cobra_db.scripts.pseudonymize_image_metadata

Module Contents

Functions

parse_arguments(→ str)

Parse the arguments for the pseudonymization process

im_meta_generator(src_mongo[, query])

Generator of im_meta dicts

im_meta_from_virtual_dataset(ds, file_source[, _id])

An alternative version of ImageMetadata.from_dataset that does not require a

process_batch(args)

process_im_meta(im_meta_dict, cfg, src_im_dao, dst_im_dao)

get_required_drive_names(src_mongo, query)

check_mount_paths(mount_paths, required_drive_names, ...)

single_proc(batches[, n_proc])

multi_proc(batches, n_proc)

query_mux(query[, image_ids])

Select one of query or image_ids

recipe_mux(base, mr, recipe)

Select the correct recipe according to the configurations

main([args, image_ids])

cobra_db.scripts.pseudonymize_image_metadata.parse_arguments(raw_args: List[str]) → str[source]

Parse the arguments for the pseudonymization process

Parameters:

raw_args – arguments from sys.argv[1:]

Returns:

a namespace with the required cfg

cobra_db.scripts.pseudonymize_image_metadata.im_meta_generator(src_mongo: dict, query: dict = {})[source]

Generator of im_meta dicts

Parameters:

  • src_mongo – kwargs for the Connector

  • query – query to select subset of the ImageMetadata collection

Yield:

dict with image metadata.

cobra_db.scripts.pseudonymize_image_metadata.im_meta_from_virtual_dataset(ds: pydicom.Dataset, file_source: cobra_db.model.FileSource, _id: bson.ObjectId = None)[source]

An alternative version of ImageMetadata.from_dataset that does not require a ds.filename

Parameters:

  • ds – Dicom dataset

  • file_source – Source of the dataset

  • _id – the id that will be stored in the dst_mongo

cobra_db.scripts.pseudonymize_image_metadata.process_batch(args)[source]
cobra_db.scripts.pseudonymize_image_metadata.process_im_meta(im_meta_dict: dict, cfg, src_im_dao: cobra_db.mongo_dao.ImageMetadataDao, dst_im_dao: cobra_db.mongo_dao.ImageMetadataDao, retries=10)[source]
cobra_db.scripts.pseudonymize_image_metadata.get_required_drive_names(src_mongo, query)[source]
cobra_db.scripts.pseudonymize_image_metadata.check_mount_paths(mount_paths, required_drive_names, dst_drive_name)[source]
cobra_db.scripts.pseudonymize_image_metadata.single_proc(batches, n_proc=1)[source]
cobra_db.scripts.pseudonymize_image_metadata.multi_proc(batches, n_proc)[source]
cobra_db.scripts.pseudonymize_image_metadata.query_mux(query, image_ids: List[bson.ObjectId] = None)[source]

Select one of query or image_ids

cobra_db.scripts.pseudonymize_image_metadata.recipe_mux(base: bool, mr: bool, recipe: Union[str, List[str]])[source]

Select the correct recipe according to the configurations

cobra_db.scripts.pseudonymize_image_metadata.main(args=None, image_ids: List[bson.ObjectId] = None)[source]