oncoray · alexzwanenburg · Sep 18, 2024 · Jul 5, 2024 · Jul 5, 2024 · Jul 5, 2024
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,28 @@
+# Version 2.3.0
+
+## Major changes
+
+- The proper ancient feature computation code running in the background of MIRP has been completely refactored. We 
+  moved from a functional backend where all features were computed per feature family to a more flexible 
+  object-oriented approach. Although this change is not visible at the user-end, it offers several new possibilities:
+  - Single features can now be computed. In addition, for some features (e.g. percentile statistics), a flexible 
+    percentile value could be passed.
+  - Creation of feature maps.
+  - Output of features and their metadata to machine-readable formats, instead of just tabular data.
+
+  **Important**: Though the *name* of features in the tabular exports has not changed, their *ordering* may have. 
+  Avoid using column position when processing or analysing feature data.
+
+- Apparent diffusion coefficient (ADC) maps, diffusion contrast-enhanced (DCE) MRI and multi-frame DICOM objects in 
+  general are now supported.
+- Planar imaging, i.e. computed radiography, digital X-ray and digital mammography DICOM files are now supported.
+- Python version 3.12 is now supported thanks to recent updates by the maintainers of `ray` and `itk`.
+  This means that `mirp` now supports Python version 3.10 and later.
+
+## Fixes
+
+- Internal use of `numpy.cross` no longer produces deprecation warnings. 
+
 # Version 2.2.4
 
 ## Fixes

diff --git a/README.md b/README.md
@@ -39,18 +39,19 @@ MIRP currently supports the following Python versions and operating systems:
 |--------|-----------|-----------|-----------|
 | 3.10   | Supported | Supported | Supported |
 | 3.11   | Supported | Supported | Supported |
+| 3.12   | Supported | Supported | Supported |
 
 ## Supported imaging and mask modalities
 
 MIRP currently supports the following image modalities:
 
-| File format | File type | Supported modality |
-|-------------|-----------|--------------------|
-| DICOM       | image     | CT, MR, PT, RTDOSE |
-| DICOM       | mask      | RTSTRUCT, SEG      |
-| NIfTI       | any       | any                |
-| NRRD        | any       | any                |
-| numpy       | any       | any                |
+| File format | File type | Supported modality                              |
+|-------------|-----------|-------------------------------------------------|
+| DICOM       | image     | CT, MR (incl. ADC, DCE), PT, RTDOSE, CR, DX, MG |
+| DICOM       | mask      | RTSTRUCT, SEG                                   |
+| NIfTI       | any       | any                                             |
+| NRRD        | any       | any                                             |
+| numpy       | any       | any                                             |
 
 NIfTI, NRRD, and numpy files support any kind of (single-channel) image. MIRP cannot process RGB or 4D images.
 

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: 92a05a2b300f0adee19d846b9e8f30a1
+config: c1f694fbbe082d73842ccd5978b8b8a0
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,8 +3,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=92fd9be5" />
+  <title>Overview: module code &mdash; mirp 2.3.0 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" />
 
 
@@ -14,8 +14,8 @@
 
         <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=4e6cfea6"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/docs/_modules/mirp/data_import/import_image_and_mask.html b/docs/_modules/mirp/data_import/import_image_and_mask.html
@@ -3,8 +3,8 @@
 <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 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.data_import.import_image_and_mask &mdash; mirp 2.3.0 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" />
 
 
@@ -14,8 +14,8 @@
 
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         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=4e6cfea6"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/docs/_modules/mirp/deep_learning_preprocessing.html b/docs/_modules/mirp/deep_learning_preprocessing.html
@@ -3,8 +3,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.deep_learning_preprocessing &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.deep_learning_preprocessing &mdash; mirp 2.3.0 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" />
 
 
@@ -14,8 +14,8 @@
 
         <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=4e6cfea6"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/docs/_modules/mirp/extract_features_and_images.html b/docs/_modules/mirp/extract_features_and_images.html
@@ -3,8 +3,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extract_features_and_images &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.extract_features_and_images &mdash; mirp 2.3.0 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" />
 
 
@@ -14,8 +14,8 @@
 
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         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=4e6cfea6"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
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diff --git a/docs/_modules/mirp/extract_image_parameters.html b/docs/_modules/mirp/extract_image_parameters.html
@@ -3,8 +3,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extract_image_parameters &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.extract_image_parameters &mdash; mirp 2.3.0 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" />
 
 
@@ -14,8 +14,8 @@
 
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         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=4e6cfea6"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/docs/_modules/mirp/extract_mask_labels.html b/docs/_modules/mirp/extract_mask_labels.html
@@ -3,8 +3,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.extract_mask_labels &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.extract_mask_labels &mdash; mirp 2.3.0 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" />
 
 
@@ -14,8 +14,8 @@
 
         <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=4e6cfea6"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/docs/_modules/mirp/settings/feature_parameters.html b/docs/_modules/mirp/settings/feature_parameters.html
@@ -3,8 +3,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.feature_parameters &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.settings.feature_parameters &mdash; mirp 2.3.0 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" />
 
 
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-        <script src="../../../_static/documentation_options.js?v=4e6cfea6"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
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diff --git a/docs/_modules/mirp/settings/general_parameters.html b/docs/_modules/mirp/settings/general_parameters.html
@@ -3,8 +3,8 @@
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   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.general_parameters &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.settings.general_parameters &mdash; mirp 2.3.0 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" />
 
 
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-        <script src="../../../_static/documentation_options.js?v=4e6cfea6"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/documentation_options.js?v=c3c8ae58"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
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diff --git a/docs/_modules/mirp/settings/generic.html b/docs/_modules/mirp/settings/generic.html
@@ -3,8 +3,8 @@
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   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>mirp.settings.generic &mdash; mirp 2.2.4 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.settings.generic &mdash; mirp 2.3.0 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" />
 
 
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diff --git a/docs/_modules/mirp/settings/image_processing_parameters.html b/docs/_modules/mirp/settings/image_processing_parameters.html
@@ -3,8 +3,8 @@
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-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.settings.image_processing_parameters &mdash; mirp 2.3.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
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diff --git a/docs/_modules/mirp/settings/interpolation_parameters.html b/docs/_modules/mirp/settings/interpolation_parameters.html
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-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.settings.interpolation_parameters &mdash; mirp 2.3.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
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diff --git a/docs/_modules/mirp/settings/perturbation_parameters.html b/docs/_modules/mirp/settings/perturbation_parameters.html
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-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=92fd9be5" />
+  <title>mirp.settings.perturbation_parameters &mdash; mirp 2.3.0 documentation</title>
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