Merge pull request #60 from MStarmans91/development

Release version 3.4.3

.gitignore

@@ -132,4 +132,4 @@ WORC/external/*
 WORC/exampledata/ICCvalues.csv
 WORC/tests/*.png
 WORC/tests/*.mat
-WORC/tests/WORC_Example_STWStrategyHN_Regression
+WORC/tests/WORC_Example_STWStrategyHN_*

.travis.yml

@@ -52,13 +52,18 @@ matrix:
         - fastr trace /tmp/WORC_Example_STWStrategyHN/__sink_data__.json --sinks classification --samples all
         - fastr trace /tmp/WORC_Example_STWStrategyHN/__sink_data__.json --sinks performance --samples all
         - fastr trace /tmp/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
-        # Change the tutorial script to also run a regression experiment,
-        # using the previously calculated features
+        # Also run a regression experiment, using the previously calculated features
         - rm -r /tmp/GS/DEBUG_0
         - python WORC/tests/WORCTutorialSimple_travis_regression.py
         - fastr trace /tmp/WORC_Example_STWStrategyHN_Regression/__sink_data__.json --sinks classification --samples all
         - fastr trace /tmp/WORC_Example_STWStrategyHN_Regression/__sink_data__.json --sinks performance --samples all
         - fastr trace /tmp/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
+        # Also run a multiclass experiment, using the previously calculated features
+        - rm -r /tmp/GS/DEBUG_0
+        - python WORC/tests/WORCTutorialSimple_travis_multiclass.py
+        - fastr trace /tmp/WORC_Example_STWStrategyHN_Multiclass/__sink_data__.json --sinks classification --samples all
+        - fastr trace /tmp/WORC_Example_STWStrategyHN_Multiclass/__sink_data__.json --sinks performance --samples all
+        - fastr trace /tmp/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
 notifications:
   slack:
     secure: 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

CHANGELOG

@@ -6,8 +6,19 @@ 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 - 2021-06-02
+------------------
+
+Fixed
+~~~~~
+- SimpleWORC and BasicWORC now support multilabel workflows.
+- SimpleWORC and BasicWORC now support use of masks.
+
+Added
+~~~~~~~
+- Unit testing for multilabel workflows.
 
-3.4.2 - Unreleased
+3.4.2 - 2021-05-27
 ------------------
 
 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/WORC.py

@@ -419,12 +419,7 @@ def defaultconfig(self):
         config['Classification']['fastr'] = 'True'
         config['Classification']['fastr_plugin'] = self.fastr_plugin
         config['Classification']['classifiers'] =\
-            'SVM, SVM, SVM, SVM, SVM, SVM, SVM, SVM, SVM, ' +\
-            'RF, RF, RF, ' +\
-            'LR, LR, LR, ' +\
-            'LDA, LDA, LDA, ' +\
-            'QDA, QDA, QDA, ' +\
-            'GaussianNB, GaussianNB, GaussianNB, ' +\
+            'SVM, RF, LR, LDA, QDA, GaussianNB, ' +\
             'AdaBoostClassifier, ' +\
             'XGBClassifier'
         config['Classification']['max_iter'] = '100000'
@@ -472,7 +467,7 @@ def defaultconfig(self):
         # Hyperparameter optimization options
         config['HyperOptimization'] = dict()
         config['HyperOptimization']['scoring_method'] = 'f1_weighted'
-        config['HyperOptimization']['test_size'] = '0.15'
+        config['HyperOptimization']['test_size'] = '0.2'
         config['HyperOptimization']['n_splits'] = '5'
         config['HyperOptimization']['N_iterations'] = '1000'
         config['HyperOptimization']['n_jobspercore'] = '500'  # only relevant when using fastr in classification
@@ -982,6 +977,7 @@ def build_training(self):
                             self.links_C1_test[label] = self.classify.inputs['features_test'][str(label)] << self.sources_features_test[label].output
                             self.links_C1_test[label].collapse = 'test'
 
+
             else:
                 raise WORCexceptions.WORCIOError("Please provide labels.")
         else:
@@ -1769,7 +1765,7 @@ def execute(self):
 
         self.network.execute(self.source_data, self.sink_data, execution_plugin=self.fastr_plugin, tmpdir=self.fastr_tmpdir)
 
-    def add_evaluation(self, label_type, modus='classification'):
+    def add_evaluation(self, label_type, modus='binary_classification'):
         """Add branch for evaluation of performance to network.
 
         Note: should be done after build, before set:

WORC/classification/crossval.py

@@ -104,6 +104,7 @@ def random_split_cross_validation(image_features, feature_labels, classes,
                 for n_patient in range(0, classes.shape[1]):
                     for n_label in range(0, classes.shape[0]):
                         classes_temp[n_patient, n_label] = classes[n_label, n_patient]
+
             else:
                 raise ae.WORCKeyError('{} is not a valid modus!').format(modus)
 

WORC/classification/fitandscore.py

@@ -432,6 +432,7 @@ def fit_and_score(X, y, scoring,
         X_test = scaler.transform(X_test)
 
     del para_estimator['FeatureScaling']
+    del para_estimator['FeatureScaling_skip_features']
 
     # Delete the object if we do not need to return it
     if not return_all:
@@ -554,6 +555,11 @@ def fit_and_score(X, y, scoring,
         else:
             raise ae.WORCKeyError(f'Model {model} is not known for SelectFromModel. Use Lasso, LR, or RF.')
 
+        if len(y_train.shape) >= 2:
+            # Multilabel or regression. Regression: second dimension has length 1
+            if y_train.shape[1] > 1 and model != 'RF':
+                raise ae.WORCValueError(f'Model {model} is not suitable for multiclass classification. Please use RF or do not use SelectFromModel.')
+
         # Prefit model
         selectestimator.fit(X_train, y_train)
 
@@ -968,6 +974,8 @@ def delete_cc_para(para):
                   'RFmin_samples_split',
                   'RFmax_depth',
                   'LRpenalty',
+                  'LR_l1_ratio',
+                  'LR_solver',
                   'LRC',
                   'LDA_solver',
                   'LDA_shrinkage',

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>