", param, "=", ";")
272 variable cpos = NumberByKey("Cpos", param, "=", ";")
273 variable csize = NumberByKey("Csize", param, "=", ";")
275 make /wave /free /n=2 result_waves
276 make /free /n=0 dest1, dest2
277 result_waves[0] = dest1
278 result_waves[1] = dest2
284 if (numtype(lcrop) != 0)
287 if (numtype(lsize) != 0)
290 if (numtype(hcrop) != 0)
293 if (numtype(hsize) != 0)
296 if (numtype(Cpos) != 0)
297 redimension /n=0 result_waves
300 if (numtype(Csize) != 0)
301 redimension /n=0 result_waves
305 variable lpos = lcrop + lsize / 2
306 variable hpos = 1 - (hcrop + hsize / 2)
311 duplicate /free dest1, lbg, hbg
313 p0 = round(lcrop * nx)
314 p1 = round((lcrop + lsize) * nx)
320 p0 = round((1 - hcrop - hsize) * nx)
321 p1 = round((1 - hcrop) * nx)
327 p0 = round((cpos - csize/2) * nx)
328 p1 = round((cpos + csize/2) * nx)
334 variable scale = (cpos - lpos) / (hpos - lpos)
336 dest1 -= scale * (hbg - lbg) + lbg
337 dest2 = sqrt(dest2 + scale^2 * (hbg + lbg))
341 sprintf s_note1, "AxisLabelD=peak integral"
342 sprintf s_note2, "KineticEnergy=%.3f", cpos * nx * dimdelta(source, 0) + dimoffset(source, 0)
354 variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
355 variable Lsize = NumberByKey("Lsize", param, "=", ";")
356 variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
357 variable Hsize = NumberByKey("Hsize", param, "=", ";")
358 variable Cpos = NumberByKey("Cpos", param, "=", ";")
359 variable Csize = NumberByKey("Csize", param, "=", ";")
361 prompt Lcrop, "Lower cropping region"
362 prompt Hcrop, "Upper cropping region"
363 prompt Lsize, "Lower background region"
364 prompt Hsize, "Upper background region"
365 prompt Cpos, "Center position"
366 prompt Csize, "Center integration region"
370 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
371 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
372 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
373 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
374 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
375 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
417 variable nx = dimsize(source, 0)
418 variable ny = dimsize(source, 1)
421 variable lcrop = NumberByKey("Lcrop", param, "=", ";")
422 variable lsize = NumberByKey("Lsize", param, "=", ";")
423 variable hcrop = NumberByKey("Hcrop", param, "=", ";")
424 variable hsize = NumberByKey("Hsize", param, "=", ";")
425 variable cpos = NumberByKey("Cpos", param, "=", ";")
426 variable csize = NumberByKey("Csize", param, "=", ";")
428 make /wave /free /n=2 result_waves
429 make /free /n=0 dest1, dest2
430 result_waves[0] = dest1
431 result_waves[1] = dest2
437 if (numtype(lcrop) != 0)
440 if (numtype(lsize) != 0)
443 if (numtype(hcrop) != 0)
446 if (numtype(hsize) != 0)
449 if (numtype(Cpos) != 0)
450 redimension /n=0 result_waves
453 if (numtype(Csize) != 0)
454 redimension /n=0 result_waves
459 variable pcl = round(lcrop * nx)
460 variable pch = round((1 - hcrop) * nx)
462 variable pfl = round((lcrop + lsize) * nx)
463 variable pfh = round((1 - hcrop - hsize) * nx)
465 variable pil = round((cpos - csize/2) * nx)
466 variable pih = round((cpos + csize/2) * nx)
469 make /n=(nx) /d /free profile, mask, fit
470 setscale /p x dimoffset(source,0), dimdelta(source,0), waveunits(source,0), profile, mask, fit
471 mask = ((p >= pcl) && (p < pfl)) || ((p >= pfh) && (p < pch))
475 variable xil = x2pnt(profile, pil)
476 variable xih = x2pnt(profile, pih)
478 make /n=3 /free /d w_coef
479 for (qq = 0; qq < ny; qq += 1)
480 profile = source[p][qq]
481 curvefit /Q /NTHR=1 /W=2 poly 3, kwCWave=w_coef, profile /M=mask
482 fit = poly(w_coef, x)
483 sp = sum(profile, xil, xih)
484 sf = sum(fit, xil, xih)
491 sprintf s_note1, "AxisLabelD=peak integral"
492 sprintf s_note2, "KineticEnergy=%.3f", cpos * nx * dimdelta(source, 0) + dimoffset(source, 0)
512 variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
513 variable Lsize = NumberByKey("Lsize", param, "=", ";")
514 variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
515 variable Hsize = NumberByKey("Hsize", param, "=", ";")
516 variable Cpos = NumberByKey("Cpos", param, "=", ";")
517 variable Csize = NumberByKey("Csize", param, "=", ";")
519 prompt Lcrop, "Lower cropping region"
520 prompt Hcrop, "Upper cropping region"
521 prompt Lsize, "Lower background region"
522 prompt Hsize, "Upper background region"
523 prompt Cpos, "Center position"
524 prompt Csize, "Center integration region"
528 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
529 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
530 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
531 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
532 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
533 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
576 variable nx = dimsize(source, 0)
577 variable ny = dimsize(source, 1)
579 duplicate /free source, source_redim
580 redimension /n=(nx * ny) source_redim
582 redimension /n=(nx, ny) source_redim
597 param = ReplaceNumberByKey("rngl", param, -inf, "=", ";")
598 param = ReplaceNumberByKey("rngh", param, inf, "=", ";")
599 param = ReplaceNumberByKey("npeaks", param, 4, "=", ";")
600 param = ReplaceNumberByKey("ybox", param, 1, "=", ";")
601 param = ReplaceNumberByKey("pos1", param, 11, "=", ";")
602 param = ReplaceNumberByKey("wid1", param, 0.1, "=", ";")
603 param = ReplaceNumberByKey("pos2", param, 12, "=", ";")
604 param = ReplaceNumberByKey("wid2", param, 0.2, "=", ";")
605 param = ReplaceNumberByKey("pos3", param, 13, "=", ";")
606 param = ReplaceNumberByKey("wid3", param, 0.3, "=", ";")
607 param = ReplaceNumberByKey("pos4", param, 14, "=", ";")
608 param = ReplaceNumberByKey("wid4", param, 0.4, "=", ";")
612 variable npk = numpnts(results) / 2
615 for (ipk = 0; ipk < npk; ipk += 1)
616 sw = "test_int_" + num2str(ipk + 1)
617 duplicate /o results[ipk], $sw
618 sw = "test_sig_" + num2str(ipk + 1)
619 duplicate /o results[ipk + npk], $sw
629 variable rngl = NumberByKey("rngl", param, "=", ";")
630 variable rngh = NumberByKey("rngh", param, "=", ";")
631 variable pos1 = NumberByKey("pos1", param, "=", ";")
632 variable wid1 = NumberByKey("wid1", param, "=", ";")
633 variable pos2 = NumberByKey("pos2", param, "=", ";")
634 variable wid2 = NumberByKey("wid2", param, "=", ";")
635 variable pos3 = NumberByKey("pos3", param, "=", ";")
636 variable wid3 = NumberByKey("wid3", param, "=", ";")
637 variable pos4 = NumberByKey("pos4", param, "=", ";")
638 variable wid4 = NumberByKey("wid4", param, "=", ";")
639 variable npeaks = NumberByKey("npeaks", param, "=", ";")
640 variable ybox = NumberByKey("ybox", param, "=", ";")
642 prompt rngl, "range low"
643 prompt rngh, "range high"
644 prompt pos1, "position 1"
645 prompt wid1, "width 1"
646 prompt pos2, "position 2"
647 prompt wid2, "width 2"
648 prompt pos3, "position 3"
649 prompt wid3, "width 3"
650 prompt pos4, "position 4"
651 prompt wid4, "width 4"
652 prompt npeaks, "number of peaks"
653 prompt ybox, "ybox (1 or 3)"
655 doprompt "
gauss4_reduction reduction parameters (1/2)", rngl, rngh, npeaks, ybox
657 param = ReplaceNumberByKey("rngl", param, rngl, "=", ";")
658 param = ReplaceNumberByKey("rngh", param, rngh, "=", ";")
659 param = ReplaceNumberByKey("npeaks", param, npeaks, "=", ";")
660 param = ReplaceNumberByKey("ybox", param, ybox, "=", ";")
662 doprompt "
gauss4_reduction reduction parameters (2/2)", pos1, wid1, pos2, wid2, pos3, wid3, pos4, wid4
664 param = ReplaceNumberByKey("pos1", param, pos1, "=", ";")
665 param = ReplaceNumberByKey("wid1", param, wid1, "=", ";")
666 param = ReplaceNumberByKey("pos2", param, pos2, "=", ";")
667 param = ReplaceNumberByKey("wid2", param, wid2, "=", ";")
668 param = ReplaceNumberByKey("pos3", param, pos3, "=", ";")
669 param = ReplaceNumberByKey("wid3", param, wid3, "=", ";")
670 param = ReplaceNumberByKey("pos4", param, pos4, "=", ";")
671 param = ReplaceNumberByKey("wid4", param, wid4, "=", ";")
722 variable nx = dimsize(source, 0)
723 variable ny = dimsize(source, 1)
726 variable rngl = NumberByKey("rngl", param, "=", ";")
727 variable rngh = NumberByKey("rngh", param, "=", ";")
728 variable pos1 = NumberByKey("pos1", param, "=", ";")
729 variable wid1 = NumberByKey("wid1", param, "=", ";")
730 variable pos2 = NumberByKey("pos2", param, "=", ";")
731 variable wid2 = NumberByKey("wid2", param, "=", ";")
732 variable pos3 = NumberByKey("pos3", param, "=", ";")
733 variable wid3 = NumberByKey("wid3", param, "=", ";")
734 variable pos4 = NumberByKey("pos4", param, "=", ";")
735 variable wid4 = NumberByKey("wid4", param, "=", ";")
736 variable npeaks = NumberByKey("npeaks", param, "=", ";")
737 variable ybox = NumberByKey("ybox", param, "=", ";")
743 duplicate /free xprof, xprof_sig
744 variable pl = max(x2pnt(xprof, rngl), 0)
745 variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
747 make /free /n=(npeaks) peak_coef
748 peak_coef = p * 3 + 2
749 variable n_coef = npeaks * 3 + 2
750 make /free /d /n=14 w_coef, W_sigma
751 w_coef[0] = {0, 0, 1, pos1, wid1, 1, pos2, wid2, 1, pos3, wid3, 1, pos4, wid4}
752 redimension /n=(n_coef) w_coef, w_sigma
758 make /free /n=(npeaks + 2, numpnts(w_coef)) cmat
759 make /free /n=(npeaks + 2) cvec
766 for (ipk=0; ipk < npeaks; ipk += 1)
768 cmat[2 + ipk][2 + ipk*3] = -1
772 make /free /n=(npeaks * 2) /wave result_waves
774 for (ipk = 0; ipk < npeaks; ipk += 1)
775 make /free /n=0 pk_int
778 sprintf s_note,
"AxisLabelD=peak %u integral" , ipk+1
780 sprintf s_note,
"KineticEnergy=%.3f" , w_coef[3 + ipk * 3]
782 result_waves[ipk] = pk_int
784 make /free /n=0 pk_sig
787 sprintf s_note,
"AxisLabelD=peak %u sigma" , ipk+1
789 sprintf s_note,
"KineticEnergy=%.3f" , w_coef[3 + ipk * 3]
791 result_waves[ipk + npeaks] = pk_sig
793 waveclear pk_int, pk_sig
798 variable p1 = dimsize(source, 1) - 1
803 p0 += ceil((ybox - 1) / 2)
804 p1 -= ceil((ybox - 1) / 2)
806 variable V_FitNumIters
808 for (pp = p0; pp <= p1; pp += 1)
810 xprof = source[p][pp]
812 xprof += source[p][pp-1] + source[p][pp+1]
814 xprof_sig = max(sqrt(xprof), 1)
819 wmin = wavemin(xprof)
820 wmax = wavemax(xprof)
824 for (ipk=0; ipk < npeaks; ipk += 1)
825 w_coef[2 + ipk*3] = wmax - wmin
827 FuncFit /H=hold /Q /NTHR=1 /N /W=2
MultiGaussLinBG_AO w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
831 if (V_FitNumIters < 40)
832 for (ipk = 0; ipk < npeaks; ipk += 1)
833 wave val = result_waves[ipk]
834 wave sig = result_waves[ipk + npeaks]
835 val[pp] = max(w_coef[peak_coef[ipk]], 0)
836 sig[pp] = max(w_sigma[peak_coef[ipk]], 0)
842 for (ipk = 0; ipk < npeaks; ipk += 1)
843 wave val = result_waves[ipk]
844 wave sig = result_waves[ipk + npeaks]
845 val *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
846 sig *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
884 function /s find_gauss4_reduction_params(spectrum, peakpos)
889 variable wmin = wavemin(spectrum)
890 variable wmax = wavemax(spectrum)
893 variable rngl = dimoffset(spectrum, 0)
894 variable rngh = dimoffset(spectrum, 0) + dimdelta(spectrum, 0) * (dimsize(spectrum, 0) - 1)
895 make /n=4 /free positions, widths
896 variable npeaks = numpnts(peakpos)
899 positions[0, npeaks-1] = peakpos[p]
902 variable n_coef = npeaks * 3 + 2
903 make /free /d /n=(n_coef) w_coef
908 make /free /n=(2+npeaks, numpnts(w_coef)) cmat
909 make /free /n=(2+npeaks) cvec
916 for (ip=0; ip < npeaks; ip += 1)
917 cmat[2 + ip][2 + ip*3] = -1
918 w_coef[2 + ip*3] = wmax - wmin
919 w_coef[3 + ip*3] = peakpos[ip]
920 w_coef[4 + ip*3] = widths[ip]
923 variable V_FitNumIters
926 for (ip=0; ip < npeaks; ip += 1)
927 positions[ip] = w_coef[3 + ip * 3]
928 widths[ip ] = abs(w_coef[4 + ip * 3])
930 for (ip=npeaks; ip < 4; ip += 1)
935 param = ReplaceNumberByKey(
"rngl" , param, rngl,
"=" ,
";" )
936 param = ReplaceNumberByKey(
"rngh" , param, rngh,
"=" ,
";" )
937 param = ReplaceNumberByKey(
"npeaks" , param, npeaks,
"=" ,
";" )
938 param = ReplaceNumberByKey(
"ybox" , param, ybox,
"=" ,
";" )
939 param = ReplaceNumberByKey(
"pos1" , param, positions[0],
"=" ,
";" )
940 param = ReplaceNumberByKey(
"wid1" , param, widths[0],
"=" ,
";" )
941 param = ReplaceNumberByKey(
"pos2" , param, positions[1],
"=" ,
";" )
942 param = ReplaceNumberByKey(
"wid2" , param, widths[1],
"=" ,
";" )
943 param = ReplaceNumberByKey(
"pos3" , param, positions[2],
"=" ,
";" )
944 param = ReplaceNumberByKey(
"wid3" , param, widths[2],
"=" ,
";" )
945 param = ReplaceNumberByKey(
"pos4" , param, positions[3],
"=" ,
";" )
946 param = ReplaceNumberByKey(
"wid4" , param, widths[3],
"=" ,
";" )
958 function test_shockley_anglefit(image, branch)
963 param = ReplaceStringByKey(
"branch" , param, num2str(branch),
"=" ,
";" )
971 string pkpos_name =
"saf_pkpos_" + s_branch
972 string pkwid_name =
"saf_pkwid_" + s_branch
974 wave /wave results = shockley_anglefit(image, param)
975 duplicate results[0], $pkpos_name
976 duplicate results[1], $pkwid_name
979 function prompt_Shockley_anglefit(param)
982 variable branch = NumberByKey(
"branch" , param,
"=" ,
";" )
984 prompt branch,
"Branch (-1 or +1)" 986 doprompt
"Shockley_anglefit_reduction Parameters" , branch
988 param = ReplaceNumberByKey(
"branch" , param, branch,
"=" ,
";" )
1016 threadsafe
function /wave Shockley_anglefit(source, param)
1020 variable nx = dimsize(source, 0)
1021 variable ny = dimsize(source, 1)
1024 variable branch = NumberByKey(
"branch" , param,
"=" ,
";" )
1027 if (numtype(branch) != 0)
1032 make /wave /free /n=2 result_waves
1033 make /free /n=0 dest1, dest2
1034 result_waves[0] = dest1
1035 result_waves[1] = dest2
1059 duplicate /free dest1, center
1060 q0 = round((y0 - dimoffset(source, 1)) / dimdelta(source, 1))
1061 q1 = round((y1 - dimoffset(source, 1)) / dimdelta(source, 1))
1063 wavestats /q/m=1 center
1064 p0 = round((v_maxloc - dimoffset(source, 0)) / dimdelta(source, 0))
1065 p1 = round((v_maxloc + 0.4 - dimoffset(source, 0)) / dimdelta(source, 0))
1068 make /n=(ny)/d/free profile
1069 setscale /p x dimoffset(source,1), dimdelta(source,1), waveunits(source,1), profile
1072 for (pp = p0; pp <= p1; pp += 1)
1073 profile = source[pp][p]
1074 curvefit /Q /NTHR=1 /W=2 gauss profile(y0,y1)
1076 dest1[pp] = w_coef[2]
1077 dest2[pp] = w_coef[3]
1083 function scienta_norm(w, x): fitfunc
1087 return w[0] * (x^2 - w[1]^2)
1090 function /wave fit_scienta_ang_transm(data, params)
1094 if (!waveexists(params))
1095 make /n=12 /o params
1097 redimension /n=12/d params
1099 variable h = wavemax(data) - wavemin(data)
1112 FuncFit /NTHR=0 /q scienta_ang_transm params data
1117 threadsafe
function scienta_ang_transm(w, x): fitfunc
1134 make /free /n=4 /d w_int
1136 w_int[1,] = w[p - 1]
1137 variable pk1 = gauss1d(w_int, x)
1138 w_int[1,] = w[p + 2]
1139 variable pk2 = gauss1d(w_int, x)
1140 w_int[1,] = w[p + 5]
1141 variable pk3 = gauss1d(w_int, x)
1142 w_int[0,2] = w[9 + p]
1144 variable bg = poly(w_int, x)
1146 return bg + pk1 + pk2 + pk3
1149 function /wave fit_scienta_poly_bg(data, params, bgterms)
1154 if (!waveexists(params))
1155 make /n=15 /o params
1157 redimension /n=15 /d params
1159 variable wmax = wavemax(data)
1160 variable wmin = wavemin(data)
1173 params[12] = (wmax - wmin) / dimdelta(data,1) / dimsize(data,1)
1177 string h =
"0000000000000" 1188 FuncFitMD /NTHR=1 /q /h=h scienta_poly_bg params data
1193 function scienta_poly_bg(w, e, a): fitfunc
1219 make /free /n=4 /d w_int
1224 w_int[2,] = w[p0 + p - 2]
1225 variable pk1 = gauss1d(w_int, a)
1228 w_int[1,] = w[p0 + p - 1]
1229 variable pk2 = gauss1d(w_int, a)
1232 w_int[1,] = w[p0 + p - 1]
1233 variable pk3 = gauss1d(w_int, a)
1236 w_int[0,2] = w[p0 + p]
1238 variable base = poly(w_int, a)
1241 w_int[0,3] = w[p0 + p]
1242 variable bg = poly(w_int, e)
1244 return bg * (base + pk1 + pk2 + pk3)
threadsafe variable MultiGaussLinBG(wave w, variable x)
multiple gaussian peaks on a linear background fit function.
-
threadsafe variable MultiGaussLinBG_AO(wave pw, wave yw, wave xw)
multiple gaussian peaks on a linear background fit function (all at once).
-
variable prompt_gauss4_reduction(string *param)
prompt for the gauss4_reduction parameters
-
threadsafe wave redim_linbg_reduction(wave source, string *param)
linear background reduction function for incorrectly dimensioned scienta image
-
variable test_gauss4_reduction(wave image)
apply the gauss4_reduction function to a single image
-
threadsafe wave ad_profile_x_w(wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
-
threadsafe variable adh5_setup_profile(wave image, wave profile, variable dim)
set up a one-dimensional wave for a line profile based on a 2D original wave.
-
variable prompt_int_quadbg_reduction(string *param)
-
threadsafe wave int_linbg_reduction(wave source, string *param)
linear-background subtracted integration reduction function.
-
threadsafe wave gauss4_reduction(wave source, string *param)
fit horizontal cuts of an image with up to four gaussian peaks on a linear background ...
-
variable prompt_redim_linbg_reduction(string *param)
parameter dialog for the redim_linbg_reduction() function
-
threadsafe wave ad_profile_y_w(wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
-
threadsafe wave int_quadbg_reduction(wave source, string *param)
integrate peak area minus a quadratic background
-
variable prompt_int_linbg_reduction(string *param)
prompt the user for integrate on linear background reduction parameters.
-
string csr_int_linbg_reduction(string win)
calculate linear background reduction parameters from cursors in a graph.
-
string capture_int_linbg_cursors()
capture linear background reduction parameters from cursors in a graph.
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
3 #pragma IgorVersion = 6.1
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4 #pragma ModuleName = PearlScientaPreprocess
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5 #include "pearl-fitfuncs"
+
6 #include "pearl-area-import"
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+
+
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+
+
+
+
+
+
+
40 variable Lcrop = NumberByKey(
"Lcrop" , param,
"=" ,
";" )
+
41 variable Lsize = NumberByKey("Lsize", param, "=", ";")
+
42 variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
+
43 variable Hsize = NumberByKey("Hsize", param, "=", ";")
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44 variable Cpos = NumberByKey("Cpos", param, "=", ";")
+
45 variable Csize = NumberByKey("Csize", param, "=", ";")
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+
47 prompt Lcrop, "Lower cropping region"
+
48 prompt Hcrop, "Upper cropping region"
+
49 prompt Lsize, "Lower background region"
+
50 prompt Hsize, "Upper background region"
+
51 prompt Cpos, "Center position"
+
52 prompt Csize, "Center integration region"
+
+
+
+
56 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
+
57 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
+
58 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
+
59 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
+
60 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
+
61 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
+
+
+
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+
+
+
+
97 svar /z global_params = root:packages:pearl_explorer:s_reduction_params
+
98 if (svar_exists(global_params))
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142 make /n=(nc) /free positions
+
+
+
145 string imagename = ""
+
146 string tracename = ""
+
+
+
149 for (ic = 0; ic < nc; ic += 1)
+
150 sc = num2char(char2num("A") + ic)
+
151 wave /z wc = CsrWaveRef($sc, win)
+
152 info = CsrInfo($sc, win)
+
153 tracename = StringByKey("TNAME", info, ":", ";")
+
154 if (waveexists(wc) && (wavedims(wc) == 2))
+
155 if (!waveexists(image))
+
+
157 imagename = tracename
+
+
159 if (cmpstr(tracename, imagename) == 0)
+
160 positions[np] = pcsr($sc, win)
+
+
+
+
+
+
166 np = floor(np / 2) * 2
+
167 redimension /n=(np) positions
+
168 sort positions, positions
+
+
170 positions = p >= np / 2 ? positions + 1 : positions
+
171 positions = positions / dimsize(image, 0)
+
+
+
174 variable ip2 = np / 2
+
175 variable ip1 = ip2 - 1
+
+
+
+
179 Cpos = (positions[ip1] + positions[ip2]) / 2
+
180 Csize = positions[ip2] - positions[ip1]
+
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+
+
+
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+
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+
+
193 Lsize = positions[ip1]
+
194 Hsize = 1 - positions[ip2]
+
+
+
197 Lsize = Cpos - Csize / 2
+
198 Hsize = 1 - (Cpos + Csize / 2)
+
+
+
+
+
+
+
+
+
207 Lcrop = positions[ip1]
+
208 Hcrop = 1 - positions[ip2]
+
+
+
211 if (dimsize(image, 0) >= 992)
+
+
+
+
+
216 Lsize = max(Lsize - Lcrop, 0)
+
217 Hsize = max(Hsize - Hcrop, 0)
+
+
+
220 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
+
221 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
+
222 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
+
223 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
+
224 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
+
225 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
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+
266 variable nx = dimsize(source, 0)
+
267 variable ny = dimsize(source, 1)
+
+
+
270 variable lcrop = NumberByKey("Lcrop", param, "=", ";")
+
271 variable lsize = NumberByKey("Lsize", param, "=", ";")
+
272 variable hcrop = NumberByKey("Hcrop", param, "=", ";")
+
273 variable hsize = NumberByKey("Hsize", param, "=", ";")
+
274 variable cpos = NumberByKey("Cpos", param, "=", ";")
+
275 variable csize = NumberByKey("Csize", param, "=", ";")
+
+
277 make /wave /free /n=2 result_waves
+
278 make /free /n=0 dest1, dest2
+
279 result_waves[0] = dest1
+
280 result_waves[1] = dest2
+
+
+
+
+
+
286 if (numtype(lcrop) != 0)
+
+
+
289 if (numtype(lsize) != 0)
+
+
+
292 if (numtype(hcrop) != 0)
+
+
+
295 if (numtype(hsize) != 0)
+
+
+
298 if (numtype(Cpos) != 0)
+
299 redimension /n=0 result_waves
+
+
+
302 if (numtype(Csize) != 0)
+
303 redimension /n=0 result_waves
+
+
+
+
307 variable lpos = lcrop + lsize / 2
+
308 variable hpos = 1 - (hcrop + hsize / 2)
+
+
+
+
+
313 duplicate /free dest1, lbg, hbg
+
+
315 p0 = round(lcrop * nx)
+
316 p1 = round((lcrop + lsize) * nx)
+
+
+
+
+
+
322 p0 = round((1 - hcrop - hsize) * nx)
+
323 p1 = round((1 - hcrop) * nx)
+
+
+
+
+
+
329 p0 = round((cpos - csize/2) * nx)
+
330 p1 = round((cpos + csize/2) * nx)
+
+
+
+
+
+
336 variable scale = (cpos - lpos) / (hpos - lpos)
+
+
338 dest1 -= scale * (hbg - lbg) + lbg
+
339 dest2 = sqrt(dest2 + scale^2 * (hbg + lbg))
+
+
+
+
343 sprintf s_note1, "AxisLabelD=peak integral"
+
344 sprintf s_note2, "KineticEnergy=%.3f", cpos * nx * dimdelta(source, 0) + dimoffset(source, 0)
+
+
+
+
+
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356 variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
+
357 variable Lsize = NumberByKey("Lsize", param, "=", ";")
+
358 variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
+
359 variable Hsize = NumberByKey("Hsize", param, "=", ";")
+
360 variable Cpos = NumberByKey("Cpos", param, "=", ";")
+
361 variable Csize = NumberByKey("Csize", param, "=", ";")
+
+
363 prompt Lcrop, "Lower cropping region"
+
364 prompt Hcrop, "Upper cropping region"
+
365 prompt Lsize, "Lower background region"
+
366 prompt Hsize, "Upper background region"
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367 prompt Cpos, "Center position"
+
368 prompt Csize, "Center integration region"
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+
+
+
372 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
+
373 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
+
374 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
+
375 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
+
376 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
+
377 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
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+
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419 variable nx = dimsize(source, 0)
+
420 variable ny = dimsize(source, 1)
+
+
+
423 variable lcrop = NumberByKey("Lcrop", param, "=", ";")
+
424 variable lsize = NumberByKey("Lsize", param, "=", ";")
+
425 variable hcrop = NumberByKey("Hcrop", param, "=", ";")
+
426 variable hsize = NumberByKey("Hsize", param, "=", ";")
+
427 variable cpos = NumberByKey("Cpos", param, "=", ";")
+
428 variable csize = NumberByKey("Csize", param, "=", ";")
+
+
430 make /wave /free /n=2 result_waves
+
431 make /free /n=0 dest1, dest2
+
432 result_waves[0] = dest1
+
433 result_waves[1] = dest2
+
+
+
+
+
+
439 if (numtype(lcrop) != 0)
+
+
+
442 if (numtype(lsize) != 0)
+
+
+
445 if (numtype(hcrop) != 0)
+
+
+
448 if (numtype(hsize) != 0)
+
+
+
451 if (numtype(Cpos) != 0)
+
452 redimension /n=0 result_waves
+
+
+
455 if (numtype(Csize) != 0)
+
456 redimension /n=0 result_waves
+
+
+
+
+
461 variable pcl = round(lcrop * nx)
+
462 variable pch = round((1 - hcrop) * nx)
+
+
464 variable pfl = round((lcrop + lsize) * nx)
+
465 variable pfh = round((1 - hcrop - hsize) * nx)
+
+
467 variable pil = round((cpos - csize/2) * nx)
+
468 variable pih = round((cpos + csize/2) * nx)
+
+
+
471 make /n=(nx) /d /free profile, mask, fit
+
472 setscale /p x dimoffset(source,0), dimdelta(source,0), waveunits(source,0), profile, mask, fit
+
473 mask = ((p >= pcl) && (p < pfl)) || ((p >= pfh) && (p < pch))
+
+
+
+
477 variable xil = x2pnt(profile, pil)
+
478 variable xih = x2pnt(profile, pih)
+
+
480 make /n=3 /free /d w_coef
+
481 for (qq = 0; qq < ny; qq += 1)
+
482 profile = source[p][qq]
+
483 curvefit /Q /NTHR=1 /W=2 poly 3, kwCWave=w_coef, profile /M=mask
+
484 fit = poly(w_coef, x)
+
485 sp = sum(profile, xil, xih)
+
486 sf = sum(fit, xil, xih)
+
+
+
+
+
+
+
493 sprintf s_note1, "AxisLabelD=peak integral"
+
494 sprintf s_note2, "KineticEnergy=%.3f", cpos * nx * dimdelta(source, 0) + dimoffset(source, 0)
+
+
+
+
+
+
+
+
+
+
+
+
514 variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
+
515 variable Lsize = NumberByKey("Lsize", param, "=", ";")
+
516 variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
+
517 variable Hsize = NumberByKey("Hsize", param, "=", ";")
+
518 variable Cpos = NumberByKey("Cpos", param, "=", ";")
+
519 variable Csize = NumberByKey("Csize", param, "=", ";")
+
+
521 prompt Lcrop, "Lower cropping region"
+
522 prompt Hcrop, "Upper cropping region"
+
523 prompt Lsize, "Lower background region"
+
524 prompt Hsize, "Upper background region"
+
525 prompt Cpos, "Center position"
+
526 prompt Csize, "Center integration region"
+
+
+
+
530 param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
+
531 param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
+
532 param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
+
533 param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
+
534 param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
+
535 param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
+
+
+
+
+
+
+
+
+
+
578 variable nx = dimsize(source, 0)
+
579 variable ny = dimsize(source, 1)
+
+
581 duplicate /free source, source_redim
+
582 redimension /n=(nx * ny) source_redim
+
+
584 redimension /n=(nx, ny) source_redim
+
+
+
+
+
+
+
+
+
+
599 param = ReplaceNumberByKey("rngl", param, -inf, "=", ";")
+
600 param = ReplaceNumberByKey("rngh", param, inf, "=", ";")
+
601 param = ReplaceNumberByKey("npeaks", param, 4, "=", ";")
+
602 param = ReplaceNumberByKey("ybox", param, 1, "=", ";")
+
603 param = ReplaceNumberByKey("pos1", param, 11, "=", ";")
+
604 param = ReplaceNumberByKey("wid1", param, 0.1, "=", ";")
+
605 param = ReplaceNumberByKey("pos2", param, 12, "=", ";")
+
606 param = ReplaceNumberByKey("wid2", param, 0.2, "=", ";")
+
607 param = ReplaceNumberByKey("pos3", param, 13, "=", ";")
+
608 param = ReplaceNumberByKey("wid3", param, 0.3, "=", ";")
+
609 param = ReplaceNumberByKey("pos4", param, 14, "=", ";")
+
610 param = ReplaceNumberByKey("wid4", param, 0.4, "=", ";")
+
+
+
+
614 variable npk = numpnts(results) / 2
+
+
+
617 for (ipk = 0; ipk < npk; ipk += 1)
+
618 sw = "test_int_" + num2str(ipk + 1)
+
619 duplicate /o results[ipk], $sw
+
620 sw = "test_sig_" + num2str(ipk + 1)
+
621 duplicate /o results[ipk + npk], $sw
+
+
+
+
+
+
+
631 variable rngl = NumberByKey("rngl", param, "=", ";")
+
632 variable rngh = NumberByKey("rngh", param, "=", ";")
+
633 variable pos1 = NumberByKey("pos1", param, "=", ";")
+
634 variable wid1 = NumberByKey("wid1", param, "=", ";")
+
635 variable pos2 = NumberByKey("pos2", param, "=", ";")
+
636 variable wid2 = NumberByKey("wid2", param, "=", ";")
+
637 variable pos3 = NumberByKey("pos3", param, "=", ";")
+
638 variable wid3 = NumberByKey("wid3", param, "=", ";")
+
639 variable pos4 = NumberByKey("pos4", param, "=", ";")
+
640 variable wid4 = NumberByKey("wid4", param, "=", ";")
+
641 variable npeaks = NumberByKey("npeaks", param, "=", ";")
+
642 variable ybox = NumberByKey("ybox", param, "=", ";")
+
+
644 prompt rngl, "range low"
+
645 prompt rngh, "range high"
+
646 prompt pos1, "position 1"
+
647 prompt wid1, "width 1"
+
648 prompt pos2, "position 2"
+
649 prompt wid2, "width 2"
+
650 prompt pos3, "position 3"
+
651 prompt wid3, "width 3"
+
652 prompt pos4, "position 4"
+
653 prompt wid4, "width 4"
+
654 prompt npeaks, "number of peaks"
+
655 prompt ybox, "ybox (1 or 3)"
+
+
657 doprompt "
gauss4_reduction reduction parameters (1/2)", rngl, rngh, npeaks, ybox
+
+
659 param = ReplaceNumberByKey("rngl", param, rngl, "=", ";")
+
660 param = ReplaceNumberByKey("rngh", param, rngh, "=", ";")
+
661 param = ReplaceNumberByKey("npeaks", param, npeaks, "=", ";")
+
662 param = ReplaceNumberByKey("ybox", param, ybox, "=", ";")
+
+
664 doprompt "
gauss4_reduction reduction parameters (2/2)", pos1, wid1, pos2, wid2, pos3, wid3, pos4, wid4
+
+
666 param = ReplaceNumberByKey("pos1", param, pos1, "=", ";")
+
667 param = ReplaceNumberByKey("wid1", param, wid1, "=", ";")
+
668 param = ReplaceNumberByKey("pos2", param, pos2, "=", ";")
+
669 param = ReplaceNumberByKey("wid2", param, wid2, "=", ";")
+
670 param = ReplaceNumberByKey("pos3", param, pos3, "=", ";")
+
671 param = ReplaceNumberByKey("wid3", param, wid3, "=", ";")
+
672 param = ReplaceNumberByKey("pos4", param, pos4, "=", ";")
+
673 param = ReplaceNumberByKey("wid4", param, wid4, "=", ";")
+
+
+
+
+
+
+
+
+
+
+
724 variable nx = dimsize(source, 0)
+
725 variable ny = dimsize(source, 1)
+
+
+
728 variable rngl = NumberByKey("rngl", param, "=", ";")
+
729 variable rngh = NumberByKey("rngh", param, "=", ";")
+
730 variable pos1 = NumberByKey("pos1", param, "=", ";")
+
731 variable wid1 = NumberByKey("wid1", param, "=", ";")
+
732 variable pos2 = NumberByKey("pos2", param, "=", ";")
+
733 variable wid2 = NumberByKey("wid2", param, "=", ";")
+
734 variable pos3 = NumberByKey("pos3", param, "=", ";")
+
735 variable wid3 = NumberByKey("wid3", param, "=", ";")
+
736 variable pos4 = NumberByKey("pos4", param, "=", ";")
+
737 variable wid4 = NumberByKey("wid4", param, "=", ";")
+
738 variable npeaks = NumberByKey("npeaks", param, "=", ";")
+
739 variable ybox = NumberByKey("ybox", param, "=", ";")
+
+
+
+
+
+
745 duplicate /free xprof, xprof_sig
+
746 variable pl = max(x2pnt(xprof, rngl), 0)
+
747 variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
+
+
749 make /free /n=(npeaks) peak_coef
+
750 peak_coef = p * 3 + 2
+
751 variable n_coef = npeaks * 3 + 2
+
752 make /free /d /n=14 w_coef, W_sigma
+
753 w_coef[0] = {0, 0, 1, pos1, wid1, 1, pos2, wid2, 1, pos3, wid3, 1, pos4, wid4}
+
754 redimension /n=(n_coef) w_coef, w_sigma
+
+
+
+
+
+
760 make /free /n=(npeaks + 2, numpnts(w_coef)) cmat
+
761 make /free /n=(npeaks + 2) cvec
+
+
+
+
+
+
+
768 for (ipk=0; ipk < npeaks; ipk += 1)
+
+
770 cmat[2 + ipk][2 + ipk*3] = -1
+
+
+
+
774 make /free /n=(npeaks * 2) /wave result_waves
+
+
776 for (ipk = 0; ipk < npeaks; ipk += 1)
+
777 make /free /n=0 pk_int
+
+
+
780 sprintf s_note,
"AxisLabelD=peak %u integral" , ipk+1
+
+
782 sprintf s_note,
"KineticEnergy=%.3f" , w_coef[3 + ipk * 3]
+
+
784 result_waves[ipk] = pk_int
+
+
786 make /free /n=0 pk_sig
+
+
+
789 sprintf s_note, "AxisLabelD=peak %u sigma", ipk+1
+
+
791 sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * 3]
+
+
793 result_waves[ipk + npeaks] = pk_sig
+
+
795 waveclear pk_int, pk_sig
+
+
+
+
+
800 variable p1 = dimsize(source, 1) - 1
+
+
+
+
+
805 p0 += ceil((ybox - 1) / 2)
+
806 p1 -= ceil((ybox - 1) / 2)
+
+
808 variable V_FitNumIters
+
+
+
811 for (pp = p0; pp <= p1; pp += 1)
+
+
813 xprof = source[p][pp]
+
+
815 xprof += source[p][pp-1] + source[p][pp+1]
+
+
817 xprof_sig = max(sqrt(xprof), 1)
+
+
+
+
+
822 wmin = wavemin(xprof)
+
823 wmax = wavemax(xprof)
+
+
+
826 for (ipk=0; ipk < npeaks; ipk += 1)
+
827 w_coef[2 + ipk*3] = wmax - wmin
+
+
+
+
831 FuncFit /H=hold /Q /NTHR=1 /N /W=2
MultiGaussLinBG_AO w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
+
+
+
+
835 if (V_FitNumIters < 40)
+
836 for (ipk = 0; ipk < npeaks; ipk += 1)
+
837 wave val = result_waves[ipk]
+
838 wave sig = result_waves[ipk + npeaks]
+
839 val[pp] = max(w_coef[peak_coef[ipk]], 0)
+
840 sig[pp] = max(w_sigma[peak_coef[ipk]], 0)
+
+
+
+
+
+
846 for (ipk = 0; ipk < npeaks; ipk += 1)
+
847 wave val = result_waves[ipk]
+
848 wave sig = result_waves[ipk + npeaks]
+
849 val *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
+
850 sig *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
+
+
+
+
+
+
+
+
+
+
860 variable nx = dimsize(source, 0)
+
861 variable ny = dimsize(source, 1)
+
+
+
864 variable rngl = NumberByKey("rngl", param, "=", ";")
+
865 variable rngh = NumberByKey("rngh", param, "=", ";")
+
866 variable pos1 = NumberByKey("pos1", param, "=", ";")
+
867 variable wid1 = NumberByKey("wid1", param, "=", ";")
+
868 variable pos2 = NumberByKey("pos2", param, "=", ";")
+
869 variable wid2 = NumberByKey("wid2", param, "=", ";")
+
870 variable pos3 = NumberByKey("pos3", param, "=", ";")
+
871 variable wid3 = NumberByKey("wid3", param, "=", ";")
+
872 variable pos4 = NumberByKey("pos4", param, "=", ";")
+
873 variable wid4 = NumberByKey("wid4", param, "=", ";")
+
874 variable pos5 = NumberByKey("pos5", param, "=", ";")
+
875 variable wid5 = NumberByKey("wid5", param, "=", ";")
+
876 variable pos6 = NumberByKey("pos6", param, "=", ";")
+
877 variable wid6 = NumberByKey("wid6", param, "=", ";")
+
878 variable npeaks = NumberByKey("npeaks", param, "=", ";")
+
879 variable ybox = NumberByKey("ybox", param, "=", ";")
+
+
+
+
+
+
885 duplicate /free xprof, xprof_sig
+
886 variable pl = max(x2pnt(xprof, rngl), 0)
+
887 variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
+
+
889 make /free /n=(npeaks) peak_coef
+
890 peak_coef = p * 3 + 2
+
891 variable n_coef = npeaks * 3 + 2
+
892 make /free /d /n=(n_coef) w_coef, W_sigma
+
893 w_coef[0] = {0, 0, 1, pos1, wid1, 1, pos2, wid2, 1, pos3, wid3, 1, pos4, wid4, 1, pos5, wid5, 1, pos6, wid6}
+
894 redimension /n=(n_coef) w_coef, w_sigma
+
+
+
+
+
+
900 make /free /n=(npeaks + 2, numpnts(w_coef)) cmat
+
901 make /free /n=(npeaks + 2) cvec
+
+
+
+
+
+
+
908 for (ipk=0; ipk < npeaks; ipk += 1)
+
+
910 cmat[2 + ipk][2 + ipk*3] = -1
+
+
+
+
914 make /free /n=(npeaks * 2) /wave result_waves
+
+
916 for (ipk = 0; ipk < npeaks; ipk += 1)
+
917 make /free /n=0 pk_int
+
+
+
920 sprintf s_note,
"AxisLabelD=peak %u integral" , ipk+1
+
+
922 sprintf s_note,
"KineticEnergy=%.3f" , w_coef[3 + ipk * 3]
+
+
924 result_waves[ipk] = pk_int
+
+
926 make /free /n=0 pk_sig
+
+
+
929 sprintf s_note, "AxisLabelD=peak %u sigma", ipk+1
+
+
931 sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * 3]
+
+
933 result_waves[ipk + npeaks] = pk_sig
+
+
935 waveclear pk_int, pk_sig
+
+
+
+
+
940 variable p1 = dimsize(source, 1) - 1
+
+
+
+
+
945 p0 += ceil((ybox - 1) / 2)
+
946 p1 -= ceil((ybox - 1) / 2)
+
+
948 variable V_FitNumIters
+
+
+
951 for (pp = p0; pp <= p1; pp += 1)
+
+
953 xprof = source[p][pp]
+
+
955 xprof += source[p][pp-1] + source[p][pp+1]
+
+
957 xprof_sig = max(sqrt(xprof), 1)
+
+
+
+
+
962 wmin = wavemin(xprof)
+
963 wmax = wavemax(xprof)
+
+
+
966 for (ipk=0; ipk < npeaks; ipk += 1)
+
967 w_coef[2 + ipk*3] = wmax - wmin
+
+
+
+
971 FuncFit /H=hold /Q /NTHR=1 /N /W=2
MultiGaussLinBG_AO w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
+
+
+
+
975 if (V_FitNumIters < 40)
+
976 for (ipk = 0; ipk < npeaks; ipk += 1)
+
977 wave val = result_waves[ipk]
+
978 wave sig = result_waves[ipk + npeaks]
+
979 val[pp] = max(w_coef[peak_coef[ipk]], 0)
+
980 sig[pp] = max(w_sigma[peak_coef[ipk]], 0)
+
+
+
+
+
+
986 for (ipk = 0; ipk < npeaks; ipk += 1)
+
987 wave val = result_waves[ipk]
+
988 wave sig = result_waves[ipk + npeaks]
+
989 val *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
+
990 sig *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
+
+
+
+
+
+
+
+
+
1030 function /s find_gauss4_reduction_params(spectrum, peakpos)
+
+
+
+
+
1035 variable wmin = wavemin(spectrum)
+
1036 variable wmax = wavemax(spectrum)
+
+
+
1039 variable rngl = dimoffset(spectrum, 0)
+
1040 variable rngh = dimoffset(spectrum, 0) + dimdelta(spectrum, 0) * (dimsize(spectrum, 0) - 1)
+
1041 make /n=4 /free positions, widths
+
1042 variable npeaks = numpnts(peakpos)
+
+
+
1045 positions[0, npeaks-1] = peakpos[p]
+
+
+
1048 variable n_coef = npeaks * 3 + 2
+
1049 make /free /d /n=(n_coef) w_coef
+
+
+
+
+
1054 make /free /n=(2+npeaks, numpnts(w_coef)) cmat
+
1055 make /free /n=(2+npeaks) cvec
+
+
+
+
+
+
+
1062 for (ip=0; ip < npeaks; ip += 1)
+
1063 cmat[2 + ip][2 + ip*3] = -1
+
1064 w_coef[2 + ip*3] = wmax - wmin
+
1065 w_coef[3 + ip*3] = peakpos[ip]
+
1066 w_coef[4 + ip*3] = widths[ip]
+
+
+
1069 variable V_FitNumIters
+
+
+
1072 for (ip=0; ip < npeaks; ip += 1)
+
1073 positions[ip] = w_coef[3 + ip * 3]
+
1074 widths[ip ] = abs(w_coef[4 + ip * 3])
+
+
1076 for (ip=npeaks; ip < 4; ip += 1)
+
+
+
+
+
1081 param = ReplaceNumberByKey(
"rngl" , param, rngl,
"=" ,
";" )
+
1082 param = ReplaceNumberByKey(
"rngh" , param, rngh,
"=" ,
";" )
+
1083 param = ReplaceNumberByKey("npeaks", param, npeaks, "=", ";")
+
1084 param = ReplaceNumberByKey("ybox", param, ybox, "=", ";")
+
1085 param = ReplaceNumberByKey("pos1", param, positions[0], "=", ";")
+
1086 param = ReplaceNumberByKey("wid1", param, widths[0], "=", ";")
+
1087 param = ReplaceNumberByKey("pos2", param, positions[1], "=", ";")
+
1088 param = ReplaceNumberByKey("wid2", param, widths[1], "=", ";")
+
1089 param = ReplaceNumberByKey("pos3", param, positions[2], "=", ";")
+
1090 param = ReplaceNumberByKey("wid3", param, widths[2], "=", ";")
+
1091 param = ReplaceNumberByKey("pos4", param, positions[3], "=", ";")
+
1092 param = ReplaceNumberByKey("wid4", param, widths[3], "=", ";")
+
+
+
+
+
1138 threadsafe function /wave voigt4_reduction(source, param)
+
+
+
+
1142 dfref orig_dfr = GetDataFolderDFR()
+
+
1144 variable nx = dimsize(source, 0)
+
1145 variable ny = dimsize(source, 1)
+
+
+
1148 variable rngl = NumberByKey("rngl", param, "=", ";")
+
1149 variable rngh = NumberByKey("rngh", param, "=", ";")
+
1150 variable pos1 = NumberByKey("pos1", param, "=", ";")
+
1151 variable wid1 = NumberByKey("wid1", param, "=", ";")
+
1152 variable shp1 = NumberByKey("shp1", param, "=", ";")
+
1153 variable pos2 = NumberByKey("pos2", param, "=", ";")
+
1154 variable wid2 = NumberByKey("wid2", param, "=", ";")
+
1155 variable shp2 = NumberByKey("shp2", param, "=", ";")
+
1156 variable pos3 = NumberByKey("pos3", param, "=", ";")
+
1157 variable wid3 = NumberByKey("wid3", param, "=", ";")
+
1158 variable shp3 = NumberByKey("shp3", param, "=", ";")
+
1159 variable pos4 = NumberByKey("pos4", param, "=", ";")
+
1160 variable wid4 = NumberByKey("wid4", param, "=", ";")
+
1161 variable shp4 = NumberByKey("shp4", param, "=", ";")
+
1162 variable npeaks = NumberByKey("npeaks", param, "=", ";")
+
+
+
+
+
+
1168 duplicate /free xprof, xprof_sig
+
1169 variable pl = max(x2pnt(xprof, rngl), 0)
+
1170 variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
+
+
1172 make /free /n=(npeaks) peak_coef
+
1173 variable coef_per_peak = 4
+
1174 peak_coef = p * coef_per_peak + 2
+
1175 variable n_coef = npeaks * coef_per_peak + 2
+
1176 make /free /d /n=18 w_coef, W_sigma
+
1177 w_coef[0] = {0, 0, 1, pos1, wid1, shp1, 1, pos2, wid2, shp2, 1, pos3, wid3, shp3, 1, pos4, wid4, shp4}
+
1178 redimension /n=(n_coef) w_coef, w_sigma
+
+
+
+
1182 make /free /n=(npeaks, numpnts(w_coef)) cmat
+
1183 make /free /n=(npeaks) cvec
+
+
+
+
+
1188 for (ipk=0; ipk < npeaks; ipk += 1)
+
+
1190 cmat[ipk][2 + ipk * coef_per_peak] = -1
+
+
+
+
1194 make /free /n=(npeaks * 2) /wave result_waves
+
+
1196 for (ipk = 0; ipk < npeaks; ipk += 1)
+
1197 make /free /n=0 pk_int
+
+
+
1200 sprintf s_note,
"AxisLabelD=peak %u integral" , ipk+1
+
+
1202 sprintf s_note,
"KineticEnergy=%.3f" , w_coef[3 + ipk * coef_per_peak]
+
+
1204 result_waves[ipk] = pk_int
+
+
1206 make /free /n=0 pk_sig
+
+
+
1209 sprintf s_note, "AxisLabelD=peak %u sigma", ipk+1
+
+
1211 sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * coef_per_peak]
+
+
1213 result_waves[ipk + npeaks] = pk_sig
+
+
1215 waveclear pk_int, pk_sig
+
+
+
+
+
1220 variable p1 = dimsize(source, 1) - 1
+
+
+
+
1224 variable V_FitNumIters
+
+
+
1227 for (pp = p0; pp <= p1; pp += 1)
+
1228 xprof = source[p][pp]
+
1229 xprof_sig = max(sqrt(xprof), 1)
+
+
+
1232 wmin = wavemin(xprof)
+
1233 wmax = wavemax(xprof)
+
+
+
+
1237 for (ipk=0; ipk < npeaks; ipk += 1)
+
1238 w_coef[2 + ipk * coef_per_peak] = wmax - wmin
+
+
+
+
1242 FuncFit /H=hold /Q /N /W=2
MultiVoigtLinBG_AO w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
+
+
+
+
1246 if (V_FitNumIters < 40)
+
1247 for (ipk = 0; ipk < npeaks; ipk += 1)
+
1248 wave val = result_waves[ipk]
+
1249 wave sig = result_waves[ipk + npeaks]
+
1250 val[pp] = max(w_coef[peak_coef[ipk]], 0)
+
1251 sig[pp] = max(w_sigma[peak_coef[ipk]], 0)
+
+
+
+
+
1256 SetDataFolder orig_dfr
+
+
+
+
+
1264 function prompt_voigt4_reduction(param)
+
+
+
1267 variable rngl = NumberByKey("rngl", param, "=", ";")
+
1268 variable rngh = NumberByKey("rngh", param, "=", ";")
+
1269 variable pos1 = NumberByKey("pos1", param, "=", ";")
+
1270 variable wid1 = NumberByKey("wid1", param, "=", ";")
+
1271 variable shp1 = NumberByKey("shp1", param, "=", ";")
+
1272 variable pos2 = NumberByKey("pos2", param, "=", ";")
+
1273 variable wid2 = NumberByKey("wid2", param, "=", ";")
+
1274 variable shp2 = NumberByKey("shp2", param, "=", ";")
+
1275 variable pos3 = NumberByKey("pos3", param, "=", ";")
+
1276 variable wid3 = NumberByKey("wid3", param, "=", ";")
+
1277 variable shp3 = NumberByKey("shp3", param, "=", ";")
+
1278 variable pos4 = NumberByKey("pos4", param, "=", ";")
+
1279 variable wid4 = NumberByKey("wid4", param, "=", ";")
+
1280 variable shp4 = NumberByKey("shp4", param, "=", ";")
+
1281 variable npeaks = NumberByKey("npeaks", param, "=", ";")
+
1282 variable dummy = nan
+
+
1284 prompt rngl, "range low"
+
1285 prompt rngh, "range high"
+
1286 prompt pos1, "position 1"
+
1287 prompt wid1, "width 1"
+
1288 prompt shp1, "shape 1"
+
1289 prompt pos2, "position 2"
+
1290 prompt wid2, "width 2"
+
1291 prompt shp2, "shape 2"
+
1292 prompt pos3, "position 3"
+
1293 prompt wid3, "width 3"
+
1294 prompt shp3, "shape 3"
+
1295 prompt pos4, "position 4"
+
1296 prompt wid4, "width 4"
+
1297 prompt shp4, "shape 4"
+
1298 prompt npeaks, "number of peaks"
+
1299 prompt dummy, "(not used)"
+
+
1301 doprompt "voigt4_reduction reduction parameters (1/2)", rngl, rngh, npeaks, dummy, pos1, pos2, pos3, pos4
+
+
1303 param = ReplaceNumberByKey("rngl", param, rngl, "=", ";")
+
1304 param = ReplaceNumberByKey("rngh", param, rngh, "=", ";")
+
1305 param = ReplaceNumberByKey("npeaks", param, npeaks, "=", ";")
+
1306 param = ReplaceNumberByKey("pos1", param, pos1, "=", ";")
+
1307 param = ReplaceNumberByKey("pos2", param, pos2, "=", ";")
+
1308 param = ReplaceNumberByKey("pos3", param, pos3, "=", ";")
+
1309 param = ReplaceNumberByKey("pos4", param, pos4, "=", ";")
+
+
1311 doprompt "voigt4_reduction reduction parameters (2/2)", wid1, shp1, wid2, shp2, wid3, shp3, wid4, shp4
+
+
1313 param = ReplaceNumberByKey("wid1", param, wid1, "=", ";")
+
1314 param = ReplaceNumberByKey("shp1", param, shp1, "=", ";")
+
1315 param = ReplaceNumberByKey("wid2", param, wid2, "=", ";")
+
1316 param = ReplaceNumberByKey("shp2", param, shp2, "=", ";")
+
1317 param = ReplaceNumberByKey("wid3", param, wid3, "=", ";")
+
1318 param = ReplaceNumberByKey("shp3", param, shp3, "=", ";")
+
1319 param = ReplaceNumberByKey("wid4", param, wid4, "=", ";")
+
1320 param = ReplaceNumberByKey("shp4", param, shp4, "=", ";")
+
+
+
+
+
+
+
+
1335 function test_shockley_anglefit(image, branch)
+
+
+
+
+
1340 param = ReplaceStringByKey("branch", param, num2str(branch), "=", ";")
+
+
+
+
+
+
+
+
1348 string pkpos_name = "saf_pkpos_" + s_branch
+
1349 string pkwid_name = "saf_pkwid_" + s_branch
+
+
1351 wave /wave results = shockley_anglefit(image, param)
+
1352 duplicate results[0], $pkpos_name
+
1353 duplicate results[1], $pkwid_name
+
+
+
1356 function prompt_Shockley_anglefit(param)
+
+
+
1359 variable branch = NumberByKey("branch", param, "=", ";")
+
+
1361 prompt branch, "Branch (-1 or +1)"
+
+
1363 doprompt "Shockley_anglefit_reduction Parameters", branch
+
+
1365 param = ReplaceNumberByKey("branch", param, branch, "=", ";")
+
+
+
+
+
+
1393 threadsafe function /wave Shockley_anglefit(source, param)
+
+
+
+
1397 variable nx = dimsize(source, 0)
+
1398 variable ny = dimsize(source, 1)
+
+
+
1401 variable branch = NumberByKey("branch", param, "=", ";")
+
+
+
1404 if (numtype(branch) != 0)
+
+
+
+
+
1409 make /wave /free /n=2 result_waves
+
1410 make /free /n=0 dest1, dest2
+
1411 result_waves[0] = dest1
+
1412 result_waves[1] = dest2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1436 duplicate /free dest1, center
+
1437 q0 = round((y0 - dimoffset(source, 1)) / dimdelta(source, 1))
+
1438 q1 = round((y1 - dimoffset(source, 1)) / dimdelta(source, 1))
+
+
1440 wavestats /q/m=1 center
+
1441 p0 = round((v_maxloc - dimoffset(source, 0)) / dimdelta(source, 0))
+
1442 p1 = round((v_maxloc + 0.4 - dimoffset(source, 0)) / dimdelta(source, 0))
+
+
+
1445 make /n=(ny)/d/free profile
+
1446 setscale /p x dimoffset(source,1), dimdelta(source,1), waveunits(source,1), profile
+
+
+
1449 for (pp = p0; pp <= p1; pp += 1)
+
1450 profile = source[pp][p]
+
1451 curvefit /Q /NTHR=1 /W=2 gauss profile(y0,y1)
+
+
1453 dest1[pp] = w_coef[2]
+
1454 dest2[pp] = w_coef[3]
+
+
+
+
+
+
1460 function scienta_norm(w, x): fitfunc
+
+
+
+
1464 return w[0] * (x^2 - w[1]^2)
+
+
+
1467 function /wave fit_scienta_ang_transm(data, params)
+
+
+
+
1471 if (!waveexists(params))
+
1472 make /n=12 /o params
+
+
1474 redimension /n=12/d params
+
+
1476 variable h = wavemax(data) - wavemin(data)
+
+
+
+
+
+
+
+
+
+
+
+
+
1489 FuncFit /NTHR=0 /q scienta_ang_transm params data
+
+
+
+
+
1494 threadsafe function scienta_ang_transm(w, x): fitfunc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1511 make /free /n=4 /d w_int
+
+
1513 w_int[1,] = w[p - 1]
+
1514 variable pk1 = gauss1d(w_int, x)
+
1515 w_int[1,] = w[p + 2]
+
1516 variable pk2 = gauss1d(w_int, x)
+
1517 w_int[1,] = w[p + 5]
+
1518 variable pk3 = gauss1d(w_int, x)
+
1519 w_int[0,2] = w[9 + p]
+
+
1521 variable bg = poly(w_int, x)
+
+
1523 return bg + pk1 + pk2 + pk3
+
+
+
1526 function /wave fit_scienta_poly_bg(data, params, bgterms)
+
+
+
+
+
1531 if (!waveexists(params))
+
1532 make /n=15 /o params
+
+
1534 redimension /n=15 /d params
+
+
1536 variable wmax = wavemax(data)
+
1537 variable wmin = wavemin(data)
+
+
+
+
+
+
+
+
+
+
+
+
+
1550 params[12] = (wmax - wmin) / dimdelta(data,1) / dimsize(data,1)
+
+
+
+
1554 string h = "0000000000000"
+
+
+
+
+
+
+
+
+
+
+
1565 FuncFitMD /NTHR=1 /q /h=h scienta_poly_bg params data
+
+
+
+
+
1570 function scienta_poly_bg(w, e, a): fitfunc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1596 make /free /n=4 /d w_int
+
+
+
+
+
1601 w_int[2,] = w[p0 + p - 2]
+
1602 variable pk1 = gauss1d(w_int, a)
+
+
+
1605 w_int[1,] = w[p0 + p - 1]
+
1606 variable pk2 = gauss1d(w_int, a)
+
+
+
1609 w_int[1,] = w[p0 + p - 1]
+
1610 variable pk3 = gauss1d(w_int, a)
+
+
+
1613 w_int[0,2] = w[p0 + p]
+
+
1615 variable base = poly(w_int, a)
+
+
+
1618 w_int[0,3] = w[p0 + p]
+
1619 variable bg = poly(w_int, e)
+
+
1621 return bg * (base + pk1 + pk2 + pk3)
+
threadsafe wave int_linbg_reduction(wave source, string *param)
linear-background subtracted integration reduction function.
variable prompt_int_linbg_reduction(string *param)
prompt the user for integrate on linear background reduction parameters.
threadsafe variable MultiVoigtLinBG_AO(wave pw, wave yw, wave xw)
multiple voigt peaks on a linear background fit function.
threadsafe variable MultiGaussLinBG_AO(wave pw, wave yw, wave xw)
multiple gaussian peaks on a linear background fit function (all at once).
string capture_int_linbg_cursors()
capture linear background reduction parameters from cursors in a graph.
threadsafe wave ad_profile_x_w(wave dataset, variable q1, variable q2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
threadsafe variable adh5_setup_profile(wave image, wave profile, variable dim)
set up a one-dimensional wave for a line profile based on a 2D original wave.
variable prompt_gauss4_reduction(string *param)
prompt for the gauss4_reduction parameters
threadsafe wave gauss6_reduction(wave source, string *param)
variable test_gauss4_reduction(wave image)
apply the gauss4_reduction function to a single image
string csr_int_linbg_reduction(string win)
calculate linear background reduction parameters from cursors in a graph.
threadsafe wave redim_linbg_reduction(wave source, string *param)
linear background reduction function for incorrectly dimensioned scienta image
threadsafe wave ad_profile_y_w(wave dataset, variable p1, variable p2, wave destwave, variable noavg=defaultValue)
1D cut through 2D dataset along X dimension, existing destination wave.
variable prompt_int_quadbg_reduction(string *param)
threadsafe wave gauss4_reduction(wave source, string *param)
fit horizontal cuts of an image with up to four gaussian peaks on a linear background
variable prompt_redim_linbg_reduction(string *param)
parameter dialog for the redim_linbg_reduction() function
threadsafe wave int_quadbg_reduction(wave source, string *param)
integrate peak area minus a quadratic background
threadsafe variable MultiGaussLinBG(wave w, variable x)
multiple gaussian peaks on a linear background fit function.
PEARL Procedures: pearl-tools.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -133,7 +135,7 @@ Functions
@@ -163,7 +165,7 @@ Functions
@@ -193,7 +195,7 @@ Functions
@@ -235,7 +237,7 @@ Functions
@@ -271,7 +273,7 @@ Functions
@@ -301,7 +303,7 @@ Functions
@@ -311,9 +313,9 @@ Functions
diff --git a/doc/html/pearl-tools_8ipf_source.html b/doc/html/pearl-tools_8ipf_source.html
index da3cecb..8d46172 100644
--- a/doc/html/pearl-tools_8ipf_source.html
+++ b/doc/html/pearl-tools_8ipf_source.html
@@ -1,9 +1,9 @@
-
+
PEARL Procedures: pearl-tools.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,24 +87,160 @@ $(document).ready(function(){initNavTree('pearl-tools_8ipf_source.html','');});
pearl-tools.ipf
-
Go to the documentation of this file. 1 #pragma rtGlobals=3 // Use modern global access method and strict wave access. 3 #pragma IgorVersion = 6.2 4 #pragma ModuleName = PearlTools 5 #include "pearl-gui-tools" 55 string wlist = WaveList(matchStr,
";" ,
"" )
56 variable n = ItemsInList(wlist, ";")
58 for (i = 0; i < n; i += 1)
59 wave w = $(StringFromList(i, wlist, ";"))
75 print getdatafolder(1)
94 if (ParamIsDefault(progress_title))
97 variable show_progress = strlen(progress_title) > 0
99 dfref origdf = GetDataFolderDFR()
102 variable abort_req = 0
105 variable ndf = CountObjectsDFR(origdf, 4)
111 objName = GetIndexedObjNameDFR(origdf, 4, index)
112 if (strlen(objName) == 0)
115 if (stringmatch(objname, matchstr))
123 curdf = $(":" + objname)
124 iterator(curdf, sdata)
-
-
-
-
-
-
-
-
+
Go to the documentation of this file. 1 #pragma TextEncoding = "UTF-8"
+
2 #pragma rtGlobals=3 // Use modern global access method and strict wave access.
+
+
4 #pragma IgorVersion = 6.2
+
5 #pragma ModuleName = PearlTools
+
6 #include "pearl-gui-tools"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
56 string wlist = WaveList(matchStr,
";" ,
"" )
+
57 variable n = ItemsInList(wlist, ";")
+
+
59 for (i = 0; i < n; i += 1)
+
60 wave w = $(StringFromList(i, wlist, ";"))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
76 print getdatafolder(1)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
95 if (ParamIsDefault(progress_title))
+
+
+
98 variable show_progress = strlen(progress_title) > 0
+
+
100 dfref origdf = GetDataFolderDFR()
+
+
+
103 variable abort_req = 0
+
+
+
106 variable ndf = CountObjectsDFR(origdf, 4)
+
+
+
+
+
+
112 objName = GetIndexedObjNameDFR(origdf, 4, index)
+
113 if (strlen(objName) == 0)
+
+
+
116 if (stringmatch(objname, matchstr))
+
+
+
+
+
+
+
+
124 curdf = $(":" + objname)
+
125 iterator(curdf, sdata)
+
+
+
+
+
+
+
+
+
+
+
PEARL Procedures: pearl-vector-operations.ipf File Reference
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -103,40 +105,40 @@ Namespaces
variable rotate2d_x (variable xx, variable yy, variable angle) rotate a 2D cartesian vector and returns its x component. More... rotate a 2D cartesian vector and returns its x component. More... variable rotate2d_y (variable xx, variable yy, variable angle) rotate a 2D cartesian vector and returns its y component. More... rotate a 2D cartesian vector and returns its y component. More... wave create_rotation_matrix_free () create a free matrix wave which represents the 3-vector identity. More... create a free matrix wave which represents the 3-vector identity. More... wave set_rotation_x (wave matrix, variable angle) calculate a matrix representing a 3-vector rotation around the x axis. More... calculate a matrix representing a 3-vector rotation around the x axis. More... wave set_rotation_y (wave matrix, variable angle) calculate a matrix representing a 3-vector rotation around the y axis More... calculate a matrix representing a 3-vector rotation around the y axis More... wave set_rotation_z (wave matrix, variable angle) calculate a matrix representing a 3-vector rotation around the z axis More... calculate a matrix representing a 3-vector rotation around the z axis More... variable rotate_x_wave (wave inout, variable angle) rotate a wave of 3-vectors about the x axis. More... rotate a wave of 3-vectors about the x axis. More... variable rotate_y_wave (wave inout, variable angle) rotates a wave of 3-vectors about the y axis More... rotates a wave of 3-vectors about the y axis More... variable rotate_z_wave (wave inout, variable angle) rotates a wave of 3-vectors about the z axis More... rotates a wave of 3-vectors about the z axis More... basic vector geometry operations.
this procedure file contains basic vector geometry functions, such as rotations.
Author matthias muntwiler, matth.nosp@m. ias..nosp@m. muntw.nosp@m. iler.nosp@m. @psi..nosp@m. ch
-
Copyright 2011-17 Paul Scherrer Institut Copyright 2011-21 Paul Scherrer Institut http://www.apache.org/licenses/LICENSE-2.0 Definition in file pearl-vector-operations.ipf .
@@ -160,7 +162,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); the matrix is initialized as identity.
Returns 3x3 identity matrix in a free wave. Definition at line 73 of file pearl-vector-operations.ipf .
+Definition at line 74 of file pearl-vector-operations.ipf .
Returns x coordinate of the rotated vector. Definition at line 45 of file pearl-vector-operations.ipf .
+Definition at line 46 of file pearl-vector-operations.ipf .
@@ -254,7 +256,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns y coordinate of the rotated vector. Definition at line 60 of file pearl-vector-operations.ipf .
+Definition at line 61 of file pearl-vector-operations.ipf .
@@ -295,7 +297,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns none Definition at line 175 of file pearl-vector-operations.ipf .
+Definition at line 176 of file pearl-vector-operations.ipf .
@@ -336,7 +338,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns none Definition at line 203 of file pearl-vector-operations.ipf .
+Definition at line 205 of file pearl-vector-operations.ipf .
@@ -377,7 +379,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns none Definition at line 231 of file pearl-vector-operations.ipf .
+Definition at line 234 of file pearl-vector-operations.ipf .
@@ -418,7 +420,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns rotation matrix. this is the same wave instance as the matrix input. Definition at line 92 of file pearl-vector-operations.ipf .
+Definition at line 93 of file pearl-vector-operations.ipf .
@@ -459,7 +461,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns rotation matrix. this is the same wave instance as the matrix input. Definition at line 120 of file pearl-vector-operations.ipf .
+Definition at line 121 of file pearl-vector-operations.ipf .
@@ -500,7 +502,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); Returns rotation matrix. this is the same wave instance as the matrix input. Definition at line 148 of file pearl-vector-operations.ipf .
+Definition at line 149 of file pearl-vector-operations.ipf .
@@ -510,9 +512,9 @@ Licensed under the Apache License, Version 2.0 (the "License"); PEARL Procedures: pearl-vector-operations.ipf Source File
PEARL Procedures
- rev-distro-2.1.1-1-gf419e92-dirty
+ rev-distro-3.0.0-0-gfa24916-dirty
Igor procedures for the analysis of PEARL data
@@ -38,18 +35,21 @@
-
+
+/* @license-end */
@@ -63,7 +63,9 @@ $(function() {
@@ -85,24 +87,157 @@ $(document).ready(function(){initNavTree('pearl-vector-operations_8ipf_source.ht
pearl-vector-operations.ipf
-
Go to the documentation of this file. 3 #pragma IgorVersion = 6.1 4 #pragma ModuleName = PearlVectorOperations 49 return xx * cos(angle * pi / 180) - yy * sin(angle * pi / 180)
64 return xx * sin(angle * pi / 180) + yy * cos(angle * pi / 180)
74 make /n=(3,3)/free matrix
96 variable si = sin(angle * pi / 180)
97 variable co = cos(angle * pi / 180)
124 variable si = sin(angle * pi / 180)
125 variable co = cos(angle * pi / 180)
152 variable si = sin(angle * pi / 180)
153 variable co = cos(angle * pi / 180)
180 make /n=3/d/free w_temp_rotate_x
182 nvec = max(DimSize(inout, 1), 1)
183 for (ivec = 0; ivec < nvec; ivec += 1)
185 w_temp_rotate_x = inout[p][ivec]
186 matrixop /free w_temp_rotate_x_result = m_rotation_x x w_temp_rotate_x
187 inout[0,2][ivec] = w_temp_rotate_x_result[p]
208 make /n=3/d/free w_temp_rotate_y
210 nvec = max(DimSize(inout, 1), 1)
211 for (ivec = 0; ivec < nvec; ivec += 1)
213 w_temp_rotate_y = inout[p][ivec]
214 matrixop /free w_temp_rotate_y_result = m_rotation_y x w_temp_rotate_y
215 inout[0,2][ivec] = w_temp_rotate_y_result[p]
236 make /n=3/d/free w_temp_rotate_z
238 nvec = max(DimSize(inout, 1), 1)
239 for (ivec = 0; ivec < nvec; ivec += 1)
241 w_temp_rotate_z = inout[p][ivec]
242 matrixop /free w_temp_rotate_z_result = m_rotation_z x w_temp_rotate_z
243 inout[0,2][ivec] = w_temp_rotate_z_result[p]
wave set_rotation_x(wave matrix, variable angle)
calculate a matrix representing a 3-vector rotation around the x axis.
-
variable rotate_x_wave(wave inout, variable angle)
rotate a wave of 3-vectors about the x axis.
-
variable rotate2d_x(variable xx, variable yy, variable angle)
rotate a 2D cartesian vector and returns its x component.
-
wave set_rotation_z(wave matrix, variable angle)
calculate a matrix representing a 3-vector rotation around the z axis
-
variable rotate_y_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the y axis
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variable rotate2d_y(variable xx, variable yy, variable angle)
rotate a 2D cartesian vector and returns its y component.
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variable rotate_z_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the z axis
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wave create_rotation_matrix_free()
create a free matrix wave which represents the 3-vector identity.
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wave set_rotation_y(wave matrix, variable angle)
calculate a matrix representing a 3-vector rotation around the y axis
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4 #pragma IgorVersion = 6.1
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5 #pragma ModuleName = PearlVectorOperations
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50 return xx * cos(angle * pi / 180) - yy * sin(angle * pi / 180)
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65 return xx * sin(angle * pi / 180) + yy * cos(angle * pi / 180)
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75 make /n=(3,3)/free matrix
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97 variable si = sin(angle * pi / 180)
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98 variable co = cos(angle * pi / 180)
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125 variable si = sin(angle * pi / 180)
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126 variable co = cos(angle * pi / 180)
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153 variable si = sin(angle * pi / 180)
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154 variable co = cos(angle * pi / 180)
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183 duplicate /free inout, out
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186 for (j = 0; j < 3; j += 1)
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187 out += m_rotation[p][j] * inout[j][q]
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212 duplicate /free inout, out
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215 for (j = 0; j < 3; j += 1)
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216 out += m_rotation[p][j] * inout[j][q]
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241 duplicate /free inout, out
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244 for (j = 0; j < 3; j += 1)
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245 out += m_rotation[p][j] * inout[j][q]
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variable rotate_y_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the y axis
wave set_rotation_y(wave matrix, variable angle)
calculate a matrix representing a 3-vector rotation around the y axis
wave set_rotation_x(wave matrix, variable angle)
calculate a matrix representing a 3-vector rotation around the x axis.
variable rotate2d_x(variable xx, variable yy, variable angle)
rotate a 2D cartesian vector and returns its x component.
wave create_rotation_matrix_free()
create a free matrix wave which represents the 3-vector identity.
variable rotate_x_wave(wave inout, variable angle)
rotate a wave of 3-vectors about the x axis.
variable rotate2d_y(variable xx, variable yy, variable angle)
rotate a 2D cartesian vector and returns its y component.
variable rotate_z_wave(wave inout, variable angle)
rotates a wave of 3-vectors about the z axis
wave set_rotation_z(wave matrix, variable angle)
calculate a matrix representing a 3-vector rotation around the z axis
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diff --git a/doc/html/search/all_0.js b/doc/html/search/all_0.js
index 0b8d528..789479b 100644
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diff --git a/doc/html/search/all_e.js b/doc/html/search/all_e.js
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index b1ded27..4377320 100644
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index dedce3b..a554ab9 100644
--- a/doc/html/search/search.js
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@@ -1,3 +1,26 @@
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+ Copyright (C) 1997-2017 by Dimitri van Heesch
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+ This program is free software; you can redistribute it and/or modify
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+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+ @licend The above is the entire license notice
+ for the JavaScript code in this file
+ */
function convertToId(search)
{
var result = '';
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index 3ea3b0e..c93a397 100644
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index 84237b6..49fe59a 100644
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index bb7f2da..cef0e70 100644
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index 548ac84..92982ac 100644
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index f1061a8..e26a98c 100644
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PEARL Procedures: DoniachSunjicStruct Struct Reference
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Igor procedures for the analysis of PEARL data
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