tools Package¶
Elastix
Module¶
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class
WORC.tools.Elastix.
Elastix
[source]¶ Bases:
object
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__dict__
= mappingproxy({'__module__': 'WORC.tools.Elastix', '__init__': <function Elastix.__init__>, 'getparametermap': <function Elastix.getparametermap>, 'create_network': <function Elastix.create_network>, 'addchangeorder': <function Elastix.addchangeorder>, 'create_bbox': <function Elastix.create_bbox>, 'execute': <function Elastix.execute>, '__dict__': <attribute '__dict__' of 'Elastix' objects>, '__weakref__': <attribute '__weakref__' of 'Elastix' objects>, '__doc__': None})¶
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__module__
= 'WORC.tools.Elastix'¶
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__weakref__
¶ list of weak references to the object (if defined)
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Evaluate
Module¶
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class
WORC.tools.Evaluate.
Evaluate
(label_type, modus='binary_classification', scores='percentages', ensemble_method='top_N', ensemble_size=100, parent=None, features=None, fastr_plugin='LinearExecution', name='Example')[source]¶ Bases:
object
Build a network that evaluates the performance of an estimator.
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__dict__
= mappingproxy({'__module__': 'WORC.tools.Evaluate', '__doc__': 'Build a network that evaluates the performance of an estimator.', '__init__': <function Evaluate.__init__>, 'create_network': <function Evaluate.create_network>, 'create_links_Standalone': <function Evaluate.create_links_Standalone>, 'create_links_Addon': <function Evaluate.create_links_Addon>, 'set': <function Evaluate.set>, 'execute': <function Evaluate.execute>, '__dict__': <attribute '__dict__' of 'Evaluate' objects>, '__weakref__': <attribute '__weakref__' of 'Evaluate' objects>})¶
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__init__
(label_type, modus='binary_classification', scores='percentages', ensemble_method='top_N', ensemble_size=100, parent=None, features=None, fastr_plugin='LinearExecution', name='Example')[source]¶ Initialize object.
- network: fastr network, default None
If you input a network, the evaluate network is added to the existing network.
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__module__
= 'WORC.tools.Evaluate'¶
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__weakref__
¶ list of weak references to the object (if defined)
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Inference
Module¶
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class
WORC.tools.Inference.
Inference
(fastr_plugin='LinearExecution', name='Example')[source]¶ Bases:
object
Build a network that can use an existing model for inference.
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__dict__
= mappingproxy({'__module__': 'WORC.tools.Inference', '__doc__': 'Build a network that can use an existing model for inference.', '__init__': <function Inference.__init__>, 'create_network': <function Inference.create_network>, '__dict__': <attribute '__dict__' of 'Inference' objects>, '__weakref__': <attribute '__weakref__' of 'Inference' objects>})¶
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__init__
(fastr_plugin='LinearExecution', name='Example')[source]¶ Initialize object.
- network: fastr network, default None
If you input a network, the evaluate network is added to the existing network.
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__module__
= 'WORC.tools.Inference'¶
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__weakref__
¶ list of weak references to the object (if defined)
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Slicer
Module¶
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class
WORC.tools.Slicer.
Slicer
(images=None, segmentations=None, network=None, fastr_plugin='ProcessPoolExecution', name='Example')[source]¶ Bases:
object
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__dict__
= mappingproxy({'__module__': 'WORC.tools.Slicer', '__init__': <function Slicer.__init__>, 'create_network': <function Slicer.create_network>, 'set': <function Slicer.set>, 'execute': <function Slicer.execute>, '__dict__': <attribute '__dict__' of 'Slicer' objects>, '__weakref__': <attribute '__weakref__' of 'Slicer' objects>, '__doc__': None})¶
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__init__
(images=None, segmentations=None, network=None, fastr_plugin='ProcessPoolExecution', name='Example')[source]¶ Build a network that evaluates the performance of an estimator.
- network: fastr network, default None
If you input a network, the evaluate network is added to the existing network.
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__module__
= 'WORC.tools.Slicer'¶
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__weakref__
¶ list of weak references to the object (if defined)
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Transformix
Module¶
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class
WORC.tools.Transformix.
Transformix
[source]¶ Bases:
object
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__dict__
= mappingproxy({'__module__': 'WORC.tools.Transformix', '__init__': <function Transformix.__init__>, 'create_network': <function Transformix.create_network>, 'execute': <function Transformix.execute>, '__dict__': <attribute '__dict__' of 'Transformix' objects>, '__weakref__': <attribute '__weakref__' of 'Transformix' objects>, '__doc__': None})¶
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__module__
= 'WORC.tools.Transformix'¶
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__weakref__
¶ list of weak references to the object (if defined)
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createfixedsplits
Module¶
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WORC.tools.createfixedsplits.
createfixedsplits
(label_file=None, label_type=None, patient_IDs=None, stratify=True, test_size=0.2, N_iterations=1, modus='singlelabel', output=None)[source]¶ Create fixed splits for a random-split cross-validation.
- label_filefilepath
CSV file containing the labels of the patients.
- label_type: list of strings
labels to extracted from the label file, e.g. [‘label1’]
- patient_IDs: list of strings
names of patients to take into account. If None, take all
- stratify: Boolean
If True, splits are stratified. In this case, you need to provide label data.
- test_size: float
Percentage of patients in test set per iteration.
- N_iterations: integer
Number of cross-validation iterations
- modus: str
singlelabel or regression. Multilabel not implemented yet.
- output: filepath
csv filename to save output to.
- df: pandas Dataframe
Fixed splits created.
fingerprinting
Module¶
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class
WORC.tools.fingerprinting.
Fingerprinter
[source]¶ Bases:
object
Fingerprinting object for WORC configuration.
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__dict__
= mappingproxy({'__module__': 'WORC.tools.fingerprinting', '__doc__': 'Fingerprinting object for WORC configuration.', '__init__': <function Fingerprinter.__init__>, 'execute': <function Fingerprinter.execute>, '__dict__': <attribute '__dict__' of 'Fingerprinter' objects>, '__weakref__': <attribute '__weakref__' of 'Fingerprinter' objects>})¶
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__module__
= 'WORC.tools.fingerprinting'¶
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__weakref__
¶ list of weak references to the object (if defined)
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