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from __future__ import print_function, unicode_literals
import argparse
import logging
import os
import re
import odil
from .dicomdir import create_dicomdir
def add_subparser(subparsers):
parser = subparsers.add_parser(
"get", help="DICOM retrieve (C-GET)",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("host", help="Remote host address")
parser.add_argument("port", type=int, help="Remote host port")
parser.add_argument(
"calling_ae_title", help="AE title of the calling application")
parser.add_argument(
"called_ae_title", help="AE title of the called application")
parser.add_argument(
"level", choices=["patient", "study"],
help="Root object of the retrieval")
parser.add_argument("keys", nargs="+", help="Retrieve keys")
parser.add_argument(
"--directory", "-d", default=os.getcwd(),
help="Directory where the output files will be stored")
parser.add_argument(
"--iso-9660", "-I", action="store_true",
help="Save file names using ISO-9660 compatible file names")
parser.add_argument(
"--layout", "-l", choices=["flat", "tree"], default="flat",
help="Save files in the same directory (flat) or in a "
"patient/study/series tree (hierarchical)")
parser.add_argument(
"--dicomdir", "-D", action="store_true",
help="Create a DICOMDIR from the retrieved files")
parser.add_argument(
"--patient-key", "-p", default=[], action="append",
help="User-defined keys for PATIENT-level records, "
"expressed as KEYWORD[:TYPE]. TYPE defaults to 3.")
parser.add_argument(
"--study-key", "-S", default=[], action="append",
help="User-defined keys for STUDY-level records")
parser.add_argument(
"--series-key", "-s", default=[], action="append",
help="User-defined keys for SERIES-level records")
parser.add_argument(
"--image-key", "-i", default=[], action="append",
help="User-defined keys for IMAGE-level records")
parser.set_defaults(function=get)
return parser
def get(
host, port, calling_ae_title, called_ae_title, level, keys, directory,
iso_9660, layout,
dicomdir, patient_key, study_key, series_key, image_key):
if dicomdir and not iso_9660:
raise Exception("Cannot create a DICOMDIR without ISO-9660 filenames")
query = odil.DataSet()
for key in keys:
key, value = key.split("=", 1)
value = value.split("\\")
tag = getattr(odil.registry, key)
vr = odil.registry.public_dictionary[tag].vr
if vr in ["DS", "FL", "FD"]:
value = [float(x) for x in value]
elif vr in ["IS", "SL", "SS", "UL", "US"]:
value = [int(x) for x in value]
query.add(tag, value)
get_syntax = getattr(
odil.registry,
"{}RootQueryRetrieveInformationModelGet".format(level.capitalize()))
transfer_syntaxes = [
odil.registry.ImplicitVRLittleEndian,
odil.registry.ExplicitVRLittleEndian
]
get_pc = odil.AssociationParameters.PresentationContext(
1, get_syntax, transfer_syntaxes,
odil.AssociationParameters.PresentationContext.Role.SCU)
abstract_syntaxes = find_abstract_syntaxes(
host, port, calling_ae_title, called_ae_title, level, keys)
if not abstract_syntaxes:
# Negotiate ALL storage syntaxes. Is there a better way to do this?
abstract_syntaxes = [
entry.key() for entry in odil.registry.uids_dictionary
if entry.data().name.endswith("Storage")
]
if len(abstract_syntaxes) > 126:
raise Exception("Too many storage syntaxes")
storage_pcs = [
odil.AssociationParameters.PresentationContext(
2*(i+1)+1, uid, transfer_syntaxes,
odil.AssociationParameters.PresentationContext.Role.SCP)
for i, uid in enumerate(abstract_syntaxes)
]
association = odil.Association()
association.set_peer_host(host)
association.set_peer_port(port)
association.update_parameters()\
.set_calling_ae_title(calling_ae_title)\
.set_called_ae_title(called_ae_title) \
.set_presentation_contexts([get_pc]+storage_pcs)
association.associate()
logging.info("Association established")
get = odil.GetSCU(association)
get.set_affected_sop_class(get_syntax)
class Callback(object):
def __init__(self, directory):
self.directory = directory
self.completed = 0
self.remaining = 0
self.failed = 0
self.warning = 0
self.stored = {}
self.files = []
self._study_ids = {}
self._series_ids = {}
def store(self, data_set):
specific_character_set = odil.Value.Strings()
if "SpecificCharacterSet" in data_set:
specific_character_set = data_set.as_string(
"SpecificCharacterSet")
as_unicode = lambda x: odil.as_unicode(x, specific_character_set)
if layout == "flat":
directory = ""
elif layout == "tree":
# Patient directory: <PatientName> or <PatientID>.
patient_directory = None
if "PatientName" in data_set and data_set.as_string("PatientName"):
patient_directory = data_set.as_string("PatientName")[0]
else:
patient_directory = data_set.as_string("PatientID")[0]
patient_directory = as_unicode(patient_directory)
# Study directory: <StudyID>_<StudyDescription>, both parts are
# optional. If both tags are missing or empty, default to a
# numeric index based on StudyInstanceUID.
study_directory = []
if "StudyID" in data_set and data_set.as_string("StudyID"):
study_directory.append(data_set.as_string("StudyID")[0])
if ("StudyDescription" in data_set and
data_set.as_string("StudyDescription")):
study_directory.append(
data_set.as_string("StudyDescription")[0])
if not study_directory:
study_instance_uid = data_set.as_string("StudyInstanceUID")[0]
study_directory.append(
self._study_ids.setdefault(
study_instance_uid, 1+len(self._study_ids)))
study_directory = "_".join(as_unicode(x) for x in study_directory)
# Study directory: <SeriesNumber>_<SeriesDescription>, both
# parts are optional. If both tags are missing or empty, default
# to a numeric index based on SeriesInstanceUID.
series_directory = []
if "SeriesNumber" in data_set and data_set.as_int("SeriesNumber"):
series_directory.append(str(data_set.as_int("SeriesNumber")[0]))
if ("SeriesDescription" in data_set and
data_set.as_string("SeriesDescription")):
series_directory.append(
data_set.as_string("SeriesDescription")[0])
if not series_directory:
series_instance_uid = data_set.as_string("series_instance_uid")[0]
series_directory.append(
self._series_ids.setdefault(
series_instance_uid, 1+len(self._series_ids)))
series_directory = "_".join(as_unicode(x) for x in series_directory)
if iso_9660:
patient_directory = to_iso_9660(patient_directory)
study_directory = to_iso_9660(study_directory)
series_directory = to_iso_9660(series_directory)
directory = os.path.join(
patient_directory, study_directory, series_directory)
if not os.path.isdir(os.path.join(self.directory, directory)):
os.makedirs(os.path.join(self.directory, directory))
else:
raise NotImplementedError()
self.stored.setdefault(directory, 0)
if iso_9660:
filename = "IM{:06d}".format(1+self.stored[directory])
else:
filename = as_unicode(data_set.as_string("SOPInstanceUID")[0])
with odil.open(os.path.join(self.directory, directory, filename), "wb") as fd:
odil.Writer.write_file(data_set, fd)
self.stored[directory] += 1
self.files.append(os.path.join(directory, filename))
def get(self, message):
for type_ in ["completed", "remaining", "failed", "warning"]:
base = "number_of_{}_sub_operations".format(type_)
if getattr(message, "has_{}".format(base))():
setattr(
self, type_, getattr(message, "get_{}".format(base))())
logging.info(
"Remaining: {}, completed: {}, failed: {}, warning: {}".format(
self.remaining, self.completed, self.failed, self.warning))
if not os.path.isdir(directory):
os.makedirs(directory)
if len(os.listdir(directory)):
logging.warning("{} is not empty".format(directory))
callback = Callback(directory)
get.get(query, callback.store, callback.get)
print(
"Completed: {}, remaining: {}, failed: {}, warning: {}".format(
callback.completed, callback.remaining, callback.failed,
callback.warning))
association.release()
logging.info("Association released")
if dicomdir:
logging.info("Creating DICOMDIR")
create_dicomdir(
[os.path.join(directory, x) for x in callback.files],
directory, patient_key, study_key, series_key, image_key)
def find_abstract_syntaxes(
host, port, calling_ae_title, called_ae_title, level, keys):
""" Return the abstract syntaxes corresponding to the query, based on
SOP Classes in Study.
"""
query = odil.DataSet()
for key in keys:
key, value = key.split("=", 1)
value = value.split("\\")
if key in ["QueryRetrieveLevel", "SOPClassesInStudy"]:
continue
tag = getattr(odil.registry, key)
vr = odil.registry.public_dictionary[tag].vr
if vr in ["DS", "FL", "FD"]:
value = [float(x) for x in value]
elif vr in ["IS", "SL", "SS", "UL", "US"]:
value = [int(x) for x in value]
query.add(tag, value)
query.add("QueryRetrieveLevel", ["STUDY"])
query.add("SOPClassesInStudy")
find_syntax = getattr(
odil.registry,
"{}RootQueryRetrieveInformationModelFind".format(level.capitalize()))
transfer_syntaxes = [
odil.registry.ImplicitVRLittleEndian,
odil.registry.ExplicitVRLittleEndian
]
find_pc = odil.AssociationParameters.PresentationContext(
1, find_syntax, transfer_syntaxes,
odil.AssociationParameters.PresentationContext.Role.SCU)
association = odil.Association()
association.set_peer_host(host)
association.set_peer_port(port)
association.update_parameters()\
.set_calling_ae_title(calling_ae_title)\
.set_called_ae_title(called_ae_title) \
.set_presentation_contexts([find_pc])
association.associate()
logging.info("Association established")
find = odil.FindSCU(association)
find.set_affected_sop_class(find_syntax)
data_sets = find.find(query)
sop_classes = set()
for data_set in data_sets:
if "SOPClassesInStudy" in data_set:
sop_classes.update(data_set.as_string("SOPClassesInStudy"))
return sop_classes
def to_iso_9660(value):
value = value[:8].upper()
value = re.sub(r"[^A-Z0-9_]", "_", value)
return value
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