Merge pull request #58 from oncoray/v2.1.1

Update documentation.
oncoray · Mar 12, 2024 · 2e0c635 · 2e0c635
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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: ff14afa94c6b07b2796c6998289270b6
+config: ab60819b912204cb527868dbfe8edebc
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,20 +1,22 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <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" />
+  <title>Overview: module code &mdash; mirp 2.1.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <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=20623aea"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+        <script src="../_static/jquery.js"></script>
+        <script src="../_static/underscore.js"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+        <script src="../_static/doctools.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 

diff --git a/docs/_modules/mirp/deepLearningPreprocessing.html b/docs/_modules/mirp/deepLearningPreprocessing.html
@@ -1,20 +1,22 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <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" />
+  <title>mirp.deepLearningPreprocessing &mdash; mirp 2.1.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css" />
+
+
   <!--[if lt IE 9]>
     <script src="../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <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=f5cff4aa"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
+        <script src="../../_static/jquery.js"></script>
+        <script src="../../_static/underscore.js"></script>
+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
+        <script src="../../_static/doctools.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -83,9 +85,7 @@ <h1>Source code for mirp.deepLearningPreprocessing</h1><div class="highlight"><p
 <span class="kn">from</span> <span class="nn">mirp.workflows.standardWorkflow</span> <span class="kn">import</span> <span class="n">StandardWorkflow</span>
 
 
-<div class="viewcode-block" id="deep_learning_preprocessing">
-<a class="viewcode-back" href="../../mirp.deepLearningPreprocessing.html#mirp.deepLearningPreprocessing.deep_learning_preprocessing">[docs]</a>
-<span class="k">def</span> <span class="nf">deep_learning_preprocessing</span><span class="p">(</span>
+<div class="viewcode-block" id="deep_learning_preprocessing"><a class="viewcode-back" href="../../mirp.deepLearningPreprocessing.html#mirp.deepLearningPreprocessing.deep_learning_preprocessing">[docs]</a><span class="k">def</span> <span class="nf">deep_learning_preprocessing</span><span class="p">(</span>
         <span class="n">output_slices</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
         <span class="n">crop_size</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">float</span><span class="p">]</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <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>
@@ -208,7 +208,6 @@ <h1>Source code for mirp.deepLearningPreprocessing</h1><div class="highlight"><p
     <span class="k">return</span> <span class="n">results</span></div>
 
 
-
 <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>
@@ -229,9 +228,7 @@ <h1>Source code for mirp.deepLearningPreprocessing</h1><div class="highlight"><p
     <span class="p">)</span>
 
 
-<div class="viewcode-block" id="deep_learning_preprocessing_generator">
-<a class="viewcode-back" href="../../mirp.deepLearningPreprocessing.html#mirp.deepLearningPreprocessing.deep_learning_preprocessing_generator">[docs]</a>
-<span class="k">def</span> <span class="nf">deep_learning_preprocessing_generator</span><span class="p">(</span>
+<div class="viewcode-block" id="deep_learning_preprocessing_generator"><a class="viewcode-back" href="../../mirp.deepLearningPreprocessing.html#mirp.deepLearningPreprocessing.deep_learning_preprocessing_generator">[docs]</a><span class="k">def</span> <span class="nf">deep_learning_preprocessing_generator</span><span class="p">(</span>
         <span class="n">output_slices</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
         <span class="n">crop_size</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">float</span><span class="p">]</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <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>
@@ -315,7 +312,6 @@ <h1>Source code for mirp.deepLearningPreprocessing</h1><div class="highlight"><p
         <span class="p">)</span></div>
 
 
-
 <span class="k">def</span> <span class="nf">_base_deep_learning_preprocessing</span><span class="p">(</span>
         <span class="n">image</span><span class="p">,</span>
         <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>

diff --git a/docs/_modules/mirp/extractFeaturesAndImages.html b/docs/_modules/mirp/extractFeaturesAndImages.html
@@ -1,20 +1,22 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <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" />
+  <title>mirp.extractFeaturesAndImages &mdash; mirp 2.1.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css" />
+
+
   <!--[if lt IE 9]>
     <script src="../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <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=f5cff4aa"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
+        <script src="../../_static/jquery.js"></script>
+        <script src="../../_static/underscore.js"></script>
+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
+        <script src="../../_static/doctools.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -84,9 +86,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
 <span class="kn">from</span> <span class="nn">mirp.workflows.standardWorkflow</span> <span class="kn">import</span> <span class="n">StandardWorkflow</span>
 
 
-<div class="viewcode-block" id="extract_features">
-<a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features">[docs]</a>
-<span class="k">def</span> <span class="nf">extract_features</span><span class="p">(</span>
+<div class="viewcode-block" id="extract_features"><a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features">[docs]</a><span class="k">def</span> <span class="nf">extract_features</span><span class="p">(</span>
         <span class="n">write_features</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <span class="n">export_features</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <span class="n">write_dir</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
@@ -132,10 +132,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
     <span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="extract_features_generator">
-<a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features_generator">[docs]</a>
-<span class="k">def</span> <span class="nf">extract_features_generator</span><span class="p">(</span>
+<div class="viewcode-block" id="extract_features_generator"><a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features_generator">[docs]</a><span class="k">def</span> <span class="nf">extract_features_generator</span><span class="p">(</span>
         <span class="n">write_features</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
         <span class="n">export_features</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
         <span class="o">**</span><span class="n">kwargs</span>
@@ -175,10 +172,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
     <span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="extract_images">
-<a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_images">[docs]</a>
-<span class="k">def</span> <span class="nf">extract_images</span><span class="p">(</span>
+<div class="viewcode-block" id="extract_images"><a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_images">[docs]</a><span class="k">def</span> <span class="nf">extract_images</span><span class="p">(</span>
         <span class="n">write_images</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
         <span class="n">export_images</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
         <span class="n">write_dir</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
@@ -224,10 +218,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
     <span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="extract_images_generator">
-<a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_images_generator">[docs]</a>
-<span class="k">def</span> <span class="nf">extract_images_generator</span><span class="p">(</span>
+<div class="viewcode-block" id="extract_images_generator"><a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_images_generator">[docs]</a><span class="k">def</span> <span class="nf">extract_images_generator</span><span class="p">(</span>
         <span class="n">write_images</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
         <span class="n">export_images</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
         <span class="o">**</span><span class="n">kwargs</span>
@@ -267,10 +258,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
     <span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="extract_features_and_images">
-<a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features_and_images">[docs]</a>
-<span class="k">def</span> <span class="nf">extract_features_and_images</span><span class="p">(</span>
+<div class="viewcode-block" id="extract_features_and_images"><a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features_and_images">[docs]</a><span class="k">def</span> <span class="nf">extract_features_and_images</span><span class="p">(</span>
         <span class="n">image_export_format</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;dict&quot;</span><span class="p">,</span>
         <span class="n">num_cpus</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <span class="o">**</span><span class="n">kwargs</span>
@@ -351,10 +339,7 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
     <span class="k">return</span> <span class="n">results</span></div>
 
 
-
-<div class="viewcode-block" id="extract_features_and_images_generator">
-<a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features_and_images_generator">[docs]</a>
-<span class="k">def</span> <span class="nf">extract_features_and_images_generator</span><span class="p">(</span>
+<div class="viewcode-block" id="extract_features_and_images_generator"><a class="viewcode-back" href="../../mirp.extractFeaturesAndImages.html#mirp.extractFeaturesAndImages.extract_features_and_images_generator">[docs]</a><span class="k">def</span> <span class="nf">extract_features_and_images_generator</span><span class="p">(</span>
         <span class="n">image_export_format</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;dict&quot;</span><span class="p">,</span>
         <span class="o">**</span><span class="n">kwargs</span>
 <span class="p">):</span>
@@ -410,7 +395,6 @@ <h1>Source code for mirp.extractFeaturesAndImages</h1><div class="highlight"><pr
         <span class="k">yield</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></div>
 
 
-
 <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>