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update pshell explorer and data import, misc. improvements

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FEATURES

- pshell: convert scienta data to true counts
- pre-process: add gauss2_reduction data reduction function
- anglescan: add set_contrast and normalize_strip_phi functions
- explorer: show info about multi-region scans
- documentation: add detailed instructions for angle-scan processing

BUGFIXES

- explorer: fix attributes notebook
- pshell: fix progress bar
- elog: increase the number of accepted attachments
This commit is contained in:
muntwiler_m
2017-09-21 12:36:30 +02:00
parent 0a436db00b
commit cf1399e59c
137 changed files with 1824 additions and 853 deletions
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195
pearl/pearl-anglescan-process.ipf
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@ -1,12 +1,12 @@
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
#pragma version = 1.7
#pragma version = 1.8
#pragma IgorVersion = 6.2
#pragma ModuleName = PearlAnglescanProcess
#include "pearl-vector-operations"
#include "pearl-polar-coordinates"
#include <New Polar Graphs>
// copyright (c) 2013-16 Paul Scherrer Institut
// copyright (c) 2013-17 Paul Scherrer Institut
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
@ -64,13 +64,13 @@
///
/// @author matthias muntwiler, matthias.muntwiler@psi.ch
///
/// @copyright 2013-16 Paul Scherrer Institut @n
/// @copyright 2013-17 Paul Scherrer Institut @n
/// 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
///
/// @version 1.6
/// @version 1.8
/// canonical orientation of spherical coordinate system.
///
@ -241,6 +241,84 @@ function normalize_strip_x(strip, [smooth_method, smooth_factor, check])
endif
end
/// divide the strip by a sine function in phi (wobble correction).
///
/// the sine function is a curve fit to the intensity integrated over detector angle
/// with a period of 360&degree;.
///
/// this normalization may be useful if the intensity varies with a 360&degree; periodicity in the azimuthal angle,
/// e.g. due to misalignment of the surface normal and the azimuthal rotation axis of the manipulator (wobble).
/// note, however, that this function does not correct other effects of wobble such as angle shifts.
///
/// the strip is normalized in place, previous data is overwritten.
///
/// @param[in,out] strip 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan
/// @param[in] theta polar manipulator angle.
/// @param[in] phi azimuthal manipulator angle, arbitrary offset.
/// @param[in] theta_offset theta value corresponding to normal emission (default 0).
/// @param[in] theta_range maximum (offset corrected) theta to consider in the sine fit (default 10).
///
/// @param check enable output of intermediate results
/// @arg 0 (default) don't create additional waves
/// @arg 1 create check waves in the current folder
/// @arg 2 calculate check waves only, do not modify strip
///
/// @return if check waves are enabled, the following waves are created (overwritten if existing):
/// @arg check_dist average theta distribution
/// @arg check_smoo smoothed distribution used to normalize the strip
///
function normalize_strip_phi(strip, theta, phi, [theta_offset, theta_range, check])
wave strip
wave theta
wave phi
variable theta_offset
variable theta_range
variable check
if (ParamIsDefault(check))
check = 0
endif
if (ParamIsDefault(theta_offset))
theta_offset = 0
endif
if (ParamIsDefault(theta_range))
theta_offset = 10
endif
// average over analyser angles
wave dist = ad_profile_y(strip, -inf, inf, "")
// smooth distribution function
duplicate /free dist, dist_smoo
duplicate /free theta, theta_int
theta_int = theta - theta_offset
duplicate /free phi, phi_int
setscale /p x phi_int[0], phi_int[1] - phi_int[0], waveunits(phi, -1), dist, dist_smoo
extract /free /indx dist, red_idx, theta_int < theta_range
duplicate /free red_idx, red_dist, red_phi
red_dist = dist[red_idx]
red_phi = phi_int[red_idx]
variable wavg = mean(red_dist)
make /n=4 /d /free coef
coef[0] = {wavg, wavg/100, pi/180, 0}
CurveFit /q /h="0010" /g /w=2 sin, kwcWave=coef, red_dist /x=red_phi
dist_smoo = coef[0] + coef[1] * sin(coef[2] * phi_int[p] + coef[3])
// divide
if (check != 2)
strip = strip / dist_smoo[q] * coef[0]
endif
// check
if (check)
duplicate /o dist, check_dist
duplicate /o dist_smoo, check_smoo
setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
endif
end
/// divide the strip by the average polar distribution.
///
/// this is a simple way to remove the polar angle dependence.
@ -2843,3 +2921,112 @@ function /wave hemi_azi_cut(nickname, pol)
return $""
endif
end
static function check_contrast(values, pcmin, pcmax, vmin, vmax)
wave values
variable pcmin
variable pcmax
variable &vmin
variable &vmax
dfref save_df = GetDataFolderDFR()
dfref dfr = NewFreeDataFolder()
setdatafolder dfr
StatsQuantiles /inan /iw /q /z values
wave index = w_quantilesindex
variable imin = round(numpnts(index) * pcmin / 100)
variable imax = round(numpnts(index) * (100 - pcmax) / 100)
vmin = values[index[imin]]
vmax = values[index[imax]]
KillDataFolder dfr
setdatafolder save_df
end
/// set the pseudocolor contrast by percentile.
///
/// set the minimum and maximum values of the pseudocolor scale
/// such that a specified percentile of the distribution lies outside the limits.
///
/// the new contrast is applied to traces and images of the selected graph
/// that have pseudocolor tables.
///
/// the function is not specific to angle scans.
/// it can be used for any pseudocolor trace or image plots except contour plots.
///
/// @param pcmin percentile below the minimum color (0-100).
/// @param pcmax percentile above the maximum color (0-100).
/// @param graphname name of graph. default: top graph.
/// @param colortable name of new colortable. default: keep current table.
///
function set_contrast(pcmin, pcmax, [graphname, colortable])
variable pcmin
variable pcmax
string graphname
string colortable
if (ParamIsDefault(graphname))
graphname = ""
endif
if (ParamIsDefault(colortable))
colortable = ""
endif
dfref save_df = GetDataFolderDFR()
string objname
string info
string wname
string ctab
variable rev
variable n
variable i
variable vmin
variable vmax
string traces = TraceNameList(graphname, ";", 1+4)
n = ItemsInList(traces, ";")
for (i = 0; i < n; i += 1)
objname = StringFromList(i, traces, ";")
info = TraceInfo(graphname, objname, 0)
if (strlen(info) > 0)
info = StringByKey("RECREATION", info, ":", ";")
info = StringByKey("zColor(x)", info, "=", ";")
if (strlen(info) > 2)
info = info[1,strlen(info)-2]
wname = StringFromList(0, info, ",")
wave w = $wname
ctab = StringFromList(3, info, ",")
rev = str2num("0" + StringFromList(4, info, ","))
if (strlen(colortable) > 0)
ctab = colortable
endif
check_contrast(w, pcmin, pcmax, vmin, vmax)
ModifyGraph /w=$graphname zColor($objname)={w, vmin, vmax, $ctab, rev}
endif
endif
endfor
string images = ImageNameList(graphname, ";")
n = ItemsInList(images, ";")
for (i = 0; i < n; i += 1)
objname = StringFromList(i, images, ";")
wave w = ImageNameToWaveRef(graphname, objname)
info = ImageInfo(graphname, objname, 0)
if (strlen(info) > 0)
info = StringByKey("RECREATION", info, ":", ";")
info = StringByKey("ctab", info, "=", ";")
if (strlen(info) > 2)
info = info[1,strlen(info)-2]
ctab = StringFromList(2, info, ",")
rev = str2num("0" + StringFromList(3, info, ","))
if (strlen(colortable) > 0)
ctab = colortable
endif
check_contrast(w, pcmin, pcmax, vmin, vmax)
ModifyImage /w=$graphname $objname ctab={vmin, vmax, $ctab, rev}
endif
endif
endfor
setdatafolder save_df
end