Merge branch 'dev2.1.0'

oncoray · Feb 7, 2024 · 9416b9e · 9416b9e
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diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,5 @@ test/data/temp
 /mirp.egg-info/
 /dist/
 docs_source/build/*
+test/data/configuration_files/settings.xml
+/test/data/temp_data/
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,38 @@
+# Version 2.1.0
+
+## Major changes
+
+- Added support for SEG DICOM files for segmentation.
+
+- Added support for processing RTDOSE files.
+
+- It is now possible to combine and split masks, and to select the largest mask or mask slice, as part of the image
+  processing workflow. Masks can be combines by setting `mask_merge = True`, which merges all available masks for an
+  image into a single mask. This can be useful when, e.g., multiple regions of interest should be assessed as a single
+  (possibly internally disconnected) mask. Masks are split using `mask_split = True`, which separates every disconnected
+  region into its own mask that is assessed separately. This is used for splitting multiple lesions inside a single mask
+  into multiple separate masks. The largest region of interest in each mask is selected by 
+  `mask_select_largest_region = True`. This can be used when, e.g., only the largest lesion of multiple lesions should be
+  assessed. Sometimes, only the largest slice (i.e. the slice containing most of the voxels in a mask) should be
+  assessed. This is done using `mask_select_largest_slice = True`. This also forces `by_slice = True`.
+
+  These mask operations are implemented in the following order: combination -> splitting -> largest region -> 
+  largest slice.
+
+- Masks from an RT-structure file that shares a frame of reference with an image but does not have a one-to-one 
+  mapping to its voxel space can now be processed. This facilitates processing of masks from RT structure sets that 
+  are, e.g., defined on CT images but applied to co-registered PET imaging, or from one MR sequence to another. 
+
+## Fixes
+
+- Providing a mask consisting of boolean values in a numpy array no longer incorrectly throws an error.
+- Configuration parameters from `xml` files are now processed in the same manner as parameters defined as function 
+  arguments. The same default values are now used, independent of the parameter source. This fixes a known issue where
+  outlier-based resegmentation would occur by default using `xml` files, whereas the intended default is that no
+  resegmentation takes place.
+- Masks can now be exported to the file system without throwing an error.
+- DICOM files from frontal or sagittal view data are now correctly processed.
+
 # Version 2.0.1
 
 ## Minor changes
@@ -51,7 +86,7 @@
 ## Minor changes
 - MIRP now uses the `ray` package for parallel processing.
 
-# Version 1.3.0 (dev - unreleased)
+# Version 1.3.0
 
 ## Minor changes
 - `SimpleITK` has been removed as a dependency. Handling of non-DICOM imaging is now done through `itk` itself.

diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 8e96e8f4f42399fb5af887be43bc900a
+config: ff14afa94c6b07b2796c6998289270b6
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; mirp 2.0.1 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=f5cff4aa"></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>

diff --git a/docs/_modules/mirp/extractImageParameters.html b/docs/_modules/mirp/extractImageParameters.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extractImageParameters &mdash; mirp 2.0.1 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=f5cff4aa"></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>
 

diff --git a/docs/_modules/mirp/importData/importImageAndMask.html b/docs/_modules/mirp/importData/importImageAndMask.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.importData.importImageAndMask &mdash; mirp 2.0.1 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=f5cff4aa"></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>