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Prepare for 3.4.3 release.
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MStarmans91 committed Jun 2, 2021
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2 changes: 1 addition & 1 deletion CHANGELOG
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The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
and this project adheres to `Semantic Versioning <http://semver.org/>`_

3.4.3 - Unreleased
3.4.3 - 2021-06-02
------------------

Fixed
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2 changes: 1 addition & 1 deletion README.md
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# WORC v3.4.2
# WORC v3.4.3
## Workflow for Optimal Radiomics Classification

## Information
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WORC v3.4.2
WORC v3.4.3
===========

Workflow for Optimal Radiomics Classification
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2 changes: 1 addition & 1 deletion WORC/doc/_build/html/.buildinfo
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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: 33f10d2ce9bf6d5dcfd26d0fd1e86e7b
config: 1a400459aca376ecf872ea4fb53480b0
tags: 645f666f9bcd5a90fca523b33c5a78b7
4 changes: 2 additions & 2 deletions WORC/doc/_build/html/_modules/WORC/IOparser/config_WORC.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.IOparser.config_WORC &mdash; WORC 3.4.2 documentation</title>
<title>WORC.IOparser.config_WORC &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.IOparser.config_io_classifier &mdash; WORC 3.4.2 documentation</title>
<title>WORC.IOparser.config_io_classifier &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.IOparser.config_preprocessing &mdash; WORC 3.4.2 documentation</title>
<title>WORC.IOparser.config_preprocessing &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.IOparser.config_segmentix &mdash; WORC 3.4.2 documentation</title>
<title>WORC.IOparser.config_segmentix &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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4 changes: 2 additions & 2 deletions WORC/doc/_build/html/_modules/WORC/IOparser/file_io.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.IOparser.file_io &mdash; WORC 3.4.2 documentation</title>
<title>WORC.IOparser.file_io &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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16 changes: 6 additions & 10 deletions WORC/doc/_build/html/_modules/WORC/WORC.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.WORC &mdash; WORC 3.4.2 documentation</title>
<title>WORC.WORC &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


Expand Down Expand Up @@ -584,12 +584,7 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;fastr&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;True&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;fastr_plugin&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fastr_plugin</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;classifiers&#39;</span><span class="p">]</span> <span class="o">=</span>\
<span class="s1">&#39;SVM, SVM, SVM, SVM, SVM, SVM, SVM, SVM, SVM, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;RF, RF, RF, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;LR, LR, LR, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;LDA, LDA, LDA, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;QDA, QDA, QDA, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;GaussianNB, GaussianNB, GaussianNB, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;SVM, RF, LR, LDA, QDA, GaussianNB, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;AdaBoostClassifier, &#39;</span> <span class="o">+</span>\
<span class="s1">&#39;XGBClassifier&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;max_iter&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;100000&#39;</span>
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<span class="c1"># Hyperparameter optimization options</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;scoring_method&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;f1_weighted&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;test_size&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;0.15&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;test_size&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;0.2&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;n_splits&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;5&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;N_iterations&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;1000&#39;</span>
<span class="n">config</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;n_jobspercore&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;500&#39;</span> <span class="c1"># only relevant when using fastr in classification</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">links_C1_test</span><span class="p">[</span><span class="n">label</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classify</span><span class="o">.</span><span class="n">inputs</span><span class="p">[</span><span class="s1">&#39;features_test&#39;</span><span class="p">][</span><span class="nb">str</span><span class="p">(</span><span class="n">label</span><span class="p">)]</span> <span class="o">&lt;&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources_features_test</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">output</span>
<span class="bp">self</span><span class="o">.</span><span class="n">links_C1_test</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">collapse</span> <span class="o">=</span> <span class="s1">&#39;test&#39;</span>


<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">WORCexceptions</span><span class="o">.</span><span class="n">WORCIOError</span><span class="p">(</span><span class="s2">&quot;Please provide labels.&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">network</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">source_data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sink_data</span><span class="p">,</span> <span class="n">execution_plugin</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">fastr_plugin</span><span class="p">,</span> <span class="n">tmpdir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">fastr_tmpdir</span><span class="p">)</span></div>

<div class="viewcode-block" id="WORC.add_evaluation"><a class="viewcode-back" href="../../autogen/WORC.html#WORC.WORC.WORC.add_evaluation">[docs]</a> <span class="k">def</span> <span class="nf">add_evaluation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label_type</span><span class="p">,</span> <span class="n">modus</span><span class="o">=</span><span class="s1">&#39;classification&#39;</span><span class="p">):</span>
<div class="viewcode-block" id="WORC.add_evaluation"><a class="viewcode-back" href="../../autogen/WORC.html#WORC.WORC.WORC.add_evaluation">[docs]</a> <span class="k">def</span> <span class="nf">add_evaluation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label_type</span><span class="p">,</span> <span class="n">modus</span><span class="o">=</span><span class="s1">&#39;binary_classification&#39;</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Add branch for evaluation of performance to network.</span>

<span class="sd"> Note: should be done after build, before set:</span>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.addexceptions &mdash; WORC 3.4.2 documentation</title>
<title>WORC.addexceptions &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.AdvancedSampler &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.AdvancedSampler &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.ObjectSampler &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.ObjectSampler &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.RankedSVM &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.RankedSVM &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.SearchCV &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.SearchCV &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.construct_classifier &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.construct_classifier &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.createfixedsplits &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.createfixedsplits &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.crossval &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.crossval &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


Expand Down Expand Up @@ -269,6 +269,7 @@ <h1>Source code for WORC.classification.crossval</h1><div class="highlight"><pre
<span class="k">for</span> <span class="n">n_patient</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">classes</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
<span class="k">for</span> <span class="n">n_label</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">classes</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
<span class="n">classes_temp</span><span class="p">[</span><span class="n">n_patient</span><span class="p">,</span> <span class="n">n_label</span><span class="p">]</span> <span class="o">=</span> <span class="n">classes</span><span class="p">[</span><span class="n">n_label</span><span class="p">,</span> <span class="n">n_patient</span><span class="p">]</span>

<span class="k">else</span><span class="p">:</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="s1">&#39;</span><span class="si">{}</span><span class="s1"> is not a valid modus!&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">modus</span><span class="p">)</span>

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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>WORC.classification.estimators &mdash; WORC 3.4.2 documentation</title>
<title>WORC.classification.estimators &mdash; WORC 3.4.3 documentation</title>



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<div class="version">
3.4.2
3.4.3
</div>


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