new features: data reduction, angle scan panel

- new data reduction interface for more efficient multi-peak fitting.
  the new interface breaks compatibility with pre-2.0 data reduction
  functions. user-defined functions must be adapted to the new
  interface.
- new angle scan processing panel for interactive data analysis.
This commit is contained in:
2018-02-06 11:39:57 +01:00
parent e1f1aa9636
commit fda49c3195
171 changed files with 7539 additions and 2554 deletions

View File

@@ -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-1.6.0-0-gcf1399e-dirty</span>
&#160;<span id="projectnumber">rev-distro-1.6.1-0-ge1f1aa9-dirty</span>
</div>
<div id="projectbrief">Igor procedures for the analysis of PEARL data</div>
</td>
@@ -211,16 +211,16 @@ Functions</h2></td></tr>
<tr class="memitem:a2c456397c36d4116bfddca452eff5954"><td class="memItemLeft" align="right" valign="top">variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#a2c456397c36d4116bfddca452eff5954">ps_scale_dataset_2</a> (wave data, wave ax, wave lo, wave hi, wave un)</td></tr>
<tr class="memdesc:a2c456397c36d4116bfddca452eff5954"><td class="mdescLeft">&#160;</td><td class="mdescRight">set the dimension scales of a dataset. <a href="#a2c456397c36d4116bfddca452eff5954">More...</a><br /></td></tr>
<tr class="separator:a2c456397c36d4116bfddca452eff5954"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1444648f9a49e7d7aeef5b5fb55594aa"><td class="memItemLeft" align="right" valign="top">string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#a1444648f9a49e7d7aeef5b5fb55594aa">psh5_load_reduced</a> (string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable progress=defaultValue)</td></tr>
<tr class="memdesc:a1444648f9a49e7d7aeef5b5fb55594aa"><td class="mdescLeft">&#160;</td><td class="mdescRight">load and reduce the ScientaImage dataset of the first scan of a PShell data file. <a href="#a1444648f9a49e7d7aeef5b5fb55594aa">More...</a><br /></td></tr>
<tr class="separator:a1444648f9a49e7d7aeef5b5fb55594aa"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3eefc2f84a09f2ce29893c71ef44ae32"><td class="memItemLeft" align="right" valign="top">string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#a3eefc2f84a09f2ce29893c71ef44ae32">psh5_load_reduced</a> (string ANickName, string APathName, string AFileName, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue)</td></tr>
<tr class="memdesc:a3eefc2f84a09f2ce29893c71ef44ae32"><td class="mdescLeft">&#160;</td><td class="mdescRight">load and reduce the ScientaImage dataset of the first scan of a PShell data file. <a href="#a3eefc2f84a09f2ce29893c71ef44ae32">More...</a><br /></td></tr>
<tr class="separator:a3eefc2f84a09f2ce29893c71ef44ae32"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a13a45e8618c1ab7406e1aa5e608e21fe"><td class="memItemLeft" align="right" valign="top">string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#a13a45e8618c1ab7406e1aa5e608e21fe">psh5_load_dataset_reduced</a> (variable fileID, string scanpath, string datasetname, funcref reduction_func, string reduction_param, variable progress=defaultValue, variable nthreads=defaultValue)</td></tr>
<tr class="memdesc:a13a45e8618c1ab7406e1aa5e608e21fe"><td class="mdescLeft">&#160;</td><td class="mdescRight">load a reduced dataset from the open PShell HDF5 file. <a href="#a13a45e8618c1ab7406e1aa5e608e21fe">More...</a><br /></td></tr>
<tr class="separator:a13a45e8618c1ab7406e1aa5e608e21fe"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a33f8faf117450af1d6dae9ef48786cd6"><td class="memItemLeft" align="right" valign="top">static threadsafe variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#a33f8faf117450af1d6dae9ef48786cd6">reduce_slab_worker</a> (funcref reduction_func)</td></tr>
<tr class="separator:a33f8faf117450af1d6dae9ef48786cd6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:acf0315ec8a3e927ef161a35cb05adb8b"><td class="memItemLeft" align="right" valign="top">static threadsafe variable&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#acf0315ec8a3e927ef161a35cb05adb8b">reduce_slab_image</a> (wave slabdata, wave image, wave profile1, wave profile2, funcref reduction_func, string reduction_param)</td></tr>
<tr class="separator:acf0315ec8a3e927ef161a35cb05adb8b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a44d495fba0dd2b82dec13760a07fd226"><td class="memItemLeft" align="right" valign="top">static threadsafe wave&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#a44d495fba0dd2b82dec13760a07fd226">reduce_slab_image</a> (wave slabdata, wave image, funcref reduction_func, string reduction_param)</td></tr>
<tr class="separator:a44d495fba0dd2b82dec13760a07fd226"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa14b28120a07a8213e5a692930704a4b"><td class="memItemLeft" align="right" valign="top">string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="pearl-pshell-import_8ipf.html#aa14b28120a07a8213e5a692930704a4b">psh5_load_info</a> (string APathName, string AFileName)</td></tr>
<tr class="memdesc:aa14b28120a07a8213e5a692930704a4b"><td class="mdescLeft">&#160;</td><td class="mdescRight">load descriptive info from a PShell data file. <a href="#aa14b28120a07a8213e5a692930704a4b">More...</a><br /></td></tr>
<tr class="separator:aa14b28120a07a8213e5a692930704a4b"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -266,7 +266,7 @@ Variables</h2></td></tr>
<p>HDF5 file import from the PShell data acquisition program. the main import functions are:</p>
<ul>
<li><a class="el" href="pearl-pshell-import_8ipf.html#a8a5ce6c2767607de194b4c148ee98c27" title="load everything from a PShell data file. ">psh5_load_complete()</a> load all scans and datasets from a file.</li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#a1444648f9a49e7d7aeef5b5fb55594aa" title="load and reduce the ScientaImage dataset of the first scan of a PShell data file. ...">psh5_load_reduced()</a> load the ScientaImage dataset of the first scan and reduce its dimensionality.</li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#a3eefc2f84a09f2ce29893c71ef44ae32" title="load and reduce the ScientaImage dataset of the first scan of a PShell data file. ...">psh5_load_reduced()</a> load the ScientaImage dataset of the first scan and reduce its dimensionality.</li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#a0a02f87e19e825964aa17c46ed51df8c" title="load all data of a selected scan from a PShell data file. ">psh5_load_scan_complete()</a> load all datasets of a selected scan.</li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#ad3b9354b137ba4f1bc3ed2e74f24dc88" title="load a preview dataset from an open PShell HDF5 file. ">psh5_load_scan_preview()</a> load a preview of a selected scan.</li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#ac4dfb90b951d29b56501e904f5cc38aa" title="load a dataset from an open PShell HDF5 file. ">psh5_load_dataset()</a> load a selected dataset.</li>
@@ -279,8 +279,13 @@ Variables</h2></td></tr>
<li><a class="el" href="pearl-pshell-import_8ipf.html#a2152f7c39a187b740cf9890767ffac3f" title="list scan groups of a PShell data file. ">psh5_list_scans()</a></li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#a4508bd507c4c935bd8463d9b2b84c6fc" title="list datasets of a PShell scan group. ">psh5_list_scan_datasets()</a></li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#aa56c25d64b3e59f74d6dd92a599cce4f" title="load metadata of a PShell scan group. ">psh5_load_scan_meta()</a></li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#aec191d0167bbf606d24396f4658104b5" title="load attributes of a PShell scan group. ">psh5_load_scan_attrs()</a> </li>
<li><a class="el" href="pearl-pshell-import_8ipf.html#aec191d0167bbf606d24396f4658104b5" title="load attributes of a PShell scan group. ">psh5_load_scan_attrs()</a></li>
</ul>
<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>2013-18 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>
<p>Definition in file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div><h2 class="groupheader">Function Documentation</h2>
@@ -309,7 +314,7 @@ Variables</h2></td></tr>
<p>find the attributes data folder </p>
<p>this is the :attr folder. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01451">1451</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01458">1458</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -357,7 +362,7 @@ Variables</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01539">1539</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01546">1546</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -386,7 +391,7 @@ Variables</h2></td></tr>
<p>find the scan folder </p>
<p>the scan folder is the one that contains the :attr folder the data and scan folders may refer to the same folder. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01434">1434</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01441">1441</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -456,7 +461,7 @@ Variables</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd>the function results are written to the lo, hi, un, and ax waves.</dd></dl>
<dl class="section version"><dt>Version</dt><dd>this function supports regions from version 1.03. check that you're in the correct data folder! </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01596">1596</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01603">1603</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -486,7 +491,7 @@ Variables</h2></td></tr>
</dl>
<dl class="section version"><dt>Version</dt><dd>this function supports regions from version 1.03. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01525">1525</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01532">1532</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -540,6 +545,7 @@ Variables</h2></td></tr>
<li><code>lo[%scan]</code> scan dimension. </li>
<li><code>lo[%data]</code> data dimension.</li>
</ul>
<p>if the data dimension labels and units are at their defaults ("value" and "arb.", respectively), the function tries to read them from the existing wave note ("AxisLabelD" and "AxisUnitD"), or based on the wave name if the name is one of the known measurement variables: "ScientaImage", "ImageAngleDistribution", "ScientaAngleDistribution", "ScientaSpectrum", "ImageEnergyDistribution", "ScientaEnergyDistribution", "SampleCurrent", "RefCurrent", "AuxCurrent", "MachineCurrent".</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">data</td><td>data wave to be scaled. dimension labels (index -1) must be set to match the limit waves.</td></tr>
@@ -552,7 +558,7 @@ Variables</h2></td></tr>
</dl>
<dl class="section version"><dt>Version</dt><dd>this function supports regions from version 1.03. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01750">1750</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01763">1763</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -575,7 +581,7 @@ Variables</h2></td></tr>
<p>the dimension labels of the dataset waves must have been set correctly, e.g. by <a class="el" href="pearl-pshell-import_8ipf.html#aba25eb98e4c6cc9066c46ef6be1cde15" title="set dimension labels according to the axis type ">ps_set_dimlabels()</a>. this is implicitly done by the high-level load functions.</p>
<dl class="section version"><dt>Version</dt><dd>this function supports regions from version 1.03. check that you're in the correct data folder! </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01479">1479</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01486">1486</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -609,7 +615,7 @@ Variables</h2></td></tr>
</ul>
</dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01358">1358</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01365">1365</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -653,7 +659,7 @@ Variables</h2></td></tr>
</ul>
</dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01377">1377</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01384">1384</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -680,7 +686,7 @@ Variables</h2></td></tr>
</dd>
</dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00132">132</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00139">139</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -727,7 +733,7 @@ Variables</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of dataset paths.</dd></dl>
<dl class="section version"><dt>Version</dt><dd>since version 1.03 this function returns paths relative to scanpath. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00432">432</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00439">439</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -766,7 +772,7 @@ Variables</h2></td></tr>
</dl>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of datagroup paths. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00473">473</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00480">480</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -794,7 +800,7 @@ Variables</h2></td></tr>
</dl>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of group paths. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00397">397</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00404">404</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
</div>
@@ -865,7 +871,7 @@ global string s_filepath in new data folder contains the full file path on disk.
<dd>
global string s_scanpaths in new data folder contains a list of scan groups inside the file. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00162">162</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00169">169</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -929,7 +935,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<dl class="section return"><dt>Returns</dt><dd>name of loaded wave if successful. empty string otherwise.</dd></dl>
<dl class="section version"><dt>Version</dt><dd>this function supports regions as of version 1.03. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00681">681</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00688">688</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -983,7 +989,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
</dl>
<dl class="section return"><dt>Returns</dt><dd>0 if successful, non-zero if an error occurred. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01066">1066</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01073">1073</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
</div>
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@@ -1042,7 +1048,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
</div><div class="memdoc">
<p>load a reduced dataset from the open PShell HDF5 file. </p>
<p>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 <code>ReducedData1</code> and <code>ReducedData2</code> waves. the raw data are discarded.</p>
<p>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 <code>ReducedData1</code>, <code>ReducedData2</code>, etc. waves. the raw data are discarded.</p>
<p>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.</p>
<p>if the reduction function requires the image waves to be scaled properly, the attributes must have been loaded by <a class="el" href="pearl-pshell-import_8ipf.html#aec191d0167bbf606d24396f4658104b5" title="load attributes of a PShell scan group. ">psh5_load_scan_attrs()</a> before. in this case, the scales of the result waves are also set by the function. otherwise, the results can also be scaled by <a class="el" href="pearl-pshell-import_8ipf.html#adc11ea797562b3d99c247f4866618d39" title="set the dimension scales of a loaded PShell Scienta dataset according to attributes. ">ps_scale_dataset()</a> later.</p>
<dl class="params"><dt>Parameters</dt><dd>
@@ -1050,7 +1056,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<tr><td class="paramname">fileID</td><td>ID of open HDF5 file from <a class="el" href="pearl-pshell-import_8ipf.html#accc20b0fc6bda95ba0cd0aea6633086f" title="open a HDF5 file created by the PShell data acquisition program and prepare the data folder...">psh5_open_file()</a>.</td></tr>
<tr><td class="paramname">scanpath</td><td>path to scan group in the HDF5 file.</td></tr>
<tr><td class="paramname">datasetname</td><td>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".</td></tr>
<tr><td class="paramname">reduction_func</td><td>custom reduction function (any user-defined function which has the same parameters as <a class="el" href="pearl-area-import_8ipf.html#a245034d7a94536a24c78a7bfe22725b7" title="function prototype for adh5_load_reduced_detector ">adh5_default_reduction()</a>).</td></tr>
<tr><td class="paramname">reduction_func</td><td>custom data reduction function. this can be any user-defined function which has the same parameters as <a class="el" href="pearl-area-import_8ipf.html#ade69cb0f82e0c9cf6082d5fcc29f742f">adh5_default_reduction</a>. some reduction functions are predefined in the <a class="el" href="namespace_pearl_scienta_preprocess.html">PearlScientaPreprocess</a> module.</td></tr>
<tr><td class="paramname">reduction_param</td><td>parameter string for the reduction function.</td></tr>
<tr><td class="paramname">progress</td><td>progress window. <ul>
<li>1 (default) show progress window </li>
@@ -1059,17 +1065,17 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
</td></tr>
<tr><td class="paramname">nthreads</td><td><ul>
<li>-1 (default) use as many threads as there are processor cores (in addition to main thread). </li>
<li>0 use main thread only (e.g. for debugging the reduction function). </li>
<li>0 use main thread only (for debugging and profiling). </li>
<li>&gt;= 1 use a fixed number of (additional) threads.</li>
</ul>
</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded waves, <code>ReducedData1</code> and <code>ReducedData2</code> if successful. empty string if an error occurred. error messages are printed to the history.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded dataset <code>ReducedData1</code>, <code>ReducedData2</code>, 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.</dd></dl>
<dl class="section version"><dt>Version</dt><dd>this function supports regions as of version 1.03. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01970">1970</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02022">2022</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>name of loaded wave if successful. empty string otherwise. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01259">1259</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01266">1266</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>name of loaded wave if successful. empty string otherwise. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01123">1123</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01130">1130</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>newline terminated string. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02286">2286</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02349">2349</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>name of loaded preview wave. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00243">243</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00250">250</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<td class="paramkey"></td>
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<td class="paramname"><em>progress</em> = <code>defaultValue</code>&#160;</td>
<td class="paramname"><em>progress</em> = <code>defaultValue</code>, </td>
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<p>load and reduce the ScientaImage dataset of the first scan of a PShell data file. </p>
<p>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.</p>
<p>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. <a class="el" href="pearl-area-import_8ipf.html#ade69cb0f82e0c9cf6082d5fcc29f742f">adh5_default_reduction</a> for further details.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">ANickName</td><td>destination folder name (top level under root).</td></tr>
<tr><td class="paramname">APathName</td><td>igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed.</td></tr>
<tr><td class="paramname">AFileName</td><td>if empty a dialog box shows up.</td></tr>
<tr><td class="paramname">reduction_func</td><td>custom reduction function (any user-defined function which has the same parameters as <a class="el" href="pearl-area-import_8ipf.html#a245034d7a94536a24c78a7bfe22725b7" title="function prototype for adh5_load_reduced_detector ">adh5_default_reduction()</a>)</td></tr>
<tr><td class="paramname">reduction_func</td><td>custom data reduction function. this can be any user-defined function which has the same parameters as <a class="el" href="pearl-area-import_8ipf.html#ade69cb0f82e0c9cf6082d5fcc29f742f">adh5_default_reduction</a>. some reduction functions are predefined in the <a class="el" href="namespace_pearl_scienta_preprocess.html">PearlScientaPreprocess</a> module.</td></tr>
<tr><td class="paramname">reduction_param</td><td>parameter string for the reduction function.</td></tr>
<tr><td class="paramname">progress</td><td>progress window. <ul>
<li>1 (default) show progress window </li>
<li>0 do not show progress window</li>
</ul>
</td></tr>
<tr><td class="paramname">nthreads</td><td><ul>
<li>-1 (default) use as many threads as there are processor cores (in addition to main thread). </li>
<li>0 use main thread only (for debugging and profiling). </li>
<li>&gt;= 1 use a fixed number of (additional) threads.</li>
</ul>
</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded waves, <code>ReducedData1</code> and <code>ReducedData2</code> if successful. empty string if an error occurred. error messages are printed to the history.</dd>
<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded dataset <code>ReducedData1</code>, <code>ReducedData2</code>, 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.</dd>
<dd>
global string s_filepath in new data folder contains the full file path on disk.</dd>
<dd>
global string s_scanpaths in new data folder contains a list of scan groups inside the file.</dd></dl>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000006">Todo:</a></b></dt><dd>load scan positions. </dd></dl>
global string s_scanpaths in new data folder contains a list of scan groups inside the file. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01846">1846</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l01893">1893</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded waves. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00546">546</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00553">553</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded data waves (excluding attributes). </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00353">353</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00360">360</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded waves. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00506">506</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00513">513</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>newline terminated string. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02333">2333</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02396">2396</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>semicolon-separated list of the loaded waves. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00614">614</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00621">621</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>name of loaded wave if successful. empty string otherwise. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00815">815</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00822">822</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>name of loaded wave if successful. empty string otherwise.</dd></dl>
<dl class="section warning"><dt>Warning</dt><dd>EXPERIMENTAL: this function is under development. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00928">928</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00935">935</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dd>
global string s_scanpaths in new data folder contains a list of scan groups inside the file. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00102">102</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00109">109</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<td class="memname">static threadsafe variable reduce_slab_image </td>
<td class="memname">static threadsafe wave reduce_slab_image </td>
<td>(</td>
<td class="paramtype">wave&#160;</td>
<td class="paramname"><em>slabdata</em>, </td>
@@ -1828,18 +1846,6 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<td class="paramtype">wave&#160;</td>
<td class="paramname"><em>image</em>, </td>
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<td class="paramname"><em>profile1</em>, </td>
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<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02258">2258</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02323">2323</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02219">2219</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02284">2284</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>selected dataset. </dd></dl>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00753">753</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00760">760</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<p>convert text wave to list. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02392">2392</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02455">2455</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<p>convert numeric wave to list. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02409">2409</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l02472">2472</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<p>Dimension label for the angle dispersive dimension of multi-dimensional datasets. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00060">60</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00067">67</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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<p>Dimension label for the data dimension. </p>
<p>This label may be used to store the parameters for the <code>setscale d</code> operation. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00067">67</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00074">74</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2069,7 +2075,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<p>multiply scienta detector intensity by this value to get actual counts. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00079">79</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00086">86</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2085,7 +2091,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<p>Dimension label for the energy dispersive dimension of multi-dimensional datasets. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00057">57</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00064">64</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2101,7 +2107,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<p>List of preferred datasets to load for preview. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00070">70</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00077">77</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2117,7 +2123,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<p>Dimension label for the scan dimension of multi-dimensional datasets. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00063">63</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00070">70</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2133,7 +2139,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<p>List of datasets that must be loaded to determine the axis scaling of a Scienta image. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00073">73</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00080">80</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2149,7 +2155,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
<p>List of datasets that should be transposed upon loading. </p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00076">76</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
<p>Definition at line <a class="el" href="pearl-pshell-import_8ipf_source.html#l00083">83</a> of file <a class="el" href="pearl-pshell-import_8ipf_source.html">pearl-pshell-import.ipf</a>.</p>
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@@ -2159,7 +2165,7 @@ global string s_scanpaths in new data folder contains a list of scan groups insi
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