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Merge pull request #48 from oncoray/dev2.0.1
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Merge version 2.0.1
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@alexzwanenburg
alexzwanenburg authored Jan 25, 2024
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16 changes: 16 additions & 0 deletions NEWS.md
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# Version 2.0.1

## Minor changes

- Randomisation in MIRP now uses the generator-based methods in `numpy.random`, replacing the legacy functions.
The generator is seeded so that results are reproducible. The seed depends on input image, mask and configuration
parameters, if applicable.

## Fixes

- Numpy arrays can now be used as direct input without throwing a `FileNotFoundError`.
- Relaxed check on orientation matrix when importing images, preventing errors when the l2-norm is around 1.000 but not
to high precision.
- To prevent high loads through internal multithreading in `numpy` and other libraries when using `ray` for parallel
processing, each ray thread is now initialised with environment parameters that prevent multi-threading.

# Version 2.0.0

## Major changes
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -6,6 +6,10 @@ Medical Image Radiomics Processor (MIRP) is an IBSI-compliant python package for
MIRP focuses on radiomics applications and supports computation of features for conventional radiomics
and image processing for deep-learning applications.

## Documentation

Documentation can be found here: https://oncoray.github.io/mirp/

## Installing MIRP
MIRP is available from PyPI and can be installed using `pip`, or other installer tools:

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1 change: 0 additions & 1 deletion VERSION.txt
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2 changes: 0 additions & 2 deletions conda/bld.bat
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2 changes: 0 additions & 2 deletions conda/conda_build_config.yaml
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# 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: 8e96e8f4f42399fb5af887be43bc900a
tags: 645f666f9bcd5a90fca523b33c5a78b7
6 changes: 3 additions & 3 deletions docs/_modules/index.html
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<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 2.0.1 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]>
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<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>
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<script src="../_static/js/theme.js"></script>
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<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
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10 changes: 7 additions & 3 deletions docs/_modules/mirp/deepLearningPreprocessing.html
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<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" />
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<script src="../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../_static/js/theme.js"></script>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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
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10 changes: 7 additions & 3 deletions docs/_modules/mirp/extractFeaturesAndImages.html
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<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" />
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<script src="../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../_static/js/theme.js"></script>
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<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>


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<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
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6 changes: 3 additions & 3 deletions docs/_modules/mirp/extractImageParameters.html
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<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 2.0.1 documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
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<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>
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<script src="../../_static/js/theme.js"></script>
Expand Down Expand Up @@ -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
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6 changes: 3 additions & 3 deletions docs/_modules/mirp/extractMaskLabels.html
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<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" />
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<script src="../../_static/jquery.js?v=5d32c60e"></script>
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<script src="../../_static/documentation_options.js?v=51b770b3"></script>
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<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../_static/js/theme.js"></script>
Expand Down Expand Up @@ -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
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6 changes: 3 additions & 3 deletions docs/_modules/mirp/importData/importImageAndMask.html
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<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 2.0.1 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]>
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<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>
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<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../../_static/js/theme.js"></script>
Expand Down Expand Up @@ -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
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<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 2.0.1 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]>
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../../_static/js/theme.js"></script>
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<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2023, Alex Zwanenburg.</p>
<p>&#169; Copyright 2024, Alex Zwanenburg.</p>
</div>

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<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 2.0.1 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
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Expand Down Expand Up @@ -148,7 +148,7 @@ <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
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<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 2.0.1 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
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<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2023, Alex Zwanenburg.</p>
<p>&#169; Copyright 2024, Alex Zwanenburg.</p>
</div>

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<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 2.0.1 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
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<script src="../../../_static/jquery.js?v=5d32c60e"></script>
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<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2023, Alex Zwanenburg.</p>
<p>&#169; Copyright 2024, Alex Zwanenburg.</p>
</div>

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