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update pshell explorer and data import, misc. improvements

Browse Source 
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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doc/html/pearl-scienta-preprocess_8ipf.html
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@@ -32,7 +32,7 @@
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">PEARL Procedures
&#160;<span id="projectnumber">rev-distro-1.4.0-0-g80a01f2</span>
&#160;<span id="projectnumber">rev-distro-1.4.0-1-g0a436db-dirty</span>
</div>
<div id="projectbrief">Igor procedures for the analysis of PEARL data</div>
</td>
@@ -116,7 +116,8 @@ $(document).ready(function(){initNavTree('pearl-scienta-preprocess_8ipf.html',''
<p>preprocessing functions for Scienta detector images.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &quot;mm-fitfuncs&quot;</code><br />
</div>
<p><a href="pearl-scienta-preprocess_8ipf_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
@@ -165,12 +166,21 @@ Functions</h2></td></tr>
<tr class="memitem:a9b3321b9ed876ff50e260fa311ebf4be"><td class="memItemLeft" align="right" valign="top">threadsafe variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-scienta-preprocess_8ipf.html#a9b3321b9ed876ff50e260fa311ebf4be">redim_linbg_reduction</a> (wave source, wave dest1, wave dest2, string *param)</td></tr>
<tr class="memdesc:a9b3321b9ed876ff50e260fa311ebf4be"><td class="mdescLeft">&#160;</td><td class="mdescRight">linear background reduction function for incorrectly dimensioned scienta image <a href="#a9b3321b9ed876ff50e260fa311ebf4be">More...</a><br /></td></tr>
<tr class="separator:a9b3321b9ed876ff50e260fa311ebf4be"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a57308c99b9e4dd48d139f6613a8a9f40"><td class="memItemLeft" align="right" valign="top">variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-scienta-preprocess_8ipf.html#a57308c99b9e4dd48d139f6613a8a9f40">test_gauss2_reduction</a> (wave image)</td></tr>
<tr class="memdesc:a57308c99b9e4dd48d139f6613a8a9f40"><td class="mdescLeft">&#160;</td><td class="mdescRight">apply the gauss2_reduction function to a single image <a href="#a57308c99b9e4dd48d139f6613a8a9f40">More...</a><br /></td></tr>
<tr class="separator:a57308c99b9e4dd48d139f6613a8a9f40"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a79eb4d0d4902a549bf92553840b884e8"><td class="memItemLeft" align="right" valign="top">variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-scienta-preprocess_8ipf.html#a79eb4d0d4902a549bf92553840b884e8">prompt_gauss2_reduction</a> (string *param)</td></tr>
<tr class="memdesc:a79eb4d0d4902a549bf92553840b884e8"><td class="mdescLeft">&#160;</td><td class="mdescRight">prompt for the gauss2_reduction parameters <a href="#a79eb4d0d4902a549bf92553840b884e8">More...</a><br /></td></tr>
<tr class="separator:a79eb4d0d4902a549bf92553840b884e8"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af9ea97d870f53a70583c53328599ff14"><td class="memItemLeft" align="right" valign="top">threadsafe variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-scienta-preprocess_8ipf.html#af9ea97d870f53a70583c53328599ff14">gauss2_reduction</a> (wave source, wave dest1, wave dest2, string *param)</td></tr>
<tr class="memdesc:af9ea97d870f53a70583c53328599ff14"><td class="mdescLeft">&#160;</td><td class="mdescRight">fit horizontal cuts of an image with two gaussian peaks on a linear background <a href="#af9ea97d870f53a70583c53328599ff14">More...</a><br /></td></tr>
<tr class="separator:af9ea97d870f53a70583c53328599ff14"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>preprocessing functions for Scienta detector images. </p>
<p>this procedure contains functions for data reduction and instrument-specific normalization.</p>
<dl class="section author"><dt>Author</dt><dd>matthias muntwiler, <a href="#" onclick="location.href='mai'+'lto:'+'mat'+'th'+'ias'+'.m'+'unt'+'wi'+'ler'+'@p'+'si.'+'ch'; return false;">matth<span style="display: none;">.nosp@m.</span>ias.<span style="display: none;">.nosp@m.</span>muntw<span style="display: none;">.nosp@m.</span>iler<span style="display: none;">.nosp@m.</span>@psi.<span style="display: none;">.nosp@m.</span>ch</a></dd></dl>
<dl class="section copyright"><dt>Copyright</dt><dd>2013-15 Paul Scherrer Institut <br />
<dl class="section copyright"><dt>Copyright</dt><dd>2013-17 Paul Scherrer Institut <br />
Licensed under the Apache License, Version 2.0 (the "License"); <br />
you may not use this file except in compliance with the License. <br />
You may obtain a copy of the License at <a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a> </dd></dl>
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<td class="memname">threadsafe variable gauss2_reduction </td>
<td>(</td>
<td class="paramtype">wave&#160;</td>
<td class="paramname"><em>source</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">wave&#160;</td>
<td class="paramname"><em>dest1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">wave&#160;</td>
<td class="paramname"><em>dest2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">string *&#160;</td>
<td class="paramname"><em>param</em>&#160;</td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td>
</tr>
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<p>fit horizontal cuts of an image with two gaussian peaks on a linear background </p>
<p>the function fits each horizontal profile (EDC) with two gaussian peaks on a linear background. the position and width of the peaks is kept fixed according to input parameters. the peak amplitude is constrained to positive value.</p>
<p>the width parameter is defined as in Igor's gauss curve fit function (standard deviation divided by the square root of two). the return value in dest1 is the integrated peak either of peak 1 or peak 2. dest2 returns the corresponding error estimate.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">source</td><td>source wave. two-dimensional distribution of counts. for correct weighting and error estimation it is important that the source wave contains actual counts (Poisson statistics). </td></tr>
<tr><td class="paramname">dest1</td><td>(out) peak area </td></tr>
<tr><td class="paramname">dest2</td><td>(out) error estimate of peak area </td></tr>
<tr><td class="paramname">param</td><td>(in, out) semicolon-separated key=value list of processing parameters. this is a pass-by-reference argument. the following parameters are required. position, width and limit parameters are on the x (energy) scale. <ul>
<li>rngl low limit of fit interval </li>
<li>rngh high limit of fit interval </li>
<li>pos1 position of peak 1 </li>
<li>wid1 width of peak 1 </li>
<li>pos2 position of peak 2 </li>
<li>wid2 width of peak 2 </li>
<li>return select result to return, either "int1" or "int2". </li>
<li>ybox box size of averaging in y direction, must be 1 or 3. other values lead to corrupt data.</li>
</ul>
</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>zero if successful, non-zero if an error occurs. </dd></dl>
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<td class="memname">variable prompt_gauss2_reduction </td>
<td>(</td>
<td class="paramtype">string *&#160;</td>
<td class="paramname"><em>param</em></td><td>)</td>
<td></td>
</tr>
</table>
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<p>prompt for the gauss2_reduction parameters </p>
<p>useful for testing or manual processing. to debug, (temporarily) remove the threadsafe attribute from the gauss2_reduction function. </p>
<p>Definition at line <a class="el" href="pearl-scienta-preprocess_8ipf_source.html#l00834">834</a> of file <a class="el" href="pearl-scienta-preprocess_8ipf_source.html">pearl-scienta-preprocess.ipf</a>.</p>
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</dl>
<dl class="section return"><dt>Returns</dt><dd>zero if the user clicked OK, non-zero if the user clicked Cancel. </dd></dl>
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<p>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</p>
<dl class="section return"><dt>Returns</dt><dd>zero if successful, non-zero if an error occurs. </dd></dl>
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<td>(</td>
<td class="paramtype">wave&#160;</td>
<td class="paramname"><em>image</em></td><td>)</td>
<td></td>
</tr>
</table>
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<p>apply the gauss2_reduction function to a single image </p>
<p>useful for testing or manual processing. to debug, (temporarily) remove the threadsafe attribute from the gauss2_reduction function. </p>
<p>Definition at line <a class="el" href="pearl-scienta-preprocess_8ipf_source.html#l00810">810</a> of file <a class="el" href="pearl-scienta-preprocess_8ipf_source.html">pearl-scienta-preprocess.ipf</a>.</p>
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@@ -699,7 +815,7 @@ Licensed under the Apache License, Version 2.0 (the "License"); <br />
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_fe5dc42579d4b99403482a3a637d9f7d.html">pearl</a></li><li class="navelem"><a class="el" href="pearl-scienta-preprocess_8ipf.html">pearl-scienta-preprocess.ipf</a></li>
<li class="footer">Generated on Tue Jul 4 2017 11:17:32 for PEARL Procedures by
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