def convert(input, output, transfer_syntax, item_length, use_group_length):
header, data_set = odil.read(input)
to_remove = [
"FileMetaInformationVersion", "MediaStorageSOPClassUID",
"MediaStorageSOPInstanceUID", "TransferSyntaxUID",
"ImplementationClassUID", "ImplementationVersionName"
]
for name in to_remove:
header.remove(getattr(odil.registry, name))
odil.write(data_set, output, header, transfer_syntax, item_length,
use_group_length)
def convert(input, output, transfer_syntax, item_length, use_group_length):
header, data_set = odil.read(input)
to_remove = [
"FileMetaInformationVersion",
"MediaStorageSOPClassUID", "MediaStorageSOPInstanceUID",
"TransferSyntaxUID",
"ImplementationClassUID", "ImplementationVersionName"
]
for name in to_remove:
header.remove(getattr(odil.registry, name))
odil.write(data_set, output, header, transfer_syntax, item_length, use_group_length)
def convert_reconstruction(bruker_directory, series, reconstruction,
iod_converter, transfer_syntax, destination,
iso_9660):
""" Convert and save a single reconstruction.
:param bruker_directory: Bruker directory object
:param series: series number in the Bruker directory
:param reconstruction: reconstruction number in the series
:param iod_converter: conversion function
:param transfer_syntax: target transfer syntax
:param destination: destination directory
:param iso_9660: whether to use ISO-9660 compatible file names
"""
logger.info("Converting {}:{}".format(series, reconstruction))
bruker_binary = bruker_directory.get_dataset("{}{:04d}".format(
series, int(reconstruction)))
bruker_json = json.loads(bruker.as_json(bruker_binary))
logger.info("Found {}:{} - {} ({})".format(
series, reconstruction,
bruker_json.get("VisuAcquisitionProtocol", ["(none)"])[0],
bruker_json.get("RECO_mode", ["none"])[0]))
bruker_json["reco_files"] = list(
bruker_directory.get_used_files("{}{:04d}".format(
series, int(reconstruction))))
dicom_binaries = iod_converter(bruker_json, transfer_syntax)
files = []
for index, dicom_binary in enumerate(dicom_binaries):
if iso_9660:
filename = "IM{:06d}".format(1 + index)
else:
filename = dicom_binary.as_string("SOPInstanceUID")[0]
destination_file = os.path.join(
destination, get_series_directory(dicom_binary, iso_9660),
reconstruction, filename)
if not os.path.isdir(os.path.dirname(destination_file)):
os.makedirs(os.path.dirname(destination_file))
odil.write(dicom_binary,
destination_file,
transfer_syntax=transfer_syntax)
files.append(destination_file)
return files
def store(self, data_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]
# 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(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(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 = data_set.as_string("SOPInstanceUID")[0]
odil.write(data_set,
os.path.join(self.directory, directory, filename))
self.stored[directory] += 1
self.files.append(os.path.join(directory, filename))
def as_binary(input, output, transfer_syntax):
_, data_set = odil.read(input)
odil.write(data_set, output, transfer_syntax=transfer_syntax)
def as_binary(input, output, transfer_syntax):
_, data_set = odil.read(input)
odil.write(data_set, output, transfer_syntax=transfer_syntax)
def store(self, data_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]
# 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(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(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 = data_set.as_string("SOPInstanceUID")[0]
odil.write(
data_set, os.path.join(self.directory, directory, filename))
self.stored[directory] += 1
self.files.append(os.path.join(directory, filename))