From 6c157259f99f96b79223ce592ec93f3fbc9089cb Mon Sep 17 00:00:00 2001
From: Alex Zwanenburg <alexander.zwanenburg@nct-dresden.de>
Date: Wed, 7 Feb 2024 09:53:56 +0100
Subject: [PATCH] Updated longform documentation.

---
 docs/.buildinfo                               |   2 +-
 docs/_modules/index.html                      |   6 +-
 .../mirp/deepLearningPreprocessing.html       |  10 +-
 .../mirp/extractFeaturesAndImages.html        |  10 +-
 .../_modules/mirp/extractImageParameters.html |   8 +-
 docs/_modules/mirp/extractMaskLabels.html     |   6 +-
 .../mirp/importData/importImageAndMask.html   |   8 +-
 .../settings/settingsFeatureExtraction.html   |  64 +++++++-
 .../mirp/settings/settingsGeneral.html        |  82 ++++++----
 .../mirp/settings/settingsGeneric.html        |  47 ++++--
 .../settings/settingsImageProcessing.html     |  37 ++++-
 .../settings/settingsImageTransformation.html | 148 +++++++++++++++---
 .../mirp/settings/settingsInterpolation.html  |  29 +++-
 .../settings/settingsMaskResegmentation.html  |  19 ++-
 .../mirp/settings/settingsPerturbation.html   |  58 ++++++-
 .../mirp/utilities/config_utilities.html      |   6 +-
 docs/_sources/mirp.importData.rst.txt         |  19 ++-
 docs/_static/documentation_options.js         |   2 +-
 docs/genindex.html                            |   6 +-
 docs/index.html                               |   6 +-
 docs/mirp.deepLearningPreprocessing.html      |   6 +-
 docs/mirp.extractFeaturesAndImages.html       |   6 +-
 docs/mirp.extractImageParameters.html         |   8 +-
 docs/mirp.extractMaskLabels.html              |   6 +-
 docs/mirp.importData.html                     |  33 ++--
 docs/mirp.settings.html                       |  20 ++-
 docs/py-modindex.html                         |   6 +-
 docs/search.html                              |   6 +-
 docs/searchindex.js                           |   2 +-
 29 files changed, 506 insertions(+), 160 deletions(-)
diff --git a/docs/.buildinfo b/docs/.buildinfo
index f255cee1..fc31f6e8 100644
--- 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
index f9b1e11a..ee704ab4 100644
--- 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
index 16d6250e..55654591 100644
--- 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
index ee8112aa..423f1f47 100644
--- 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
index b4b20097..69330e42 100644
--- 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
index 061eaa37..59794496 100644
--- 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
index bc549728..3af39d96 100644
--- 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
diff --git a/docs/_modules/mirp/settings/settingsFeatureExtraction.html b/docs/_modules/mirp/settings/settingsFeatureExtraction.html
index 63a9dacb..3bac3f26 100644
--- a/docs/_modules/mirp/settings/settingsFeatureExtraction.html
+++ b/docs/_modules/mirp/settings/settingsFeatureExtraction.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsFeatureExtraction &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsFeatureExtraction &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>
@@ -74,11 +74,14 @@
            <div itemprop="articleBody">
              
   <h1>Source code for mirp.settings.settingsFeatureExtraction</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span>
+<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 
 <div class="viewcode-block" id="FeatureExtractionSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsFeatureExtraction.FeatureExtractionSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">FeatureExtractionSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to feature computation. Many are conditional on the type of features that will be computed (</span>
@@ -94,6 +97,9 @@ <h1>Source code for mirp.settings.settingsFeatureExtraction</h1><div class="high
 <span class="sd">        Disables approximation of features, such as Geary&#39;s c-measure. Can be True or False (default). See</span>
 <span class="sd">        :class:`~mirp.settings.settingsGeneral.GeneralSettingsClass`.</span>
 
+<span class="sd">    ibsi_compliant: bool, optional, default: True</span>
+<span class="sd">        Limits computation of features to those features that have a reference value in the IBSI reference standard.</span>
+
 <span class="sd">    base_feature_families: str or list of str, optional, default: &quot;none&quot;</span>
 <span class="sd">        Determines the feature families for which features are computed. Radiomics features are implemented as</span>
 <span class="sd">        defined in the IBSI reference manual. The following feature families are currently present, and can be added</span>
@@ -668,6 +674,56 @@ <h1>Source code for mirp.settings.settingsFeatureExtraction</h1><div class="high
 
         <span class="k">return</span> <span class="n">x</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_feature_extraction_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;ibsi_compliant&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;base_feature_families&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;feature_families&quot;</span><span class="p">,</span> <span class="s2">&quot;families&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;families&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;all&quot;</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;base_discretisation_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;discretisation_method&quot;</span><span class="p">,</span> <span class="s2">&quot;discr_method&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;discretisation_method&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;fixed_bin_size&quot;</span><span class="p">,</span> <span class="s2">&quot;fixed_bin_number&quot;</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;base_discretisation_n_bins&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;discretisation_n_bins&quot;</span><span class="p">,</span> <span class="s2">&quot;discr_n_bins&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;discretisation_n_bins&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">10</span><span class="p">,</span> <span class="mi">33</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;base_discretisation_bin_width&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;discretisation_bin_width&quot;</span><span class="p">,</span> <span class="s2">&quot;discr_bin_width&quot;</span><span class="p">],</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;discretisation_bin_width&quot;</span><span class="p">,</span>
+            <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">10.0</span><span class="p">,</span> <span class="mf">34.0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;ivh_discretisation_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ivh_discretisation_method&quot;</span><span class="p">,</span> <span class="s2">&quot;ivh_discr_method&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;ivh_discretisation_method&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;fixed_bin_size&quot;</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;ivh_discretisation_n_bins&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ivh_discretisation_n_bins&quot;</span><span class="p">,</span> <span class="s2">&quot;ivh_discr_n_bins&quot;</span><span class="p">],</span>
+            <span class="n">test</span><span class="o">=</span><span class="mi">20</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;ivh_discretisation_bin_width&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ivh_discretisation_bin_width&quot;</span><span class="p">,</span> <span class="s2">&quot;ivh_discr_bin_width&quot;</span><span class="p">],</span>
+            <span class="n">test</span><span class="o">=</span><span class="mf">30.0</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;glcm_distance&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;glcm_distance&quot;</span><span class="p">,</span> <span class="s2">&quot;glcm_dist&quot;</span><span class="p">],</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">2.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;glcm_spatial_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;2d_average&quot;</span><span class="p">,</span> <span class="s2">&quot;2d_slice_merge&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;glrlm_spatial_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;2d_average&quot;</span><span class="p">,</span> <span class="s2">&quot;2d_slice_merge&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;glszm_spatial_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;2d&quot;</span><span class="p">,</span> <span class="s2">&quot;2.5d&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gldzm_spatial_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;2d&quot;</span><span class="p">,</span> <span class="s2">&quot;2.5d&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;ngtdm_spatial_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;2d&quot;</span><span class="p">,</span> <span class="s2">&quot;2.5d&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;ngldm_distance&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ngldm_distance&quot;</span><span class="p">,</span> <span class="s2">&quot;ngldm_dist&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;ngldm_dist&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">2.5</span><span class="p">,</span> <span class="mf">3.5</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;ngldm_difference_level&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;ngldm_difference_level&quot;</span><span class="p">,</span> <span class="s2">&quot;ngldm_diff_lvl&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;ngldm_diff_lvl&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.9</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;ngldm_spatial_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;2d&quot;</span><span class="p">,</span> <span class="s2">&quot;2.5d&quot;</span><span class="p">])</span>
+    <span class="p">]</span>
 </pre></div>
 
            </div>
@@ -677,7 +733,7 @@ <h1>Source code for mirp.settings.settingsFeatureExtraction</h1><div class="high
   <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/settings/settingsGeneral.html b/docs/_modules/mirp/settings/settingsGeneral.html
index ef02b009..a2c35ea3 100644
--- a/docs/_modules/mirp/settings/settingsGeneral.html
+++ b/docs/_modules/mirp/settings/settingsGeneral.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsGeneral &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsGeneral &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>
@@ -74,11 +74,15 @@
            <div itemprop="articleBody">
              
   <h1>Source code for mirp.settings.settingsGeneral</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
+<span></span><span class="kn">import</span> <span class="nn">warnings</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 
 <div class="viewcode-block" id="GeneralSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsGeneral.GeneralSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">GeneralSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Set of overall process parameters. The most important parameter here is ``by_slice`` which affects how images are</span>
@@ -86,9 +90,22 @@ <h1>Source code for mirp.settings.settingsGeneral</h1><div class="highlight"><pr
 
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
-<span class="sd">    by_slice: str or bool, optional, default: False</span>
-<span class="sd">        Defines whether calculations should be performed in 2D (True) or 3D (False), or alternatively only in the</span>
-<span class="sd">        largest slice (&quot;largest&quot;).</span>
+<span class="sd">    by_slice: bool, optional, default: False</span>
+<span class="sd">        Defines whether image processing and computations should be performed in 2D (True) or 3D (False).</span>
+
+<span class="sd">    mask_merge: bool, optional, default: False</span>
+<span class="sd">        Defines whether multiple mask objects should be combined into a single mask.</span>
+
+<span class="sd">    mask_split: bool, optional, default: False</span>
+<span class="sd">        Defines whether a mask that contains multiple regions should be split into separate mask objects.</span>
+
+<span class="sd">    mask_select_largest_region: bool, optional, default: False</span>
+<span class="sd">        Defines whether the largest region within a mask object should be selected. For example, in a mask that</span>
+<span class="sd">        contains multiple separate lesions. ``mask_select_largest_region = True`` will remove all but the largest</span>
+<span class="sd">        lesion.</span>
+
+<span class="sd">    mask_select_largest_slice: bool, optional, default: False</span>
+<span class="sd">        Defines whether the largest slice within a mask object should be selected.</span>
 
 <span class="sd">    config_str: str, optional</span>
 <span class="sd">        Sets a configuration string, which can be used to differentiate results obtained using other settings.</span>
@@ -103,35 +120,30 @@ <h1>Source code for mirp.settings.settingsGeneral</h1><div class="highlight"><pr
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
             <span class="bp">self</span><span class="p">,</span>
-            <span class="n">by_slice</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">by_slice</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">mask_merge</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">mask_split</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">mask_select_largest_region</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">mask_select_largest_slice</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">config_str</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
             <span class="n">no_approximation</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="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 
-        <span class="c1"># Parse and check slice information.</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">by_slice</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-            <span class="k">if</span> <span class="n">by_slice</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;true&quot;</span><span class="p">,</span> <span class="s2">&quot;t&quot;</span><span class="p">,</span> <span class="s2">&quot;1&quot;</span><span class="p">]:</span>
-                <span class="n">by_slice</span> <span class="o">=</span> <span class="kc">True</span>
-                <span class="n">select_slice</span> <span class="o">=</span> <span class="s2">&quot;all&quot;</span>
-            <span class="k">elif</span> <span class="n">by_slice</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;false&quot;</span><span class="p">,</span> <span class="s2">&quot;f&quot;</span><span class="p">,</span> <span class="s2">&quot;0&quot;</span><span class="p">]:</span>
-                <span class="n">by_slice</span> <span class="o">=</span> <span class="kc">False</span>
-                <span class="n">select_slice</span> <span class="o">=</span> <span class="s2">&quot;all&quot;</span>
-            <span class="k">elif</span> <span class="n">by_slice</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;largest&quot;</span><span class="p">]:</span>
-                <span class="n">by_slice</span> <span class="o">=</span> <span class="kc">True</span>
-                <span class="n">select_slice</span> <span class="o">=</span> <span class="s2">&quot;largest&quot;</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                    <span class="sa">f</span><span class="s2">&quot;The by_slice parameter should be true, false, t, f, 1, 0 or largest. Found: </span><span class="si">{</span><span class="n">by_slice</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-
-        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">by_slice</span><span class="p">,</span> <span class="nb">bool</span><span class="p">):</span>
-            <span class="n">select_slice</span> <span class="o">=</span> <span class="s2">&quot;all&quot;</span>
-
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;The by_slice parameter should be a string or boolean.&quot;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">by_slice</span><span class="p">,</span> <span class="nb">bool</span><span class="p">):</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;The by_slice parameter should be a boolean.&quot;</span><span class="p">)</span>
 
         <span class="c1"># Set by_slice and select_slice parameters.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">by_slice</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="n">by_slice</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">select_slice</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">select_slice</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">mask_merge</span> <span class="o">=</span> <span class="n">mask_merge</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">mask_split</span> <span class="o">=</span> <span class="n">mask_split</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">mask_select_largest_region</span> <span class="o">=</span> <span class="n">mask_select_largest_region</span>
+
+        <span class="k">if</span> <span class="n">mask_select_largest_slice</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">by_slice</span><span class="p">:</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;A 2D approach is used as the largest slice is selected.&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">by_slice</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">mask_select_largest_slice</span> <span class="o">=</span> <span class="n">mask_select_largest_slice</span>
 
         <span class="c1"># Set configuration string.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">config_str</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">config_str</span>
@@ -139,6 +151,18 @@ <h1>Source code for mirp.settings.settingsGeneral</h1><div class="highlight"><pr
         <span class="c1"># Set approximation of features.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">no_approximation</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="n">no_approximation</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_general_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;by_slice&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;mask_merge&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;mask_split&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;mask_select_largest_region&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;mask_select_largest_slice&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;config_str&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;test_config&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;no_approximation&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="p">]</span>
 </pre></div>
 
            </div>
@@ -148,7 +172,7 @@ <h1>Source code for mirp.settings.settingsGeneral</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/settings/settingsGeneric.html b/docs/_modules/mirp/settings/settingsGeneric.html
index baeb09ba..bf005a13 100644
--- a/docs/_modules/mirp/settings/settingsGeneric.html
+++ b/docs/_modules/mirp/settings/settingsGeneric.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsGeneric &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsGeneric &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>
@@ -74,7 +74,9 @@
            <div itemprop="articleBody">
              
   <h1>Source code for mirp.settings.settingsGeneric</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">mirp.settings.settingsFeatureExtraction</span> <span class="kn">import</span> <span class="n">FeatureExtractionSettingsClass</span>
+<span></span><span class="kn">import</span> <span class="nn">copy</span>
+
+<span class="kn">from</span> <span class="nn">mirp.settings.settingsFeatureExtraction</span> <span class="kn">import</span> <span class="n">FeatureExtractionSettingsClass</span>
 <span class="kn">from</span> <span class="nn">mirp.settings.settingsGeneral</span> <span class="kn">import</span> <span class="n">GeneralSettingsClass</span>
 <span class="kn">from</span> <span class="nn">mirp.settings.settingsImageProcessing</span> <span class="kn">import</span> <span class="n">ImagePostProcessingClass</span>
 <span class="kn">from</span> <span class="nn">mirp.settings.settingsImageTransformation</span> <span class="kn">import</span> <span class="n">ImageTransformationSettingsClass</span>
@@ -157,11 +159,17 @@ <h1>Source code for mirp.settings.settingsGeneric</h1><div class="highlight"><pr
             <span class="n">img_transform_settings</span><span class="p">:</span> <span class="kc">None</span> <span class="o">|</span> <span class="n">ImageTransformationSettingsClass</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
             <span class="o">**</span><span class="n">kwargs</span>
     <span class="p">):</span>
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
         <span class="c1"># General settings.</span>
         <span class="k">if</span> <span class="n">general_settings</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">general_settings</span> <span class="o">=</span> <span class="n">GeneralSettingsClass</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">general</span> <span class="o">=</span> <span class="n">general_settings</span>
 
+        <span class="c1"># Remove by_slice and no_approximation from the keyword arguments to avoid double passing.</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s2">&quot;by_slice&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s2">&quot;no_approximation&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
         <span class="c1"># Image interpolation settings.</span>
         <span class="k">if</span> <span class="n">img_interpolate_settings</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">img_interpolate_settings</span> <span class="o">=</span> <span class="n">ImageInterpolationSettingsClass</span><span class="p">(</span>
@@ -203,13 +211,32 @@ <h1>Source code for mirp.settings.settingsGeneric</h1><div class="highlight"><pr
         <span class="k">if</span> <span class="n">img_transform_settings</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">img_transform_settings</span> <span class="o">=</span> <span class="n">ImageTransformationSettingsClass</span><span class="p">(</span>
                 <span class="n">by_slice</span><span class="o">=</span><span class="n">general_settings</span><span class="o">.</span><span class="n">by_slice</span><span class="p">,</span>
-                <span class="n">response_map_feature_settings</span><span class="o">=</span><span class="n">FeatureExtractionSettingsClass</span><span class="p">(</span>
-                    <span class="n">by_slice</span><span class="o">=</span><span class="n">general_settings</span><span class="o">.</span><span class="n">by_slice</span><span class="p">,</span>
-                    <span class="n">no_approximation</span><span class="o">=</span><span class="n">general_settings</span><span class="o">.</span><span class="n">no_approximation</span><span class="p">,</span>
-                    <span class="o">**</span><span class="n">kwargs</span>
-                <span class="p">)</span>
+                <span class="o">**</span><span class="n">kwargs</span>
             <span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">img_transform</span> <span class="o">=</span> <span class="n">img_transform_settings</span></div>
+        <span class="bp">self</span><span class="o">.</span><span class="n">img_transform</span> <span class="o">=</span> <span class="n">img_transform_settings</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="vm">__class__</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">general</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">general</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">img_interpolate</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">img_interpolate</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">roi_interpolate</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">roi_interpolate</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">post_process</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">post_process</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">perturbation</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">perturbation</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">roi_resegment</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">roi_resegment</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">feature_extr</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">feature_extr</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">img_transform</span> <span class="o">!=</span> <span class="n">other</span><span class="o">.</span><span class="n">img_transform</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+
+        <span class="k">return</span> <span class="kc">True</span></div>
 
 </pre></div>
 
@@ -220,7 +247,7 @@ <h1>Source code for mirp.settings.settingsGeneric</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/settings/settingsImageProcessing.html b/docs/_modules/mirp/settings/settingsImageProcessing.html
index ee6b26e6..83510015 100644
--- a/docs/_modules/mirp/settings/settingsImageProcessing.html
+++ b/docs/_modules/mirp/settings/settingsImageProcessing.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsImageProcessing &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsImageProcessing &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>
@@ -74,13 +74,16 @@
            <div itemprop="articleBody">
              
   <h1>Source code for mirp.settings.settingsImageProcessing</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Tuple</span>
+<span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 
 <div class="viewcode-block" id="ImagePostProcessingClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsImageProcessing.ImagePostProcessingClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">ImagePostProcessingClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to image processing. Note that parameters concerning image perturbation / augmentation and</span>
@@ -390,6 +393,30 @@ <h1>Source code for mirp.settings.settingsImageProcessing</h1><div class="highli
         <span class="c1"># Set tissue_mask_range.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">tissue_mask_range</span><span class="p">:</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">float</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">tissue_mask_range</span><span class="p">)</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_post_processing_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;bias_field_correction&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;bias_field_correction_n_fitting_levels&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;n_fitting_levels&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;n_fitting_levels&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mi">2</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;bias_field_correction_n_max_iterations&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;n_max_iterations&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;n_max_iterations&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">1000</span><span class="p">,</span> <span class="mi">1000</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;bias_field_convergence_threshold&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;convergence_threshold&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;convergence_threshold&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">0.1</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;intensity_normalisation&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;relative_range&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;intensity_normalisation_range&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.10</span><span class="p">,</span> <span class="mf">0.90</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;intensity_normalisation_saturation&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.00</span><span class="p">,</span> <span class="mf">10.00</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;tissue_mask_type&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;range&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;tissue_mask_range&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.00</span><span class="p">,</span> <span class="mf">10.00</span><span class="p">])</span>
+    <span class="p">]</span>
 </pre></div>
 
            </div>
@@ -399,7 +426,7 @@ <h1>Source code for mirp.settings.settingsImageProcessing</h1><div class="highli
   <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/settings/settingsImageTransformation.html b/docs/_modules/mirp/settings/settingsImageTransformation.html
index 9e6db15d..363fff62 100644
--- a/docs/_modules/mirp/settings/settingsImageTransformation.html
+++ b/docs/_modules/mirp/settings/settingsImageTransformation.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsImageTransformation &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsImageTransformation &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>
@@ -75,15 +75,18 @@
              
   <h1>Source code for mirp.settings.settingsImageTransformation</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">copy</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
 <span class="kn">from</span> <span class="nn">mirp.settings.settingsFeatureExtraction</span> <span class="kn">import</span> <span class="n">FeatureExtractionSettingsClass</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 
 <div class="viewcode-block" id="ImageTransformationSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsImageTransformation.ImageTransformationSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">ImageTransformationSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to image transformation using filters. Many parameters are conditional on the selected image</span>
@@ -405,7 +408,7 @@ <h1>Source code for mirp.settings.settingsImageTransformation</h1><div class="hi
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
             <span class="bp">self</span><span class="p">,</span>
             <span class="n">by_slice</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
-            <span class="n">response_map_feature_settings</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">FeatureExtractionSettingsClass</span><span class="p">,</span> <span class="kc">None</span><span class="p">],</span>
+            <span class="n">response_map_feature_settings</span><span class="p">:</span> <span class="n">FeatureExtractionSettingsClass</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
             <span class="n">response_map_feature_families</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]]</span> <span class="o">=</span> <span class="s2">&quot;statistical&quot;</span><span class="p">,</span>
             <span class="n">response_map_discretisation_method</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]]</span> <span class="o">=</span> <span class="s2">&quot;fixed_bin_number&quot;</span><span class="p">,</span>
             <span class="n">response_map_discretisation_n_bins</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">int</span><span class="p">]]</span> <span class="o">=</span> <span class="mi">16</span><span class="p">,</span>
@@ -492,31 +495,31 @@ <h1>Source code for mirp.settings.settingsImageTransformation</h1><div class="hi
         <span class="p">]</span> <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="n">response_map_feature_families</span><span class="p">]</span>
 
         <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">valid_families</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;One or more families in the base_feature_families parameter were not recognised: &quot;</span>
-                             <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">response_map_feature_families</span><span class="p">[</span><span class="n">ii</span><span class="p">]</span><span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="n">ii</span><span class="p">,</span><span class="w"> </span><span class="n">is_valid</span><span class="w"> </span><span class="ow">in</span><span class="w"> </span><span class="nb">enumerate</span><span class="p">(</span><span class="n">valid_families</span><span class="p">)</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="ow">not</span><span class="w"> </span><span class="n">is_valid</span><span class="p">])</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s2">&quot;One or more families in the base_feature_families parameter were not recognised: &quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">response_map_feature_families</span><span class="p">[</span><span class="n">ii</span><span class="p">]</span><span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="n">ii</span><span class="p">,</span><span class="w"> </span><span class="n">is_valid</span><span class="w"> </span><span class="ow">in</span><span class="w"> </span><span class="nb">enumerate</span><span class="p">(</span><span class="n">valid_families</span><span class="p">)</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="ow">not</span><span class="w"> </span><span class="n">is_valid</span><span class="p">])</span><span class="si">}</span><span class="s2">&quot;</span>
+            <span class="p">)</span>
 
         <span class="c1"># Create a temporary feature settings object. If response_map_feature_settings is not present, this object is</span>
         <span class="c1"># used. Otherwise, response_map_feature_settings is copied, and then updated.</span>
-        <span class="n">temp_feature_settings</span> <span class="o">=</span> <span class="n">FeatureExtractionSettingsClass</span><span class="p">(</span>
-            <span class="n">by_slice</span><span class="o">=</span><span class="n">by_slice</span><span class="p">,</span>
-            <span class="n">no_approximation</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-            <span class="n">base_feature_families</span><span class="o">=</span><span class="n">response_map_feature_families</span><span class="p">,</span>
-            <span class="n">base_discretisation_method</span><span class="o">=</span><span class="n">response_map_discretisation_method</span><span class="p">,</span>
-            <span class="n">base_discretisation_bin_width</span><span class="o">=</span><span class="n">response_map_discretisation_bin_width</span><span class="p">,</span>
-            <span class="n">base_discretisation_n_bins</span><span class="o">=</span><span class="n">response_map_discretisation_n_bins</span><span class="p">)</span>
-
-        <span class="k">if</span> <span class="n">response_map_feature_settings</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="n">filter_feature_settings</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">response_map_feature_settings</span><span class="p">)</span>
-            <span class="n">filter_feature_settings</span><span class="o">.</span><span class="n">families</span> <span class="o">=</span> <span class="n">temp_feature_settings</span><span class="o">.</span><span class="n">families</span>
-            <span class="n">filter_feature_settings</span><span class="o">.</span><span class="n">discretisation_method</span> <span class="o">=</span> <span class="n">temp_feature_settings</span><span class="o">.</span><span class="n">discretisation_method</span>
-            <span class="n">filter_feature_settings</span><span class="o">.</span><span class="n">discretisation_n_bins</span> <span class="o">=</span> <span class="n">temp_feature_settings</span><span class="o">.</span><span class="n">discretisation_n_bins</span>
-            <span class="n">filter_feature_settings</span><span class="o">.</span><span class="n">discretisation_bin_width</span> <span class="o">=</span> <span class="n">temp_feature_settings</span><span class="o">.</span><span class="n">discretisation_bin_width</span>
-
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">filter_feature_settings</span> <span class="o">=</span> <span class="n">temp_feature_settings</span>
+        <span class="k">if</span> <span class="n">response_map_feature_settings</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">kwargs</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+                <span class="s2">&quot;base_feature_families&quot;</span><span class="p">:</span> <span class="n">response_map_feature_families</span><span class="p">,</span>
+                <span class="s2">&quot;base_discretisation_method&quot;</span><span class="p">:</span> <span class="n">response_map_discretisation_method</span><span class="p">,</span>
+                <span class="s2">&quot;base_discretisation_bin_width&quot;</span><span class="p">:</span> <span class="n">response_map_discretisation_bin_width</span><span class="p">,</span>
+                <span class="s2">&quot;base_discretisation_n_bins&quot;</span><span class="p">:</span> <span class="n">response_map_discretisation_n_bins</span>
+            <span class="p">})</span>
+
+            <span class="n">response_map_feature_settings</span> <span class="o">=</span> <span class="n">FeatureExtractionSettingsClass</span><span class="p">(</span>
+                <span class="n">by_slice</span><span class="o">=</span><span class="n">by_slice</span><span class="p">,</span>
+                <span class="n">no_approximation</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span>
 
         <span class="c1"># Set feature settings.</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">feature_settings</span><span class="p">:</span> <span class="n">FeatureExtractionSettingsClass</span> <span class="o">=</span> <span class="n">filter_feature_settings</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">feature_settings</span><span class="p">:</span> <span class="n">FeatureExtractionSettingsClass</span> <span class="o">=</span> <span class="n">response_map_feature_settings</span>
 
         <span class="c1"># Check boundary condition.</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">boundary_condition</span> <span class="o">=</span> <span class="n">boundary_condition</span>
@@ -1182,6 +1185,101 @@ <h1>Source code for mirp.settings.settingsImageTransformation</h1><div class="hi
 
         <span class="k">return</span> <span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="nb">any</span><span class="p">(</span><span class="n">filter_kernel</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;riesz_steered&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="n">filter_kernel</span> <span class="ow">in</span> <span class="n">x</span><span class="p">)</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_image_transformation_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;response_map_feature_families&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;feature_families&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;families&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;statistical&quot;</span><span class="p">,</span> <span class="s2">&quot;glcm&quot;</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;response_map_discretisation_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;discretisation_method&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;discretisation_method&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;fixed_bin_size&quot;</span><span class="p">,</span> <span class="s2">&quot;fixed_bin_number&quot;</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;response_map_discretisation_n_bins&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;discretisation_n_bins&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;discretisation_n_bins&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">10</span><span class="p">,</span> <span class="mi">33</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;response_map_discretisation_bin_width&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;discretisation_bin_width&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;discretisation_bin_width&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">10.0</span><span class="p">,</span> <span class="mf">34.0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;filter_kernels&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;filter_kernels&quot;</span><span class="p">,</span> <span class="s2">&quot;spatial_filters&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;spatial_filters&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span>
+                <span class="s2">&quot;separable_wavelet&quot;</span><span class="p">,</span> <span class="s2">&quot;nonseparable_wavelet&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_nonseparable_wavelet&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;riesz_steered_nonseparable_wavelet&quot;</span><span class="p">,</span> <span class="s2">&quot;gaussian&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_gaussian&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_steered_gaussian&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;laplacian_of_gaussian&quot;</span><span class="p">,</span> <span class="s2">&quot;log&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_laplacian_of_gaussian&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_steered_laplacian_of_gaussian&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;riesz_log&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_steered_log&quot;</span><span class="p">,</span> <span class="s2">&quot;laws&quot;</span><span class="p">,</span> <span class="s2">&quot;gabor&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_gabor&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_steered_gabor&quot;</span><span class="p">,</span> <span class="s2">&quot;mean&quot;</span>
+            <span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;nearest&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;separable_wavelet_families&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;coif4&quot;</span><span class="p">,</span> <span class="s2">&quot;coif5&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;separable_wavelet_set&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;separable_wavelet_filter_set&quot;</span><span class="p">,</span>
+            <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;hhh&quot;</span><span class="p">,</span> <span class="s2">&quot;lll&quot;</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;separable_wavelet_stationary&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">False</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;separable_wavelet_decomposition_level&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;separable_wavelet_rotation_invariance&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">False</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;separable_wavelet_pooling_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;mean&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;separable_wavelet_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;nonseparable_wavelet_families&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;simoncelli&quot;</span><span class="p">,</span> <span class="s2">&quot;shannon&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;nonseparable_wavelet_decomposition_level&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;nonseparable_wavelet_response&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;magnitude&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;nonseparable_wavelet_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gaussian_sigma&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gaussian_kernel_truncate&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;gaussian_sigma_truncate&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">10.0</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;gaussian_kernel_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;gaussian_boundary_condition&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;laplacian_of_gaussian_sigma&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;laplacian_of_gaussian_sigma&quot;</span><span class="p">,</span> <span class="s2">&quot;log_sigma&quot;</span><span class="p">],</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;log_sigma&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;laplacian_of_gaussian_kernel_truncate&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span>
+            <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;laplacian_of_gaussian_kernel_truncate&quot;</span><span class="p">,</span> <span class="s2">&quot;log_sigma_truncate&quot;</span><span class="p">],</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;log_sigma_truncate&quot;</span><span class="p">,</span>
+            <span class="n">test</span><span class="o">=</span><span class="mf">10.0</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;laplacian_of_gaussian_pooling_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;log_pooling_method&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;mean&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;laplacian_of_gaussian_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;log_boundary_condition&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;laws_kernel&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;l5e5s5&quot;</span><span class="p">,</span> <span class="s2">&quot;w5r5l3&quot;</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;laws_compute_energy&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;laws_calculate_energy&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;laws_calculate_energy&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;laws_delta&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">5</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;laws_rotation_invariance&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;laws_rotation_invariance&quot;</span><span class="p">,</span> <span class="s2">&quot;laws_rot_invar&quot;</span><span class="p">],</span> <span class="n">test</span><span class="o">=</span><span class="kc">False</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;laws_pooling_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;mean&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;laws_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_sigma&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_lambda&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_gamma&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.75</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_theta&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">5.0</span><span class="p">,</span> <span class="mf">15.0</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_theta_step&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">None</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_response&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;magnitude&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;gabor_rotation_invariance&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;gabor_rotation_invariance&quot;</span><span class="p">,</span> <span class="s2">&quot;gabor_rot_invar&quot;</span><span class="p">],</span> <span class="n">test</span><span class="o">=</span><span class="kc">False</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_pooling_method&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;mean&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;gabor_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;mean_filter_kernel_size&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;mean_filter_kernel_size&quot;</span><span class="p">,</span> <span class="s2">&quot;mean_filter_size&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;mean_filter_size&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">7</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;mean_filter_boundary_condition&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="s2">&quot;constant&quot;</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;riesz_filter_order&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;riesz_filter_order&quot;</span><span class="p">,</span> <span class="s2">&quot;riesz_order&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;riesz_order&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;riesz_filter_tensor_sigma&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">3.0</span><span class="p">,</span> <span class="mf">5.0</span><span class="p">])</span>
+    <span class="p">]</span>
 </pre></div>
 
            </div>
@@ -1191,7 +1289,7 @@ <h1>Source code for mirp.settings.settingsImageTransformation</h1><div class="hi
   <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/settings/settingsInterpolation.html b/docs/_modules/mirp/settings/settingsInterpolation.html
index 1a6f9102..83fabf2c 100644
--- a/docs/_modules/mirp/settings/settingsInterpolation.html
+++ b/docs/_modules/mirp/settings/settingsInterpolation.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsInterpolation &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsInterpolation &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>
@@ -74,11 +74,14 @@
            <div itemprop="articleBody">
              
   <h1>Source code for mirp.settings.settingsInterpolation</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Iterable</span>
+<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Iterable</span><span class="p">,</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 
 <div class="viewcode-block" id="ImageInterpolationSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsInterpolation.ImageInterpolationSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">ImageInterpolationSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to image interpolating / resampling. Images in a dataset are typically resampled to uniform</span>
@@ -222,8 +225,18 @@ <h1>Source code for mirp.settings.settingsInterpolation</h1><div class="highligh
 
 
 
+<span class="k">def</span> <span class="nf">get_image_interpolation_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;new_spacing&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;spline_order&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mi">2</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;anti_aliasing&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="kc">False</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;smoothing_beta&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">0.75</span><span class="p">)</span>
+    <span class="p">]</span>
+
+
 <div class="viewcode-block" id="MaskInterpolationSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsInterpolation.MaskInterpolationSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">MaskInterpolationSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to mask interpolation / resampling. MIRP registers the mask to an interpolated image based,</span>
@@ -269,6 +282,14 @@ <h1>Source code for mirp.settings.settingsInterpolation</h1><div class="highligh
 
         <span class="bp">self</span><span class="o">.</span><span class="n">incl_threshold</span> <span class="o">=</span> <span class="n">roi_interpolation_mask_inclusion_threshold</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_mask_interpolation_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;roi_spline_order&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;spline_order&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;spline_order&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mi">2</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;roi_interpolation_mask_inclusion_threshold&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;incl_threshold&quot;</span><span class="p">,</span>
+                    <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;incl_threshold&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">0.25</span><span class="p">)</span>
+    <span class="p">]</span>
 </pre></div>
 
            </div>
@@ -278,7 +299,7 @@ <h1>Source code for mirp.settings.settingsInterpolation</h1><div class="highligh
   <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/settings/settingsMaskResegmentation.html b/docs/_modules/mirp/settings/settingsMaskResegmentation.html
index 569b1600..e4b371e2 100644
--- a/docs/_modules/mirp/settings/settingsMaskResegmentation.html
+++ b/docs/_modules/mirp/settings/settingsMaskResegmentation.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsMaskResegmentation &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsMaskResegmentation &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>
@@ -75,12 +75,15 @@
              
   <h1>Source code for mirp.settings.settingsMaskResegmentation</h1><div class="highlight"><pre>
 <span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
 
 <div class="viewcode-block" id="ResegmentationSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsMaskResegmentation.ResegmentationSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">ResegmentationSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to mask resegmentation. Resegmentation is used to remove parts of the mask that correspond to</span>
@@ -156,6 +159,16 @@ <h1>Source code for mirp.settings.settingsMaskResegmentation</h1><div class="hig
 
         <span class="bp">self</span><span class="o">.</span><span class="n">sigma</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="n">resegmentation_sigma</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_mask_resegmentation_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;resegmentation_intensity_range&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;intensity_range&quot;</span><span class="p">,</span> <span class="s2">&quot;g_thresh&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;intensity_range&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mf">10.0</span><span class="p">,</span> <span class="mf">30.0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;resegmentation_sigma&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;sigma&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;sigma&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">1.0</span><span class="p">)</span>
+    <span class="p">]</span>
 </pre></div>
 
            </div>
@@ -165,7 +178,7 @@ <h1>Source code for mirp.settings.settingsMaskResegmentation</h1><div class="hig
   <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/settings/settingsPerturbation.html b/docs/_modules/mirp/settings/settingsPerturbation.html
index 7359af4e..6511dadb 100644
--- a/docs/_modules/mirp/settings/settingsPerturbation.html
+++ b/docs/_modules/mirp/settings/settingsPerturbation.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.settingsPerturbation &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.settings.settingsPerturbation &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>
@@ -74,11 +74,14 @@
            <div itemprop="articleBody">
              
   <h1>Source code for mirp.settings.settingsPerturbation</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span>
+<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
+<span class="kn">from</span> <span class="nn">mirp.settings.utilities</span> <span class="kn">import</span> <span class="n">setting_def</span>
 
 
 <div class="viewcode-block" id="ImagePerturbationSettingsClass">
 <a class="viewcode-back" href="../../../mirp.settings.html#mirp.settings.settingsPerturbation.ImagePerturbationSettingsClass">[docs]</a>
+<span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">ImagePerturbationSettingsClass</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parameters related to image and mask perturbation / augmentation. By default images and masks are not perturbed or</span>
@@ -288,6 +291,53 @@ <h1>Source code for mirp.settings.settingsPerturbation</h1><div class="highlight
         <span class="bp">self</span><span class="o">.</span><span class="n">translate_y</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">translate_z</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">get_perturbation_settings</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]:</span>
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;crop_around_roi&quot;</span><span class="p">,</span> <span class="s2">&quot;bool&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;crop_around_roi&quot;</span><span class="p">,</span> <span class="s2">&quot;resect&quot;</span><span class="p">],</span> <span class="n">test</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span><span class="s2">&quot;crop_distance&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">10.0</span><span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_noise_repetitions&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;noise_repetitions&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;noise_repetitions&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mi">10</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_noise_level&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;noise_level&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;noise_level&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">0.75</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_rotation_angles&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;rotation_angles&quot;</span><span class="p">,</span> <span class="s2">&quot;rot_angles&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;rotation_angles&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mf">33.0</span><span class="p">,</span> <span class="mf">33.0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_translation_fraction&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;translation_fraction&quot;</span><span class="p">,</span> <span class="s2">&quot;translate_frac&quot;</span><span class="p">],</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;translation_fraction&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.25</span><span class="p">,</span> <span class="mf">0.75</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_roi_adapt_type&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;roi_adapt_type&quot;</span><span class="p">,</span> <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;roi_adapt_type&quot;</span><span class="p">,</span>
+            <span class="n">test</span><span class="o">=</span><span class="s2">&quot;fraction&quot;</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_roi_adapt_size&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;roi_adapt_size&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;roi_adapt_size&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">0.8</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.2</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_roi_adapt_max_erosion&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;roi_adapt_max_erosion&quot;</span><span class="p">,</span> <span class="s2">&quot;eroded_vol_fract&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;max_volume_erosion&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">0.2</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;perturbation_randomise_roi_repetitions&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;roi_random_rep&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;roi_random_rep&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mi">100</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;roi_split_boundary_size&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">to_list</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="s2">&quot;roi_boundary_size&quot;</span><span class="p">,</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;roi_boundary_size&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="p">[</span><span class="mf">2.0</span><span class="p">,</span> <span class="mf">5.0</span><span class="p">]</span>
+        <span class="p">),</span>
+        <span class="n">setting_def</span><span class="p">(</span>
+            <span class="s2">&quot;roi_split_max_erosion&quot;</span><span class="p">,</span> <span class="s2">&quot;float&quot;</span><span class="p">,</span> <span class="n">xml_key</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;roi_split_max_erosion&quot;</span><span class="p">,</span> <span class="s2">&quot;bulk_min_vol_fract&quot;</span><span class="p">],</span>
+            <span class="n">class_key</span><span class="o">=</span><span class="s2">&quot;max_bulk_volume_erosion&quot;</span><span class="p">,</span> <span class="n">test</span><span class="o">=</span><span class="mf">0.2</span>
+        <span class="p">)</span>
+    <span class="p">]</span>
+
 </pre></div>
 
            </div>
@@ -297,7 +347,7 @@ <h1>Source code for mirp.settings.settingsPerturbation</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
diff --git a/docs/_modules/mirp/utilities/config_utilities.html b/docs/_modules/mirp/utilities/config_utilities.html
index 90923c2d..d0234195 100644
--- a/docs/_modules/mirp/utilities/config_utilities.html
+++ b/docs/_modules/mirp/utilities/config_utilities.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.utilities.config_utilities &mdash; mirp 2.0.0 documentation</title>
+  <title>mirp.utilities.config_utilities &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>
@@ -168,7 +168,7 @@ <h1>Source code for mirp.utilities.config_utilities</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
diff --git a/docs/_sources/mirp.importData.rst.txt b/docs/_sources/mirp.importData.rst.txt
index 6a026a40..b9ff8279 100644
--- a/docs/_sources/mirp.importData.rst.txt
+++ b/docs/_sources/mirp.importData.rst.txt
@@ -195,9 +195,9 @@ MIRP processes and analyses images and masks. There are multiple ways to provide
       .. warning::
         While it is possible to provide multiple masks for each image, in practice there is no safe way to do so. The
         only way to associate image and masks is by their image dimension, which may be the same for different images.
-        with its masks, e.g. on sample name or frame of reference. Hence, providing one mask per image is recommended.
-        MIRP will treat image and mask lists of equal length as being sorted by element, and associate the first mask
-        with the first image, the second mask with the second image, and so forth.
+        Hence, providing one mask per image is recommended. MIRP will treat image and mask lists of equal length as
+        being sorted by element, and associate the first mask with the first image, the second mask with the second
+        image, and so forth.
 
 * By specifying the configuration in a stand-alone data ``xml`` file. An empty copy of the ``xml`` file can be
   created using :func:`mirp.utilities.config_utilities.get_data_xml`. The tags of the``xml`` file are the same as the
@@ -241,10 +241,15 @@ On occasion, input should be more selective. This can be done by specifying addi
 * Select image files based on image modality using ``image_modality``:
     MIRP can filter image files based on the image modality. Aside from generic image modality, MIRP specifically
     checks for the following modalities:
+
     * Computed tomography (CT): ``"ct"``
+
     * Positron emission tomography (PET): ``"pet"`` or ``"pt"``
+
     * Magnetic resonance imaging (MRI): ``"mri"`` or ``"mr"``
 
+    * Radiotherapy dose (RTDOSE): ``"rtdose"``
+
     Images from other modalities are currently not fully supported, and a default ``"generic"`` image modality will
     be assigned.
 
@@ -260,14 +265,18 @@ On occasion, input should be more selective. This can be done by specifying addi
 
 * Select mask files based on mask modality using ``mask_modality``:
     MIRP can filter mask files based on the modality of the mask. Aside form generic masks, MIRP specifically checks for
-    radiotherapy structure (RTSTRUCT) files.
+    DICOM radiotherapy structure (RTSTRUCT) and DICOM segmentation (SEG) files.
 
     .. note::
         Only DICOM images contain metadata concerning mask modality. Masks from other file types are interpreted as
         ``"generic_mask"`` by default and cannot be filtered using ``mask_modality``.
 
     .. note::
-        Support for DICOM segmentation (SEG) files is being implemented.
+        Since version ``2.1.0`` MIRP does not require that images and masks have the exact same dimensions, origin,
+        spacing and orientation, with the exception of numpy images and masks. This is explicitly true for DICOM
+        radiotherapy structure (RTSTRUCT) sets. These are either mapped to the corresponding image if image slices
+        are referenced in the structure set, or use internal data to generate a voxel-based mask. However, images and
+        their masks should share the same frame of reference.
 
 * Select the specific regions of interest using ``roi_name``:
     A mask file may contain multiple masks. By default, MIRP will assess all masks in a file. The ``roi_name`` argument
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 7f51004a..42ebe091 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '2.0.0',
+    VERSION: '2.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/genindex.html b/docs/genindex.html
index c98c66b0..3cba6517 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; mirp 2.0.0 documentation</title>
+  <title>Index &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>
@@ -301,7 +301,7 @@ <h2 id="S">S</h2>
   <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/index.html b/docs/index.html
index 1c272700..e01a8d2e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Welcome to MIRP &mdash; mirp 2.0.0 documentation</title>
+  <title>Welcome to MIRP &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -121,7 +121,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
   <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/mirp.deepLearningPreprocessing.html b/docs/mirp.deepLearningPreprocessing.html
index 49e4136b..8396dff5 100644
--- a/docs/mirp.deepLearningPreprocessing.html
+++ b/docs/mirp.deepLearningPreprocessing.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Preprocess images for deep learning &mdash; mirp 2.0.0 documentation</title>
+  <title>Preprocess images for deep learning &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -228,7 +228,7 @@ <h2>Example<a class="headerlink" href="#example" title="Link to this heading">
   <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/mirp.extractFeaturesAndImages.html b/docs/mirp.extractFeaturesAndImages.html
index f74ae399..beeec8be 100644
--- a/docs/mirp.extractFeaturesAndImages.html
+++ b/docs/mirp.extractFeaturesAndImages.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Process image and compute quantitative image features &mdash; mirp 2.0.0 documentation</title>
+  <title>Process image and compute quantitative image features &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -459,7 +459,7 @@ <h2>API documentation<a class="headerlink" href="#api-documentation" title="Link
   <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/mirp.extractImageParameters.html b/docs/mirp.extractImageParameters.html
index e96c4ced..9f371476 100644
--- a/docs/mirp.extractImageParameters.html
+++ b/docs/mirp.extractImageParameters.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Extract image metadata &mdash; mirp 2.0.0 documentation</title>
+  <title>Extract image metadata &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -125,7 +125,7 @@ <h2>Example<a class="headerlink" href="#example" title="Link to this heading">
 setting sample names.</p></li>
 <li><p><strong>image_file_type</strong> (<em>{&quot;dicom&quot;</em><em>, </em><em>&quot;nifti&quot;</em><em>, </em><em>&quot;nrrd&quot;</em><em>, </em><em>&quot;numpy&quot;</em><em>, </em><em>&quot;itk&quot;}</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – The type of file that is expected. If None, the file type is not used for filtering files.
 “itk” comprises “nifti” and “nrrd” file types.</p></li>
-<li><p><strong>image_modality</strong> (<em>{&quot;ct&quot;</em><em>, </em><em>&quot;pet&quot;</em><em>, </em><em>&quot;pt&quot;</em><em>, </em><em>&quot;mri&quot;</em><em>, </em><em>&quot;mr&quot;</em><em>, </em><em>&quot;generic&quot;}</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – The type of modality that is expected. If None, modality is not used for filtering files. Note that only
+<li><p><strong>image_modality</strong> (<em>{&quot;ct&quot;</em><em>, </em><em>&quot;pet&quot;</em><em>, </em><em>&quot;pt&quot;</em><em>, </em><em>&quot;mri&quot;</em><em>, </em><em>&quot;mr&quot;</em><em>, </em><em>&quot;rtdose&quot;</em><em>, </em><em>&quot;generic&quot;}</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – The type of modality that is expected. If None, modality is not used for filtering files. Note that only
 DICOM files contain metadata concerning modality.</p></li>
 <li><p><strong>image_sub_folder</strong> (<em>str</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – Fixed directory substructure where image files are located. If None, the directory substructure is not used
 for filtering files.</p></li>
@@ -161,7 +161,7 @@ <h2>Example<a class="headerlink" href="#example" title="Link to this heading">
   <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/mirp.extractMaskLabels.html b/docs/mirp.extractMaskLabels.html
index f6e52b62..034ab711 100644
--- a/docs/mirp.extractMaskLabels.html
+++ b/docs/mirp.extractMaskLabels.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Extract mask labels &mdash; mirp 2.0.0 documentation</title>
+  <title>Extract mask labels &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -156,7 +156,7 @@ <h2>Example<a class="headerlink" href="#example" title="Link to this heading">
   <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/mirp.importData.html b/docs/mirp.importData.html
index a50f4c0c..633ef628 100644
--- a/docs/mirp.importData.html
+++ b/docs/mirp.importData.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Configure image and mask import &mdash; mirp 2.0.0 documentation</title>
+  <title>Configure image and mask import &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -280,9 +280,9 @@ <h2>Specifying input<a class="headerlink" href="#specifying-input" title="Link t
 <p class="admonition-title">Warning</p>
 <p>While it is possible to provide multiple masks for each image, in practice there is no safe way to do so. The
 only way to associate image and masks is by their image dimension, which may be the same for different images.
-with its masks, e.g. on sample name or frame of reference. Hence, providing one mask per image is recommended.
-MIRP will treat image and mask lists of equal length as being sorted by element, and associate the first mask
-with the first image, the second mask with the second image, and so forth.</p>
+Hence, providing one mask per image is recommended. MIRP will treat image and mask lists of equal length as
+being sorted by element, and associate the first mask with the first image, the second mask with the second
+image, and so forth.</p>
 </div>
 </li>
 </ul>
@@ -335,10 +335,13 @@ <h2>Selecting specific images and masks<a class="headerlink" href="#selecting-sp
 </li>
 <li><dl>
 <dt>Select image files based on image modality using <code class="docutils literal notranslate"><span class="pre">image_modality</span></code>:</dt><dd><p>MIRP can filter image files based on the image modality. Aside from generic image modality, MIRP specifically
-checks for the following modalities:
-* Computed tomography (CT): <code class="docutils literal notranslate"><span class="pre">&quot;ct&quot;</span></code>
-* Positron emission tomography (PET): <code class="docutils literal notranslate"><span class="pre">&quot;pet&quot;</span></code> or <code class="docutils literal notranslate"><span class="pre">&quot;pt&quot;</span></code>
-* Magnetic resonance imaging (MRI): <code class="docutils literal notranslate"><span class="pre">&quot;mri&quot;</span></code> or <code class="docutils literal notranslate"><span class="pre">&quot;mr&quot;</span></code></p>
+checks for the following modalities:</p>
+<ul class="simple">
+<li><p>Computed tomography (CT): <code class="docutils literal notranslate"><span class="pre">&quot;ct&quot;</span></code></p></li>
+<li><p>Positron emission tomography (PET): <code class="docutils literal notranslate"><span class="pre">&quot;pet&quot;</span></code> or <code class="docutils literal notranslate"><span class="pre">&quot;pt&quot;</span></code></p></li>
+<li><p>Magnetic resonance imaging (MRI): <code class="docutils literal notranslate"><span class="pre">&quot;mri&quot;</span></code> or <code class="docutils literal notranslate"><span class="pre">&quot;mr&quot;</span></code></p></li>
+<li><p>Radiotherapy dose (RTDOSE): <code class="docutils literal notranslate"><span class="pre">&quot;rtdose&quot;</span></code></p></li>
+</ul>
 <p>Images from other modalities are currently not fully supported, and a default <code class="docutils literal notranslate"><span class="pre">&quot;generic&quot;</span></code> image modality will
 be assigned.</p>
 <div class="admonition note">
@@ -358,7 +361,7 @@ <h2>Selecting specific images and masks<a class="headerlink" href="#selecting-sp
 </li>
 <li><dl>
 <dt>Select mask files based on mask modality using <code class="docutils literal notranslate"><span class="pre">mask_modality</span></code>:</dt><dd><p>MIRP can filter mask files based on the modality of the mask. Aside form generic masks, MIRP specifically checks for
-radiotherapy structure (RTSTRUCT) files.</p>
+DICOM radiotherapy structure (RTSTRUCT) and DICOM segmentation (SEG) files.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <p>Only DICOM images contain metadata concerning mask modality. Masks from other file types are interpreted as
@@ -366,7 +369,11 @@ <h2>Selecting specific images and masks<a class="headerlink" href="#selecting-sp
 </div>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Support for DICOM segmentation (SEG) files is being implemented.</p>
+<p>Since version <code class="docutils literal notranslate"><span class="pre">2.1.0</span></code> MIRP does not require that images and masks have the exact same dimensions, origin,
+spacing and orientation, with the exception of numpy images and masks. This is explicitly true for DICOM
+radiotherapy structure (RTSTRUCT) sets. These are either mapped to the corresponding image if image slices
+are referenced in the structure set, or use internal data to generate a voxel-based mask. However, images and
+their masks should share the same frame of reference.</p>
 </div>
 </dd>
 </dl>
@@ -416,7 +423,7 @@ <h2>API documentation<a class="headerlink" href="#api-documentation" title="Link
 setting sample names.</p></li>
 <li><p><strong>image_file_type</strong> (<em>{&quot;dicom&quot;</em><em>, </em><em>&quot;nifti&quot;</em><em>, </em><em>&quot;nrrd&quot;</em><em>, </em><em>&quot;numpy&quot;</em><em>, </em><em>&quot;itk&quot;}</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – The type of file that is expected. If None, the file type is not used for filtering files.
 “itk” comprises “nifti” and “nrrd” file types.</p></li>
-<li><p><strong>image_modality</strong> (<em>{&quot;ct&quot;</em><em>, </em><em>&quot;pet&quot;</em><em>, </em><em>&quot;pt&quot;</em><em>, </em><em>&quot;mri&quot;</em><em>, </em><em>&quot;mr&quot;</em><em>, </em><em>&quot;generic&quot;}</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – The type of modality that is expected. If None, modality is not used for filtering files. Note that only
+<li><p><strong>image_modality</strong> (<em>{&quot;ct&quot;</em><em>, </em><em>&quot;pet&quot;</em><em>, </em><em>&quot;pt&quot;</em><em>, </em><em>&quot;mri&quot;</em><em>, </em><em>&quot;mr&quot;</em><em>, </em><em>&quot;rtdose&quot;</em><em>, </em><em>&quot;generic&quot;}</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – The type of modality that is expected. If None, modality is not used for filtering files. Note that only
 DICOM files contain metadata concerning modality.</p></li>
 <li><p><strong>image_sub_folder</strong> (<em>str</em><em>, </em><em>optional</em><em>, </em><em>default: None</em>) – Fixed directory substructure where image files are located. If None, the directory substructure is not used
 for filtering files.</p></li>
@@ -488,7 +495,7 @@ <h2>API documentation<a class="headerlink" href="#api-documentation" title="Link
   <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/mirp.settings.html b/docs/mirp.settings.html
index 176489c0..8349ced1 100644
--- a/docs/mirp.settings.html
+++ b/docs/mirp.settings.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Configure the image processing and feature extraction workflow &mdash; mirp 2.0.0 documentation</title>
+  <title>Configure the image processing and feature extraction workflow &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]>
@@ -13,7 +13,7 @@
   
         <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>
@@ -132,15 +132,20 @@ <h1>Configure the image processing and feature extraction workflow<a class="head
 <span id="general-settings"></span><h2>General settings<a class="headerlink" href="#module-mirp.settings.settingsGeneral" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="mirp.settings.settingsGeneral.GeneralSettingsClass">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mirp.settings.settingsGeneral.</span></span><span class="sig-name descname"><span class="pre">GeneralSettingsClass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">by_slice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config_str</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_approximation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mirp/settings/settingsGeneral.html#GeneralSettingsClass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mirp.settings.settingsGeneral.GeneralSettingsClass" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mirp.settings.settingsGeneral.</span></span><span class="sig-name descname"><span class="pre">GeneralSettingsClass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">by_slice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_merge</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_split</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_select_largest_region</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_select_largest_slice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config_str</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_approximation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mirp/settings/settingsGeneral.html#GeneralSettingsClass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mirp.settings.settingsGeneral.GeneralSettingsClass" title="Link to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Set of overall process parameters. The most important parameter here is <code class="docutils literal notranslate"><span class="pre">by_slice</span></code> which affects how images are
 processed and features are computed.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>by_slice</strong> (<em>str</em><em> or </em><em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Defines whether calculations should be performed in 2D (True) or 3D (False), or alternatively only in the
-largest slice (“largest”).</p></li>
+<li><p><strong>by_slice</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Defines whether image processing and computations should be performed in 2D (True) or 3D (False).</p></li>
+<li><p><strong>mask_merge</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Defines whether multiple mask objects should be combined into a single mask.</p></li>
+<li><p><strong>mask_split</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Defines whether a mask that contains multiple regions should be split into separate mask objects.</p></li>
+<li><p><strong>mask_select_largest_region</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Defines whether the largest region within a mask object should be selected. For example, in a mask that
+contains multiple separate lesions. <code class="docutils literal notranslate"><span class="pre">mask_select_largest_region</span> <span class="pre">=</span> <span class="pre">True</span></code> will remove all but the largest
+lesion.</p></li>
+<li><p><strong>mask_select_largest_slice</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Defines whether the largest slice within a mask object should be selected.</p></li>
 <li><p><strong>config_str</strong> (<em>str</em><em>, </em><em>optional</em>) – Sets a configuration string, which can be used to differentiate results obtained using other settings.</p></li>
 <li><p><strong>no_approximation</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Disables approximation within MIRP. This currently only affects computation of features such as Geary’s
 c-measure. Can be True or False (default). False means that approximation is performed.</p></li>
@@ -371,6 +376,7 @@ <h1>Configure the image processing and feature extraction workflow<a class="head
 largest slice (“largest”). See <a class="reference internal" href="#mirp.settings.settingsGeneral.GeneralSettingsClass" title="mirp.settings.settingsGeneral.GeneralSettingsClass"><code class="xref py py-class docutils literal notranslate"><span class="pre">GeneralSettingsClass</span></code></a>.</p></li>
 <li><p><strong>no_approximation</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: False</em>) – Disables approximation of features, such as Geary’s c-measure. Can be True or False (default). See
 <a class="reference internal" href="#mirp.settings.settingsGeneral.GeneralSettingsClass" title="mirp.settings.settingsGeneral.GeneralSettingsClass"><code class="xref py py-class docutils literal notranslate"><span class="pre">GeneralSettingsClass</span></code></a>.</p></li>
+<li><p><strong>ibsi_compliant</strong> (<em>bool</em><em>, </em><em>optional</em><em>, </em><em>default: True</em>) – Limits computation of features to those features that have a reference value in the IBSI reference standard.</p></li>
 <li><p><strong>base_feature_families</strong> (<em>str</em><em> or </em><em>list</em><em> of </em><em>str</em><em>, </em><em>optional</em><em>, </em><em>default: &quot;none&quot;</em>) – <p>Determines the feature families for which features are computed. Radiomics features are implemented as
 defined in the IBSI reference manual. The following feature families are currently present, and can be added
 using the following tags:</p>
@@ -525,7 +531,7 @@ <h1>Configure the image processing and feature extraction workflow<a class="head
 <span id="image-transformation-settings"></span><h2>Image transformation settings<a class="headerlink" href="#module-mirp.settings.settingsImageTransformation" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="mirp.settings.settingsImageTransformation.ImageTransformationSettingsClass">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mirp.settings.settingsImageTransformation.</span></span><span class="sig-name descname"><span class="pre">ImageTransformationSettingsClass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">by_slice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_feature_settings</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#mirp.settings.settingsFeatureExtraction.FeatureExtractionSettingsClass" title="mirp.settings.settingsFeatureExtraction.FeatureExtractionSettingsClass"><span class="pre">FeatureExtractionSettingsClass</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_feature_families</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'statistical'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_discretisation_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'fixed_bin_number'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_discretisation_n_bins</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">16</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_discretisation_bin_width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_kernels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mirror'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_families</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_set</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_stationary</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_decomposition_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_rotation_invariance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'max'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_families</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_decomposition_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_response</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'real'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gaussian_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gaussian_kernel_truncate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">4.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gaussian_kernel_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_kernel_truncate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">4.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_kernel</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_delta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">7</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_compute_energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_rotation_invariance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'max'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_lambda</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_gamma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_theta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_theta_step</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_response</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'modulus'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_rotation_invariance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'max'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean_filter_kernel_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean_filter_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">riesz_filter_order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">riesz_filter_tensor_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mirp/settings/settingsImageTransformation.html#ImageTransformationSettingsClass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mirp.settings.settingsImageTransformation.ImageTransformationSettingsClass" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mirp.settings.settingsImageTransformation.</span></span><span class="sig-name descname"><span class="pre">ImageTransformationSettingsClass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">by_slice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_feature_settings</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#mirp.settings.settingsFeatureExtraction.FeatureExtractionSettingsClass" title="mirp.settings.settingsFeatureExtraction.FeatureExtractionSettingsClass"><span class="pre">FeatureExtractionSettingsClass</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_feature_families</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'statistical'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_discretisation_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'fixed_bin_number'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_discretisation_n_bins</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">16</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">response_map_discretisation_bin_width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_kernels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mirror'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_families</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_set</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_stationary</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_decomposition_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_rotation_invariance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'max'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separable_wavelet_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_families</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_decomposition_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_response</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'real'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonseparable_wavelet_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gaussian_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gaussian_kernel_truncate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">4.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gaussian_kernel_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_kernel_truncate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">4.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laplacian_of_gaussian_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_kernel</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_delta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">7</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_compute_energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_rotation_invariance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'max'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">laws_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_lambda</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_gamma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_theta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_theta_step</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_response</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'modulus'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_rotation_invariance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_pooling_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'max'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gabor_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean_filter_kernel_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mean_filter_boundary_condition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">riesz_filter_order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">riesz_filter_tensor_sigma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mirp/settings/settingsImageTransformation.html#ImageTransformationSettingsClass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mirp.settings.settingsImageTransformation.ImageTransformationSettingsClass" title="Link to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Parameters related to image transformation using filters. Many parameters are conditional on the selected image
 filter (<code class="docutils literal notranslate"><span class="pre">filter_kernels</span></code>). By default, only statistical features are computed from filtered images.</p>
@@ -859,7 +865,7 @@ <h2>Creating a settings xml file<a class="headerlink" href="#creating-a-settings
   <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/py-modindex.html b/docs/py-modindex.html
index b1e58c9a..3180f2ec 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Python Module Index &mdash; mirp 2.0.0 documentation</title>
+  <title>Python Module Index &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>
@@ -157,7 +157,7 @@ <h1>Python Module Index</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/search.html b/docs/search.html
index debc52fc..a0a71e94 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; mirp 2.0.0 documentation</title>
+  <title>Search &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" />
     
@@ -13,7 +13,7 @@
   
         <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>
@@ -95,7 +95,7 @@
   <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/searchindex.js b/docs/searchindex.js
index d75a0ea0..2a093394 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
