stable release

momentoscope · Mar 31, 2021 · 85b0894 · 85b0894
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diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/example/01_readdaq.doctree b/docs/doctrees/example/01_readdaq.doctree
diff --git a/docs/doctrees/example/02_parquet.doctree b/docs/doctrees/example/02_parquet.doctree
diff --git a/docs/doctrees/example/03_binning.doctree b/docs/doctrees/example/03_binning.doctree
diff --git a/docs/doctrees/example/04_nobinning.doctree b/docs/doctrees/example/04_nobinning.doctree
diff --git a/docs/doctrees/example/05_corrections.doctree b/docs/doctrees/example/05_corrections.doctree
diff --git a/docs/doctrees/example/06_fullexample.doctree b/docs/doctrees/example/06_fullexample.doctree
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/library/DldFlashDataframeCreator.doctree b/docs/doctrees/library/DldFlashDataframeCreator.doctree
diff --git a/docs/doctrees/library/DldProcessor.doctree b/docs/doctrees/library/DldProcessor.doctree
diff --git a/docs/doctrees/library/pah.doctree b/docs/doctrees/library/pah.doctree
diff --git a/docs/doctrees/library/utils/calibration.doctree b/docs/doctrees/library/utils/calibration.doctree
diff --git a/docs/doctrees/library/utils/diagnostics.doctree b/docs/doctrees/library/utils/diagnostics.doctree
diff --git a/docs/doctrees/library/utils/io.doctree b/docs/doctrees/library/utils/io.doctree
diff --git a/docs/doctrees/library/utils/masking.doctree b/docs/doctrees/library/utils/masking.doctree
diff --git a/docs/doctrees/library/utils/misc.doctree b/docs/doctrees/library/utils/misc.doctree
diff --git a/docs/doctrees/library/utils/vis.doctree b/docs/doctrees/library/utils/vis.doctree
diff --git a/docs/doctrees/misc/howtomaintain.doctree b/docs/doctrees/misc/howtomaintain.doctree
diff --git a/docs/doctrees/misc/listofterms.doctree b/docs/doctrees/misc/listofterms.doctree
diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: eba9baad041dd5c812d690ed0fb15975
+config: e689ffa809719ac3337c9db822b9225c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
@@ -1,28 +1,23 @@
 
 
 <!DOCTYPE html>
-<html class="writer-html5" lang="English" >
+<!--[if IE 8]><html class="no-js lt-ie9" lang="English" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="English" > <!--<![endif]-->
 <head>
   <meta charset="utf-8">
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview: module code &mdash; hextof-processor 1.0.3 documentation</title>
+  <title>Overview: module code &mdash; hextof-processor 1.0.4 documentation</title>
 
 
 
-  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
-
 
 
 
 
 
-  <!--[if lt IE 9]>
-    <script src="../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
+  <script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -35,6 +30,10 @@
     <script type="text/javascript" src="../_static/js/theme.js"></script>
 
 
+
+
+  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
 </head>
@@ -50,7 +49,7 @@
 
 
 
-            <a href="../index.html" class="icon icon-home" alt="Documentation Home"> hextof-processor
+            <a href="../index.html" class="icon icon-home"> hextof-processor
 
 
 
@@ -60,7 +59,7 @@
 
 
               <div class="version">
-                1.0.3
+                1.0.4
               </div>
 
 
@@ -77,7 +76,6 @@
 
         </div>
 
-
         <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
 
 
@@ -118,7 +116,6 @@
 
 
         </div>
-
       </div>
     </nav>
 
@@ -157,7 +154,7 @@
 
   <ul class="wy-breadcrumbs">
 
-      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
+      <li><a href="../index.html">Docs</a> &raquo;</li>
 
       <li>Overview: module code</li>
 
@@ -195,19 +192,11 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>
-
         &copy; Copyright 2018-2020, momentoscope team
 
     </p>
   </div>
-
-
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-    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
-    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
-    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
 
 </footer>
 
@@ -219,6 +208,7 @@ <h1>All modules for which code is available</h1>
   </div>
 
 
+
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);

diff --git a/docs/html/_modules/processor/DldFlashDataframeCreator.html b/docs/html/_modules/processor/DldFlashDataframeCreator.html
diff --git a/docs/html/_modules/processor/DldProcessor.html b/docs/html/_modules/processor/DldProcessor.html
diff --git a/docs/html/_modules/processor/pah.html b/docs/html/_modules/processor/pah.html
@@ -1,28 +1,23 @@
 
 
 <!DOCTYPE html>
-<html class="writer-html5" lang="English" >
+<!--[if IE 8]><html class="no-js lt-ie9" lang="English" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="English" > <!--<![endif]-->
 <head>
   <meta charset="utf-8">
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>processor.pah &mdash; hextof-processor 1.0.3 documentation</title>
+  <title>processor.pah &mdash; hextof-processor 1.0.4 documentation</title>
 
 
 
-  <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-
-
 
 
 
 
 
-  <!--[if lt IE 9]>
-    <script src="../../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
+  <script type="text/javascript" src="../../_static/js/modernizr.min.js"></script>
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
@@ -35,6 +30,10 @@
     <script type="text/javascript" src="../../_static/js/theme.js"></script>
 
 
+
+
+  <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
 </head>
@@ -50,7 +49,7 @@
 
 
 
-            <a href="../../index.html" class="icon icon-home" alt="Documentation Home"> hextof-processor
+            <a href="../../index.html" class="icon icon-home"> hextof-processor
 
 
 
@@ -60,7 +59,7 @@
 
 
               <div class="version">
-                1.0.3
+                1.0.4
               </div>
 
 
@@ -77,7 +76,6 @@
 
         </div>
 
-
         <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
 
 
@@ -118,7 +116,6 @@
 
 
         </div>
-
       </div>
     </nav>
 
@@ -157,7 +154,7 @@
 
   <ul class="wy-breadcrumbs">
 
-      <li><a href="../../index.html" class="icon icon-home"></a> &raquo;</li>
+      <li><a href="../../index.html">Docs</a> &raquo;</li>
 
           <li><a href="../index.html">Module code</a> &raquo;</li>
 
@@ -185,6 +182,8 @@ <h1>Source code for processor.pah</h1><div class="highlight"><pre>
 
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">h5py</span>
+
 
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">camp.pah.beamtimedaqaccess</span> <span class="kn">import</span> <span class="n">BeamtimeDaqAccess</span> <span class="k">as</span> <span class="n">_BeamtimeDaqAccess</span><span class="p">,</span> <span class="n">H5FileDataAccess</span> <span class="k">as</span> <span class="n">_H5FileDataAccess</span><span class="p">,</span> \
@@ -260,7 +259,32 @@ <h1>Source code for processor.pah</h1><div class="highlight"><pre>
                <span class="ow">or</span> <span class="n">channelName</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;/Photon Diagnostic/&#39;</span><span class="p">)</span> \
                <span class="ow">or</span> <span class="n">channelName</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;/Electron Diagnostic/&#39;</span><span class="p">)</span> \
                <span class="ow">or</span> <span class="n">channelName</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;/Beamlines/&#39;</span><span class="p">)</span> \
-               <span class="ow">or</span> <span class="n">channelName</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;/Timing/&#39;</span><span class="p">)</span>  <span class="c1"># &lt;--for datasets before 08-2018</span></div></div>
+               <span class="ow">or</span> <span class="n">channelName</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;/Timing/&#39;</span><span class="p">)</span>  <span class="c1"># &lt;--for datasets before 08-2018</span></div>
+
+    <span class="k">def</span> <span class="nf">filledInDesiredDataSets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sortedDesiredDataSets</span><span class="p">):</span>
+        <span class="k">assert</span> <span class="n">sortedDesiredDataSets</span><span class="p">,</span> <span class="s2">&quot;Precond.: desiredDataSets not empty&quot;</span>
+
+        <span class="c1"># finding largest datumsShape</span>
+        <span class="n">largestShape</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="k">for</span> <span class="n">currentDataset</span> <span class="ow">in</span> <span class="n">sortedDesiredDataSets</span><span class="p">:</span>
+            <span class="k">with</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">currentDataset</span><span class="o">.</span><span class="n">fileMeta</span><span class="o">.</span><span class="n">fileName</span><span class="p">(),</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">h5file</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">h5file</span><span class="p">[</span><span class="n">currentDataset</span><span class="o">.</span><span class="n">channelName</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&gt;</span> <span class="n">largestShape</span><span class="p">:</span>
+                    <span class="n">largestDataset</span> <span class="o">=</span> <span class="n">currentDataset</span>
+                    <span class="n">largestShape</span> <span class="o">=</span> <span class="n">h5file</span><span class="p">[</span><span class="n">currentDataset</span><span class="o">.</span><span class="n">channelName</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">largestDataset</span><span class="o">.</span><span class="n">desiredDatasetInitializedFromFile</span><span class="p">()</span>
+
+        <span class="c1"># all the result parts need to be the same shape. Therefore, they need to be the largest possible</span>
+        <span class="n">result</span><span class="o">=</span> <span class="p">[</span><span class="n">sortedDesiredDataSets</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">desiredDatasetInitializedFromSample</span><span class="p">(</span><span class="n">largestDataset</span><span class="p">)]</span>
+        <span class="n">preceedingDataset</span><span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">currentDataset</span> <span class="ow">in</span> <span class="n">sortedDesiredDataSets</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+            <span class="k">if</span> <span class="n">currentDataset</span><span class="o">.</span><span class="n">pulseIdInterval</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">preceedingDataset</span><span class="o">.</span><span class="n">pulseIdInterval</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">nanDataSet</span><span class="o">=</span> <span class="n">_H5FileDataAccess</span><span class="o">.</span><span class="n">NaNDesiredDataSet</span><span class="p">((</span><span class="n">preceedingDataset</span><span class="o">.</span><span class="n">pulseIdInterval</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">currentDataset</span><span class="o">.</span><span class="n">pulseIdInterval</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">preceedingDataset</span><span class="p">)</span>
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">nanDataSet</span><span class="p">)</span>
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">currentDataset</span><span class="o">.</span><span class="n">desiredDatasetInitializedFromSample</span><span class="p">(</span><span class="n">preceedingDataset</span><span class="p">))</span>
+            <span class="n">preceedingDataset</span><span class="o">=</span> <span class="n">currentDataset</span>
+        <span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">hasNoGapsBetween</span><span class="p">(</span><span class="n">result</span><span class="p">),</span> <span class="s2">&quot;Postcond.: No gaps between file chunks.&quot;</span>
+        <span class="k">return</span> <span class="n">result</span></div>
 
 
 <div class="viewcode-block" id="H5FileManager"><a class="viewcode-back" href="../../library/pah.html#processor.pah.H5FileManager">[docs]</a><span class="k">class</span> <span class="nc">H5FileManager</span><span class="p">(</span><span class="n">_H5FileManager</span><span class="p">):</span>
@@ -281,19 +305,11 @@ <h1>Source code for processor.pah</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-
         &copy; Copyright 2018-2020, momentoscope team
 
     </p>
   </div>
-
-
-
-    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
-
-    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
-
-    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
 
 </footer>
 
@@ -305,6 +321,7 @@ <h1>Source code for processor.pah</h1><div class="highlight"><pre>
   </div>
 
 
+
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);