Merge pull request #63 from MStarmans91/development

Release v3.5.0

CHANGELOG

@@ -7,6 +7,26 @@ The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
 and this project adheres to `Semantic Versioning <http://semver.org/>`_
 
 
+3.5.0 - 2021-08-18
+------------
+
+Fixed
+~~~~~
+- Bug in plotting 2D images when ranking the posteriors or percentages.
+- Bug in Evaluate for Regression.
+- Bug in BasicWORC for supplying label files.
+- There is a bug in SimpleITK 2.1.0, which leads it to not be able
+  to read certain NIFTI files. See: https://github.com/InsightSoftwareConsortium/ITK/issues/2674
+  Reverting to SimpleITK 2.0.2 for now
+
+Changed
+~~~~~~~
+- Defaults for splitting jobs in hyperoptimization: now more parallelized.
+
+Added
+~~~~~~~
+- Documentation on additional functionality.
+
 3.4.5 - 2021-07-09
 ------------------
  Unit tests moved from Travis to Github Workflow from this verion on.

README.md

@@ -1,4 +1,4 @@
-# WORC v3.4.5
+# WORC v3.5.0
 ## Workflow for Optimal Radiomics Classification
 
 ## Information

README.rst

@@ -1,4 +1,4 @@
-WORC v3.4.5
+WORC v3.5.0
 ===========
 
 Workflow for Optimal Radiomics Classification

WORC/WORC.py

@@ -30,6 +30,9 @@
 import WORC.addexceptions as WORCexceptions
 import WORC.IOparser.config_WORC as config_io
 from WORC.detectors.detectors import DebugDetector
+from WORC.export.hyper_params_exporter import export_hyper_params_to_latex
+from urllib.parse import urlparse
+from urllib.request import url2pathname
 
 
 class WORC(object):
@@ -471,7 +474,7 @@ def defaultconfig(self):
         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
+        config['HyperOptimization']['n_jobspercore'] = '200'  # only relevant when using fastr in classification
         config['HyperOptimization']['maxlen'] = '100'
         config['HyperOptimization']['ranking_score'] = 'test_score'
         config['HyperOptimization']['memory'] = '3G'
@@ -1752,6 +1755,12 @@ def execute(self):
         except graphviz.backend.CalledProcessError as e:
             print(f'[WORC WARNING] Graphviz executable gave an error: not drawing network diagram. Original error: {e}')
 
+        # export hyper param. search space to LaTeX table
+        for config in self.fastrconfigs:
+            config_path = Path(url2pathname(urlparse(config).path))
+            tex_path = f'{config_path.parent.absolute() / config_path.stem}_hyperparams_space.tex'
+            export_hyper_params_to_latex(config_path, tex_path)
+
         if DebugDetector().do_detection():
             print("Source Data:")
             for k in self.source_data.keys():

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: 90b87bcebef0f13f3ee4eda0aa38d0c3
+config: 200f1b705b4d367101e0261a187b00d0
 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 3.4.5 documentation</title>
+  <title>WORC.IOparser.config_WORC &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.IOparser.config_io_classifier &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.IOparser.config_preprocessing &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.IOparser.config_segmentix &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.IOparser.file_io &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.WORC &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </div>
 
 
@@ -195,6 +195,9 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">WORC.addexceptions</span> <span class="k">as</span> <span class="nn">WORCexceptions</span>
 <span class="kn">import</span> <span class="nn">WORC.IOparser.config_WORC</span> <span class="k">as</span> <span class="nn">config_io</span>
 <span class="kn">from</span> <span class="nn">WORC.detectors.detectors</span> <span class="k">import</span> <span class="n">DebugDetector</span>
+<span class="kn">from</span> <span class="nn">WORC.export.hyper_params_exporter</span> <span class="k">import</span> <span class="n">export_hyper_params_to_latex</span>
+<span class="kn">from</span> <span class="nn">urllib.parse</span> <span class="k">import</span> <span class="n">urlparse</span>
+<span class="kn">from</span> <span class="nn">urllib.request</span> <span class="k">import</span> <span class="n">url2pathname</span>
 
 
 <div class="viewcode-block" id="WORC"><a class="viewcode-back" href="../../autogen/WORC.html#WORC.WORC.WORC">[docs]</a><span class="k">class</span> <span class="nc">WORC</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
@@ -636,7 +639,7 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
         <span class="n">config</span><span class="p">[</span><span class="s1">&#39;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>
+        <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;200&#39;</span>  <span class="c1"># only relevant when using fastr in classification</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;maxlen&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;100&#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;ranking_score&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;test_score&#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;memory&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;3G&#39;</span>
@@ -1917,6 +1920,12 @@ <h1>Source code for WORC.WORC</h1><div class="highlight"><pre>
         <span class="k">except</span> <span class="n">graphviz</span><span class="o">.</span><span class="n">backend</span><span class="o">.</span><span class="n">CalledProcessError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
             <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s1">&#39;[WORC WARNING] Graphviz executable gave an error: not drawing network diagram. Original error: </span><span class="si">{e}</span><span class="s1">&#39;</span><span class="p">)</span>
 
+        <span class="c1"># export hyper param. search space to LaTeX table</span>
+        <span class="k">for</span> <span class="n">config</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fastrconfigs</span><span class="p">:</span>
+            <span class="n">config_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">url2pathname</span><span class="p">(</span><span class="n">urlparse</span><span class="p">(</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">path</span><span class="p">))</span>
+            <span class="n">tex_path</span> <span class="o">=</span> <span class="n">f</span><span class="s1">&#39;{config_path.parent.absolute() / config_path.stem}_hyperparams_space.tex&#39;</span>
+            <span class="n">export_hyper_params_to_latex</span><span class="p">(</span><span class="n">config_path</span><span class="p">,</span> <span class="n">tex_path</span><span class="p">)</span>
+
         <span class="k">if</span> <span class="n">DebugDetector</span><span class="p">()</span><span class="o">.</span><span class="n">do_detection</span><span class="p">():</span>
             <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Source Data:&quot;</span><span class="p">)</span>
             <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">source_data</span><span class="o">.</span><span class="n">keys</span><span class="p">():</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 3.4.5 documentation</title>
+  <title>WORC.addexceptions &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.AdvancedSampler &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.ObjectSampler &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.RankedSVM &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.SearchCV &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.construct_classifier &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.createfixedsplits &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </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 3.4.5 documentation</title>
+  <title>WORC.classification.crossval &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </div>
 
 

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 3.4.5 documentation</title>
+  <title>WORC.classification.estimators &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </div>
 
 

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 3.4.5 documentation</title>
+  <title>WORC.classification.fitandscore &mdash; WORC 3.5.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.4.5
+                3.5.0
               </div>