Merge pull request #65 from oncoray/v2.2.0

Release version 2.2.0

CONTRIBUTING.md

@@ -2,10 +2,15 @@
 
 If you have ideas or code to contribute, please first open an [issue](https://github.com/oncoray/mirp/issues). We will then discuss your ideas and create an implementation roadmap.
 
-Please keep the following in mind when contributiing:
+Please keep the following in mind when contributing:
 
-- The main branch of `mirp` is protected. You can therefore make a pull request for your contribution to a development branch of the intended future version.
-- If you introduce new functionality, this functionality should be tested as part of the tests in `test`.
-- Code is styled according to [PEP8](https://peps.python.org/pep-0008/).
+- The main branch of `mirp` is protected. You can therefore make a pull request for your contribution to a 
+  development branch of the intended future version.
+- If you introduce new functionality, this functionality should be tested as part of the tests in the `test`directory. 
+  After implementation, please ensure that all tests complete without errors by running `pytest` from your IDE or 
+  console using `python -m pytest test` from the mirp main directory.  
+- Code is styled according to [PEP8](https://peps.python.org/pep-0008/). Using a linter or IDE with automated linter 
+  is recommended.
 - Function, class and method documentation is done using Numpy-flavoured [docstrings](https://numpydoc.readthedocs.io/en/latest/format.html).
-  [Long-form documentation](https://oncoray.github.io/mirp/) is partially created from function, class and method documention, embedded in restructured text files in `docs_source`.
+  [Long-form documentation](https://oncoray.github.io/mirp/) is partially created from function, class and method 
+  documentation, embedded in restructured text files in `docs_source`.

NEWS.md

@@ -1,3 +1,29 @@
+# Version 2.2.0
+
+## Major changes
+
+- Added support for intensity scaling using the `intensity_scaling` parameter. Intensity scaling multiplies 
+  intensities by a scalar value. Intensity scaling occurs after intensity normalisation (if any) and prior to adding 
+  noise (if any). For example, intensity scaling can be used after intensity normalisation to scale intensities to a 
+  different range. `intensity_normalisation = "range"` with `intensity_scaling = 1000.0` maps image intensities to 
+  [1000.0, 0.0] instead of [1.0, 0.0].
+
+- Added support for intensity transformation filters: square root (`"pyradiomics_square_root"`), square 
+  (`"pyradiomics_square"`), logarithm (`"pyradiomics_logarithm"`) and exponential (`"pyradiomics_exponential"`). 
+  These implementations are based on the definitions in the `pyradiomics` 
+  [documentation](https://pyradiomics.readthedocs.io/en/latest/radiomics.html#module-radiomics.imageoperations). 
+  Since these filters do not currently have an IBSI reference standard, these are mostly intended for reproducing 
+  and validating radiomics models based on features extracted from pyradiomics.
+
+- Modules were renamed according to the PEP8 standard. This does not affect the documented public interface, but may 
+  affect external extensions. Public and private parts of the API are now indicated. 
+
+## Minor changes
+
+- Added support for Python version 3.10 using `typing-extensions`.
+- Several changes were made to ensure proper functioning of MIRP with future versions of `pandas`.
+- Some changes were made prevent deprecation warnings in future version of `numpy`.
+
 # Version 2.1.1
 
 ## Fixes

README.md

@@ -159,6 +159,9 @@ mask_labels = extract_mask_labels(
 A publication for MIRP is forthcoming. For now, please cite the following work:
 ```Zwanenburg A, Leger S, Agolli L, Pilz K, Troost EG, Richter C, Löck S. Assessing robustness of radiomic features by image perturbation. Scientific reports. 2019 Jan 24;9(1):614.```
 
+# Contributing
+If you have ideas for improving MIRP, please read the short [contribution guide](./CONTRIBUTING.md).
+
 # Developers and contributors
 
 MIRP is developed by:

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: ab60819b912204cb527868dbfe8edebc
+config: 17cbf7e65c49e001bf222ac3d01664cc
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_modules/index.html

@@ -1,22 +1,22 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; mirp 2.1.1 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
+  <title>Overview: module code &mdash; mirp 2.2.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=92fd9be5" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
 
 
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-        <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
-        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script src="../_static/doctools.js"></script>
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=b21de401"></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>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -75,19 +75,19 @@
            <div itemprop="articleBody">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="mirp/deepLearningPreprocessing.html">mirp.deepLearningPreprocessing</a></li>
-<li><a href="mirp/extractFeaturesAndImages.html">mirp.extractFeaturesAndImages</a></li>
-<li><a href="mirp/extractImageParameters.html">mirp.extractImageParameters</a></li>
-<li><a href="mirp/extractMaskLabels.html">mirp.extractMaskLabels</a></li>
-<li><a href="mirp/importData/importImageAndMask.html">mirp.importData.importImageAndMask</a></li>
-<li><a href="mirp/settings/settingsFeatureExtraction.html">mirp.settings.settingsFeatureExtraction</a></li>
-<li><a href="mirp/settings/settingsGeneral.html">mirp.settings.settingsGeneral</a></li>
-<li><a href="mirp/settings/settingsGeneric.html">mirp.settings.settingsGeneric</a></li>
-<li><a href="mirp/settings/settingsImageProcessing.html">mirp.settings.settingsImageProcessing</a></li>
-<li><a href="mirp/settings/settingsImageTransformation.html">mirp.settings.settingsImageTransformation</a></li>
-<li><a href="mirp/settings/settingsInterpolation.html">mirp.settings.settingsInterpolation</a></li>
-<li><a href="mirp/settings/settingsMaskResegmentation.html">mirp.settings.settingsMaskResegmentation</a></li>
-<li><a href="mirp/settings/settingsPerturbation.html">mirp.settings.settingsPerturbation</a></li>
+<ul><li><a href="mirp/data_import/import_image_and_mask.html">mirp.data_import.import_image_and_mask</a></li>
+<li><a href="mirp/deep_learning_preprocessing.html">mirp.deep_learning_preprocessing</a></li>
+<li><a href="mirp/extract_features_and_images.html">mirp.extract_features_and_images</a></li>
+<li><a href="mirp/extract_image_parameters.html">mirp.extract_image_parameters</a></li>
+<li><a href="mirp/extract_mask_labels.html">mirp.extract_mask_labels</a></li>
+<li><a href="mirp/settings/feature_parameters.html">mirp.settings.feature_parameters</a></li>
+<li><a href="mirp/settings/general_parameters.html">mirp.settings.general_parameters</a></li>
+<li><a href="mirp/settings/generic.html">mirp.settings.generic</a></li>
+<li><a href="mirp/settings/image_processing_parameters.html">mirp.settings.image_processing_parameters</a></li>
+<li><a href="mirp/settings/interpolation_parameters.html">mirp.settings.interpolation_parameters</a></li>
+<li><a href="mirp/settings/perturbation_parameters.html">mirp.settings.perturbation_parameters</a></li>
+<li><a href="mirp/settings/resegmentation_parameters.html">mirp.settings.resegmentation_parameters</a></li>
+<li><a href="mirp/settings/transformation_parameters.html">mirp.settings.transformation_parameters</a></li>
 <li><a href="mirp/utilities/config_utilities.html">mirp.utilities.config_utilities</a></li>
 </ul>