Merge pull request #59 from MStarmans91/development

Release version 3.4.2
MStarmans91 · May 27, 2021 · 375e768 · 375e768
2 parents f9349c0 + 2a21c1d
commit 375e768
Show file tree

Hide file tree

Showing 93 changed files with 670 additions and 578 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -7,6 +7,21 @@ The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
 and this project adheres to `Semantic Versioning <http://semver.org/>`_
 
 
+3.4.2 - Unreleased
+------------------
+
+Fixed
+~~~~~
+- Bug in flattening of plot_ranked_posteriors function.
+- Bug in plot_images: could not handle 2D images when applying slicing.
+- Bug in precision-recall curve.
+- Bug in performance estimation plotting.
+- Preflighcheck now also accepts labels from txt or XNAT.
+
+Added
+~~~~~~~
+- Label file can now also be separated by semicolons.
+
 3.4.1 - 2021-05-18
 ------------------
 

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# WORC v3.4.1
+# WORC v3.4.2
 ## Workflow for Optimal Radiomics Classification
 
 ## Information

diff --git a/README.rst b/README.rst
@@ -1,4 +1,4 @@
-WORC v3.4.1
+WORC v3.4.2
 ===========
 
 Workflow for Optimal Radiomics Classification

diff --git a/WORC/WORC.py b/WORC/WORC.py
@@ -409,7 +409,7 @@ def defaultconfig(self):
             'RandomUnderSampling, RandomOverSampling, NearMiss, ' +\
             'NeighbourhoodCleaningRule, ADASYN, BorderlineSMOTE, SMOTE, ' +\
             'SMOTEENN, SMOTETomek'
-        config['Resampling']['sampling_strategy'] = 'majority, minority, not minority, not majority, all'
+        config['Resampling']['sampling_strategy'] = 'auto, majority, minority, not minority, not majority, all'
         config['Resampling']['n_neighbors'] = '3, 12'
         config['Resampling']['k_neighbors'] = '5, 15'
         config['Resampling']['threshold_cleaning'] = '0.25, 0.5'

diff --git a/WORC/doc/_build/doctrees/autogen/WORC.plotting.doctree b/WORC/doc/_build/doctrees/autogen/WORC.plotting.doctree
diff --git a/WORC/doc/_build/doctrees/autogen/WORC.processing.doctree b/WORC/doc/_build/doctrees/autogen/WORC.processing.doctree
diff --git a/WORC/doc/_build/doctrees/environment.pickle b/WORC/doc/_build/doctrees/environment.pickle
diff --git a/WORC/doc/_build/doctrees/static/changelog.doctree b/WORC/doc/_build/doctrees/static/changelog.doctree
diff --git a/WORC/doc/_build/doctrees/static/configuration.doctree b/WORC/doc/_build/doctrees/static/configuration.doctree
diff --git a/WORC/doc/_build/html/.buildinfo b/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: 73f1da5a99fea16f90c552d633d66cea
+config: 33f10d2ce9bf6d5dcfd26d0fd1e86e7b
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/WORC/doc/_build/html/_modules/WORC/IOparser/config_WORC.html b/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 3.4.1 documentation</title>
+  <title>WORC.IOparser.config_WORC &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/IOparser/config_io_classifier.html b/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 3.4.1 documentation</title>
+  <title>WORC.IOparser.config_io_classifier &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/IOparser/config_preprocessing.html b/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 3.4.1 documentation</title>
+  <title>WORC.IOparser.config_preprocessing &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/IOparser/config_segmentix.html b/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 3.4.1 documentation</title>
+  <title>WORC.IOparser.config_segmentix &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/IOparser/file_io.html b/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 3.4.1 documentation</title>
+  <title>WORC.IOparser.file_io &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/WORC.html b/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 3.4.1 documentation</title>
+  <title>WORC.WORC &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 
@@ -574,7 +574,7 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
             <span class="s1">&#39;RandomUnderSampling, RandomOverSampling, NearMiss, &#39;</span> <span class="o">+</span>\
             <span class="s1">&#39;NeighbourhoodCleaningRule, ADASYN, BorderlineSMOTE, SMOTE, &#39;</span> <span class="o">+</span>\
             <span class="s1">&#39;SMOTEENN, SMOTETomek&#39;</span>
-        <span class="n">config</span><span class="p">[</span><span class="s1">&#39;Resampling&#39;</span><span class="p">][</span><span class="s1">&#39;sampling_strategy&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;majority, minority, not minority, not majority, all&#39;</span>
+        <span class="n">config</span><span class="p">[</span><span class="s1">&#39;Resampling&#39;</span><span class="p">][</span><span class="s1">&#39;sampling_strategy&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;auto, majority, minority, not minority, not majority, all&#39;</span>
         <span class="n">config</span><span class="p">[</span><span class="s1">&#39;Resampling&#39;</span><span class="p">][</span><span class="s1">&#39;n_neighbors&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;3, 12&#39;</span>
         <span class="n">config</span><span class="p">[</span><span class="s1">&#39;Resampling&#39;</span><span class="p">][</span><span class="s1">&#39;k_neighbors&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;5, 15&#39;</span>
         <span class="n">config</span><span class="p">[</span><span class="s1">&#39;Resampling&#39;</span><span class="p">][</span><span class="s1">&#39;threshold_cleaning&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;0.25, 0.5&#39;</span>

diff --git a/WORC/doc/_build/html/_modules/WORC/addexceptions.html b/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 3.4.1 documentation</title>
+  <title>WORC.addexceptions &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.AdvancedSampler &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.ObjectSampler &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.RankedSVM &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.SearchCV &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/construct_classifier.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.construct_classifier &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.createfixedsplits &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/crossval.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.crossval &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/estimators.html b/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 3.4.1 documentation</title>
+  <title>WORC.classification.estimators &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html b/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.classification.fitandscore &mdash; WORC 3.4.1 documentation</title>
+  <title>WORC.classification.fitandscore &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/metrics.html b/WORC/doc/_build/html/_modules/WORC/classification/metrics.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.classification.metrics &mdash; WORC 3.4.1 documentation</title>
+  <title>WORC.classification.metrics &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/parameter_optimization.html b/WORC/doc/_build/html/_modules/WORC/classification/parameter_optimization.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.classification.parameter_optimization &mdash; WORC 3.4.1 documentation</title>
+  <title>WORC.classification.parameter_optimization &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>
 
 

diff --git a/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html b/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.classification.trainclassifier &mdash; WORC 3.4.1 documentation</title>
+  <title>WORC.classification.trainclassifier &mdash; WORC 3.4.2 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.1
+                3.4.2
               </div>