Merge pull request #90 from oncoray/dev2.2.3

Release version 2.2.3
oncoray · Jun 5, 2024 · 31d2b8a · 31d2b8a
2 parents b57db79 + 5866cf9
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,16 @@
+# Version 2.2.3
+
+## Minor changes
+
+- Tables with feature values now contain extra columns. These columns specify the file name (for non-DICOM input), 
+  the directory path of the image and masks and several DICOM tags for identifying the input.
+
+- MIRP now checks whether there are potential problems between the frames of reference of image and mask files.
+
+# Fixes
+
+- Fixed an error that occurs when attempting to create a deep copy `ImageITKFile` objects.
+
 # Version 2.2.2
 
 ## Minor changes

diff --git a/README.md b/README.md
@@ -44,8 +44,8 @@ pip install mirp
 
 MIRP can be used to compute quantitative features from regions of interest in images in an IBSI-compliant manner 
 using a standardized workflow This requires both images and masks. MIRP can process DICOM, NIfTI, NRRD and numpy 
-images. Masks are DICOM radiotherapy structure sets (RTSTRUCT), or volumetric data with integer labels (e.g. 1, 2, 
-etc.).
+images. Masks are DICOM radiotherapy structure sets (RTSTRUCT), DICOM segmentation (SEG) or volumetric data with 
+integer labels (e.g. 1, 2, etc.).
 
 Below is a minimal working example for extracting features from a single image file and its mask.
 

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: 4e548bc695306a4ce61e35d5a23229c6
+config: b7d3c05f6bec86800f0a1510ac564b73
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_images/tutorial_compute_radiomics_features_mr_8_0.png b/docs/_images/tutorial_compute_radiomics_features_mr_8_0.png
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 2.2.2 documentation</title>
+  <title>Overview: module code &mdash; mirp 2.2.3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
 
@@ -14,7 +14,7 @@
 
         <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=219dea72"></script>
+        <script src="../_static/documentation_options.js?v=85e56e6b"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>

diff --git a/docs/_modules/mirp/data_import/import_image_and_mask.html b/docs/_modules/mirp/data_import/import_image_and_mask.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.data_import.import_image_and_mask &mdash; mirp 2.2.1 documentation</title>
+  <title>mirp.data_import.import_image_and_mask &mdash; mirp 2.2.3 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
 
@@ -14,7 +14,7 @@
 
         <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=16656018"></script>
+        <script src="../../../_static/documentation_options.js?v=85e56e6b"></script>
         <script src="../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
@@ -51,7 +51,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorial_compute_radiomics_features_mr.html">Tutorial: Computing radiomics features</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorial_apply_image_filter.html">Tutorial: Applying image filters</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../tutorial_apply_image_filter.html#Applying-filters">Applying filters</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Deep Dive</span></p>
 <ul>
@@ -61,10 +60,13 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../mask_labels.html">Extract mask labels</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../deep_learning.html">Preprocess images for deep learning</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../quantitative_image_analysis.html">Process image and compute quantitative image features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../features_names.html">Feature name references</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Contributing</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../contributing.html">Contributing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../design.html">General design</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../contributing_tests.html">Tests</a></li>
 </ul>
 
         </div>