Updated longform documentation.

oncoray · Feb 7, 2024 · 6c15725 · 6c15725
1 parent 362dd39
commit 6c15725
Show file tree

Hide file tree

Showing 29 changed files with 506 additions and 160 deletions.
diff --git a/docs/.buildinfo b/docs/.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: 9c9bf8ce1e6064b92ac7bf61594b8542
+config: ff14afa94c6b07b2796c6998289270b6
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; mirp 2.0.0 documentation</title>
+  <title>Overview: module code &mdash; mirp 2.1.0 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=51b770b3"></script>
+        <script src="../_static/documentation_options.js?v=20623aea"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -96,7 +96,7 @@ <h1>All modules for which code is available</h1>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, Alex Zwanenburg.</p>
+    <p>&#169; Copyright 2024, Alex Zwanenburg.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/mirp/deepLearningPreprocessing.html b/docs/_modules/mirp/deepLearningPreprocessing.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.deepLearningPreprocessing &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.deepLearningPreprocessing &mdash; mirp 2.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=51b770b3"></script>
+        <script src="../../_static/documentation_options.js?v=f5cff4aa"></script>
         <script src="../../_static/doctools.js?v=888ff710"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
@@ -217,6 +217,10 @@ <h1>Source code for mirp.deepLearningPreprocessing</h1><div class="highlight"><p
         <span class="n">image_export_format</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;numpy&quot;</span><span class="p">,</span>
         <span class="n">write_file_format</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;numpy&quot;</span>
 <span class="p">):</span>
+    <span class="c1"># Limit internal threading by third-party libraries.</span>
+    <span class="kn">from</span> <span class="nn">mirp.utilities.parallel</span> <span class="kn">import</span> <span class="n">limit_inner_threads</span>
+    <span class="n">limit_inner_threads</span><span class="p">()</span>
+
     <span class="k">return</span> <span class="n">workflow</span><span class="o">.</span><span class="n">deep_learning_conversion</span><span class="p">(</span>
         <span class="n">output_slices</span><span class="o">=</span><span class="n">output_slices</span><span class="p">,</span>
         <span class="n">crop_size</span><span class="o">=</span><span class="n">crop_size</span><span class="p">,</span>
@@ -482,7 +486,7 @@ <h1>Source code for mirp.deepLearningPreprocessing</h1><div class="highlight"><p
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, Alex Zwanenburg.</p>
+    <p>&#169; Copyright 2024, Alex Zwanenburg.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/mirp/extractFeaturesAndImages.html b/docs/_modules/mirp/extractFeaturesAndImages.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extractFeaturesAndImages &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.extractFeaturesAndImages &mdash; mirp 2.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=51b770b3"></script>
+        <script src="../../_static/documentation_options.js?v=f5cff4aa"></script>
         <script src="../../_static/doctools.js?v=888ff710"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
@@ -413,6 +413,10 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
 
 <span class="nd">@ray</span><span class="o">.</span><span class="n">remote</span>
 <span class="k">def</span> <span class="nf">_ray_extractor</span><span class="p">(</span><span class="n">workflow</span><span class="p">:</span> <span class="n">StandardWorkflow</span><span class="p">,</span> <span class="n">image_export_format</span><span class="o">=</span><span class="s2">&quot;dict&quot;</span><span class="p">):</span>
+    <span class="c1"># Limit internal threading by third-party libraries.</span>
+    <span class="kn">from</span> <span class="nn">mirp.utilities.parallel</span> <span class="kn">import</span> <span class="n">limit_inner_threads</span>
+    <span class="n">limit_inner_threads</span><span class="p">()</span>
+
     <span class="k">return</span> <span class="n">workflow</span><span class="o">.</span><span class="n">standard_extraction</span><span class="p">(</span><span class="n">image_export_format</span><span class="o">=</span><span class="n">image_export_format</span><span class="p">)</span>
 
 
@@ -603,7 +607,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, Alex Zwanenburg.</p>
+    <p>&#169; Copyright 2024, Alex Zwanenburg.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/mirp/extractImageParameters.html b/docs/_modules/mirp/extractImageParameters.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extractImageParameters &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.extractImageParameters &mdash; mirp 2.1.0 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=51b770b3"></script>
+        <script src="../../_static/documentation_options.js?v=20623aea"></script>
         <script src="../../_static/doctools.js?v=888ff710"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
@@ -119,7 +119,7 @@ <h1>Source code for mirp.extractImageParameters</h1><div class="highlight"><pre>
 <span class="sd">        The type of file that is expected. If None, the file type is not used for filtering files.</span>
 <span class="sd">        &quot;itk&quot; comprises &quot;nifti&quot; and &quot;nrrd&quot; file types.</span>
 
-<span class="sd">    image_modality: {&quot;ct&quot;, &quot;pet&quot;, &quot;pt&quot;, &quot;mri&quot;, &quot;mr&quot;, &quot;generic&quot;}, optional, default: None</span>
+<span class="sd">    image_modality: {&quot;ct&quot;, &quot;pet&quot;, &quot;pt&quot;, &quot;mri&quot;, &quot;mr&quot;, &quot;rtdose&quot;, &quot;generic&quot;}, optional, default: None</span>
 <span class="sd">        The type of modality that is expected. If None, modality is not used for filtering files. Note that only</span>
 <span class="sd">        DICOM files contain metadata concerning modality.</span>
 
@@ -195,7 +195,7 @@ <h1>Source code for mirp.extractImageParameters</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, Alex Zwanenburg.</p>
+    <p>&#169; Copyright 2024, Alex Zwanenburg.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/mirp/extractMaskLabels.html b/docs/_modules/mirp/extractMaskLabels.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extractMaskLabels &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.extractMaskLabels &mdash; mirp 2.0.1 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=51b770b3"></script>
+        <script src="../../_static/documentation_options.js?v=f5cff4aa"></script>
         <script src="../../_static/doctools.js?v=888ff710"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
@@ -197,7 +197,7 @@ <h1>Source code for mirp.extractMaskLabels</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, Alex Zwanenburg.</p>
+    <p>&#169; Copyright 2024, Alex Zwanenburg.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/mirp/importData/importImageAndMask.html b/docs/_modules/mirp/importData/importImageAndMask.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.importData.importImageAndMask &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.importData.importImageAndMask &mdash; mirp 2.1.0 documentation</title>
       <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -12,7 +12,7 @@
 
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=51b770b3"></script>
+        <script src="../../../_static/documentation_options.js?v=20623aea"></script>
         <script src="../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
@@ -132,7 +132,7 @@ <h1>Source code for mirp.importData.importImageAndMask</h1><div class="highlight
 <span class="sd">        The type of file that is expected. If None, the file type is not used for filtering files.</span>
 <span class="sd">        &quot;itk&quot; comprises &quot;nifti&quot; and &quot;nrrd&quot; file types.</span>
 
-<span class="sd">    image_modality: {&quot;ct&quot;, &quot;pet&quot;, &quot;pt&quot;, &quot;mri&quot;, &quot;mr&quot;, &quot;generic&quot;}, optional, default: None</span>
+<span class="sd">    image_modality: {&quot;ct&quot;, &quot;pet&quot;, &quot;pt&quot;, &quot;mri&quot;, &quot;mr&quot;, &quot;rtdose&quot;, &quot;generic&quot;}, optional, default: None</span>
 <span class="sd">        The type of modality that is expected. If None, modality is not used for filtering files. Note that only</span>
 <span class="sd">        DICOM files contain metadata concerning modality.</span>
 
@@ -389,7 +389,7 @@ <h1>Source code for mirp.importData.importImageAndMask</h1><div class="highlight
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2023, Alex Zwanenburg.</p>
+    <p>&#169; Copyright 2024, Alex Zwanenburg.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a