def remove_private_identifiers(dicom_files,
save=True,
overwrite=False,
output_folder=None,
force=True):
"""remove_private_identifiers is a wrapper for the
simple call to dicom.remove_private_tags, it simply
reads in the files for the user and saves accordingly
"""
updated_files = []
if not isinstance(dicom_files, list):
dicom_files = [dicom_files]
for dicom_file in dicom_files:
dicom = read_file(dicom_file, force=force)
dicom.remove_private_tags()
dicom_name = os.path.basename(dicom_file)
bot.debug("Removed private identifiers for %s" % dicom_name)
if save:
dicom = save_dicom(
dicom=dicom,
dicom_file=dicom_file,
output_folder=output_folder,
overwrite=overwrite,
)
updated_files.append(dicom)
return updated_files
def save(self, filename, overwrite=False):
"""After a parse action, the user can choose to save the dicom to file."""
filename = filename or self.dicom_file
ds = save_dicom(
dicom=self.dicom,
dicom_file=os.path.basename(filename),
output_folder=os.path.dirname(filename),
overwrite=overwrite,
)
return ds
def replace_identifiers(
dicom_files,
ids=None,
deid=None,
save=False,
overwrite=False,
output_folder=None,
force=True,
config=None,
strip_sequences=False,
remove_private=False,
):
"""replace identifiers using pydicom, can be slow when writing
and saving new files. If you want to replace sequences, they need
to be extracted with get_identifiers and expand_sequences to True.
"""
if not isinstance(dicom_files, list):
dicom_files = [dicom_files]
# Warn the user that we use the default deid recipe
if not deid:
bot.warning("No deid specification provided, will use defaults.")
# ids (a lookup) is not required
ids = ids or {}
# Parse through dicom files, update headers, and save
updated_files = []
for dicom_file in dicom_files:
parser = DicomParser(dicom_file, force=force, config=config, recipe=deid)
# If a custom lookup was provided, update the parser
if parser.dicom_file in ids:
parser.lookup.update(ids[parser.dicom_file])
parser.parse(strip_sequences=strip_sequences, remove_private=remove_private)
# Save to file, otherwise return updated objects
if save is True:
ds = save_dicom(
dicom=parser.dicom,
dicom_file=parser.dicom_file,
output_folder=output_folder,
overwrite=overwrite,
)
updated_files.append(ds)
else:
updated_files.append(parser.dicom)
return updated_files
def replace_identifiers(
dicom_files,
ids=None,
deid=None,
save=True,
overwrite=False,
output_folder=None,
force=True,
config=None,
strip_sequences=True,
remove_private=True,
):
"""replace identifiers using pydicom, can be slow when writing
and saving new files. If you want to replace sequences, they need
to be extracted with get_identifiers and expand_sequences to True.
"""
dicom_files, recipe, config = _prepare_replace_config(dicom_files,
deid=deid,
config=config)
# ids (a lookup) is not required
ids = ids or {}
# Parse through dicom files, update headers, and save
updated_files = []
for _, dicom_file in enumerate(dicom_files):
if isinstance(dicom_file, Dataset):
dicom = dicom_file
dicom_file = dicom.filename
else:
dicom = read_file(dicom_file, force=force)
dicom_name = os.path.basename(dicom_file)
# Remove sequences first, maintained in DataStore
if strip_sequences is True:
dicom = remove_sequences(dicom)
# Remove private tags at the onset, if requested
if remove_private:
try:
dicom.remove_private_tags()
except:
bot.error(
"""Private tags for %s could not be completely removed, usually
this is due to invalid data type. Removing others."""
% dicom_name)
private_tags = get_private(dicom)
for ptag in private_tags:
del dicom[ptag.tag]
continue
# Include private tags (if not removed) plus dicom.dir
fields = dicom_dir(dicom)
if recipe.deid is not None:
if dicom_file not in ids:
ids[dicom_file] = {}
# Prepare additional lists of values and fields (updates item)
if recipe.has_values_lists():
for group, actions in recipe.get_values_lists().items():
ids[dicom_file][group] = extract_values_list(
dicom=dicom, actions=actions)
if recipe.has_fields_lists():
for group, actions in recipe.get_fields_lists().items():
ids[dicom_file][group] = extract_fields_list(
dicom=dicom, actions=actions)
for action in recipe.get_actions():
dicom = perform_action(dicom=dicom,
item=ids[dicom_file],
action=action)
# Next perform actions in default config, only if not done
for action in config["put"]["actions"]:
if action["field"] in fields:
dicom = perform_action(dicom=dicom, action=action)
# Assemble a new dataset, again accounting for private tags
ds = Dataset()
for field in dicom_dir(dicom):
try:
# Most fields are strings
if isinstance(field, str):
ds.add(dicom.data_element(field))
# Remainder are tags
else:
ds.add(dicom.get(field))
except:
pass
# Copy original data attributes
attributes = [
"is_little_endian",
"is_implicit_VR",
"is_decompressed",
"read_encoding",
"read_implicit_vr",
"read_little_endian",
"_parent_encoding",
]
# We aren't including preamble, we will reset to be empty 128 bytes
ds.preamble = b"\0" * 128
for attribute in attributes:
if hasattr(dicom, attribute):
ds.__setattr__(attribute, dicom.__getattribute__(attribute))
# Original meta data # or default empty dataset
file_metas = getattr(dicom, "file_meta", Dataset())
# Media Storage SOP Instance UID can be identifying
if hasattr(file_metas, "MediaStorageSOPInstanceUID"):
file_metas.MediaStorageSOPInstanceUID = ""
# Save meta data
ds.file_meta = file_metas
# Save to file?
if save is True:
ds = save_dicom(
dicom=ds,
dicom_file=dicom_file,
output_folder=output_folder,
overwrite=overwrite,
)
updated_files.append(ds)
return updated_files