PREDICT.genetics package

Submodules

PREDICT.genetics.genetic_processing module

PREDICT.genetics.genetic_processing.findmutationdata(patientinfo, mutation_type, filenames, image_features_temp=None)

Load the label data and match to the unage features.

Args:
patientinfo (string): file with patient label data mutation_type (string): name of the label read out from patientinfo filenames (list): names of the patient feature files, used for matching image_features (np.array or list): array of the features
Returns:
mutation_data (dict): contains patient ids, their labels and the mutation name
PREDICT.genetics.genetic_processing.load_config_XNAT(config_file_path)

Configparser for retreiving patient data from XNAT.

PREDICT.genetics.genetic_processing.load_genetic_XNAT(genetic_info)

Load the patient IDs and genetic 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:

mutation_names (numpy array): Names of the different genetic mutations patient_ID (numpy array): IDs of patients for which genetic data is

loaded
mutation_status (numpy array): The status of the different mutations
for each patient
PREDICT.genetics.genetic_processing.load_genetic_file(input_file)

Load the patient IDs and genetic data from the genetic file

Args:
input_file (string): Path of the genetic file
Returns:

mutation_names (numpy array): Names of the different genetic mutations patient_ID (numpy array): IDs of patients for which genetic data is

loaded
mutation_status (numpy array): The status of the different mutations
for each patient
PREDICT.genetics.genetic_processing.load_mutation_status(genetic_file, mutation_type)

Loads the mutation data from a genetic file

Args:
genetic_file (string): The path to the genetic file mutation_type (list): List of the genetic mutations to load
Returns:
dict: A dict containing ‘patient_IDs’, ‘mutation_label’ and
‘mutation_type’

Module contents