processing Package¶
ExtractNLargestBlobsn
Module¶
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WORC.processing.ExtractNLargestBlobsn.
ExtractNLargestBlobsn
(binaryImage, numberToExtract=1)[source]¶ Extract N largest blobs from binary image.
- Arguments:
binaryImage: boolean numpy array one or several contours. numberToExtract: number of blobs to extract (integer).
- Returns:
- binaryImage: boolean numpy are containing only the N
extracted blobs.
classes
Module¶
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class
WORC.processing.classes.
switch
(value)[source]¶ Bases:
object
Object to mimic the MATLAB switch - case statement.
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__dict__
= mappingproxy({'__module__': 'WORC.processing.classes', '__doc__': ' Object to mimic the MATLAB switch - case statement.', '__init__': <function switch.__init__>, '__iter__': <function switch.__iter__>, 'match': <function switch.match>, '__dict__': <attribute '__dict__' of 'switch' objects>, '__weakref__': <attribute '__weakref__' of 'switch' objects>})¶
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__module__
= 'WORC.processing.classes'¶
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__weakref__
¶ list of weak references to the object (if defined)
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label_processing
Module¶
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WORC.processing.label_processing.
findlabeldata
(patientinfo, label_type, filenames=None, objects=None, pids=None)[source]¶ Load the label data and match to the unage features.
- Args:
patientinfo (string): file with patient label data label_type (string): name of the label read out from patientinfo filenames (list): names of the patient feature files, used for matching objects (np.array or list): array of objects you want to order as well
- Returns:
label_data (dict): contains patient ids, their labels and the label name
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WORC.processing.label_processing.
load_config_XNAT
(config_file_path)[source]¶ Configparser for retreiving patient data from XNAT.
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WORC.processing.label_processing.
load_label_XNAT
(label_info)[source]¶ Load the patient IDs and label data from XNAT, Only works if you have a file /resources/GENETICS/files/genetics.json for each patient containing a single dictionary of all labels.
- Args:
url (string): XNAT URL project: XNAT project ID
- Returns:
label_names (numpy array): Names of the different labels patient_ID (numpy array): IDs of patients for which label data is
loaded
- label_status (numpy array): The status of the different labels
for each patient
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WORC.processing.label_processing.
load_label_csv
(input_file)[source]¶ Load the patient IDs and label data from the label file
- Args:
input_file (string): Path of the label file
- Returns:
label_names (numpy array): Names of the different labels patient_ID (numpy array): IDs of patients for which label data is
loaded
- label_status (numpy array): The status of the different labels
for each patient
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WORC.processing.label_processing.
load_label_txt
(input_file)[source]¶ Load the patient IDs and label data from the label file
- Args:
input_file (string): Path of the label file
- Returns:
label_names (numpy array): Names of the different labels patient_ID (numpy array): IDs of patients for which label data is
loaded
- label_status (numpy array): The status of the different labels
for each patient
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WORC.processing.label_processing.
load_labels
(label_file, label_type)[source]¶ Loads the label data from a label file
- Args:
label_file (string): The path to the label file label_type (list): List of the names of the labels to load
- Returns:
- dict: A dict containing ‘patient_IDs’, ‘label’ and
‘label_type’
preprocessing
Module¶
segmentix
Module¶
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WORC.processing.segmentix.
dilate_contour
(contour, radius=5)[source]¶ Dilate the contour
- contour: numpy array
Array containing the contour
- radius: int, default 5
Radius of ring to be extracted.
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WORC.processing.segmentix.
get_ring
(contour, radius=5)[source]¶ Get a ring on the boundary of the contour.
- contour: numpy array
Array containing the contour
- radius: int, default 5
Radius of ring to be extracted.
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WORC.processing.segmentix.
mask_contour
(contour, mask, method='multiply')[source]¶ Apply a mask to a contour.
- contour: numpy array
Array containing the contour
- mask: string
path referring to the mask used for the final segmentation. Should be a format compatible with ITK, e.g. .nii, .nii.gz, .mhd, .raw, .tiff, .nrrd.
- method: string
How masking is applied: can be subtract or pairwise
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WORC.processing.segmentix.
segmentix
(parameters, image=None, segmentation=None, output=None, metadata_file=None, mask=None)[source]¶ Segmentix is a mixture of processing methods that can be applied to agument a segmentation. Examples include selecting only the largest blob and the application of morphological operations.
- parameters: string, mandatory
Contains the path referring to a .ini file in which the parameters to be used are specified. See the Github Wiki for more details on the format and content.
- image: string, optional
Note implemented yet! Image to be used for automatic segmentation.
- segmentation: string, currently mandatory
path referring to the input segmentation file. Should be a format compatible with ITK, e.g. .nii, .nii.gz, .mhd, .raw, .tiff, .nrrd.
- output: string, mandatory
path referring to the output segmentation file. Should be a format compatible with ITK, e.g. .nii, .nii.gz, .mhd, .raw, .tiff, .nrrd.
- metadata_file: string, optional
Note implemented yet! Path referring to the .dcm from which fields can be used as metadata for segmentation.
- mask: string, optional
path referring to the mask used for the final segmentation. Should be a format compatible with ITK, e.g. .nii, .nii.gz, .mhd, .raw, .tiff, .nrrd.