def print_data_set(
data_set, decode_uids, padding, max_length, specific_character_set):
for tag, element in data_set.items():
name = "{:04x},{:04x}".format(tag.group, tag.element)
if tag in odil.registry.public_dictionary:
entry = odil.registry.public_dictionary[tag]
name = entry.name
if tag == odil.registry.SpecificCharacterSet:
specific_character_set = element.as_string()
if element.is_data_set():
value = "(sequence, {} item{})".format(
len(element), "s" if len(element)>1 else "")
elif element.is_binary():
lengths = [len(x) for x in element.as_binary()]
value = "(binary, {} item{}, {} byte{})".format(
len(element), "s" if len(element)>1 else "",
"+".join(str(x) for x in lengths),
"s" if sum(lengths)>1 else "")
else:
getter = None
if element.empty():
getter = lambda: []
elif element.is_int():
getter = element.as_int
elif element.is_real():
getter = element.as_real
elif element.is_string():
getter = lambda: [
odil.as_unicode(x, specific_character_set)
for x in element.as_string()]
value = [x for x in getter()]
if decode_uids and element.vr == odil.VR.UI:
value = [
odil.registry.uids_dictionary[uid].name
if uid in odil.registry.uids_dictionary else uid
for uid in value
]
print("{}{}{} {:04x},{:04x} {} {}".format(
padding,
name, (max_length-len(name)-len(padding))*" ",
tag.group, tag.element, element.vr,
value))
if element.is_data_set():
sequence = element.as_data_set()
if sequence:
for item in sequence[:-1]:
print_data_set(
item, decode_uids, padding+" ", max_length,
specific_character_set)
print()
print_data_set(
sequence[-1], decode_uids, padding+" ", max_length,
specific_character_set)
def print_data_set(data_set, decode_uids, padding, max_length,
specific_character_set):
for tag, element in data_set.items():
name = "{:04x},{:04x}".format(tag.group, tag.element)
if tag in odil.registry.public_dictionary:
entry = odil.registry.public_dictionary[tag]
name = entry.name
if tag == odil.registry.SpecificCharacterSet:
specific_character_set = element.as_string()
if element.is_data_set():
value = "(sequence, {} item{})".format(
len(element), "s" if len(element) > 1 else "")
elif element.is_binary():
lengths = [len(x) for x in element.as_binary()]
value = "(binary, {} item{}, {} byte{})".format(
len(element), "s" if len(element) > 1 else "",
"+".join(str(x) for x in lengths),
"s" if sum(lengths) > 1 else "")
else:
getter = None
if element.empty():
getter = lambda: []
elif element.is_int():
getter = element.as_int
elif element.is_real():
getter = element.as_real
elif element.is_string():
getter = lambda: [
odil.as_unicode(x, specific_character_set)
for x in element.as_string()
]
value = [x for x in getter()]
if decode_uids and element.vr == odil.VR.UI:
value = [
odil.registry.uids_dictionary[uid].name
if uid in odil.registry.uids_dictionary else uid
for uid in value
]
print("{}{}{} {:04x},{:04x} {} {}".format(
padding, name, (max_length - len(name) - len(padding)) * " ",
tag.group, tag.element, element.vr, value))
if element.is_data_set():
sequence = element.as_data_set()
if sequence:
for item in sequence[:-1]:
print_data_set(item, decode_uids, padding + " ",
max_length, specific_character_set)
print()
print_data_set(sequence[-1], decode_uids, padding + " ",
max_length, specific_character_set)
def convert_element(element, specific_character_set):
""" Convert a DICOM element to its NIfTI+JSON representation: the "Value"
(or "InlineBinary") attribute of its standard DICOM JSON
representation.
"""
result = None
# element can be None because a get is called above
if element is None:
result = None
elif element.empty():
result = None
elif element.is_int():
result = list(element.as_int())
elif element.is_real():
result = list(element.as_real())
elif element.vr == odil.VR.PN:
data_set = odil.DataSet()
if specific_character_set:
data_set.add("SpecificCharacterSet", specific_character_set)
data_set.add(odil.registry.PersonName, element.as_string(), element.vr)
json_data_set = json.loads(odil.as_json(data_set))
result = json_data_set[str(odil.registry.PersonName)]["Value"]
elif element.is_string():
result = list(
odil.as_unicode(x, specific_character_set)
for x in element.as_string())
elif element.is_data_set():
result = [
convert_data_set(x, specific_character_set)
for x in element.as_data_set()
]
elif element.is_binary():
result = [
base64.b64encode(x.get_memory_view().tobytes()).decode()
for x in element.as_binary()
]
else:
raise Exception("Unknown element type")
return result
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 decode(value):
return odil.as_unicode(
value,
data_set.as_string("SpecificCharacterSet")
if "SpecificCharacterSet" in data_set else odil.Value.Strings())
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_series_directory(data_set, iso_9660):
""" Return the directory associated with the patient, study and series of
the DICOM data set.
"""
# Patient directory: <PatientName> or <PatientID>.
patient_directory = None
if "PatientName" in data_set and data_set.as_string("PatientName"):
patient_directory = odil.as_unicode(
data_set.as_string("PatientName")[0],
data_set.as_string("SpecificCharacterSet")
if "SpecificCharacterSet" in data_set else odil.Value.Strings())
else:
patient_directory = odil.as_unicode(
data_set.as_string("PatientID")[0],
data_set.as_string("SpecificCharacterSet")
if "SpecificCharacterSet" in data_set else odil.Value.Strings())
# Study directory: <StudyID>_<StudyDescription>, both parts are
# optional. If both tags are missing or empty, raise an exception
study_directory = []
if "StudyID" in data_set and data_set.as_string("StudyID"):
study_directory.append(
odil.as_unicode(
data_set.as_string("StudyID")[0],
data_set.as_string("SpecificCharacterSet")
if "SpecificCharacterSet" in data_set else odil.Value.Strings()))
if "StudyDescription" in data_set and data_set.as_string("StudyDescription"):
study_directory.append(
odil.as_unicode(
data_set.as_string("StudyDescription")[0],
data_set.as_string("SpecificCharacterSet")
if "SpecificCharacterSet" in data_set else odil.Value.Strings()))
if not study_directory:
raise Exception("Study ID and Study Description are both missing")
study_directory = "_".join(study_directory)
# Study directory: <SeriesNumber>_<SeriesDescription>, both
# parts are optional. If both tags are missing or empty, raise an exception
series_directory = []
if "SeriesNumber" in data_set and data_set.as_int("SeriesNumber"):
series_number = data_set.as_int("SeriesNumber")[0]
if series_number > 2**16:
# Bruker ID based on experiment number and reconstruction number is
# not readable: separate the two values
series_directory.append(str(divmod(series_number, 2**16)[0]))
else:
series_directory.append(str(series_number))
if not iso_9660:
if "SeriesDescription" in data_set and data_set.as_string("SeriesDescription"):
series_directory.append(
odil.as_unicode(
data_set.as_string("SeriesDescription")[0],
data_set.as_string("SpecificCharacterSet")
if "SpecificCharacterSet" in data_set else odil.Value.Strings()))
if not series_directory:
raise Exception("Series Number and Series Description are both missing")
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)
return os.path.join(patient_directory, study_directory, series_directory)