Source code for large_image_source_dicom.dicomweb_utils

from large_image_source_dicom.dicom_metadata import extract_dicom_metadata
from large_image_source_dicom.dicom_tags import dicom_key_to_tag

[docs] def get_dicomweb_metadata(client, study_uid, series_uid): # Many series-level metadata items are available if we explicitly # request for them in the `search_for_series()` calls. # However, some things are not available in the series-level # metadata - in particular, the specimen information is only # on the instance-level metadata. # It seems that, for the most part, all WSI DICOM instances in a # series have virtually identical metadata (except one or two things, # such as the suffix on the serial number, and sometimes one of the # items in the specimen metadata). # We will do as the SLIM viewer does: grab a single volume instance # and use that for the metadata. volume_metadata = get_first_wsi_volume_metadata(client, study_uid, series_uid) if not volume_metadata: # No metadata return None from pydicom import Dataset dataset = Dataset.from_json(volume_metadata) return extract_dicom_metadata(dataset)
[docs] def get_first_wsi_volume_metadata(client, study_uid, series_uid): # Find the first WSI Volume and return the DICOMweb metadata from wsidicom.uid import WSI_SOP_CLASS_UID image_type_tag = dicom_key_to_tag('ImageType') instance_uid_tag = dicom_key_to_tag('SOPInstanceUID') # We can't include the SOPClassUID as a search filter because Imaging Data Commons # produces an error if we do. Perform the filtering manually instead. class_uid_tag = dicom_key_to_tag('SOPClassUID') fields = [ image_type_tag, instance_uid_tag, class_uid_tag, ] wsi_instances = client.search_for_instances( study_uid, series_uid, fields=fields) volume_instance = None for instance in wsi_instances: class_type = instance.get(class_uid_tag, {}).get('Value') if not class_type or class_type[0] != WSI_SOP_CLASS_UID: # Only look at WSI classes continue image_type = instance.get(image_type_tag, {}).get('Value') # It would be nice if we could have a search filter for this, but # I didn't see one... if image_type and len(image_type) > 2 and image_type[2] == 'VOLUME': volume_instance = instance break if not volume_instance: # No volumes were found... return None instance_uid = volume_instance[instance_uid_tag]['Value'][0] return client.retrieve_instance_metadata(study_uid, series_uid, instance_uid)