diff --git a/CHANGELOG b/CHANGELOG
index fd0d62dc..3def1932 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -7,6 +7,21 @@ The format is based on `Keep a Changelog
'RandomUnderSampling, RandomOverSampling, NearMiss, ' +\
'NeighbourhoodCleaningRule, ADASYN, BorderlineSMOTE, SMOTE, ' +\
'SMOTEENN, SMOTETomek'
- config['Resampling']['sampling_strategy'] = 'majority, minority, not minority, not majority, all'
+ config['Resampling']['sampling_strategy'] = 'auto, majority, minority, not minority, not majority, all'
config['Resampling']['n_neighbors'] = '3, 12'
config['Resampling']['k_neighbors'] = '5, 15'
config['Resampling']['threshold_cleaning'] = '0.25, 0.5'
diff --git a/WORC/doc/_build/html/_modules/WORC/addexceptions.html b/WORC/doc/_build/html/_modules/WORC/addexceptions.html
index 8a639224..8724bda4 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 3.4.1 documentation
+ WORC.addexceptions — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html b/WORC/doc/_build/html/_modules/WORC/classification/AdvancedSampler.html
index 100a8667..bb0b2570 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 3.4.1 documentation
+ WORC.classification.AdvancedSampler — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html b/WORC/doc/_build/html/_modules/WORC/classification/ObjectSampler.html
index ca4599c1..70ee7457 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 3.4.1 documentation
+ WORC.classification.ObjectSampler — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html b/WORC/doc/_build/html/_modules/WORC/classification/RankedSVM.html
index 2c4fa8e9..e65a8523 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 3.4.1 documentation
+ WORC.classification.RankedSVM — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html b/WORC/doc/_build/html/_modules/WORC/classification/SearchCV.html
index 14ffc5a5..c080ac63 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 3.4.1 documentation
+ WORC.classification.SearchCV — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 04661d10..a91f836c 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 3.4.1 documentation
+ WORC.classification.construct_classifier — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html b/WORC/doc/_build/html/_modules/WORC/classification/createfixedsplits.html
index 98f6df04..de4e1ff2 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 3.4.1 documentation
+ WORC.classification.createfixedsplits — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/crossval.html b/WORC/doc/_build/html/_modules/WORC/classification/crossval.html
index 9be782fd..0c547ace 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 3.4.1 documentation
+ WORC.classification.crossval — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/estimators.html b/WORC/doc/_build/html/_modules/WORC/classification/estimators.html
index 3c9d67e1..ff0758df 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 3.4.1 documentation
+ WORC.classification.estimators — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html b/WORC/doc/_build/html/_modules/WORC/classification/fitandscore.html
index 2de33967..4a58ef1f 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 3.4.1 documentation
+ WORC.classification.fitandscore — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/metrics.html b/WORC/doc/_build/html/_modules/WORC/classification/metrics.html
index 3d1d27e5..249ebde5 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 3.4.1 documentation
+ WORC.classification.metrics — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 8ab9f86b..fe3f54d3 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 3.4.1 documentation
+ WORC.classification.parameter_optimization — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html b/WORC/doc/_build/html/_modules/WORC/classification/trainclassifier.html
index c6ab2f8b..2b7377cf 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 3.4.1 documentation
+ WORC.classification.trainclassifier — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html b/WORC/doc/_build/html/_modules/WORC/detectors/detectors.html
index 498be7d1..36b2a40e 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 3.4.1 documentation
+ WORC.detectors.detectors — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html b/WORC/doc/_build/html/_modules/WORC/exampledata/datadownloader.html
index d1681573..d6f3c75a 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 3.4.1 documentation
+ WORC.exampledata.datadownloader — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Imputer.html
index a51d8091..fc0e437d 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 3.4.1 documentation
+ WORC.featureprocessing.Imputer — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/Relief.html
index 6ffe0991..0a653930 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 3.4.1 documentation
+ WORC.featureprocessing.Relief — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectGroups.html
index 3d79a990..06082e39 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 3.4.1 documentation
+ WORC.featureprocessing.SelectGroups — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/SelectIndividuals.html
index 229b87b3..749ece2c 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 3.4.1 documentation
+ WORC.featureprocessing.SelectIndividuals — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestFeatures.html
index e4e1569b..fde8914b 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 3.4.1 documentation
+ WORC.featureprocessing.StatisticalTestFeatures — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/StatisticalTestThreshold.html
index f43e4179..8e6c55d5 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 3.4.1 documentation
+ WORC.featureprocessing.StatisticalTestThreshold — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html b/WORC/doc/_build/html/_modules/WORC/featureprocessing/VarianceThreshold.html
index 2f8cb34b..21eb34d3 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 3.4.1 documentation
+ WORC.featureprocessing.VarianceThreshold — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 6fd92282..e66a8eb6 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 3.4.1 documentation
+ WORC.plotting.compute_CI — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html b/WORC/doc/_build/html/_modules/WORC/plotting/linstretch.html
index ecb37c57..c09ed18b 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 3.4.1 documentation
+ WORC.plotting.linstretch — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 68806217..5988eda7 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 3.4.1 documentation
+ WORC.plotting.plot_ROC — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
@@ -190,6 +190,7 @@ Source code for WORC.plotting.plot_ROC
from WORC.plotting.compute_CI import compute_confidence as CI
import numpy as np
from sklearn.metrics import roc_auc_score, auc
+from sklearn.metrics import precision_recall_curve
import csv
from WORC.plotting.plot_estimator_performance import plot_estimator_performance
@@ -280,13 +281,6 @@ Source code for WORC.plotting.plot_ROC
y_score = y_score[inds]
# Compute the TPR and FPR for all possible thresholds
- FP = 0
- TP = 0
- precision = list()
- tpr = list()
- thresholds = list()
- fprev = -np.inf
- i = 0
N = float(np.bincount(y_truth)[0])
if len(np.bincount(y_truth)) == 1:
# No class = 1 present.
@@ -296,29 +290,19 @@ Source code for WORC.plotting.plot_ROC
if N == 0:
print('[WORC Warning] No negative class samples found, cannot determine PRC. Skipping iteration.')
- return precision, tpr, thresholds
+ return list(), list(), list()
elif P == 0:
print('[WORC Warning] No positive class samples found, cannot determine PRC. Skipping iteration.')
- return precision, tpr, thresholds
-
- while i < len(y_truth_sorted):
- if y_score[i] != fprev:
- if TP == 0:
- # Prevent division by zero
- precision.append(0)
- else:
- precision.append(TP/(TP + FP))
+ return list(), list(), list()
- tpr.append(1 - TP/P)
- thresholds.append(y_score[i])
- fprev = y_score[i]
+ precision, tpr, thresholds =\
+ precision_recall_curve(y_truth_sorted, y_score)
- if y_truth_sorted[i] == 1:
- TP += 1
- else:
- FP += 1
+ # Convert to lists
+ precision = precision.tolist()
+ tpr = tpr.tolist()
+ thresholds = thresholds.tolist()
- i += 1
if verbose or returnplot:
prc_auc = auc(tpr, precision)
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 cdc38940..341cdcdc 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 3.4.1 documentation
+ WORC.plotting.plot_barchart — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 13b9868c..1e73883e 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 3.4.1 documentation
+ WORC.plotting.plot_images — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
@@ -233,19 +233,24 @@ Source code for WORC.plotting.plot_images
if mask is not None:
mask = sitk.GetArrayFromImage(mask)
- # Determine which axial slice has the largest area
- if index is None:
+ if len(image.shape) == 2:
+ # 2D image, so image and mask are already single slices
+ imslice = image
+ maskslice = mask
+ else:
+ # Determine which axial slice has the largest area
+ if index is None:
+ if mask is not None:
+ areas = np.sum(mask, axis=1).tolist()
+ index = areas.index(max(areas))
+ else:
+ index = int(image.shape[0]/2)
+
+ imslice = image[index, :, :]
if mask is not None:
- areas = np.sum(mask, axis=1).tolist()
- index = areas.index(max(areas))
+ maskslice = mask[index, :, :]
else:
- index = int(image.shape[0]/2)
-
- imslice = image[index, :, :]
- if mask is not None:
- maskslice = mask[index, :, :]
- else:
- maskslice = None
+ maskslice = None
# Rotate, as this is not done automatically
if flip:
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 e3e9187b..8048a6f1 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 3.4.1 documentation
+ WORC.plotting.plot_ranked_scores — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
@@ -165,7 +165,7 @@
Source code for WORC.plotting.plot_ranked_scores
#!/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");
@@ -268,6 +268,18 @@ Source code for WORC.plotting.plot_ranked_scores
output_zip=output_zip)
+[docs]def flatten_object(input):
+ """Flatten various objects to a 1D list."""
+ out = []
+ for x in input:
+ if isinstance(x, (list, pd.core.series.Series, np.ndarray)):
+ out += flatten_object(x)
+ else:
+ out.append(x)
+
+ return out
+
+
[docs]def plot_ranked_percentages(estimator, pinfo, label_type=None,
ensemble=50, output_csv=None):
@@ -423,10 +435,10 @@ Source code for WORC.plotting.plot_ranked_scores
scores = dict()
truths = dict()
- y_truths_flat = [item for sublist in y_truths for item in sublist]
- #y_scores_flat = [item for sublist in y_scores for item in sublist]
- y_scores_flat = np.array(y_scores).flatten()
- PIDs_scores_flat = [item for sublist in PIDs_scores for item in sublist]
+ y_truths_flat = flatten_object(y_truths)
+ y_scores_flat = flatten_object(y_scores)
+ PIDs_scores_flat = flatten_object(PIDs_scores)
+
for yt, ys, pid in zip(y_truths_flat, y_scores_flat, PIDs_scores_flat):
if pid not in scores.keys():
# No scores yet for patient, create list
diff --git a/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html b/WORC/doc/_build/html/_modules/WORC/plotting/scatterplot.html
index 4f572bf0..3e4d5d96 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 3.4.1 documentation
+ WORC.plotting.scatterplot — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html b/WORC/doc/_build/html/_modules/WORC/processing/ExtractNLargestBlobsn.html
index 5c2d039e..f565344f 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 3.4.1 documentation
+ WORC.processing.ExtractNLargestBlobsn — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/processing/classes.html b/WORC/doc/_build/html/_modules/WORC/processing/classes.html
index 5e58c3ab..18cea5d9 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 3.4.1 documentation
+ WORC.processing.classes — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 d0a8961b..021457f9 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 3.4.1 documentation
+ WORC.processing.label_processing — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
@@ -165,7 +165,7 @@
Source code for WORC.processing.label_processing
#!/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");
@@ -191,7 +191,7 @@ Source code for WORC.processing.label_processing
import pandas as pd
-[docs]def load_labels(label_file, label_type):
+[docs]def load_labels(label_file, label_type=None):
"""Loads the label data from a label file
Args:
@@ -218,6 +218,10 @@ Source code for WORC.processing.label_processing
else:
raise ae.WORCIOError(extension + ' is not valid label file extension.')
+ if label_type is None:
+ print("Label_type given is None, extracting all labels.")
+ label_type = label_names
+
print("Label names to extract: " + str(label_type))
labels = list()
for i_label in label_type:
@@ -227,6 +231,7 @@ Source code for WORC.processing.label_processing
else:
labels.append(label_status[:, label_index])
+ # Create object to return
label_data = dict()
label_data['patient_IDs'] = patient_IDs
label_data['label'] = labels
@@ -283,7 +288,7 @@ Source code for WORC.processing.label_processing
label_status (numpy array): The status of the different labels
for each patient
"""
- data = pd.read_csv(input_file, header=0)
+ data = pd.read_csv(input_file, sep=None, header=0)
# Load and check the header
header = data.keys()
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 972222eb..24d11ac5 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 3.4.1 documentation
+ WORC.resources.fastr_tests.CalcFeatures_test — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 d955ead4..96eccd95 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 3.4.1 documentation
+ WORC.resources.fastr_tests.elastix_test — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
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 6d34bfc8..b3ae104d 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 3.4.1 documentation
+ WORC.resources.fastr_tests.segmentix_test — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html b/WORC/doc/_build/html/_modules/WORC/tools/Elastix.html
index 03b2db21..5955d50d 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 3.4.1 documentation
+ WORC.tools.Elastix — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html b/WORC/doc/_build/html/_modules/WORC/tools/Evaluate.html
index ef8bc1ba..b21014c8 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 3.4.1 documentation
+ WORC.tools.Evaluate — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html b/WORC/doc/_build/html/_modules/WORC/tools/Slicer.html
index eda5f151..a9cab5c1 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 3.4.1 documentation
+ WORC.tools.Slicer — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html b/WORC/doc/_build/html/_modules/WORC/tools/Transformix.html
index c567adac..5ebf9dbe 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 3.4.1 documentation
+ WORC.tools.Transformix — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html b/WORC/doc/_build/html/_modules/WORC/tools/createfixedsplits.html
index c32b166a..cbc9352d 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 3.4.1 documentation
+ WORC.tools.createfixedsplits — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_modules/index.html b/WORC/doc/_build/html/_modules/index.html
index c8ec64c3..b08b7ade 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 3.4.1 documentation
+ Overview: module code — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/_static/documentation_options.js b/WORC/doc/_build/html/_static/documentation_options.js
index a939770b..04328768 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: '3.4.1',
+ VERSION: '3.4.2',
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 4e5e4ba7..9e9df36f 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 3.4.1 documentation
+ IOparser Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.classification.html b/WORC/doc/_build/html/autogen/WORC.classification.html
index 77e525b0..78f08102 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 3.4.1 documentation
+ classification Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.config.html b/WORC/doc/_build/html/autogen/WORC.config.html
index 81312838..8c03634d 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 3.4.1 documentation
+ <no title> — WORC 3.4.2 documentation
@@ -62,7 +62,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.detectors.html b/WORC/doc/_build/html/autogen/WORC.detectors.html
index 68d42fc2..9a0c240c 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 3.4.1 documentation
+ detectors Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.exampledata.html b/WORC/doc/_build/html/autogen/WORC.exampledata.html
index 91b2fce6..76b0cba7 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 3.4.1 documentation
+ exampledata Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.facade.html b/WORC/doc/_build/html/autogen/WORC.facade.html
index 1b4cdabc..83b08a0d 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 3.4.1 documentation
+ facade Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.featureprocessing.html b/WORC/doc/_build/html/autogen/WORC.featureprocessing.html
index c9d2c759..404e1ab5 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 3.4.1 documentation
+ featureprocessing Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.html b/WORC/doc/_build/html/autogen/WORC.html
index 8fce2ee4..a87276c0 100644
--- a/WORC/doc/_build/html/autogen/WORC.html
+++ b/WORC/doc/_build/html/autogen/WORC.html
@@ -8,7 +8,7 @@
- WORC Package — WORC 3.4.1 documentation
+ WORC Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.plotting.html b/WORC/doc/_build/html/autogen/WORC.plotting.html
index 043f1c2f..c68aa283 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 3.4.1 documentation
+ plotting Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
@@ -560,6 +560,12 @@
WORC.plotting.plot_ranked_scores.
example
()[source]¶
+
+-
+
WORC.plotting.plot_ranked_scores.
flatten_object
(input)[source]¶
+Flatten various objects to a 1D list.
+
+
-
WORC.plotting.plot_ranked_scores.
main
()[source]¶
diff --git a/WORC/doc/_build/html/autogen/WORC.processing.html b/WORC/doc/_build/html/autogen/WORC.processing.html
index fefbf246..999e8cf0 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 3.4.1 documentation
+ processing Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
@@ -382,7 +382,7 @@ processing Package
-
-
WORC.processing.label_processing.
load_labels
(label_file, label_type)[source]¶
+WORC.processing.label_processing.
load_labels
(label_file, label_type=None)[source]¶
Loads the label data from a label file
- Args:
label_file (string): The path to the label file
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 bca8ae92..4c38b3c1 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 3.4.1 documentation
+ fastr_tests Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
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 fc835fcd..1a808e7d 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 3.4.1 documentation
+ fastr_tools Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.resources.html b/WORC/doc/_build/html/autogen/WORC.resources.html
index a8ce308b..9bc82e18 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 3.4.1 documentation
+ resources Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/autogen/WORC.tools.html b/WORC/doc/_build/html/autogen/WORC.tools.html
index 00bd318a..3d286739 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 3.4.1 documentation
+ tools Package — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/genindex.html b/WORC/doc/_build/html/genindex.html
index 83522074..1555a998 100644
--- a/WORC/doc/_build/html/genindex.html
+++ b/WORC/doc/_build/html/genindex.html
@@ -9,7 +9,7 @@
- Index — WORC 3.4.1 documentation
+ Index — WORC 3.4.2 documentation
@@ -63,7 +63,7 @@
- 3.4.1
+ 3.4.2
@@ -927,6 +927,8 @@ F
- fit_and_score() (in module WORC.classification.fitandscore)
- fit_thresholds() (in module WORC.plotting.plot_estimator_performance)
+
+ - flatten_object() (in module WORC.plotting.plot_ranked_scores)
- fullprint() (WORC.facade.helpers.configbuilder.ConfigBuilder method)
diff --git a/WORC/doc/_build/html/index.html b/WORC/doc/_build/html/index.html
index d9dd5243..12ed2621 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 3.4.1 documentation
+ WORC: Workflow for Optimal Radiomics Classification — WORC 3.4.2 documentation
@@ -63,7 +63,7 @@
- 3.4.1
+ 3.4.2
@@ -361,133 +361,138 @@ WORC DocumentationResource File Formats
- Changelog
-- 3.4.1 - 2021-05-18
+- 3.4.2 - Unreleased
-- 3.4.0 - 2021-02-02
-- Fixed
-- Changed
-- Added
+- 3.4.1 - 2021-05-18
-- 3.3.5 - 2020-10-21
-- Fixed
-- Changed
-- Added
+- 3.4.0 - 2021-02-02
-- 3.3.4 - 2020-10-06
-- Fixed
-- Changed
-- Added
+- 3.3.5 - 2020-10-21
-- 3.3.3 - 2020-09-11
-- Fixed
-- Changed
-- Added
+- 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
+- 3.3.2 - 2020-08-19
-- 3.3.0 - 2020-07-28
-- Added
-- Changed
-- Fixed
+- 3.3.1 - 2020-07-31
+
+- 3.3.0 - 2020-07-28
-- 3.2.2 - 2020-07-14
-- Added
-- Changed
-- Fixed
+- 3.2.2 - 2020-07-14
-- 3.2.1 - 2020-07-02
-- Added
-- Changed
-- Fixed
+- 3.2.1 - 2020-07-02
-- 3.2.0 - 2020-06-26
-- Added
-- Changed
-- Fixed
+- 3.2.0 - 2020-06-26
-- 3.1.4 - 2020-05-26
-- Added
-- Changed
-- Fixed
+- 3.1.4 - 2020-05-26
-- 3.1.3 - 2020-01-24
-- Added
-- Changed
-- Fixed
+- 3.1.3 - 2020-01-24
-- 3.1.2 - 2019-12-09
-- Added
-- Changed
-- Fixed
+- 3.1.2 - 2019-12-09
-- 3.1.1 - 2019-11-28
-- Added
-- Changed
-- Fixed
+- 3.1.1 - 2019-11-28
-- 3.1.0 - 2019-10-16
-- Added
-- Changed
-- Fixed
+- 3.1.0 - 2019-10-16
-- 3.0.0 - 2019-05-08
-- Added
-- Changed
-- Fixed
+- 3.0.0 - 2019-05-08
-- 2.1.3 - 2019-04-08
-- Changed
+- 2.1.3 - 2019-04-08
-- 2.1.2 - 2019-04-02
-- Added
-- Changed
-- Fixed
+- 2.1.2 - 2019-04-02
-- 2.1.1 - 2019-02-15
-- Added
-- Changed
-- Fixed
+- 2.1.1 - 2019-02-15
-- 2.1.0 - 2018-08-09
-- Added
-- Changed
-- Fixed
+- 2.1.0 - 2018-08-09
-- 2.0.0 - 2018-02-13
-- Added
-- Changed
-- Fixed
+- 2.0.0 - 2018-02-13
- 1.0.0rc1 - 2017-05-08
diff --git a/WORC/doc/_build/html/objects.inv b/WORC/doc/_build/html/objects.inv
index b1c98011..ed9db615 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 4d681cce..0e8fa800 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 3.4.1 documentation
+ Python Module Index — WORC 3.4.2 documentation
@@ -65,7 +65,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/search.html b/WORC/doc/_build/html/search.html
index 8361a0fd..68592fd4 100644
--- a/WORC/doc/_build/html/search.html
+++ b/WORC/doc/_build/html/search.html
@@ -8,7 +8,7 @@
- Search — WORC 3.4.1 documentation
+ Search — WORC 3.4.2 documentation
@@ -63,7 +63,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/searchindex.js b/WORC/doc/_build/html/searchindex.js
index a291c660..e2364eb8 100644
--- a/WORC/doc/_build/html/searchindex.js
+++ b/WORC/doc/_build/html/searchindex.js
@@ -1 +1 @@
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Package","IOparser Package","classification Package","<no title>","detectors Package","exampledata Package","facade Package","helpers Package","fastrconfig Package","featureprocessing Package","plotting Package","processing Package","resources Package","fastr_tests Package","fastr_tools Package","statistics Package","tests Package","tools Package","validators Package","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","<no title>","WORC: Workflow for Optimal Radiomics Classification","Additional functionality","Changelog","Configuration","Data Mining Methods","Developer documentation","FAQ","Radiomics Features","Resource File Formats","Introduction","Quick start guide","User Manual"],titleterms:{"0rc1":61,"boolean":65,"class":11,"function":60,"import":69,Added:61,Adding:64,The:[69,70],actual:69,addexcept:[0,65],addit:60,advancedsampl:2,analysi:[63,69],arrai:65,attribut:70,basicworc:6,begin:65,bigr:65,bin:66,binari:66,bootstrap:62,calcfeatures_test:13,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,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,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: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],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,optim:[59,68],orient:66,other:66,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:[63,66],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:68,start:69,statist:[15,63],statisticaltestfeatur:9,statisticaltestthreshold:9,submit:65,subpackag:[0,6,12],surviv:63,tabl:59,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:61,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_regress:16,worcvalueerror:65,work:65,workflow:59,would:65,your: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 6ef7115f..56e4d2aa 100644
--- a/WORC/doc/_build/html/static/changelog.html
+++ b/WORC/doc/_build/html/static/changelog.html
@@ -8,7 +8,7 @@
- Changelog — WORC 3.4.1 documentation
+ Changelog — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
@@ -99,133 +99,138 @@
- Developer documentation
- Resource File Formats
- Changelog
-- 3.4.1 - 2021-05-18
+- 3.4.2 - Unreleased
-- 3.4.0 - 2021-02-02
-- Fixed
-- Changed
-- Added
+- 3.4.1 - 2021-05-18
-- 3.3.5 - 2020-10-21
-- Fixed
-- Changed
-- Added
+- 3.4.0 - 2021-02-02
-- 3.3.4 - 2020-10-06
-- Fixed
-- Changed
-- Added
+- 3.3.5 - 2020-10-21
-- 3.3.3 - 2020-09-11
-- Fixed
-- Changed
-- Added
+- 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
+- 3.3.2 - 2020-08-19
-- 3.3.0 - 2020-07-28
-- Added
-- Changed
-- Fixed
+- 3.3.1 - 2020-07-31
+
+- 3.3.0 - 2020-07-28
-- 3.2.2 - 2020-07-14
-- Added
-- Changed
-- Fixed
+- 3.2.2 - 2020-07-14
-- 3.2.1 - 2020-07-02
-- Added
-- Changed
-- Fixed
+- 3.2.1 - 2020-07-02
-- 3.2.0 - 2020-06-26
-- Added
-- Changed
-- Fixed
+- 3.2.0 - 2020-06-26
-- 3.1.4 - 2020-05-26
-- Added
-- Changed
-- Fixed
+- 3.1.4 - 2020-05-26
-- 3.1.3 - 2020-01-24
-- Added
-- Changed
-- Fixed
+- 3.1.3 - 2020-01-24
-- 3.1.2 - 2019-12-09
-- Added
-- Changed
-- Fixed
+- 3.1.2 - 2019-12-09
-- 3.1.1 - 2019-11-28
-- Added
-- Changed
-- Fixed
+- 3.1.1 - 2019-11-28
-- 3.1.0 - 2019-10-16
-- Added
-- Changed
-- Fixed
+- 3.1.0 - 2019-10-16
-- 3.0.0 - 2019-05-08
-- Added
-- Changed
-- Fixed
+- 3.0.0 - 2019-05-08
-- 2.1.3 - 2019-04-08
-- Changed
+- 2.1.3 - 2019-04-08
-- 2.1.2 - 2019-04-02
-- Added
-- Changed
-- Fixed
+- 2.1.2 - 2019-04-02
-- 2.1.1 - 2019-02-15
-- Added
-- Changed
-- Fixed
+- 2.1.1 - 2019-02-15
-- 2.1.0 - 2018-08-09
-- Added
-- Changed
-- Fixed
+- 2.1.0 - 2018-08-09
-- 2.0.0 - 2018-02-13
-- Added
-- Changed
-- Fixed
+- 2.0.0 - 2018-02-13
- 1.0.0rc1 - 2017-05-08
@@ -303,11 +308,30 @@ ChangelogKeep a Changelog
and this project adheres to Semantic Versioning
-
-3.4.1 - 2021-05-18¶
+
+3.4.2 - Unreleased¶
Fixed¶
+Bug in flattening of plot_ranked_posteriors function.
+Bug in plot_images: could not handle 2D images when applying slicing.
+Bug in precision-recall curve.
+Bug in performance estimation plotting.
+Preflighcheck now also accepts labels from txt or XNAT.
+
+
+
+Added¶
+
+Label file can now also be separated by semicolons.
+
+
+
+
+3.4.1 - 2021-05-18¶
+
+Fixed¶
+
Bugfix when PCA cannot be fitted.
Bugfix when using LOO cross-validation in performance evaluation.
Fix XGboost verson, as newest version automatically uses multihreading,
@@ -327,8 +351,8 @@
Changed
-Added¶
+
+Added¶
-
-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.
@@ -351,16 +375,16 @@ 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.
-
-Added¶
+
-
-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.
-
-Added¶
+
-
-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.
@@ -409,16 +433,16 @@ 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.
@@ -470,16 +494,16 @@ 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.
@@ -518,8 +542,8 @@ 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.
@@ -533,8 +557,8 @@ 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
@@ -629,8 +653,8 @@
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.
@@ -675,8 +699,8 @@ Added
Combat: in WORK workflow.
-
-Changed¶
+
+Changed¶
Resampling of objects is now after feature selection.
Made plot_SVM function more memory efficient.
@@ -690,8 +714,8 @@ 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.
@@ -719,8 +743,8 @@ 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,
@@ -731,18 +755,18 @@
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,
@@ -752,38 +776,38 @@
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.
@@ -822,8 +846,8 @@ 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.
@@ -837,8 +861,8 @@ 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.
@@ -879,8 +903,8 @@ 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.
@@ -889,8 +913,8 @@ 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.
@@ -943,26 +967,26 @@ 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.
@@ -984,8 +1008,8 @@ 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.
@@ -1019,8 +1043,8 @@ 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.
diff --git a/WORC/doc/_build/html/static/configuration.html b/WORC/doc/_build/html/static/configuration.html
index cd43e87c..1227e50c 100644
--- a/WORC/doc/_build/html/static/configuration.html
+++ b/WORC/doc/_build/html/static/configuration.html
@@ -8,7 +8,7 @@
- Configuration — WORC 3.4.1 documentation
+ Configuration — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
@@ -1937,7 +1937,7 @@ Contentssampling_strategy
-majority, minority, not minority, not majority, all
+auto, majority, minority, not minority, not majority, all
auto, majority, not minority, not majority, all
n_neighbors
diff --git a/WORC/doc/_build/html/static/file_description.html b/WORC/doc/_build/html/static/file_description.html
index 3fe8812e..7a9d917b 100644
--- a/WORC/doc/_build/html/static/file_description.html
+++ b/WORC/doc/_build/html/static/file_description.html
@@ -8,7 +8,7 @@
- Resource File Formats — WORC 3.4.1 documentation
+ Resource File Formats — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/static/introduction.html b/WORC/doc/_build/html/static/introduction.html
index d144a5bc..881cb6ad 100644
--- a/WORC/doc/_build/html/static/introduction.html
+++ b/WORC/doc/_build/html/static/introduction.html
@@ -8,7 +8,7 @@
- Introduction — WORC 3.4.1 documentation
+ Introduction — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/static/quick_start.html b/WORC/doc/_build/html/static/quick_start.html
index 8d684ac4..abc1e775 100644
--- a/WORC/doc/_build/html/static/quick_start.html
+++ b/WORC/doc/_build/html/static/quick_start.html
@@ -8,7 +8,7 @@
- Quick start guide — WORC 3.4.1 documentation
+ Quick start guide — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/_build/html/static/user_manual.html b/WORC/doc/_build/html/static/user_manual.html
index 853eca66..7fd53e80 100644
--- a/WORC/doc/_build/html/static/user_manual.html
+++ b/WORC/doc/_build/html/static/user_manual.html
@@ -8,7 +8,7 @@
- User Manual — WORC 3.4.1 documentation
+ User Manual — WORC 3.4.2 documentation
@@ -64,7 +64,7 @@
- 3.4.1
+ 3.4.2
diff --git a/WORC/doc/autogen/config/WORC.config_Resampling_defopts.rst b/WORC/doc/autogen/config/WORC.config_Resampling_defopts.rst
index 50c7ac39..9e00647e 100644
--- a/WORC/doc/autogen/config/WORC.config_Resampling_defopts.rst
+++ b/WORC/doc/autogen/config/WORC.config_Resampling_defopts.rst
@@ -3,7 +3,7 @@ Subkey Default
================== ================================================================================================================================== ==================================================================================================================================
Use 0.20 Float
Method RandomUnderSampling, RandomOverSampling, NearMiss, NeighbourhoodCleaningRule, ADASYN, BorderlineSMOTE, SMOTE, SMOTEENN, SMOTETomek RandomUnderSampling, RandomOverSampling, NearMiss, NeighbourhoodCleaningRule, ADASYN, BorderlineSMOTE, SMOTE, SMOTEENN, SMOTETomek
-sampling_strategy majority, minority, not minority, not majority, all auto, majority, not minority, not majority, all
+sampling_strategy auto, majority, minority, not minority, not majority, all auto, majority, not minority, not majority, all
n_neighbors 3, 12 Two Integers: loc and scale
k_neighbors 5, 15 Two Integers: loc and scale
threshold_cleaning 0.25, 0.5 Two Floats: loc and scale
diff --git a/WORC/plotting/plot_ROC.py b/WORC/plotting/plot_ROC.py
index 5d1e0e4b..37b68b73 100644
--- a/WORC/plotting/plot_ROC.py
+++ b/WORC/plotting/plot_ROC.py
@@ -25,6 +25,7 @@
from WORC.plotting.compute_CI import compute_confidence as CI
import numpy as np
from sklearn.metrics import roc_auc_score, auc
+from sklearn.metrics import precision_recall_curve
import csv
from WORC.plotting.plot_estimator_performance import plot_estimator_performance
@@ -115,13 +116,6 @@ def plot_single_PRC(y_truth, y_score, verbose=False, returnplot=False):
y_score = y_score[inds]
# Compute the TPR and FPR for all possible thresholds
- FP = 0
- TP = 0
- precision = list()
- tpr = list()
- thresholds = list()
- fprev = -np.inf
- i = 0
N = float(np.bincount(y_truth)[0])
if len(np.bincount(y_truth)) == 1:
# No class = 1 present.
@@ -131,29 +125,19 @@ def plot_single_PRC(y_truth, y_score, verbose=False, returnplot=False):
if N == 0:
print('[WORC Warning] No negative class samples found, cannot determine PRC. Skipping iteration.')
- return precision, tpr, thresholds
+ return list(), list(), list()
elif P == 0:
print('[WORC Warning] No positive class samples found, cannot determine PRC. Skipping iteration.')
- return precision, tpr, thresholds
-
- while i < len(y_truth_sorted):
- if y_score[i] != fprev:
- if TP == 0:
- # Prevent division by zero
- precision.append(0)
- else:
- precision.append(TP/(TP + FP))
+ return list(), list(), list()
- tpr.append(1 - TP/P)
- thresholds.append(y_score[i])
- fprev = y_score[i]
+ precision, tpr, thresholds =\
+ precision_recall_curve(y_truth_sorted, y_score)
- if y_truth_sorted[i] == 1:
- TP += 1
- else:
- FP += 1
+ # Convert to lists
+ precision = precision.tolist()
+ tpr = tpr.tolist()
+ thresholds = thresholds.tolist()
- i += 1
if verbose or returnplot:
prc_auc = auc(tpr, precision)
diff --git a/WORC/plotting/plot_estimator_performance.py b/WORC/plotting/plot_estimator_performance.py
index 4bccd000..b33f01d7 100644
--- a/WORC/plotting/plot_estimator_performance.py
+++ b/WORC/plotting/plot_estimator_performance.py
@@ -704,11 +704,20 @@ def plot_estimator_performance(prediction, label_data, label_type,
for i_ID in patient_classification_list:
percentage_right = patient_classification_list[i_ID]['N_correct'] / float(patient_classification_list[i_ID]['N_test'])
- if i_ID in patient_IDs:
- label = labels[0][np.where(i_ID == patient_IDs)]
+ # Check if this is exactly the label of the patient within the label file
+ check_id = i_ID
+ if check_id not in patient_IDs:
+ print(f'[WORC WARNING] Patient {check_id} is not found the patient labels, removing underscore.')
+ check_id = check_id.split("_")[0]
+ if check_id not in patient_IDs:
+ print(f'[WORC WARNING] Did not help, excluding patient {check_id}.')
+ continue
+
+ if check_id in patient_IDs:
+ label = labels[0][np.where(check_id == patient_IDs)]
else:
# Multiple instance of one patient
- label = labels[0][np.where(i_ID.split('_')[0] == patient_IDs)]
+ label = labels[0][np.where(check_id.split('_')[0] == patient_IDs)]
label = label[0][0]
percentages[i_ID] = str(label) + ': ' + str(round(percentage_right, 2) * 100) + '%'
diff --git a/WORC/plotting/plot_images.py b/WORC/plotting/plot_images.py
index 986560bf..00e9e221 100644
--- a/WORC/plotting/plot_images.py
+++ b/WORC/plotting/plot_images.py
@@ -68,19 +68,24 @@ def slicer(image, mask=None, output_name=None, output_name_zoom=None,
if mask is not None:
mask = sitk.GetArrayFromImage(mask)
- # Determine which axial slice has the largest area
- if index is None:
+ if len(image.shape) == 2:
+ # 2D image, so image and mask are already single slices
+ imslice = image
+ maskslice = mask
+ else:
+ # Determine which axial slice has the largest area
+ if index is None:
+ if mask is not None:
+ areas = np.sum(mask, axis=1).tolist()
+ index = areas.index(max(areas))
+ else:
+ index = int(image.shape[0]/2)
+
+ imslice = image[index, :, :]
if mask is not None:
- areas = np.sum(mask, axis=1).tolist()
- index = areas.index(max(areas))
+ maskslice = mask[index, :, :]
else:
- index = int(image.shape[0]/2)
-
- imslice = image[index, :, :]
- if mask is not None:
- maskslice = mask[index, :, :]
- else:
- maskslice = None
+ maskslice = None
# Rotate, as this is not done automatically
if flip:
diff --git a/WORC/plotting/plot_ranked_scores.py b/WORC/plotting/plot_ranked_scores.py
index be426f13..33c4efb9 100644
--- a/WORC/plotting/plot_ranked_scores.py
+++ b/WORC/plotting/plot_ranked_scores.py
@@ -1,6 +1,6 @@
#!/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");
@@ -103,6 +103,18 @@ def main():
output_zip=output_zip)
+def flatten_object(input):
+ """Flatten various objects to a 1D list."""
+ out = []
+ for x in input:
+ if isinstance(x, (list, pd.core.series.Series, np.ndarray)):
+ out += flatten_object(x)
+ else:
+ out.append(x)
+
+ return out
+
+
def plot_ranked_percentages(estimator, pinfo, label_type=None,
ensemble=50, output_csv=None):
@@ -258,10 +270,10 @@ def plot_ranked_posteriors(estimator, pinfo, label_type=None,
scores = dict()
truths = dict()
- y_truths_flat = [item for sublist in y_truths for item in sublist]
- #y_scores_flat = [item for sublist in y_scores for item in sublist]
- y_scores_flat = np.array(y_scores).flatten()
- PIDs_scores_flat = [item for sublist in PIDs_scores for item in sublist]
+ y_truths_flat = flatten_object(y_truths)
+ y_scores_flat = flatten_object(y_scores)
+ PIDs_scores_flat = flatten_object(PIDs_scores)
+
for yt, ys, pid in zip(y_truths_flat, y_scores_flat, PIDs_scores_flat):
if pid not in scores.keys():
# No scores yet for patient, create list
diff --git a/WORC/processing/label_processing.py b/WORC/processing/label_processing.py
index 36dbe660..69fe8607 100644
--- a/WORC/processing/label_processing.py
+++ b/WORC/processing/label_processing.py
@@ -1,6 +1,6 @@
#!/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");
@@ -26,7 +26,7 @@
import pandas as pd
-def load_labels(label_file, label_type):
+def load_labels(label_file, label_type=None):
"""Loads the label data from a label file
Args:
@@ -53,6 +53,10 @@ def load_labels(label_file, label_type):
else:
raise ae.WORCIOError(extension + ' is not valid label file extension.')
+ if label_type is None:
+ print("Label_type given is None, extracting all labels.")
+ label_type = label_names
+
print("Label names to extract: " + str(label_type))
labels = list()
for i_label in label_type:
@@ -62,6 +66,7 @@ def load_labels(label_file, label_type):
else:
labels.append(label_status[:, label_index])
+ # Create object to return
label_data = dict()
label_data['patient_IDs'] = patient_IDs
label_data['label'] = labels
@@ -118,7 +123,7 @@ def load_label_csv(input_file):
label_status (numpy array): The status of the different labels
for each patient
"""
- data = pd.read_csv(input_file, header=0)
+ data = pd.read_csv(input_file, sep=None, header=0)
# Load and check the header
header = data.keys()
diff --git a/WORC/validators/preflightcheck.py b/WORC/validators/preflightcheck.py
index feadb2f5..683ac65d 100644
--- a/WORC/validators/preflightcheck.py
+++ b/WORC/validators/preflightcheck.py
@@ -1,6 +1,23 @@
+#!/usr/bin/env python
+
+# 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");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
from abc import ABC, abstractmethod
-from WORC.processing.label_processing import load_label_csv
+from WORC.processing.label_processing import load_labels
import WORC.addexceptions as ae
import os
@@ -103,13 +120,15 @@ def _validate(self, simpleworc):
raise ae.WORCValueError(f'Given label file {labels_file_train} does not exist.')
try:
- labels, subjects, _ = load_label_csv(labels_file_train)
+ label_data = load_labels(labels_file_train)
except ae.WORCAssertionError as wae:
if 'First column should be patient ID' in str(wae):
# TODO: print wrong column name and file so that it is clear what needs to be replaced in which file
raise ae.WORCValueError(f'First column in the file given to SimpleWORC().labels_from_this_file(**) needs to be named Patient.')
# check labels for substrings of eachother
+ labels = label_data['label_name']
+ subjects = label_data['patient_IDs']
labels_matches = self._get_all_substrings_for_array(labels)
if labels_matches:
diff --git a/setup.py b/setup.py
index 6cc3364c..c706c42b 100644
--- a/setup.py
+++ b/setup.py
@@ -93,7 +93,7 @@ def run_tests(self):
setup(
name='WORC',
- version='3.4.1',
+ version='3.4.2',
description='Workflow for Optimal Radiomics Classification.',
long_description=_description,
url='https://github.com/MStarmans91/WORC',
diff --git a/version b/version
index 47b322c9..4d9d11cf 100644
--- a/version
+++ b/version
@@ -1 +1 @@
-3.4.1
+3.4.2