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’