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Prepare for 3.6.3 release
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MStarmans91 committed Aug 15, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG
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Expand Up @@ -6,7 +6,7 @@ All notable changes to this project will be documented in this file.
The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
and this project adheres to `Semantic Versioning <http://semver.org/>`_

3.6.3 - Unreleased
3.6.3 - 2023-08-15
------------------

Fixed
Expand All @@ -19,6 +19,7 @@ Fixed
and test set and thus bootstrapping should be used.
- Bug in PREDICT was fixed that mixed up the mode in shape feature extraction (2D / 2.5D)
- Bug in performance calculation of multiclass classification.
- Bugs in statistical feature testing.

Changed
~~~~~~~
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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: 385a6cf65021e68246010618f9e139d5
config: 9f4f6a5f34b465687f7ac7c47dd3b2c4
tags: 645f666f9bcd5a90fca523b33c5a78b7
90 changes: 63 additions & 27 deletions WORC/doc/_build/html/_modules/WORC/IOparser/config_WORC.html
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<title>WORC.IOparser.config_WORC &mdash; WORC 3.6.2 documentation</title>
<title>WORC.IOparser.config_WORC &mdash; WORC 3.6.3 documentation</title>



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<div class="version">
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3.6.3
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Expand All @@ -164,7 +171,7 @@
<h1>Source code for WORC.IOparser.config_WORC</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python</span>

<span class="c1"># Copyright 2016-2020 Biomedical Imaging Group Rotterdam, Departments of</span>
<span class="c1"># Copyright 2016-2023 Biomedical Imaging Group Rotterdam, Departments of</span>
<span class="c1"># Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands</span>
<span class="c1">#</span>
<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
Expand Down Expand Up @@ -195,20 +202,21 @@ <h1>Source code for WORC.IOparser.config_WORC</h1><div class="highlight"><pre>
<span class="sd"> settings_dict: dictionary containing all parsed settings.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">config_file_path</span><span class="p">):</span>
<span class="n">e</span> <span class="o">=</span> <span class="n">f</span><span class="s1">&#39;File </span><span class="si">{config_file_path}</span><span class="s1"> does not exist!&#39;</span>
<span class="n">e</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;File </span><span class="si">{</span><span class="n">config_file_path</span><span class="si">}</span><span class="s1"> does not exist!&#39;</span>
<span class="k">raise</span> <span class="n">ae</span><span class="o">.</span><span class="n">WORCKeyError</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>

<span class="n">settings</span> <span class="o">=</span> <span class="n">configparser</span><span class="o">.</span><span class="n">ConfigParser</span><span class="p">()</span>
<span class="n">settings</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">config_file_path</span><span class="p">)</span>

<span class="n">settings_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;ImageFeatures&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;General&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span>
<span class="s1">&#39;SVMFeatures&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">()}</span>
<span class="n">settings_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;Preprocessing&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;ImageFeatures&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;General&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span>
<span class="s1">&#39;SVMFeatures&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;Ensemble&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span>
<span class="s1">&#39;Labels&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">()}</span>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;ImageFeatures&#39;</span><span class="p">][</span><span class="s1">&#39;image_type&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;ImageFeatures&#39;</span><span class="p">][</span><span class="s1">&#39;image_type&#39;</span><span class="p">])</span>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;FeatureCalculators&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
<span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;[]&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
<span class="n">settings</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;FeatureCalculators&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;Preprocessing&#39;</span><span class="p">]</span> <span class="o">=</span>\
Expand All @@ -219,28 +227,57 @@ <h1>Source code for WORC.IOparser.config_WORC</h1><div class="highlight"><pre>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;Segmentix&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="n">settings</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">getboolean</span><span class="p">(</span><span class="s1">&#39;Segmentix&#39;</span><span class="p">)</span>

<span class="c1"># Settings for ensembling</span>
<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Method&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Method&#39;</span><span class="p">])</span>
<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Size&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Size&#39;</span><span class="p">])</span>

<span class="c1"># Label settings</span>
<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Labels&#39;</span><span class="p">][</span><span class="s1">&#39;label_names&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
<span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Labels&#39;</span><span class="p">][</span><span class="s1">&#39;label_names&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Labels&#39;</span><span class="p">][</span><span class="s1">&#39;modus&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Labels&#39;</span><span class="p">][</span><span class="s1">&#39;modus&#39;</span><span class="p">])</span>

<span class="c1"># Whether to use some methods or not</span>
<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;ComBat&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;ComBat&#39;</span><span class="p">])</span>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;Fingerprint&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;Fingerprint&#39;</span><span class="p">])</span>

<span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Preprocessing&#39;</span><span class="p">][</span><span class="s1">&#39;Resampling&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Preprocessing&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">getboolean</span><span class="p">(</span><span class="s1">&#39;Resampling&#39;</span><span class="p">)</span>

<span class="k">return</span> <span class="n">settings_dict</span></div>
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&copy; Copyright 2016 -- 2023, Biomedical Imaging Group Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
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Expand All @@ -249,7 +286,6 @@ <h1>Source code for WORC.IOparser.config_WORC</h1><div class="highlight"><pre>
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