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
[docs]class WORC(object):
@@ -636,7 +639,7 @@ Source code for WORC.WORC
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'
@@ -1917,6 +1920,12 @@ Source code for WORC.WORC
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():
diff --git a/WORC/doc/_build/html/_modules/WORC/addexceptions.html b/WORC/doc/_build/html/_modules/WORC/addexceptions.html
index 09da74f1..b751c379 100644
--- a/WORC/doc/_build/html/_modules/WORC/addexceptions.html
+++ b/WORC/doc/_build/html/_modules/WORC/addexceptions.html
@@ -8,7 +8,7 @@
- WORC.addexceptions — WORC 3.4.5 documentation
+ WORC.addexceptions — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html b/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html
index 0327e748..7422e845 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html
@@ -8,7 +8,7 @@
- WORC.classification.AdvancedSampler — WORC 3.4.5 documentation
+ WORC.classification.AdvancedSampler — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html b/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html
index 9f91cabc..0ba21179 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html
@@ -8,7 +8,7 @@
- WORC.classification.ObjectSampler — WORC 3.4.5 documentation
+ WORC.classification.ObjectSampler — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html b/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html
index 94256185..d6cacddb 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html
@@ -8,7 +8,7 @@
- WORC.classification.RankedSVM — WORC 3.4.5 documentation
+ WORC.classification.RankedSVM — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html b/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html
index 779f7125..6702946e 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html
@@ -8,7 +8,7 @@
- WORC.classification.SearchCV — WORC 3.4.5 documentation
+ WORC.classification.SearchCV — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/construct_classifier.html b/WORC/doc/_build/html/_modules/WORC/classification/construct_classifier.html
index 916e4053..141a37e3 100644
--- 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 @@
- WORC.classification.construct_classifier — WORC 3.4.5 documentation
+ WORC.classification.construct_classifier — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html b/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html
index 95fd6354..e0d020d0 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html
@@ -8,7 +8,7 @@
- WORC.classification.createfixedsplits — WORC 3.4.5 documentation
+ WORC.classification.createfixedsplits — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/crossval.html b/WORC/doc/_build/html/_modules/WORC/classification/crossval.html
index 77c44f82..5212ca1b 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/crossval.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/crossval.html
@@ -8,7 +8,7 @@
- WORC.classification.crossval — WORC 3.4.5 documentation
+ WORC.classification.crossval — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/estimators.html b/WORC/doc/_build/html/_modules/WORC/classification/estimators.html
index 526c246c..9f233b4f 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/estimators.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/estimators.html
@@ -8,7 +8,7 @@
- WORC.classification.estimators — WORC 3.4.5 documentation
+ WORC.classification.estimators — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html b/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html
index d1f608f2..6b8a2046 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html
@@ -8,7 +8,7 @@
- WORC.classification.fitandscore — WORC 3.4.5 documentation
+ WORC.classification.fitandscore — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/metrics.html b/WORC/doc/_build/html/_modules/WORC/classification/metrics.html
index a0413f15..187375f8 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/metrics.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/metrics.html
@@ -8,7 +8,7 @@
- WORC.classification.metrics — WORC 3.4.5 documentation
+ WORC.classification.metrics — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/parameter_optimization.html b/WORC/doc/_build/html/_modules/WORC/classification/parameter_optimization.html
index 97a1f176..7ca0ce99 100644
--- 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 @@
- WORC.classification.parameter_optimization — WORC 3.4.5 documentation
+ WORC.classification.parameter_optimization — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html b/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html
index 04758345..9942bfa6 100644
--- a/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html
+++ b/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html
@@ -8,7 +8,7 @@
- WORC.classification.trainclassifier — WORC 3.4.5 documentation
+ WORC.classification.trainclassifier — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html b/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html
index 9f5031a2..e1f7f1e6 100644
--- a/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html
+++ b/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html
@@ -8,7 +8,7 @@
- WORC.detectors.detectors — WORC 3.4.5 documentation
+ WORC.detectors.detectors — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html b/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html
index 2e43ffc5..58bb52ed 100644
--- a/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html
+++ b/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html
@@ -8,7 +8,7 @@
- WORC.exampledata.datadownloader — WORC 3.4.5 documentation
+ WORC.exampledata.datadownloader — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html
index 857090b7..79e9df03 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.Imputer — WORC 3.4.5 documentation
+ WORC.featureprocessing.Imputer — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html
index a1445ff1..474d322b 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.Relief — WORC 3.4.5 documentation
+ WORC.featureprocessing.Relief — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html
index 65f27892..21fd4d03 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.SelectGroups — WORC 3.4.5 documentation
+ WORC.featureprocessing.SelectGroups — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html
index 5e8d703b..aa873206 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.SelectIndividuals — WORC 3.4.5 documentation
+ WORC.featureprocessing.SelectIndividuals — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html
index cbdfcc36..a5797ff2 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.StatisticalTestFeatures — WORC 3.4.5 documentation
+ WORC.featureprocessing.StatisticalTestFeatures — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html
index 2e5c735a..2be7d257 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.StatisticalTestThreshold — WORC 3.4.5 documentation
+ WORC.featureprocessing.StatisticalTestThreshold — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html
index a2132204..133a13ef 100644
--- a/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html
+++ b/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html
@@ -8,7 +8,7 @@
- WORC.featureprocessing.VarianceThreshold — WORC 3.4.5 documentation
+ WORC.featureprocessing.VarianceThreshold — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/compute_CI.html b/WORC/doc/_build/html/_modules/WORC/plotting/compute_CI.html
index d13676d7..22dbb49e 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/compute_CI.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/compute_CI.html
@@ -8,7 +8,7 @@
- WORC.plotting.compute_CI — WORC 3.4.5 documentation
+ WORC.plotting.compute_CI — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html b/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html
index 8ce23965..68675c31 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html
@@ -8,7 +8,7 @@
- WORC.plotting.linstretch — WORC 3.4.5 documentation
+ WORC.plotting.linstretch — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/plot_ROC.html b/WORC/doc/_build/html/_modules/WORC/plotting/plot_ROC.html
index fe730fa8..fa6d0c04 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/plot_ROC.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/plot_ROC.html
@@ -8,7 +8,7 @@
- WORC.plotting.plot_ROC — WORC 3.4.5 documentation
+ WORC.plotting.plot_ROC — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/plot_barchart.html b/WORC/doc/_build/html/_modules/WORC/plotting/plot_barchart.html
index 7a889843..525984b0 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/plot_barchart.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/plot_barchart.html
@@ -8,7 +8,7 @@
- WORC.plotting.plot_barchart — WORC 3.4.5 documentation
+ WORC.plotting.plot_barchart — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/plot_images.html b/WORC/doc/_build/html/_modules/WORC/plotting/plot_images.html
index 26730e4f..426ad077 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/plot_images.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/plot_images.html
@@ -8,7 +8,7 @@
- WORC.plotting.plot_images — WORC 3.4.5 documentation
+ WORC.plotting.plot_images — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
@@ -218,21 +218,29 @@ Source code for WORC.plotting.plot_images
[docs]def slicer(image, mask=None, output_name=None, output_name_zoom=None,
thresholds=[-240, 160], zoomfactor=4, dpi=500, normalize=False,
expand=False, boundary=False, square=False, flip=True, rot90=0,
- alpha=0.40, axis='axial', index=None, color='cyan'):
+ alpha=0.40, axis='axial', index=None, color='cyan', radius=2):
"""Plot slice of image where mask is largest, with mask as overlay.
image and mask should both be arrays
"""
# Determine figure size by spacing
- spacing = [float(image.GetSpacing()[0]), float(image.GetSpacing()[1]), float(image.GetSpacing()[2])]
- imsize = [float(image.GetSize()[0]), float(image.GetSize()[1]), float(image.GetSize()[2])]
-
- if axis == 'axial':
+ if len(image.GetSize()) == 2:
+ # 2D Image
+ spacing = [float(image.GetSpacing()[0]), float(image.GetSpacing()[1])]
+ imsize = [float(image.GetSize()[0]), float(image.GetSize()[1])]
figsize = (imsize[0]*spacing[0]/100.0, imsize[1]*spacing[1]/100.0)
- elif axis == 'coronal':
- figsize = (imsize[0]*spacing[0]/100.0, imsize[2]*spacing[2]/100.0)
- elif axis == 'transversal':
- figsize = (imsize[1]*spacing[1]/100.0, imsize[2]*spacing[2]/100.0)
+ else:
+ # 3D Image
+ # Determine figure size by spacing
+ spacing = [float(image.GetSpacing()[0]), float(image.GetSpacing()[1]), float(image.GetSpacing()[2])]
+ imsize = [float(image.GetSize()[0]), float(image.GetSize()[1]), float(image.GetSize()[2])]
+
+ if axis == 'axial':
+ figsize = (imsize[0]*spacing[0]/100.0, imsize[1]*spacing[1]/100.0)
+ elif axis == 'coronal':
+ figsize = (imsize[0]*spacing[0]/100.0, imsize[2]*spacing[2]/100.0)
+ elif axis == 'transversal':
+ figsize = (imsize[1]*spacing[1]/100.0, imsize[2]*spacing[2]/100.0)
# Convert images to numpy arrays
image = sitk.GetArrayFromImage(image)
@@ -299,7 +307,7 @@ Source code for WORC.plotting.plot_images
if mask is not None:
if boundary:
print('\t Extracting boundary.')
- maskslice = extract_boundary(maskslice)
+ maskslice = extract_boundary(maskslice, radius)
if normalize:
print('\t Normalizing.')
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/plot_ranked_scores.html b/WORC/doc/_build/html/_modules/WORC/plotting/plot_ranked_scores.html
index 52a89a53..5975ad66 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/plot_ranked_scores.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/plot_ranked_scores.html
@@ -8,7 +8,7 @@
- WORC.plotting.plot_ranked_scores — WORC 3.4.5 documentation
+ WORC.plotting.plot_ranked_scores — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html b/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html
index 176f7231..1548d97c 100644
--- a/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html
+++ b/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html
@@ -8,7 +8,7 @@
- WORC.plotting.scatterplot — WORC 3.4.5 documentation
+ WORC.plotting.scatterplot — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html b/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html
index 41e8083d..8e42e888 100644
--- a/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html
+++ b/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html
@@ -8,7 +8,7 @@
- WORC.processing.ExtractNLargestBlobsn — WORC 3.4.5 documentation
+ WORC.processing.ExtractNLargestBlobsn — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/classes.html b/WORC/doc/_build/html/_modules/WORC/processing/classes.html
index 5b9b3783..d0ab7331 100644
--- a/WORC/doc/_build/html/_modules/WORC/processing/classes.html
+++ b/WORC/doc/_build/html/_modules/WORC/processing/classes.html
@@ -8,7 +8,7 @@
- WORC.processing.classes — WORC 3.4.5 documentation
+ WORC.processing.classes — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/label_processing.html b/WORC/doc/_build/html/_modules/WORC/processing/label_processing.html
index 74bb27d4..b18156c8 100644
--- a/WORC/doc/_build/html/_modules/WORC/processing/label_processing.html
+++ b/WORC/doc/_build/html/_modules/WORC/processing/label_processing.html
@@ -8,7 +8,7 @@
- WORC.processing.label_processing — WORC 3.4.5 documentation
+ WORC.processing.label_processing — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/CalcFeatures_test.html b/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/CalcFeatures_test.html
index 0bc9fdb4..c622b99b 100644
--- a/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/CalcFeatures_test.html
+++ b/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/CalcFeatures_test.html
@@ -8,7 +8,7 @@
- WORC.resources.fastr_tests.CalcFeatures_test — WORC 3.4.5 documentation
+ WORC.resources.fastr_tests.CalcFeatures_test — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/elastix_test.html b/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/elastix_test.html
index 2c5e2be0..b7cf49e8 100644
--- a/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/elastix_test.html
+++ b/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/elastix_test.html
@@ -8,7 +8,7 @@
- WORC.resources.fastr_tests.elastix_test — WORC 3.4.5 documentation
+ WORC.resources.fastr_tests.elastix_test — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/segmentix_test.html b/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/segmentix_test.html
index 07b538ac..ab190e36 100644
--- a/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/segmentix_test.html
+++ b/WORC/doc/_build/html/_modules/WORC/resources/fastr_tests/segmentix_test.html
@@ -8,7 +8,7 @@
- WORC.resources.fastr_tests.segmentix_test — WORC 3.4.5 documentation
+ WORC.resources.fastr_tests.segmentix_test — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html b/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html
index b2ab73a7..8edc4f5e 100644
--- a/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html
+++ b/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html
@@ -8,7 +8,7 @@
- WORC.tools.Elastix — WORC 3.4.5 documentation
+ WORC.tools.Elastix — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html b/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html
index 36bbf99d..f69b4016 100644
--- a/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html
+++ b/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html
@@ -8,7 +8,7 @@
- WORC.tools.Evaluate — WORC 3.4.5 documentation
+ WORC.tools.Evaluate — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
@@ -594,8 +594,8 @@ Source code for WORC.tools.Evaluate
self.links_STest_Features[name] =\
self.network.create_link(self.parent.ComBat.outputs['features_train_out'], self.node_STest.inputs['features'])
- self.links_decomposition_Features[name] =\
- self.network.create_link(self.parent.ComBat.outputs['features_train_out'], self.node_decomposition.inputs['features'])
+ self.links_decomposition_Features[name] =\
+ self.network.create_link(self.parent.ComBat.outputs['features_train_out'], self.node_decomposition.inputs['features'])
self.links_Boxplots_Features[name] =\
self.network.create_link(self.parent.ComBat.outputs['features_train_out'], self.node_Boxplots_Features.inputs['features'])
@@ -603,8 +603,8 @@ Source code for WORC.tools.Evaluate
# All features should be input at once
if 'classification' in self.modus:
self.links_STest_Features[name].collapse = 'ComBat'
+ self.links_decomposition_Features[name].collapse = 'ComBat'
- self.links_decomposition_Features[name].collapse = 'ComBat'
self.links_Boxplots_Features[name].collapse = 'ComBat'
else:
@@ -619,8 +619,8 @@ Source code for WORC.tools.Evaluate
self.links_STest_Features[name] =\
self.node_STest.inputs['features'][name] << node.outputs['feat_out']
- self.links_decomposition_Features[name] =\
- self.node_decomposition.inputs['features'][name] << node.outputs['feat_out']
+ self.links_decomposition_Features[name] =\
+ self.node_decomposition.inputs['features'][name] << node.outputs['feat_out']
self.links_Boxplots_Features[name] =\
self.node_Boxplots_Features.inputs['features'][name] << node.outputs['feat_out']
@@ -628,8 +628,8 @@ Source code for WORC.tools.Evaluate
# All features should be input at once
if 'classification' in self.modus:
self.links_STest_Features[name].collapse = 'train'
+ self.links_decomposition_Features[name].collapse = 'train'
- self.links_decomposition_Features[name].collapse = 'train'
self.links_Boxplots_Features[name].collapse = 'train'
else:
# Feature are precomputed and given as sources
@@ -639,16 +639,17 @@ Source code for WORC.tools.Evaluate
self.links_STest_Features[name] =\
self.node_STest.inputs['features'][name] << node.output
- self.links_decomposition_Features[name] =\
- self.node_decomposition.inputs['features'][name] << node.output
+ self.links_decomposition_Features[name] =\
+ self.node_decomposition.inputs['features'][name] << node.output
+
self.links_Boxplots_Features[name] =\
self.node_Boxplots_Features.inputs['features'][name] << node.output
# All features should be input at once
if 'classification' in self.modus:
self.links_STest_Features[name].collapse = 'train'
+ self.links_decomposition_Features[name].collapse = 'train'
- self.links_decomposition_Features[name].collapse = 'train'
self.links_Boxplots_Features[name].collapse = 'train'
else:
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html b/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html
index 440871e0..6ba8c334 100644
--- a/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html
+++ b/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html
@@ -8,7 +8,7 @@
- WORC.tools.Slicer — WORC 3.4.5 documentation
+ WORC.tools.Slicer — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html b/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html
index 1a6242f8..de97124c 100644
--- a/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html
+++ b/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html
@@ -8,7 +8,7 @@
- WORC.tools.Transformix — WORC 3.4.5 documentation
+ WORC.tools.Transformix — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html b/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html
index 01945e09..ad86b30a 100644
--- a/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html
+++ b/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html
@@ -8,7 +8,7 @@
- WORC.tools.createfixedsplits — WORC 3.4.5 documentation
+ WORC.tools.createfixedsplits — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/_modules/index.html b/WORC/doc/_build/html/_modules/index.html
index 4090ef76..b928ae95 100644
--- a/WORC/doc/_build/html/_modules/index.html
+++ b/WORC/doc/_build/html/_modules/index.html
@@ -8,7 +8,7 @@
- Overview: module code — WORC 3.4.5 documentation
+ Overview: module code — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
@@ -185,6 +185,7 @@ All modules for which code is available
WORC.detectors.detectors
WORC.exampledata.create_example_data
WORC.exampledata.datadownloader
+WORC.export.hyper_params_exporter
WORC.facade.basicworc
WORC.facade.helpers.configbuilder
WORC.facade.helpers.exceptions
diff --git a/WORC/doc/_build/html/_sources/autogen/WORC.rst.txt b/WORC/doc/_build/html/_sources/autogen/WORC.rst.txt
index 53de38f4..6872a9c8 100644
--- a/WORC/doc/_build/html/_sources/autogen/WORC.rst.txt
+++ b/WORC/doc/_build/html/_sources/autogen/WORC.rst.txt
@@ -37,6 +37,7 @@ Subpackages
WORC.classification
WORC.detectors
WORC.exampledata
+ WORC.export
WORC.facade
WORC.fastrconfig
WORC.featureprocessing
diff --git a/WORC/doc/_build/html/_sources/index.rst.txt b/WORC/doc/_build/html/_sources/index.rst.txt
index 2870f00d..77ec657c 100644
--- a/WORC/doc/_build/html/_sources/index.rst.txt
+++ b/WORC/doc/_build/html/_sources/index.rst.txt
@@ -12,7 +12,9 @@ a radiomics study is effectively reduced to a black box with a push button, wher
your data and WORC will adapt the workflow to your application. Thus, WORC is especially suitable
for the fast development of signatures and probing datasets for new biomarkers.
-.. note:: Despite the name, besides classification, WORC can actually also be used for regression and multilabel classification. Survival is WIP.
+.. note:: Despite the name, besides classification, WORC can actually also be
+ used for regression and multilabel classification. See for more details the
+ :ref:`additonalfunctionality-chapter` chapter.
We aim to establish a general radiomics platform supporting easy
integration of other tools. With our modular build and support of
@@ -37,7 +39,8 @@ For more information regarding radiomics, we recommend the following book chapte
`M. P. A. Starmans, S. R. van der Voort, J. M. Castillo T., J. F. Veenland, S. Klein, W. J. Niessen. "Radiomics: Data mining using quantitative medical image features" Handbook of Medical Image Computing and Computer Assisted Intervention (MICCAI) 2020 `_
- `M. P. A. Starmans, C. J. Els, F. Fiduzi, W. J. Niessen, S.Klein, R. S. Dwarkasing. "Radiomics model to predict hepatocellular carcinoma on liver MRI of high-risk patients in surveillance: a proof-of-concept study." European Congress of Radiology (ECR) 2020 `_
`M. P. A. Starmans, R. Miclea, S. R. van der Voort, W. J. Niessen, M. G. Thomeer and S. Klein. "Classification of malignant and benign liver tumors using a radiomics approach." Proceedings Volume 10574, Medical Imaging 2018: Image Processing; 105741D (2018) . `_
- `M. J. M. Timbergen, M. P. A. Starmans, M. Vos, S. R. van der Voort, G. A. Padmos, W. Kessels, W. J. Niessen, G. J. L. H. van Leenders, D. J. Grünhagen, S. Sleijfer, C. Verhoef, S. Klein, J. J. Visser. "Mutation stratification of desmoid-type fibromatosis using a Radiomics approach." Desmoid Tumor Research Foundation (DTRF) 2018. `_
-
- M. Vos, M. P. A. Starmans, M. J.M. Timbergen, S. R. van der Voort, G. A. Padmos, W. Kessels, W. J. Niessen, G. J. L. H. van Leenders, D. J. Grünhagen, S. Sleijfer, C. Verhoef, S. Klein, J. J. Visser. "Differentiating well-differentiated liposarcomas from lipomas using a Radiomics approach." Connective Tissue Oncology Society (CTOS) conference 2018.
-
- M. J. M. Timbergen, M. P. A. Starmans, M. Vos, S. R. van der Voort, G. A. Padmos, W. Kessels, W. J. Niessen, G. J. L. H. van Leenders, D. J. Grünhagen, S. Sleijfer, C. Verhoef, S. Klein, J. J. Visser. "Mutation stratification of desmoid-type fibromatosis using a Radiomics approach." Connective Tissue Oncology Society (CTOS) conference 2018.
-
WORC is made possible by contributions from the following people: Martijn P. A. Starmans, Sebastian R. van der Voort, Thomas Phil, and Stefan Klein
diff --git a/WORC/doc/_build/html/_sources/static/user_manual.rst.txt b/WORC/doc/_build/html/_sources/static/user_manual.rst.txt
index e2a03444..a8cb3dae 100644
--- a/WORC/doc/_build/html/_sources/static/user_manual.rst.txt
+++ b/WORC/doc/_build/html/_sources/static/user_manual.rst.txt
@@ -294,7 +294,7 @@ Within these evaluation settings, the following performance evaluation methods a
In bootstrapping, 95% confidence intervals are created using the ''standard'' method according to a normal distribution: see Table 6, method 1 in `Efron B., Tibshirani R. Bootstrap Methods for Standard Errors,
Confidence Intervals, and Other Measures of Statistical Accuracy, Statistical Science Vol.1, No,1, 54-77, 1986`.
-2. ROC curve with 95% confidence intervals using the fixed-width bands method, see `Macskassy S. A., Provost F., Rosset S. ROC Confidence Bands: An Empirical Evaluation. In: Proceedings of the 22nd international conference on Machine learning. 2005.`
+2. ROC and PRC curves with 95% confidence intervals using the fixed-width bands method, see `Macskassy S. A., Provost F., Rosset S. ROC Confidence Bands: An Empirical Evaluation. In: Proceedings of the 22nd international conference on Machine learning. 2005.`
3. Univariate statistical testing of the features using:
diff --git a/WORC/doc/_build/html/_static/documentation_options.js b/WORC/doc/_build/html/_static/documentation_options.js
index 33eafdf3..1d0981c2 100644
--- a/WORC/doc/_build/html/_static/documentation_options.js
+++ b/WORC/doc/_build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '3.4.5',
+ VERSION: '3.5.0',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
diff --git a/WORC/doc/_build/html/autogen/WORC.IOparser.html b/WORC/doc/_build/html/autogen/WORC.IOparser.html
index 25f88af6..120cb57b 100644
--- a/WORC/doc/_build/html/autogen/WORC.IOparser.html
+++ b/WORC/doc/_build/html/autogen/WORC.IOparser.html
@@ -8,7 +8,7 @@
- IOparser Package — WORC 3.4.5 documentation
+ IOparser Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -119,6 +119,7 @@
classification Package
detectors Package
exampledata Package
+export Package
facade Package
fastrconfig Package
featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.classification.html b/WORC/doc/_build/html/autogen/WORC.classification.html
index 66ac0136..92008c45 100644
--- a/WORC/doc/_build/html/autogen/WORC.classification.html
+++ b/WORC/doc/_build/html/autogen/WORC.classification.html
@@ -8,7 +8,7 @@
- classification Package — WORC 3.4.5 documentation
+ classification Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -124,6 +124,7 @@
detectors Package
exampledata Package
+export Package
facade Package
fastrconfig Package
featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.config.html b/WORC/doc/_build/html/autogen/WORC.config.html
index fb37156b..6ceb0649 100644
--- a/WORC/doc/_build/html/autogen/WORC.config.html
+++ b/WORC/doc/_build/html/autogen/WORC.config.html
@@ -8,7 +8,7 @@
- <no title> — WORC 3.4.5 documentation
+ <no title> — WORC 3.5.0 documentation
@@ -62,7 +62,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/autogen/WORC.detectors.html b/WORC/doc/_build/html/autogen/WORC.detectors.html
index d373c411..a8cf4925 100644
--- a/WORC/doc/_build/html/autogen/WORC.detectors.html
+++ b/WORC/doc/_build/html/autogen/WORC.detectors.html
@@ -8,7 +8,7 @@
- detectors Package — WORC 3.4.5 documentation
+ detectors Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -113,6 +113,7 @@
exampledata Package
+export Package
facade Package
fastrconfig Package
featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.exampledata.html b/WORC/doc/_build/html/autogen/WORC.exampledata.html
index 2131b268..e8f1602e 100644
--- a/WORC/doc/_build/html/autogen/WORC.exampledata.html
+++ b/WORC/doc/_build/html/autogen/WORC.exampledata.html
@@ -8,7 +8,7 @@
- exampledata Package — WORC 3.4.5 documentation
+ exampledata Package — WORC 3.5.0 documentation
@@ -36,7 +36,7 @@
-
+
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -114,6 +114,7 @@
datadownloader Moduleexport Package
facade Package
fastrconfig Package
featureprocessing Package
@@ -234,7 +235,7 @@ exampledata Package
- Next
+ Next
Previous
diff --git a/WORC/doc/_build/html/autogen/WORC.facade.html b/WORC/doc/_build/html/autogen/WORC.facade.html
index 0d291427..984195ba 100644
--- a/WORC/doc/_build/html/autogen/WORC.facade.html
+++ b/WORC/doc/_build/html/autogen/WORC.facade.html
@@ -8,7 +8,7 @@
- facade Package — WORC 3.4.5 documentation
+ facade Package — WORC 3.5.0 documentation
@@ -37,7 +37,7 @@
-
+
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
classification Package
detectors Package
exampledata Package
+export Package
facade Package
facade Packagebasicworc Module
Ranking of patients based on percentage / posterior
Decompositions (e.g. PCA, t-SNE)
-See the WORC documentation for additional info.
+See the WORC documentation for additional info.
diff --git a/WORC/doc/_build/html/autogen/WORC.featureprocessing.html b/WORC/doc/_build/html/autogen/WORC.featureprocessing.html
index 04816df0..71ebd779 100644
--- a/WORC/doc/_build/html/autogen/WORC.featureprocessing.html
+++ b/WORC/doc/_build/html/autogen/WORC.featureprocessing.html
@@ -8,7 +8,7 @@
- featureprocessing Package — WORC 3.4.5 documentation
+ featureprocessing Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
classification Package
detectors Package
exampledata Package
+export Package
facade Package
fastrconfig Package
featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.html b/WORC/doc/_build/html/autogen/WORC.html
index e853aa2f..cd76b6a0 100644
--- a/WORC/doc/_build/html/autogen/WORC.html
+++ b/WORC/doc/_build/html/autogen/WORC.html
@@ -8,7 +8,7 @@
- WORC Package — WORC 3.4.5 documentation
+ WORC Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
@@ -578,6 +579,10 @@ Subpackagesdatadownloader Module
+export Package
+
facade Package
facade Packagebasicworc Moduleplotting Package — WORC 3.4.5 documentation
+ plotting Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
@@ -538,7 +539,7 @@
-
-
WORC.plotting.plot_images.slicer(image, mask=None, output_name=None, output_name_zoom=None, thresholds=[-240, 160], zoomfactor=4, dpi=500, normalize=False, expand=False, boundary=False, square=False, flip=True, rot90=0, alpha=0.4, axis='axial', index=None, color='cyan')[source]¶
+WORC.plotting.plot_images.slicer(image, mask=None, output_name=None, output_name_zoom=None, thresholds=[-240, 160], zoomfactor=4, dpi=500, normalize=False, expand=False, boundary=False, square=False, flip=True, rot90=0, alpha=0.4, axis='axial', index=None, color='cyan', radius=2)[source]¶
Plot slice of image where mask is largest, with mask as overlay.
image and mask should both be arrays
diff --git a/WORC/doc/_build/html/autogen/WORC.processing.html b/WORC/doc/_build/html/autogen/WORC.processing.html
index b0a7aea5..6f34f570 100644
--- a/WORC/doc/_build/html/autogen/WORC.processing.html
+++ b/WORC/doc/_build/html/autogen/WORC.processing.html
@@ -8,7 +8,7 @@
- processing Package — WORC 3.4.5 documentation
+ processing Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.resources.fastr_tests.html b/WORC/doc/_build/html/autogen/WORC.resources.fastr_tests.html
index ac349337..d1f9ee00 100644
--- a/WORC/doc/_build/html/autogen/WORC.resources.fastr_tests.html
+++ b/WORC/doc/_build/html/autogen/WORC.resources.fastr_tests.html
@@ -8,7 +8,7 @@
- fastr_tests Package — WORC 3.4.5 documentation
+ fastr_tests Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.resources.fastr_tools.html b/WORC/doc/_build/html/autogen/WORC.resources.fastr_tools.html
index 609d4cec..e218762d 100644
--- a/WORC/doc/_build/html/autogen/WORC.resources.fastr_tools.html
+++ b/WORC/doc/_build/html/autogen/WORC.resources.fastr_tools.html
@@ -8,7 +8,7 @@
- fastr_tools Package — WORC 3.4.5 documentation
+ fastr_tools Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.resources.html b/WORC/doc/_build/html/autogen/WORC.resources.html
index 877baba7..ac656c76 100644
--- a/WORC/doc/_build/html/autogen/WORC.resources.html
+++ b/WORC/doc/_build/html/autogen/WORC.resources.html
@@ -8,7 +8,7 @@
- resources Package — WORC 3.4.5 documentation
+ resources Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
diff --git a/WORC/doc/_build/html/autogen/WORC.tools.html b/WORC/doc/_build/html/autogen/WORC.tools.html
index 6a6f0c12..ea7350b0 100644
--- a/WORC/doc/_build/html/autogen/WORC.tools.html
+++ b/WORC/doc/_build/html/autogen/WORC.tools.html
@@ -8,7 +8,7 @@
- tools Package — WORC 3.4.5 documentation
+ tools Package — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -110,6 +110,7 @@
- classification Package
- detectors Package
- exampledata Package
+- export Package
- facade Package
- fastrconfig Package
- featureprocessing Package
diff --git a/WORC/doc/_build/html/genindex.html b/WORC/doc/_build/html/genindex.html
index b9fb49a5..d91a03fb 100644
--- a/WORC/doc/_build/html/genindex.html
+++ b/WORC/doc/_build/html/genindex.html
@@ -9,7 +9,7 @@
- Index — WORC 3.4.5 documentation
+ Index — WORC 3.5.0 documentation
@@ -63,7 +63,7 @@
- 3.4.5
+ 3.5.0
@@ -857,6 +857,8 @@ E
- exp_uniform (class in WORC.classification.AdvancedSampler)
+
+ - export_hyper_params_to_latex() (in module WORC.export.hyper_params_exporter)
- extract_boundary() (in module WORC.plotting.plot_images)
@@ -1459,6 +1461,8 @@ W
- WORC.exampledata.create_example_data (module)
- WORC.exampledata.datadownloader (module)
+
+ - WORC.export.hyper_params_exporter (module)
- WORC.facade (module)
@@ -1517,11 +1521,11 @@ W
- WORC.IOparser.file_io (module)
- WORC.plotting (module)
-
- - WORC.plotting.compute_CI (module)
+ - WORC.plotting.compute_CI (module)
+
- WORC.plotting.linstretch (module)
- WORC.plotting.plot_barchart (module)
diff --git a/WORC/doc/_build/html/index.html b/WORC/doc/_build/html/index.html
index 3a38a896..d014a85f 100644
--- a/WORC/doc/_build/html/index.html
+++ b/WORC/doc/_build/html/index.html
@@ -8,7 +8,7 @@
-
WORC: Workflow for Optimal Radiomics Classification — WORC 3.4.5 documentation
+ WORC: Workflow for Optimal Radiomics Classification — WORC 3.5.0 documentation
@@ -63,7 +63,7 @@
- 3.4.5
+ 3.5.0
@@ -177,7 +177,9 @@ Welcome to the WORC documentation!
Note
-Despite the name, besides classification, WORC can actually also be used for regression and multilabel classification. Survival is WIP.
+Despite the name, besides classification, WORC can actually also be
+used for regression and multilabel classification. See for more details the
+Additional functionality chapter.
We aim to establish a general radiomics platform supporting easy
integration of other tools. With our modular build and support of
@@ -196,11 +198,14 @@
Welcome to the WORC documentation!M. P. A. Starmans, S. R. van der Voort, J. M. Castillo T., J. F. Veenland, S. Klein, W. J. Niessen. “Radiomics: Data mining using quantitative medical image features” Handbook of Medical Image Computing and Computer Assisted Intervention (MICCAI) 2020
-
The article on WORC is currently in preparation. WORC has been presented at the following conferences:
+The article on WORC is currently in preparation. WORC among others has been
+presented at the following conferences:
+
+
WORC has among others been used in the following studies:
@@ -209,32 +214,10 @@ Welcome to the WORC documentation!J. M. Castillo T., M. Arif, W. J. Niessen, S. Klein, C. H. Bangma, I. G. Schoots, J. F. Veenland. “A Multi-Center, Multi-Vendor Study to Evaluate the Generalizability of a Radiomics Model for Classifying Prostate Cancer: High Grade vs. Low Grade.” Diagnostics 2021
-
-
-
-
-
-
-
-
-
-
-
-Vos, M. P. A. Starmans, M. J.M. Timbergen, S. R. van der Voort, G. A. Padmos, W. Kessels, W. J. Niessen, G. J. L. H. van Leenders, D. J. Grünhagen, S. Sleijfer, C. Verhoef, S. Klein, J. J. Visser. “Differentiating well-differentiated liposarcomas from lipomas using a Radiomics approach.” Connective Tissue Oncology Society (CTOS) conference 2018.
-
-
-
-Timbergen, M. P. A. Starmans, M. Vos, S. R. van der Voort, G. A. Padmos, W. Kessels, W. J. Niessen, G. J. L. H. van Leenders, D. J. Grünhagen, S. Sleijfer, C. Verhoef, S. Klein, J. J. Visser. “Mutation stratification of desmoid-type fibromatosis using a Radiomics approach.” Connective Tissue Oncology Society (CTOS) conference 2018.
-
-
WORC is made possible by contributions from the following people: Martijn P. A. Starmans, Sebastian R. van der Voort, Thomas Phil, and Stefan Klein
@@ -333,9 +316,11 @@ WORC DocumentationAdditional functionality
- FAQ
@@ -365,156 +350,162 @@ WORC DocumentationResource File Formats
- Changelog
-- 3.4.5 - 2021-07-09
+- 3.5.0 - 2021-08-18
-- 3.4.4 - 2021-07-01
+- 3.4.5 - 2021-07-09
-- 3.4.3 - 2021-06-02
+- 3.4.4 - 2021-07-01
-- 3.4.2 - 2021-05-27
-- Fixed
-- Added
+- 3.4.3 - 2021-06-02
-- 3.4.1 - 2021-05-18
-- Fixed
-- Changed
+- 3.4.2 - 2021-05-27
-- 3.4.0 - 2021-02-02
+- 3.4.1 - 2021-05-18
-- 3.3.5 - 2020-10-21
+- 3.4.0 - 2021-02-02
-- 3.3.4 - 2020-10-06
+- 3.3.5 - 2020-10-21
-- 3.3.3 - 2020-09-11
+- 3.3.4 - 2020-10-06
-- 3.3.2 - 2020-08-19
-- Fixed
-- Added
-- Changed
+- 3.3.3 - 2020-09-11
-- 3.3.1 - 2020-07-31
-- Changed
-- Fixed
+- 3.3.2 - 2020-08-19
-- 3.3.0 - 2020-07-28
-- Added
+- 3.3.1 - 2020-07-31
-- 3.2.2 - 2020-07-14
+- 3.3.0 - 2020-07-28
-- 3.2.1 - 2020-07-02
+- 3.2.2 - 2020-07-14
-- 3.2.0 - 2020-06-26
+- 3.2.1 - 2020-07-02
-- 3.1.4 - 2020-05-26
+- 3.2.0 - 2020-06-26
-- 3.1.3 - 2020-01-24
+- 3.1.4 - 2020-05-26
-- 3.1.2 - 2019-12-09
+- 3.1.3 - 2020-01-24
-- 3.1.1 - 2019-11-28
+- 3.1.2 - 2019-12-09
-- 3.1.0 - 2019-10-16
+- 3.1.1 - 2019-11-28
-- 3.0.0 - 2019-05-08
+- 3.1.0 - 2019-10-16
-- 2.1.3 - 2019-04-08
-- Changed
+- 3.0.0 - 2019-05-08
-- 2.1.2 - 2019-04-02
-- Added
-- Changed
-- Fixed
+- 2.1.3 - 2019-04-08
-- 2.1.1 - 2019-02-15
+- 2.1.2 - 2019-04-02
-- 2.1.0 - 2018-08-09
+- 2.1.1 - 2019-02-15
-- 2.0.0 - 2018-02-13
@@ -569,6 +560,10 @@ WORC Developer Module referencedatadownloader Module
+- export Package
+
- facade Package
facade Packagebasicworc ModulePython Module Index — WORC 3.4.5 documentation
+ Python Module Index — WORC 3.5.0 documentation
@@ -65,7 +65,7 @@
- 3.4.5
+ 3.5.0
@@ -265,6 +265,11 @@ Python Module Index
WORC.exampledata.datadownloader
+
+
+ WORC.export.hyper_params_exporter
+
diff --git a/WORC/doc/_build/html/search.html b/WORC/doc/_build/html/search.html
index 76381b72..ed4e0c2d 100644
--- a/WORC/doc/_build/html/search.html
+++ b/WORC/doc/_build/html/search.html
@@ -8,7 +8,7 @@
- Search — WORC 3.4.5 documentation
+ Search — WORC 3.5.0 documentation
@@ -63,7 +63,7 @@
- 3.4.5
+ 3.5.0
diff --git a/WORC/doc/_build/html/searchindex.js b/WORC/doc/_build/html/searchindex.js
index 78b5b125..6e2e48e0 100644
--- a/WORC/doc/_build/html/searchindex.js
+++ b/WORC/doc/_build/html/searchindex.js
@@ -1 +1 @@
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Manual"],titleterms:{"0rc1":62,"boolean":66,"class":12,"default":66,"export":6,"function":61,"import":70,Added:62,Adding:65,The:[70,71],actual:70,addexcept:[0,66],addit:61,advancedsampl:2,alter:66,analysi:[64,70],arrai:66,attribut:71,basicworc:7,begin:66,bigr:66,bin:67,binari:67,bootstrap:63,calcfeatures_test:14,can:66,chang:62,changelog:62,choic:67,classif:[2,60,61,63,64],classifi:[],cluster:66,column:66,combat:[10,61,63],command:71,compon:64,comput:66,compute_ci:11,config_io_classifi:1,config_io_combat:1,config_io_pyradiom:1,config_preprocess:1,config_segmentix:1,config_worc:1,configbuild:8,configur:63,construct:71,construct_classifi:2,content:63,convert:66,crash:66,create_example_data:5,createfixedsplit:[2,18],creation:63,crossval:2,crossvalid:63,data:[64,65,71],datadownload:5,debug:71,decomposit:10,definit:71,delet:66,delong:16,depend:67,detector:4,develop:[60,65],dicom:67,differ:[66,67],dimension:64,document:[60,65],elastix:18,elastix_para:71,elastix_test:14,ensembl:63,entri:66,error:66,estim:[],evalu:[18,63,71],exampl:[65,71],exampledata:5,except:8,execut:[66,71],experi:[66,70],extract:67,extractnlargestblobsn:12,facad:7,fals:66,faq:66,fastr:69,fastr_test:14,fastr_tool:15,fastrconfig:9,feat_out_0:66,featpreprocess:63,featsel:63,featur:[61,64,65,66,67,71],featureconvert:10,featureprocess:10,featuresc:63,file:[66,68,71],file_io:1,filter:67,first:66,fitandscor:2,fix:[62,67],format:[66,68],found:66,from:64,full:67,function_bas:66,gabor:67,gaussian:67,gener:63,given:66,glcm:67,gldm:67,glrlm:67,glszm:67,grai:67,groupwis:64,guid:70,hdf5:66,helper:[8,12],histogram:67,hyper_params_export:6,hyperoptim:[63,65],icc:[],iccthreshold:10,imag:[61,67,71],imagefeatur:63,imput:[10,63,64],indexerror:66,indic:[60,66],infer:18,input:[70,71],instal:[66,70],instead:66,integ:66,interact:[63,71],introduct:[63,69],iopars:1,job:66,keep:66,label:[63,66,71],label_process:12,labels_from_this_fil:66,laplacian:67,lbp:67,learn:64,length:67,level:67,lib:66,like:66,line:66,linstretch:11,local:67,log:67,look:66,machin:64,manual:71,mask:71,matrix:67,metadata:71,method:[64,65],metric:2,mine:64,model:64,modul:[0,1,2,4,5,6,7,8,9,10,11,12,14,16,17,18,19,60,66],modular:69,modulenotfounderror:66,multilabel:61,must:66,name:66,need:66,neighborhood:67,network:71,ngtdm:67,numpi:66,obj:66,object:71,objectsampl:2,occur:67,onehotencod:[63,64],onehotencoderwrapp:10,ones:66,optim:[60,69],orient:67,other:[66,67],own:66,packag:[0,1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,66,70],paramet:67,parameter_optim:2,patient:66,pattern:67,pca:64,phase:67,plot:11,plot_barchart:11,plot_boxplot_featur:11,plot_boxplot_perform:11,plot_error:11,plot_estimator_perform:11,plot_hyperparamet:11,plot_imag:11,plot_pvalues_featur:11,plot_ranked_scor:11,plot_roc:11,plotminmaxrespons:11,preflightcheck:19,preprocess:[12,61,63],preprocessor:10,princip:64,process:[8,12,65],pyradiom:63,queue:66,quick:70,radiom:[60,67,69],rankedsvm:[],reduct:64,refer:[60,61],registr:61,regress:[61,64],regressor:2,relief:[10,64],resampl:[63,64],resourc:[13,68],result:70,roi:67,run:[67,70],scale:[61,64],scaler:10,scatterplot:[],searchcv:2,segment:71,segmentix:[12,63],segmentix_test:14,select:[64,66,67],selectfeatgroup:63,selectgroup:10,selectindividu:10,semant:[67,71],shape:67,simpleworc:[7,66],site:66,size:67,slicer:18,some:66,sourc:71,standard:[66,69],start:70,statist:[16,64],statisticaltestfeatur:10,statisticaltestthreshold:10,submit:66,subpackag:[0,7,13],surviv:64,tabl:60,tell:66,terminolog:69,test:[17,64,65],test_combat:17,test_help:17,test_iccthreshold:17,test_plot_error:17,test_valid:17,textur:67,tip:70,tone:67,tool:18,toolbox:65,trainclassifi:2,transformix:18,trick:70,tutori:70,type:66,univari:64,unreleas:[],use:66,used:66,user:[60,71],valid:19,varianc:64,variancethreshold:10,vessel:67,wavelet:67,welcom:60,where:66,width:67,worc:[0,60,66,71],worc_config:9,worckeyerror:66,worctutorialsimple_travis_multiclass:[],worctutorialsimple_travis_regress:[],worctutorialsimple_unittest_multiclass:17,worctutorialsimple_unittest_regress:17,worcvalueerror:66,work:66,workflow:60,would:66,your:[66,71],zone:67}})
\ No newline at end of file
diff --git a/WORC/doc/_build/html/static/changelog.html b/WORC/doc/_build/html/static/changelog.html
index a9aa173f..3c8da0a3 100644
--- a/WORC/doc/_build/html/static/changelog.html
+++ b/WORC/doc/_build/html/static/changelog.html
@@ -8,7 +8,7 @@
- Changelog — WORC 3.4.5 documentation
+ Changelog — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -99,156 +99,162 @@
- Developer documentation
- Resource File Formats
- Changelog
-- 3.4.5 - 2021-07-09
+- 3.5.0 - 2021-08-18
-- 3.4.4 - 2021-07-01
+- 3.4.5 - 2021-07-09
-- 3.4.3 - 2021-06-02
+- 3.4.4 - 2021-07-01
-- 3.4.2 - 2021-05-27
-- Fixed
-- Added
+- 3.4.3 - 2021-06-02
-- 3.4.1 - 2021-05-18
-- Fixed
-- Changed
+- 3.4.2 - 2021-05-27
-- 3.4.0 - 2021-02-02
+- 3.4.1 - 2021-05-18
-- 3.3.5 - 2020-10-21
+- 3.4.0 - 2021-02-02
-- 3.3.4 - 2020-10-06
+- 3.3.5 - 2020-10-21
-- 3.3.3 - 2020-09-11
+- 3.3.4 - 2020-10-06
-- 3.3.2 - 2020-08-19
-- Fixed
-- Added
-- Changed
+- 3.3.3 - 2020-09-11
-- 3.3.1 - 2020-07-31
-- Changed
-- Fixed
+- 3.3.2 - 2020-08-19
-- 3.3.0 - 2020-07-28
-- Added
+- 3.3.1 - 2020-07-31
-- 3.2.2 - 2020-07-14
+- 3.3.0 - 2020-07-28
-- 3.2.1 - 2020-07-02
+- 3.2.2 - 2020-07-14
-- 3.2.0 - 2020-06-26
+- 3.2.1 - 2020-07-02
-- 3.1.4 - 2020-05-26
+- 3.2.0 - 2020-06-26
-- 3.1.3 - 2020-01-24
+- 3.1.4 - 2020-05-26
-- 3.1.2 - 2019-12-09
+- 3.1.3 - 2020-01-24
-- 3.1.1 - 2019-11-28
+- 3.1.2 - 2019-12-09
-- 3.1.0 - 2019-10-16
+- 3.1.1 - 2019-11-28
-- 3.0.0 - 2019-05-08
+- 3.1.0 - 2019-10-16
-- 2.1.3 - 2019-04-08
-- Changed
+- 3.0.0 - 2019-05-08
-- 2.1.2 - 2019-04-02
-- Added
-- Changed
-- Fixed
+- 2.1.3 - 2019-04-08
-- 2.1.1 - 2019-02-15
+- 2.1.2 - 2019-04-02
-- 2.1.0 - 2018-08-09
+- 2.1.1 - 2019-02-15
-- 2.0.0 - 2018-02-13
@@ -325,36 +331,62 @@ ChangelogKeep a Changelog
and this project adheres to Semantic Versioning
-3.4.5 - 2021-07-09¶
-
-Unit tests moved from Travis to Github Workflow from this verion on.
-
+3.5.0 - 2021-08-18¶
Fixed¶
-Bug in plotting images when ranking the posteriors or percentages.
Linting issues.
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¶
-Removed deprecated scatterplot, RankedSVM functions.
Defaults for splitting jobs in hyperoptimization: now more parallelized.
+
+
+Added¶
+
+Documentation on additional functionality.
-3.4.4 - 2021-07-01¶
+3.4.5 - 2021-07-09¶
+
+Unit tests moved from Travis to Github Workflow from this verion on.
+
Fixed¶
+Bug in plotting images when ranking the posteriors or percentages.
Linting issues.
+
+
+Changed¶
+
+Removed deprecated scatterplot, RankedSVM functions.
+
+
+
+3.4.4 - 2021-07-01¶
+
+Fixed¶
+
Bug where most recent added estimators were not valid in SimpleWORC.
SelectorMixin is now imported directly from sklearn.feature_selection,
as sklearn.feature_selection.base is deprecated and will be removed.
-
-Changed¶
+
+Changed¶
Apply variance threshold selection before feature scaling, otherwise
variance is always the same for all features.
Changed
use changed from 0.20 to 0.275.
-
-Added¶
+
+Added¶
Functionality in plotting images functions.
Documentation on how to use your own features.
-
-3.4.3 - 2021-06-02¶
-
-Fixed¶
+
+3.4.3 - 2021-06-02¶
+
+Fixed¶
SimpleWORC and BasicWORC now support multilabel workflows.
SimpleWORC and BasicWORC now support use of masks.
-
-
-3.4.2 - 2021-05-27¶
-
-Fixed¶
+
+3.4.2 - 2021-05-27¶
+
+Fixed¶
Bug in flattening of plot_ranked_posteriors function.
Bug in plot_images: could not handle 2D images when applying slicing.
Fixed¶
Preflighcheck now also accepts labels from txt or XNAT.
-
-
-3.4.1 - 2021-05-18¶
-
-Fixed¶
+
+3.4.1 - 2021-05-18¶
+
+Fixed¶
Bugfix when PCA cannot be fitted.
Bugfix when using LOO cross-validation in performance evaluation.
Fixed
Several fixes for using 2D images.
-
-Changed¶
+
+Changed¶
Reverted back to weighted f1-score without predictproba for optimization,
more stable.
Updated regressors in SimpleWORC.
-
-
-3.4.0 - 2021-02-02¶
-
-Fixed¶
+
+3.4.0 - 2021-02-02¶
+
+Fixed¶
MAJOR: Bug in SearchCV sorting of output files.
Bug in StatisticalTest for Manhattan plot.
Fixed
Fix random states in boosting estimators.
-
-Changed¶
+
+Changed¶
IMPORTANT: previously, used f1_score based on estimator.predict function.
Now, use predict_proba.
New defaults for random-search and ensemble.
-
-
-3.3.5 - 2020-10-21¶
-
-Fixed¶
+
+3.3.5 - 2020-10-21¶
+
+Fixed¶
Some function cleaning: removing redundant parts / variables.
-
-Changed¶
+
+Changed¶
Part of developper documentation for addinf methods to hyperoptimization.
Default config: SelectFromModel incorporated, so now also use
that in feature selection step.
-
-
-3.3.4 - 2020-10-06¶
-
-Fixed¶
+
+3.3.4 - 2020-10-06¶
+
+Fixed¶
Bugfixes in some error messages.
If a classifier cannot give a score, use the prediction instead.
Fixed
Bugfix: use f1-weighted score in SimpleWORC binary classification.
-
-Changed¶
+
+Changed¶
There are no longer ‘’patient_features’’ in PREDICT: these are extracted
from the DICOM tags and are thus now called ‘’dicom_features.
As bootstrapping is now more efficient, increase default to 1000 iterations.
-
-
-3.3.3 - 2020-09-11¶
-
-Fixed¶
+
+3.3.3 - 2020-09-11¶
+
+Fixed¶
-
-Changed¶
+
+Changed¶
By default, semantic features are skipped in scaling, as the robust scaler
cannot deal well with categorical variables.
Wrapped scalers in single WORC scaler object to allow above for all scalers.
-
-
-3.3.2 - 2020-08-19¶
-
-Fixed¶
+
+3.3.2 - 2020-08-19¶
+
+Fixed¶
Bug in fit and score when using scaling: was incorrectly parsed as string
and always set to None.
Fixed
Typo in configuration documentation.
-
-Added¶
+
+Added¶
New type of scaler (robust z-scoring)
Resampling of image and mask in preprocessing (preprocessing and segmentix
nodes)
-
-
-3.3.1 - 2020-07-31¶
-
-Changed¶
+
+3.3.1 - 2020-07-31¶
+
+Changed¶
-
-
-3.3.0 - 2020-07-28¶
-
-Added¶
+
+3.3.0 - 2020-07-28¶
+
+Added¶
Graphviz vizualization of network is now nicely grouped.
Properly integrated ObjectSampler: various resampling options now available.
Added
FAQ version to documentation
-
-Changed¶
+
+Changed¶
Upgraded to new versions of sklearn (0.23.1) and imbalanced learn (0.7.0)
Some defaults, based on computation time.
ChangedL1 penalty does not work with new standard LR solver. Removed L1 penalty.
-
-
-3.2.2 - 2020-07-14¶
-
-Added¶
+
+3.2.2 - 2020-07-14¶
+
+Added¶
In classify node, when using temporary saves, start from where
the process previously stopped instead of from the beginning.
Imputation to ComBat.
-
-Changed¶
+
+Changed¶
-
-
-3.2.1 - 2020-07-02¶
-
-Added¶
+
+3.2.1 - 2020-07-02¶
+
+Added¶
Major documentation update.
-
-Changed¶
+
+Changed¶
-
-
-3.2.0 - 2020-06-26¶
-
-Added¶
+
+3.2.0 - 2020-06-26¶
+
+Added¶
Labelprocessing can now also handle having patient ID in the feature files.
Was required for ComBat.
-
-Changed¶
+
+Changed¶
Output of plot_SVM function is better ordered.
Several defaults, as we now have PyRadiomics fully embedded, resulting in
@@ -731,8 +763,8 @@
ChangedNo more overrides for the full config, as the default now is the full config.
-
-
-3.1.4 - 2020-05-26¶
-
-Added¶
+
+3.1.4 - 2020-05-26¶
+
+Added¶
Catch error if number of segmentations supplied does not match number of
images.
Added
Combat: in WORK workflow.
-
-Changed¶
+
+Changed¶
Resampling of objects is now after feature selection.
Made plot_SVM function more memory efficient.
ChangedSegmentix tool is cleaned up. Segmentix script is moved to processing.
-
-
-3.1.3 - 2020-01-24¶
-
-Added¶
+
+3.1.3 - 2020-01-24¶
+
+Added¶
Some options for the plot_images slicer function.
Validators to check your inputs before executing experiment.
Added
Error when config file cannot be found.
-
-Changed¶
+
+Changed¶
Preprocessor slows down progress and is not always neccesary. Made it optional.
Moved the preprocessor to the SearchCV script to do once on the training set,
@@ -833,18 +865,18 @@
ChangedJoblib now uses by default only 1 core and threading backend.
-
-Fixed¶
+
+Fixed¶
Bug in patient naming of plotting function: if ensembling was done in training,
do not re-ensemble.
-
-3.1.2 - 2019-12-09¶
-
-Added¶
+
+3.1.2 - 2019-12-09¶
+
+Added¶
Support for Oncoradiomics RadiomiX tool
Groupwise Search includes GLDZM, Fractal, location, NGTDM, NGLDM, wavelet,
@@ -854,38 +886,38 @@
Added
are ran. Mostly to detect possible faults/errors in the data.
-
-Changed¶
+
+Changed¶
On runtime, copy config.d file if it does not exist yet.
-
-Fixed¶
+
+Fixed¶
KNN imputation gave an error if >80% of the feature values were missing.
Added preprocessing function to remove these features.
-
-3.1.1 - 2019-11-28¶
-
-Added¶
+
+3.1.1 - 2019-11-28¶
+
+Added¶
Travis continuous integration for Windows.
Removed RT Struct Reader, as it was buggy and not used.
-
-Changed¶
+
+Changed¶
SimpleWORC now properly uses the fastr FileSystem plugin, instead
of supplying the absolute filepaths.
-
-
-3.1.0 - 2019-10-16¶
-
-Added¶
+
+3.1.0 - 2019-10-16¶
+
+Added¶
Thresholding option in plot_SVM.
NPV (Negative Preditive Value) to classification metrics.
Added
Various detectors.
-
-Changed¶
+
+Changed¶
Plot_SVR is removed: it’s now embedded in plot_SVM.
Moved statistical feature selection to last step in fit and score.
ChangedUse inspect to find packagedir
-
-
-3.0.0 - 2019-05-08¶
-
-Added¶
+
+3.0.0 - 2019-05-08¶
+
+Added¶
Now ported to Python3.6+ (Python 2 is no longer supported!). Thereby also
to fastr3.
Added
Config is now also a sink.
-
-Changed¶
+
+Changed¶
PCE and DTI node removed, as they were not open source.
Pinfo file can now also be a csv. Txt is still supported.
ChangedWhen the conffidence interval cannot be computed, just use the mean.
-
-
-2.1.3 - 2019-04-08¶
-
-Changed¶
+
+2.1.3 - 2019-04-08¶
+
+Changed¶
PREDICT was updated, so had to update the requirements. Changed it
to a minimum of PREDICT to prevent these issues in the future.
-
-2.1.2 - 2019-04-02¶
-
-Added¶
+
+2.1.2 - 2019-04-02¶
+
+Added¶
Dummy workflow in segmentix and calcfeatures PREDICT tools.
Added several new PREDICT parameters.
Slicer tool.
-
-Changed¶
+
+Changed¶
Memory for elastix tool is now larger.
-
-
-2.1.1 - 2019-02-15¶
-
-Added¶
+
+2.1.1 - 2019-02-15¶
+
+Added¶
Several new PREDICT variables to the config.
Multilabel classification workflow.
Added
RankedSVM multilabel classification and Relief feature selection.
-
-Changed¶
+
+Changed¶
Major reduction in memory usage, especially due to PREDICT updates.
Only use first configuration in the classify config.
Outputs are now in multiple subfolders instead of one big folder.
-
-Fixed¶
+
+Fixed¶
Minor bug in test workflow: needed str of label in appending to classify.
There was a bug in using a .ini file as a config.
-
-2.1.0 - 2018-08-09¶
-
-Added¶
+
+2.1.0 - 2018-08-09¶
+
+Added¶
Feature imputation settings in WORC config.
PCA settings in WORC config.
Added
whether a temporary save will be made after each cross validation.
-
-Changed¶
+
+Changed¶
-
-
-2.0.0 - 2018-02-13¶
-
-Added¶
+
+2.0.0 - 2018-02-13¶
+
+Added¶
Elastix and transformix as separate workflow in the tools folder. Can be used
through the WORC.Tools attribute.
Added
trainclassifier tool in terms of inputs and outputs.
-
-Changed¶
+
+Changed¶
-
-Fixed¶
+
+Fixed¶
Proper combining of features from multiple modalities to classify tool.
Minor bugs in segmentix tool.
Configuration — WORC 3.4.5 documentation
+ Configuration — WORC 3.5.0 documentation
@@ -64,7 +64,7 @@
- 3.4.5
+ 3.5.0
@@ -550,7 +550,7 @@ Contentsthe additional functionality chapter.
+the additional functionality chapter.
Description: