Prepare for 3.4.3 release.

CHANGELOG

@@ -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/>`_
 
-3.4.3 - Unreleased
+3.4.3 - 2021-06-02
 ------------------
 
 Fixed

README.md

@@ -1,4 +1,4 @@
-# WORC v3.4.2
+# WORC v3.4.3
 ## Workflow for Optimal Radiomics Classification
 
 ## Information

README.rst

@@ -1,4 +1,4 @@
-WORC v3.4.2
+WORC v3.4.3
 ===========
 
 Workflow for Optimal Radiomics Classification

WORC/doc/_build/html/.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: 33f10d2ce9bf6d5dcfd26d0fd1e86e7b
+config: 1a400459aca376ecf872ea4fb53480b0
 tags: 645f666f9bcd5a90fca523b33c5a78b7

WORC/doc/_build/html/_modules/WORC/IOparser/config_WORC.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/IOparser/config_io_classifier.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/IOparser/config_preprocessing.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/IOparser/config_segmentix.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/IOparser/file_io.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/WORC.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 
@@ -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>
@@ -637,7 +632,7 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
         <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>
@@ -1147,6 +1142,7 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
                             <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>
@@ -1934,7 +1930,7 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
 
         <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>

WORC/doc/_build/html/_modules/WORC/addexceptions.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/construct_classifier.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/classification/crossval.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>
 
 
@@ -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>
 

WORC/doc/_build/html/_modules/WORC/classification/estimators.html

@@ -8,7 +8,7 @@
 
   <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>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.2
+                3.4.3
               </div>