def create_client(url):
''' Function to create the dicomweb client for future requests'''
webclient = DICOMwebClient(url=url,
qido_url_prefix='rs',
wado_url_prefix='rs',
stow_url_prefix='rs')
return webclient
def _search_for_series(args):
'''Searches for Series and writes metadata to standard output.'''
params = _parse_search_parameters(args)
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
series = client.search_for_series(args.study_instance_uid, **params)
_print_metadata(series, args.prettify, args.dicomize)
def _retrieve_bulkdata(args):
'''Retrieves bulk data and either writes them to standard output or to a
file on disk.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
data = client.retrieve_bulkdata(args.bulkdata_uri, args.media_type)
print(data)
print('\n')
def _retrieve_instance_metadata(args):
'''Retrieves metadata for an individual Instances and either
writes it to standard output or to a file on disk.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
metadata = client.retrieve_instance_metadata(args.study_instance_uid,
args.series_instance_uid,
args.sop_instance_uid)
if args.save:
_save_metadata(metadata, args.output_dir, args.sop_instance_uid,
args.prettify, args.dicomize)
else:
_print_metadata(metadata, args.prettify, args.dicomize)
def _retrieve_study_metadata(args):
'''Retrieves metadata for all Instances of a given Study and either
writes it to standard output or to files on disk.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
metadata = client.retrieve_study_metadata(args.study_instance_uid)
if args.save:
for md in metadata:
tag = client.lookup_tag('SOPInstanceUID')
sop_instance_uid = md[tag]['Value'][0]
_save_metadata(md, args.output_dir, sop_instance_uid,
args.prettify, args.dicomize)
else:
_print_metadata(metadata, args.prettify, args.dicomize)
def _retrieve_instance(args):
'''Retrieves an Instances and either writes it to standard output or to a
file on disk.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
instance = client.retrieve_instance(
args.study_instance_uid,
args.series_instance_uid,
args.sop_instance_uid,
media_types=args.media_types,
)
if args.save:
_save_instance(instance, args.output_dir, args.sop_instance_uid)
else:
_print_instance(instance)
def _retrieve_study(args):
'''Retrieves all Instances of a given Study and either writes them to
standard output or to files on disk.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
instances = client.retrieve_study(
args.study_instance_uid,
media_types=args.media_types,
)
for inst in instances:
sop_instance_uid = inst.SOPInstanceUID
if args.save:
_save_instance(inst, args.output_dir, sop_instance_uid)
else:
_print_instance(inst)
def _retrieve_instance_frames(args):
'''Retrieves frames for an individual instances and either
writes them to standard output or files on disk or displays them in a GUI
(depending on the requested content type).
Frames can only be saved and shown if they are retrieved using
image media types.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
pixel_data = client.retrieve_instance_frames(
args.study_instance_uid,
args.series_instance_uid,
args.sop_instance_uid,
args.frame_numbers,
media_types=args.media_types,
)
for i, data in enumerate(pixel_data):
if args.save or args.show:
try:
image = Image.open(BytesIO(data))
except Exception:
try:
import jpeg_ls
image = jpeg_ls.decode(np.fromstring(data, dtype=np.uint8))
except Exception:
raise IOError('Cannot load retrieved frame as an image.')
if args.save:
filename = (
'{sop_instance_uid}_{frame_number}.{extension}'.format(
sop_instance_uid=args.sop_instance_uid,
frame_number=args.frame_numbers[i],
extension=image.format.lower()))
filepath = os.path.join(args.output_dir, filename)
_save_image(image, filepath)
elif args.show:
_show_image(image)
else:
_print_pixel_data(data)
