config['Featsel'] = dict()
config['Featsel']['Variance'] = '1.0'
config['Featsel']['GroupwiseSearch'] = 'True'
- config['Featsel']['SelectFromModel'] = '0.2'
+ config['Featsel']['SelectFromModel'] = '0.275'
config['Featsel']['SelectFromModel_estimator'] = 'Lasso, LR, RF'
config['Featsel']['SelectFromModel_lasso_alpha'] = '0.1, 1.4'
config['Featsel']['SelectFromModel_n_trees'] = '10, 90'
- config['Featsel']['UsePCA'] = '0.2'
+ config['Featsel']['UsePCA'] = '0.275'
config['Featsel']['PCAType'] = '95variance, 10, 50, 100'
- config['Featsel']['StatisticalTestUse'] = '0.2'
+ config['Featsel']['StatisticalTestUse'] = '0.275'
config['Featsel']['StatisticalTestMetric'] = 'MannWhitneyU'
config['Featsel']['StatisticalTestThreshold'] = '-3, 2.5'
- config['Featsel']['ReliefUse'] = '0.2'
+ config['Featsel']['ReliefUse'] = '0.275'
config['Featsel']['ReliefNN'] = '2, 4'
config['Featsel']['ReliefSampleSize'] = '0.75, 0.2'
config['Featsel']['ReliefDistanceP'] = '1, 3'
@@ -615,10 +615,11 @@ Source code for WORC.WORC
# Based on https://towardsdatascience.com/doing-xgboost-hyper-parameter-tuning-the-smart-way-part-1-of-2-f6d255a45dde
# and https://www.analyticsvidhya.com/blog/2016/03/complete-guide-parameter-tuning-xgboost-with-codes-python/
+ # and https://medium.com/data-design/xgboost-hi-im-gamma-what-can-i-do-for-you-and-the-tuning-of-regularization-a42ea17e6ab6
config['Classification']['XGB_boosting_rounds'] = config['Classification']['RFn_estimators']
config['Classification']['XGB_max_depth'] = '3, 12'
config['Classification']['XGB_learning_rate'] = config['Classification']['AdaBoost_learning_rate']
- config['Classification']['XGB_gamma'] = '0.01, 0.99'
+ config['Classification']['XGB_gamma'] = '0.01, 9.99'
config['Classification']['XGB_min_child_weight'] = '1, 6'
config['Classification']['XGB_colsample_bytree'] = '0.3, 0.7'
diff --git a/WORC/doc/_build/html/_modules/WORC/addexceptions.html b/WORC/doc/_build/html/_modules/WORC/addexceptions.html
index 6ea3064d..e100b436 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 3.4.3 documentation
+ WORC.addexceptions — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html b/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html
index 7408c95f..fb298fa8 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 3.4.3 documentation
+ WORC.classification.AdvancedSampler — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html b/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html
index fb08b036..099712da 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 3.4.3 documentation
+ WORC.classification.ObjectSampler — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html b/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html
index e9a7dae8..0099013a 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 3.4.3 documentation
+ WORC.classification.RankedSVM — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html b/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html
index 9fcd0385..d91951fd 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 3.4.3 documentation
+ WORC.classification.SearchCV — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -757,6 +757,9 @@ Source code for WORC.classification.SearchCV
if self.best_groupsel is not None:
X = self.best_groupsel.transform(X)
+ if self.best_varsel is not None:
+ X = self.best_varsel.transform(X)
+
if not training and hasattr(self, 'overfit_scaler') and self.overfit_scaler:
# Overfit the feature scaling on the test set
# NOTE: Never use this in an actual model, only to assess how
@@ -773,9 +776,6 @@ Source code for WORC.classification.SearchCV
if self.best_scaler is not None:
X = self.best_scaler.transform(X)
- if self.best_varsel is not None:
- X = self.best_varsel.transform(X)
-
if self.best_reliefsel is not None:
X = self.best_reliefsel.transform(X)
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 a6642d40..621f5e83 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 3.4.3 documentation
+ WORC.classification.construct_classifier — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -490,8 +490,8 @@ Source code for WORC.classification.construct_classifier
scale
=config['AdaBoost_n_estimators'][1])
param_grid['AdaBoost_learning_rate'] =\
-
scipy.stats.uniform(loc=config['AdaBoost_learning_rate'][0],
-
scale=config['AdaBoost_learning_rate'][1])
+
log_uniform(loc=config['AdaBoost_learning_rate'][0],
+
scale=config['AdaBoost_learning_rate'][1])
# XGDBoost parameters
param_grid['XGB_boosting_rounds'] =\
@@ -503,8 +503,8 @@
Source code for WORC.classification.construct_classifier
scale
=config['XGB_max_depth'][1])
param_grid['XGB_learning_rate'] =\
-
scipy.stats.uniform(loc=config['XGB_learning_rate'][0],
-
scale=config['XGB_learning_rate'][1])
+
log_uniform(loc=config['XGB_learning_rate'][0],
+
scale=config['XGB_learning_rate'][1])
param_grid['XGB_gamma'] =\
scipy.stats.uniform(loc=config['XGB_gamma'][0],
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html b/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html
index 9d111ccd..db4319fb 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 3.4.3 documentation
+
WORC.classification.createfixedsplits — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/crossval.html b/WORC/doc/_build/html/_modules/WORC/classification/crossval.html
index 2b0a9074..585b7d70 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 3.4.3 documentation
+
WORC.classification.crossval — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/estimators.html b/WORC/doc/_build/html/_modules/WORC/classification/estimators.html
index 69f1d45a..8e66ad51 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 3.4.3 documentation
+
WORC.classification.estimators — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html b/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html
index f4d639c4..674682c2 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 3.4.3 documentation
+
WORC.classification.fitandscore — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -364,6 +364,7 @@
Source code for WORC.classification.fitandscore
<
print("\n")
print('#######################################')
print('Starting fit and score of new workflow.')
+
para_estimator = parameters.copy()
estimator = cc.construct_classifier(para_estimator)
@@ -571,38 +572,6 @@
Source code for WORC.classification.fitandscore
<
else:
return ret
-
# ------------------------------------------------------------------------
-
# Feature scaling
-
if verbose and para_estimator['FeatureScaling'] != 'None':
-
print(f'Fitting scaler and transforming features, method ' +
-
f'{para_estimator["FeatureScaling"]}.')
-
-
scaling_method = para_estimator['FeatureScaling']
-
if scaling_method == 'None':
-
scaler = None
-
else:
-
skip_features = para_estimator['FeatureScaling_skip_features']
-
n_skip_feat = len([i for i in feature_labels[0] if any(e in i for e in skip_features)])
-
if n_skip_feat == len(X_train[0]):
-
# Don't need to scale any features
-
if verbose:
-
print('[WORC Warning] Skipping scaling, only skip features selected.')
-
scaler = None
-
else:
-
scaler = WORCScaler(method=scaling_method, skip_features=skip_features)
-
scaler.fit(X_train, feature_labels[0])
-
-
if scaler is not None:
-
X_train = scaler.transform(X_train)
-
X_test = scaler.transform(X_test)
-
-
del para_estimator['FeatureScaling']
-
del para_estimator['FeatureScaling_skip_features']
-
-
# Delete the object if we do not need to return it
-
if not return_all:
-
del scaler
-
# --------------------------------------------------------------------
# Feature selection based on variance
if para_estimator['Featsel_Variance'] == 'True':
@@ -639,6 +608,39 @@
Source code for WORC.classification.fitandscore
<
else:
return ret
+
# ------------------------------------------------------------------------
+
# Feature scaling
+
if verbose and para_estimator['FeatureScaling'] != 'None':
+
print(f'Fitting scaler and transforming features, method ' +
+
f'{para_estimator["FeatureScaling"]}.')
+
+
scaling_method = para_estimator['FeatureScaling']
+
if scaling_method == 'None':
+
scaler = None
+
else:
+
skip_features = para_estimator['FeatureScaling_skip_features']
+
n_skip_feat = len([i for i in feature_labels[0] if any(e in i for e in skip_features)])
+
if n_skip_feat == len(X_train[0]):
+
# Don't need to scale any features
+
if verbose:
+
print('[WORC Warning] Skipping scaling, only skip features selected.')
+
scaler = None
+
else:
+
scaler = WORCScaler(method=scaling_method, skip_features=skip_features)
+
scaler.fit(X_train, feature_labels[0])
+
+
if scaler is not None:
+
X_train = scaler.transform(X_train)
+
X_test = scaler.transform(X_test)
+
+
del para_estimator['FeatureScaling']
+
del para_estimator['FeatureScaling_skip_features']
+
+
# Delete the object if we do not need to return it
+
if not return_all:
+
del scaler
+
+
# --------------------------------------------------------------------
# Relief feature selection, possibly multi classself.
# Needs to be done after scaling!
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/metrics.html b/WORC/doc/_build/html/_modules/WORC/classification/metrics.html
index 7f960555..483b60bf 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 3.4.3 documentation
+
WORC.classification.metrics — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 fb17b7d1..2ffbaf44 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 3.4.3 documentation
+
WORC.classification.parameter_optimization — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html b/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html
index bf3adfd2..9f452a13 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 3.4.3 documentation
+
WORC.classification.trainclassifier — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html b/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html
index b420e204..2bbe8b34 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 3.4.3 documentation
+
WORC.detectors.detectors — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html b/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html
index 5854d271..df78d60e 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 3.4.3 documentation
+
WORC.exampledata.datadownloader — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html
index c4f2363c..a14bcb94 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 3.4.3 documentation
+
WORC.featureprocessing.Imputer — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html
index 4add0057..82359d8c 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 3.4.3 documentation
+
WORC.featureprocessing.Relief — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -165,7 +165,7 @@
Source code for WORC.featureprocessing.Relief
#!/usr/bin/env python
-# Copyright 2016-2019 Biomedical Imaging Group Rotterdam, Departments of
+# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -181,7 +181,7 @@ Source code for WORC.featureprocessing.Relief
# limitations under the License.
from sklearn.base import BaseEstimator
-from sklearn.feature_selection.base import SelectorMixin
+from sklearn.feature_selection import SelectorMixin
import numpy as np
import sklearn.neighbors as nn
# from skrebate import ReliefF
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html
index e2cfa1e9..ec4ebc55 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 3.4.3 documentation
+ WORC.featureprocessing.SelectGroups — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -165,7 +165,7 @@
Source code for WORC.featureprocessing.SelectGroups
#!/usr/bin/env python
-# Copyright 2016-2020 Biomedical Imaging Group Rotterdam, Departments of
+# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -181,7 +181,7 @@ Source code for WORC.featureprocessing.SelectGroups
# limitations under the License.
from sklearn.base import BaseEstimator
-
from sklearn.feature_selection.base import SelectorMixin
+
from sklearn.feature_selection import SelectorMixin
import numpy as np
@@ -189,6 +189,29 @@
Source code for WORC.featureprocessing.SelectGroups
'''
Object to fit feature selection based on the type group the feature belongs
to. The label for the feature is used for this procedure.
+
+
The following groups can be selected, and are detected through looking for
+
the following substrings in the feature label:
+
- histogram_features: hf_
+
- shape_features: sf_
+
- orientation_features: of_
+
- semantic_features: semf_
+
- dicom_features: df_
+
- coliage_features_ cf_
+
- phase_features: phasef_
+
- vessel_features: vf_
+
- texture_Gabor_features: Gabor
+
- texture_GLCM_features: GLCM_
+
- texture_GLCMMS_features: GLCMMS_
+
- texture_GLRLM_features: GLRLM_
+
- texture_GLSZM_features: GLSZM_
+
- texture_GLDZM_features: GLDZM_
+
- texture_NGTDM_features: NGTDM_
+
- texture_NGLDM_features: NGLDM_
+
- texture_LBP_features: LBP_
+
- fractal_features: fracf_
+
- location_features: locf_
+
- RGRD_features: rgrdf_
'''
[docs] def __init__(self, parameters, toolboxes=['PREDICT']):
'''
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html
index f428b473..a349a0d0 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 3.4.3 documentation
+
WORC.featureprocessing.SelectIndividuals — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -181,7 +181,7 @@
Source code for WORC.featureprocessing.SelectIndividuals
# limitations under the License.
from sklearn.base import BaseEstimator
-
from sklearn.feature_selection.base import SelectorMixin
+
from sklearn.feature_selection import SelectorMixin
import numpy as np
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html
index 26d45990..8b1eac60 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 3.4.3 documentation
+
WORC.featureprocessing.StatisticalTestFeatures — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html
index 9ad3840e..3d9c32d5 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 3.4.3 documentation
+
WORC.featureprocessing.StatisticalTestThreshold — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -181,7 +181,7 @@
Source code for WORC.featureprocessing.StatisticalTestThreshold
# limitations under the License.
from sklearn.base import BaseEstimator
-
from sklearn.feature_selection.base import SelectorMixin
+
from sklearn.feature_selection import SelectorMixin
import numpy as np
from scipy.stats import ttest_ind, ranksums, mannwhitneyu
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html
index 0ad6b596..557e4e21 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 3.4.3 documentation
+
WORC.featureprocessing.VarianceThreshold — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -182,7 +182,7 @@
Source code for WORC.featureprocessing.VarianceThreshold
from
sklearn.feature_selection import VarianceThreshold
from sklearn.base import BaseEstimator
-
from sklearn.feature_selection.base import SelectorMixin
+
from sklearn.feature_selection import SelectorMixin
import numpy as np
import WORC.addexceptions as ae
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 1affdc67..8d59232b 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 3.4.3 documentation
+
WORC.plotting.compute_CI — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html b/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html
index 0e20769f..367cf7b0 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 3.4.3 documentation
+
WORC.plotting.linstretch — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 c32b0b4d..eb3547de 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 3.4.3 documentation
+
WORC.plotting.plot_ROC — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 977cbaaf..a6f7fa03 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 3.4.3 documentation
+
WORC.plotting.plot_barchart — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 0bf577ea..6d868753 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 3.4.3 documentation
+
WORC.plotting.plot_images — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
@@ -217,18 +217,25 @@
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,
-
alpha=0.40, index=None, color='cyan'):
+
expand=False, boundary=False, square=False, flip=True, rot90=0,
+
alpha=0.40, axis='axial', index=None, color='cyan'):
"""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])
-
imsize = [float(image.GetSize()[0]), float(image.GetSize()[1])]
-
figsize = (imsize[0]*spacing/100.0, imsize[1]*spacing/100.0)
+
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
+
figsize = (30, 1)
image = sitk.GetArrayFromImage(image)
if mask is not None:
mask = sitk.GetArrayFromImage(mask)
@@ -241,18 +248,49 @@
Source code for WORC.plotting.plot_images
# Determine which axial slice has the largest area
if index is None:
if mask is not None:
- areas = np.sum(mask, axis=1).tolist()
+ if axis == 'axial':
+ areas = np.sum(mask, axis=2).tolist()
+ elif axis == 'coronal':
+ areas = np.sum(mask, axis=1).tolist()
+ elif axis == 'transversal':
+ areas = np.sum(mask, axis=0).tolist()
+
index = areas.index(max(areas))
else:
- index = int(image.shape[0]/2)
+ if axis == 'axial':
+ index = int(image.shape[2]/2)
+ elif axis == 'coronal':
+ index = int(image.shape[1]/2)
+ elif axis == 'transversal':
+ index = int(image.shape[0]/2)
+
+ if axis == 'axial':
+ imslice = image[index, :, :]
+ elif axis == 'coronal':
+ imslice = image[:, index, :]
+ elif axis == 'transversal':
+ imslice = image[:, :, index]
+ else:
+ raise ValueError(f'{axis} is not a valid value for the axis, should be axial, coronal, or transversal.')
- imslice = image[index, :, :]
if mask is not None:
- maskslice = mask[index, :, :]
+ if axis == 'axial':
+ maskslice = mask[index, :, :]
+ elif axis == 'coronal':
+ maskslice = mask[:, index, :]
+ elif axis == 'transversal':
+ maskslice = mask[:, :, index]
+ else:
+ raise ValueError(f'{axis} is not a valid value for the axis, should be axial, coronal, or transversal.')
else:
maskslice = None
- # Rotate, as this is not done automatically
+ if rot90 != 0:
+ print(f'\t Rotating {rot90 * 90} degrees.')
+ imslice = np.rot90(imslice, rot90)
+ if mask is not None:
+ maskslice = np.rot90(maskslice, rot90)
+
if flip:
print('\t Flipping up-down.')
imslice = np.flipud(imslice)
@@ -307,9 +345,12 @@ Source code for WORC.plotting.plot_images
maskslice = sitk.Expand(maskslice, newsize)
# Adjust the size
- spacing = float(imslice.GetSpacing()[0])
- imsize = [float(imslice.GetSize()[0]), float(imslice.GetSize()[1])]
- figsize = (imsize[0]*spacing/100.0, imsize[1]*spacing/100.0)
+ 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)
imslice = sitk.GetArrayFromImage(imslice)
if mask is not None:
@@ -371,6 +412,10 @@ Source code for WORC.plotting.plot_images
if mask is not None:
ax.imshow(mask, cmap=cmap, norm=normO, alpha=alpha, interpolation="bilinear")
+ # Alter aspect ratio according to figure size
+ aspect = figsize[0]/figsize[1]
+ ax.set_aspect(aspect)
+
# Set locator to zero to make sure padding is removed upon saving
ax.xaxis.set_major_locator(NullLocator())
ax.yaxis.set_major_locator(NullLocator())
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 46eef16b..dee10390 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 3.4.3 documentation
+ WORC.plotting.plot_ranked_scores — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html b/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html
index e8c4be28..af8a119f 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 3.4.3 documentation
+ WORC.plotting.scatterplot — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html b/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html
index 9e845400..59d5f6ee 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 3.4.3 documentation
+ WORC.processing.ExtractNLargestBlobsn — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/classes.html b/WORC/doc/_build/html/_modules/WORC/processing/classes.html
index d5926857..0c1e3808 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 3.4.3 documentation
+ WORC.processing.classes — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 b0e6bb8c..21c363cf 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 3.4.3 documentation
+ WORC.processing.label_processing — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 2786ef8d..bbf50684 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 3.4.3 documentation
+ WORC.resources.fastr_tests.CalcFeatures_test — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 83b37df0..19df6606 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 3.4.3 documentation
+ WORC.resources.fastr_tests.elastix_test — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
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 711a6cd1..d7a4f803 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 3.4.3 documentation
+ WORC.resources.fastr_tests.segmentix_test — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html b/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html
index e7cdbede..fdf6f054 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 3.4.3 documentation
+ WORC.tools.Elastix — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html b/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html
index c5b8f9a5..0ede8ad4 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 3.4.3 documentation
+ WORC.tools.Evaluate — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html b/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html
index 397ffdf4..b6b74165 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 3.4.3 documentation
+ WORC.tools.Slicer — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html b/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html
index 20aa2c0a..27627d61 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 3.4.3 documentation
+ WORC.tools.Transformix — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html b/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html
index 54c57e77..85b580b0 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 3.4.3 documentation
+ WORC.tools.createfixedsplits — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_modules/index.html b/WORC/doc/_build/html/_modules/index.html
index 205e9050..2f9a19cd 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 3.4.3 documentation
+ Overview: module code — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/_sources/static/quick_start.rst.txt b/WORC/doc/_build/html/_sources/static/quick_start.rst.txt
index b77c9ab0..a1cca080 100644
--- a/WORC/doc/_build/html/_sources/static/quick_start.rst.txt
+++ b/WORC/doc/_build/html/_sources/static/quick_start.rst.txt
@@ -1,7 +1,10 @@
+.. _quickstart-chapter:
+
Quick start guide
=================
This manual will show users how to install WORC, configure WORC and construct and run a simple experiment.
+It's exactly the same as the `WORC Tutorial `_.
.. _installation-chapter:
@@ -11,7 +14,6 @@ Installation
You can install WORC either using pip, or from the source code. We strongly advice you to install ``WORC`` in a `virtualenv `_.
-
**Installing via pip**
@@ -89,8 +91,9 @@ First, import WORC and some additional python packages.
# Define the folder this script is in, so we can easily find the example data
script_path = os.path.dirname(os.path.abspath(__file__))
- # Determine whether you would like to use WORC for classification or regression
- modus = 'classification'
+ # Determine whether you would like to use WORC for binary_classification,
+ # multiclass_classification or regression
+ modus = 'binary_classification'
Input
`````
@@ -139,13 +142,17 @@ Identify our data structure: change the fields below accordingly if you use your
label_file = os.path.join(data_path, 'Examplefiles', 'pinfo_HN.csv')
# Name of the label you want to predict
- if modus == 'classification':
+ if modus == 'binary_classification':
# Classification: predict a binary (0 or 1) label
- label_name = 'imaginary_label_1'
+ label_name = ['imaginary_label_1']
elif modus == 'regression':
# Regression: predict a continuous label
- label_name = 'Age'
+ label_name = ['Age']
+
+ elif modus == 'multiclass_classification':
+ # Multiclass classification: predict several mutually exclusive binaru labels together
+ label_name = ['imaginary_label_1', 'complement_label_1']
# Determine whether we want to do a coarse quick experiment, or a full lengthy
# one. Again, change this accordingly if you use your own data.
@@ -174,13 +181,15 @@ After defining the inputs, the following code can be used to run your first expe
experiment.segmentations_from_this_directory(imagedatadir,
segmentation_file_name=segmentation_file_name)
experiment.labels_from_this_file(label_file)
- experiment.predict_labels([label_name])
+ experiment.predict_labels(label_name)
- # Use the standard workflow for binary classification or regression
- if modus == 'classification':
+ # Use the standard workflow for your specific modus
+ if modus == 'binary_classification':
experiment.binary_classification(coarse=coarse)
elif modus == 'regression':
experiment.regression(coarse=coarse)
+ elif modus == 'multiclass_classification':
+ experiment.multiclass_classification(coarse=coarse)
# Set the temporary directory
experiment.set_tmpdir(tmpdir)
@@ -241,6 +250,9 @@ Tips and Tricks
For tips and tricks on running a full experiment instead of this simple
example, adding more evaluation options, debugging a crashed network etcetera,
please go to :ref:`User Manual ` chapter.
+We advice you to look at the docstrings of the SimpleWORC functions
+introduced in this tutorial, and explore the other SimpleWORC functions,
+s SimpleWORC offers much more functionality than presented here.
Some things we would advice to always do:
diff --git a/WORC/doc/_build/html/_static/documentation_options.js b/WORC/doc/_build/html/_static/documentation_options.js
index 79dd7988..f129f9a2 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: '3.4.3',
+ VERSION: '3.4.4',
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 817ff1eb..1406b6de 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 3.4.3 documentation
+ IOparser Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.classification.html b/WORC/doc/_build/html/autogen/WORC.classification.html
index be50c4a5..491f88fa 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 3.4.3 documentation
+ classification Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.config.html b/WORC/doc/_build/html/autogen/WORC.config.html
index a1f790a6..4981ba3d 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 3.4.3 documentation
+ <no title> — WORC 3.4.4 documentation
@@ -62,7 +62,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.detectors.html b/WORC/doc/_build/html/autogen/WORC.detectors.html
index 1246e656..9da28409 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 3.4.3 documentation
+ detectors Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.exampledata.html b/WORC/doc/_build/html/autogen/WORC.exampledata.html
index 8b695037..5e8b9a40 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 3.4.3 documentation
+ exampledata Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.facade.html b/WORC/doc/_build/html/autogen/WORC.facade.html
index 86eda425..783b573a 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 3.4.3 documentation
+ facade Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.featureprocessing.html b/WORC/doc/_build/html/autogen/WORC.featureprocessing.html
index 592f20f6..6fe0eb02 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 3.4.3 documentation
+ featureprocessing Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
@@ -772,6 +772,32 @@
Bases: sklearn.base.BaseEstimator, sklearn.feature_selection._base.SelectorMixin
Object to fit feature selection based on the type group the feature belongs
to. The label for the feature is used for this procedure.
+The following groups can be selected, and are detected through looking for
+the following substrings in the feature label:
+
+
-
__abstractmethods__ = frozenset({})
diff --git a/WORC/doc/_build/html/autogen/WORC.html b/WORC/doc/_build/html/autogen/WORC.html
index 9a2a9060..ab65c93c 100644
--- a/WORC/doc/_build/html/autogen/WORC.html
+++ b/WORC/doc/_build/html/autogen/WORC.html
@@ -8,7 +8,7 @@
- WORC Package — WORC 3.4.3 documentation
+ WORC Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.plotting.html b/WORC/doc/_build/html/autogen/WORC.plotting.html
index a0420317..aa19b8fd 100644
--- a/WORC/doc/_build/html/autogen/WORC.plotting.html
+++ b/WORC/doc/_build/html/autogen/WORC.plotting.html
@@ -8,7 +8,7 @@
- plotting Package — WORC 3.4.3 documentation
+ plotting Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
@@ -539,7 +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, alpha=0.4, 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')[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 88b112f8..0a670a8c 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 3.4.3 documentation
+ processing Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
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 0a4aa4ff..252a7097 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 3.4.3 documentation
+ fastr_tests Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
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 45830455..6ff8f3c4 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 3.4.3 documentation
+ fastr_tools Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.resources.html b/WORC/doc/_build/html/autogen/WORC.resources.html
index ea40d83e..73c7051e 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 3.4.3 documentation
+ resources Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/autogen/WORC.tools.html b/WORC/doc/_build/html/autogen/WORC.tools.html
index 6c1029b4..e1b03c1c 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 3.4.3 documentation
+ tools Package — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/genindex.html b/WORC/doc/_build/html/genindex.html
index deb51e58..11aecd74 100644
--- a/WORC/doc/_build/html/genindex.html
+++ b/WORC/doc/_build/html/genindex.html
@@ -9,7 +9,7 @@
- Index — WORC 3.4.3 documentation
+ Index — WORC 3.4.4 documentation
@@ -63,7 +63,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/index.html b/WORC/doc/_build/html/index.html
index fec192a9..4062227b 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 3.4.3 documentation
+ WORC: Workflow for Optimal Radiomics Classification — WORC 3.4.4 documentation
@@ -63,7 +63,7 @@
- 3.4.3
+ 3.4.4
@@ -344,13 +344,18 @@ - Execution
- Developer documentation
- Changelog
-- 3.4.3 - 2021-06-02
+- 3.4.4 - 2021-07-01
-- 3.4.2 - 2021-05-27
+- 3.4.3 - 2021-06-02
-- 3.4.1 - 2021-05-18
+- 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
diff --git a/WORC/doc/_build/html/objects.inv b/WORC/doc/_build/html/objects.inv
index d1cd87d5..d69bf8d0 100644
Binary files a/WORC/doc/_build/html/objects.inv and b/WORC/doc/_build/html/objects.inv differ
diff --git a/WORC/doc/_build/html/py-modindex.html b/WORC/doc/_build/html/py-modindex.html
index 7e9ac6e0..7edf180b 100644
--- a/WORC/doc/_build/html/py-modindex.html
+++ b/WORC/doc/_build/html/py-modindex.html
@@ -8,7 +8,7 @@
- Python Module Index — WORC 3.4.3 documentation
+ Python Module Index — WORC 3.4.4 documentation
@@ -65,7 +65,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/search.html b/WORC/doc/_build/html/search.html
index f71ad058..c4330a40 100644
--- a/WORC/doc/_build/html/search.html
+++ b/WORC/doc/_build/html/search.html
@@ -8,7 +8,7 @@
- Search — WORC 3.4.3 documentation
+ Search — WORC 3.4.4 documentation
@@ -63,7 +63,7 @@
- 3.4.3
+ 3.4.4
diff --git a/WORC/doc/_build/html/searchindex.js b/WORC/doc/_build/html/searchindex.js
index 74d0c890..370cf0d1 100644
--- a/WORC/doc/_build/html/searchindex.js
+++ b/WORC/doc/_build/html/searchindex.js
@@ -1 +1 @@
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Manual"],titleterms:{"0rc1":61,"boolean":65,"class":11,"default":65,"function":60,"import":69,Added:61,Adding:64,The:[69,70],actual:69,addexcept:[0,65],addit:60,advancedsampl:2,alter:65,analysi:[63,69],arrai:65,attribut:70,basicworc:6,begin:65,bigr:65,bin:66,binari:66,bootstrap:62,calcfeatures_test:13,can:65,chang:61,changelog:61,choic:66,classif:[2,59,62,63],classifi:60,cluster:65,column:65,combat:[9,60,62],command:70,compon:63,comput:65,compute_ci:10,config_io_classifi:1,config_io_combat:1,config_io_pyradiom:1,config_preprocess:1,config_segmentix:1,config_worc:1,configbuild:7,configur:62,construct:70,construct_classifi:2,content:62,convert:65,crash:65,create_example_data:5,createfixedsplit:[2,17],creation:62,crossval:2,crossvalid:62,data:[63,64,70],datadownload:5,debug:70,decomposit:9,definit:70,delet:65,delong:15,depend:66,detector:4,develop:[59,64],dicom:66,differ:[65,66],dimension:63,document:[59,64],elastix:17,elastix_para:70,elastix_test:13,ensembl:62,entri:65,error:65,estim:2,evalu:[17,62,70],exampl:[64,70],exampledata:5,except:7,execut:[65,70],experi:[65,69],extract:66,extractnlargestblobsn:11,facad:6,fals:65,faq:65,fastr:68,fastr_test:13,fastr_tool:14,fastrconfig:8,feat_out_0:65,featpreprocess:62,featsel:62,featur:[63,64,65,66,70],featureconvert:9,featureprocess:9,featuresc:62,file:[65,67,70],file_io:1,filter:66,first:65,fitandscor:2,fix:[61,66],format:[65,67],found:65,from:63,full:66,function_bas:65,gabor:66,gaussian:66,gener:62,given:65,glcm:66,gldm:66,glrlm:66,glszm:66,grai:66,groupwis:63,guid:69,hdf5:65,helper:[7,11],histogram:66,hyperoptim:[62,64],icc:60,iccthreshold:9,imag:[60,66,70],imagefeatur:62,imput:[9,62,63],indexerror:65,indic:[59,65],infer:17,input:[69,70],instal:[65,69],instead:65,integ:65,interact:[62,70],introduct:[62,68],iopars:1,job:65,keep:65,label:[62,65,70],label_process:11,labels_from_this_fil:65,laplacian:66,lbp:66,learn:63,length:66,level:66,lib:65,like:65,line:65,linstretch:10,local:66,log:66,look:65,machin:63,manual:70,mask:70,matrix:66,metadata:70,method:[63,64],metric:2,mine:63,model:63,modul:[0,1,2,4,5,6,7,8,9,10,11,13,15,16,17,18,59,65],modular:68,modulenotfounderror:65,must:65,name:65,need:65,neighborhood:66,network:70,ngtdm:66,numpi:65,obj:65,object:70,objectsampl:2,occur:66,onehotencod:[62,63],onehotencoderwrapp:9,ones:65,optim:[59,68],orient:66,other:[65,66],own:65,packag:[0,1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,65,69],paramet:66,parameter_optim:2,patient:65,pattern:66,pca:63,phase:66,plot:10,plot_barchart:10,plot_boxplot_featur:10,plot_boxplot_perform:10,plot_error:10,plot_estimator_perform:10,plot_hyperparamet:10,plot_imag:10,plot_pvalues_featur:10,plot_ranked_scor:10,plot_roc:10,plotminmaxrespons:10,preflightcheck:18,preprocess:[11,60,62],preprocessor:9,princip:63,process:[7,11,64],pyradiom:62,queue:65,quick:69,radiom:[59,66,68],rankedsvm:2,reduct:63,refer:59,registr:60,regress:63,regressor:2,relief:[9,63],resampl:[62,63],resourc:[12,67],result:69,roi:66,run:[66,69],scale:63,scaler:9,scatterplot:10,searchcv:2,segment:70,segmentix:[11,62],segmentix_test:13,select:[63,65,66],selectfeatgroup:62,selectgroup:9,selectindividu:9,semant:[66,70],shape:66,simpleworc:[6,65],site:65,size:66,slicer:17,some:65,sourc:70,standard:[65,68],start:69,statist:[15,63],statisticaltestfeatur:9,statisticaltestthreshold:9,submit:65,subpackag:[0,6,12],surviv:63,tabl:59,tell:65,terminolog:68,test:[16,63,64],test_combat:16,test_help:16,test_iccthreshold:16,test_plot_error:16,test_valid:16,textur:66,tip:69,tone:66,tool:17,toolbox:64,trainclassifi:2,transformix:17,trick:69,tutori:69,type:65,univari:63,unreleas:[],use:65,used:65,user:[59,70],valid:18,varianc:63,variancethreshold:9,vessel:66,wavelet:66,welcom:59,where:65,width:66,worc:[0,59,65,70],worc_config:8,worckeyerror:65,worctutorialsimple_travis_multiclass:16,worctutorialsimple_travis_regress:16,worcvalueerror:65,work:65,workflow:59,would:65,your:[65,70],zone:66}})
\ 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 19f60235..d275ad08 100644
--- a/WORC/doc/_build/html/static/changelog.html
+++ b/WORC/doc/_build/html/static/changelog.html
@@ -8,7 +8,7 @@
- Changelog — WORC 3.4.3 documentation
+ Changelog — WORC 3.4.4 documentation
@@ -64,7 +64,7 @@
- 3.4.3
+ 3.4.4
@@ -99,145 +99,151 @@
- Developer documentation
- Resource File Formats
- Changelog
-- 3.4.3 - 2021-06-02
+- 3.4.4 - 2021-07-01
-- 3.4.2 - 2021-05-27
+- 3.4.3 - 2021-06-02
-- 3.4.1 - 2021-05-18
+- 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
@@ -314,26 +320,53 @@ Changelog
and this project adheres to Semantic Versioning
-
3.4.3 - 2021-06-02
+
3.4.4 - 2021-07-01
Fixed
-SimpleWORC and BasicWORC now support multilabel workflows.
SimpleWORC and BasicWORC now support use of masks.
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
+
+Apply variance threshold selection before feature scaling, otherwise
+variance is always the same for all features.
RELIEF, selection using a model, PCA, and univariate testing default
+use changed from 0.20 to 0.275.
Added
-Unit testing for multilabel workflows.
Functionality in plotting images functions.
Documentation on how to use your own features.
-
3.4.2 - 2021-05-27
+
3.4.3 - 2021-06-02
+
+
+
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.
Bug in precision-recall curve.
Fixed
-
-
-
3.4.1 - 2021-05-18
-
-
Fixed
+
+
3.4.1 - 2021-05-18
+
-
-
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
+
-
-
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
+
-
-
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
+
-
-
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
+
-
-
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
+
-
-
Added
+
-
-
-
3.3.1 - 2020-07-31
-
-
Changed
+
+
3.3.1 - 2020-07-31
+
-
-
-
3.3.0 - 2020-07-28
-
-
Added
+
+
3.3.0 - 2020-07-28
+
-
-
Changed
+
+
Changed
Upgraded to new versions of sklearn (0.23.1) and imbalanced learn (0.7.0)
Some defaults, based on computation time.
Changed
-
-
-
3.2.2 - 2020-07-14
-
-
Added
+
+
3.2.2 - 2020-07-14
+
-
-
Changed
+
-
-
-
3.2.1 - 2020-07-02
-
-
Added
+
+
3.2.1 - 2020-07-02
+
-
-
Changed
+
+
Changed
PyRadiomics setup not dependent on pre-install of numpy anymore, so altered
travis, yml, setup, and documentation.
Changed
-
-
-
3.2.0 - 2020-06-26
-
-
Added
+
+
3.2.0 - 2020-06-26
+
-
-
Changed
+
+
Changed
Output of plot_SVM function is better ordered.
Several defaults, as we now have PyRadiomics fully embedded, resulting in
@@ -674,8 +707,8 @@
Changed
-
-
-
3.1.4 - 2020-05-26
-
-
Added
+
+
3.1.4 - 2020-05-26
+
-
-
Changed
+
-
-
-
3.1.3 - 2020-01-24
-
-
Added
+
+
3.1.3 - 2020-01-24
+
-
-
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,
@@ -776,18 +809,18 @@
Changed
-
-
-
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,
@@ -797,38 +830,38 @@
Added
-
-
Changed
+
-
-
-
3.1.1 - 2019-11-28
-
-
Added
+
+
3.1.1 - 2019-11-28
+
-
-
Changed
+
-
-
Fixed
+
+
Fixed
Under Windows, creation of the fastr home folder if it did not exist
did not work when using pip for installing. We now use a new feature
@@ -840,10 +873,10 @@
Fixed
-
-
3.1.0 - 2019-10-16
-
-
Added
+
+
3.1.0 - 2019-10-16
+
-
-
Changed
+
-
-
-
3.0.0 - 2019-05-08
-
-
Added
+
+
3.0.0 - 2019-05-08
+
-
-
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.
Changed
-
-
-
2.1.3 - 2019-04-08
-
-
Changed
+
-
-
2.1.2 - 2019-04-02
-
-
Added
+
+
2.1.2 - 2019-04-02
+
-
-
Changed
+
-
-
Fixed
+
+
Fixed
-Evaluate framework now correctly adopts the name you give it.
-
-
2.1.1 - 2019-02-15
-
-
Added
+
+
2.1.1 - 2019-02-15
+
-
-
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.
-
-
-
2.1.0 - 2018-08-09
-
-
Added
+
+
2.1.0 - 2018-08-09
+
-
-
Changed
+
-
-
Fixed
+
+
Fixed
Patientclass ID was used for both test and training. Now given separate names.
When elastix is used but segmentix isn’t, there was a bug.
Fixed
-