def process(self, element):
key, dir_prefix = element
fs = beam.io.gcsio.GcsIO()
gcs_path = os.path.join(self._gcs_bucket, dir_prefix)
files = fs.list_prefix(gcs_path)
dicom_paths = [fname for fname in files if '.dcm' in fname]
dicom_list = [
pydicom.dcmread(fs.open(path, 'rb'),
defer_size=None,
stop_before_pixels=False,
force=False) for path in dicom_paths
]
try:
result = dicom_array_to_nifti(dicom_list, None, False)
except ConversionValidationError:
dicom2nifti.settings.disable_validate_sliceincrement()
result = dicom_array_to_nifti(dicom_list, None, False)
dicom2nifti.settings.enable_validate_sliceincrement()
series_id = dicom_list[0].SeriesInstanceUID
del dicom_list
gc.collect()
yield key, series_id, result['NII']
def process(self, element):
key, dir_prefix = element
fs = beam.io.gcsio.GcsIO()
gcs_path = os.path.join(self._gcs_bucket, dir_prefix)
files = fs.list_prefix(gcs_path)
dicom_paths = [fname for fname in files if '.dcm' in fname]
dicom_list = [
pydicom.dcmread(fs.open(path, 'rb'),
defer_size=None,
stop_before_pixels=False,
force=False) for path in dicom_paths
]
try:
result = dicom_array_to_nifti(dicom_list, None, False)['NII']
except ConversionValidationError:
dicom2nifti.settings.disable_validate_sliceincrement()
result = dicom_array_to_nifti(dicom_list, None, False)['NII']
dicom2nifti.settings.enable_validate_sliceincrement()
series_id = dicom_list[0].SeriesInstanceUID
del dicom_list
gc.collect()
resampled = processing.resample_to_output(result)
del result
qoffset = list(resampled.header.get_sform()[:3, -1])
npy_arr = np.ascontiguousarray(
np.rot90(np.swapaxes(
resampled.get_fdata(dtype=np.float32).astype(np.int16), 0, 2),
k=2,
axes=(0, 2)))
del resampled
gc.collect()
path = os.path.join(self._gcs_save_dir, key + '.npy')
self.save_array(path, npy_arr)
del npy_arr
gc.collect()
yield key, series_id, qoffset, path
def convert_directory(dicom_directory, output_folder, compression=True, reorient=True):
"""
This function will order all dicom files by series and order them one by one
:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
:param output_folder: folder to write the nifti files to
:param dicom_directory: directory with dicom files
"""
# sort dicom files by series uid
dicom_series = {}
for root, _, files in os.walk(dicom_directory):
for dicom_file in files:
file_path = os.path.join(root, dicom_file)
# noinspection PyBroadException
try:
if compressed_dicom.is_dicom_file(file_path):
# read the dicom as fast as possible
# (max length for SeriesInstanceUID is 64 so defer_size 100 should be ok)
dicom_headers = compressed_dicom.read_file(file_path,
defer_size="1 KB",
stop_before_pixels=False,
force=dicom2nifti.settings.pydicom_read_force)
if not _is_valid_imaging_dicom(dicom_headers):
logger.info("Skipping: %s" % file_path)
continue
logger.info("Organizing: %s" % file_path)
if dicom_headers.SeriesInstanceUID not in dicom_series:
dicom_series[dicom_headers.SeriesInstanceUID] = []
dicom_series[dicom_headers.SeriesInstanceUID].append(dicom_headers)
except: # Explicitly capturing all errors here to be able to continue processing all the rest
logger.warning("Unable to read: %s" % file_path)
traceback.print_exc()
# start converting one by one
for series_id, dicom_input in iteritems(dicom_series):
base_filename = ""
# noinspection PyBroadException
try:
# construct the filename for the nifti
base_filename = ""
if 'SeriesNumber' in dicom_input[0]:
base_filename = _remove_accents('%s' % dicom_input[0].SeriesNumber)
if 'SeriesDescription' in dicom_input[0]:
base_filename = _remove_accents('%s_%s' % (base_filename,
dicom_input[0].SeriesDescription))
elif 'SequenceName' in dicom_input[0]:
base_filename = _remove_accents('%s_%s' % (base_filename,
dicom_input[0].SequenceName))
elif 'ProtocolName' in dicom_input[0]:
base_filename = _remove_accents('%s_%s' % (base_filename,
dicom_input[0].ProtocolName))
else:
base_filename = _remove_accents(dicom_input[0].SeriesInstanceUID)
logger.info('--------------------------------------------')
logger.info('Start converting %s' % base_filename)
if compression:
nifti_file = os.path.join(output_folder, base_filename + '.nii.gz')
else:
nifti_file = os.path.join(output_folder, base_filename + '.nii')
convert_dicom.dicom_array_to_nifti(dicom_input, nifti_file, reorient)
gc.collect()
except: # Explicitly capturing app exceptions here to be able to continue processing
logger.info("Unable to convert: %s" % base_filename)
traceback.print_exc()
def convert_directory(dicom_directory, output_folder, compression=True, reorient=True):
"""
This function will order all dicom files by series and order them one by one
:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
:param output_folder: folder to write the nifti files to
:param dicom_directory: directory with dicom files
"""
# sort dicom files by series uid
dicom_series = {}
for root, _, files in os.walk(dicom_directory):
for dicom_file in files:
file_path = os.path.join(root, dicom_file)
# noinspection PyBroadException
try:
if compressed_dicom.is_dicom_file(file_path):
# read the dicom as fast as possible
# (max length for SeriesInstanceUID is 64 so defer_size 100 should be ok)
dicom_headers = compressed_dicom.read_file(file_path,
defer_size="1 KB",
stop_before_pixels=False,
force=dicom2nifti.settings.pydicom_read_force)
if not _is_valid_imaging_dicom(dicom_headers):
logger.info("Skipping: %s" % file_path)
continue
logger.info("Organizing: %s" % file_path)
if dicom_headers.SeriesInstanceUID not in dicom_series:
dicom_series[dicom_headers.SeriesInstanceUID] = []
dicom_series[dicom_headers.SeriesInstanceUID].append(dicom_headers)
except: # Explicitly capturing all errors here to be able to continue processing all the rest
logger.warning("Unable to read: %s" % file_path)
traceback.print_exc()
# start converting one by one
for series_id, dicom_input in dicom_series.items():
base_filename = ""
# noinspection PyBroadException
try:
# construct the filename for the nifti
base_filename = ""
if 'SeriesNumber' in dicom_input[0]:
base_filename = _remove_accents('%s' % dicom_input[0].SeriesNumber)
if 'SeriesDescription' in dicom_input[0]:
base_filename = _remove_accents('%s_%s' % (base_filename,
dicom_input[0].SeriesDescription))
elif 'SequenceName' in dicom_input[0]:
base_filename = _remove_accents('%s_%s' % (base_filename,
dicom_input[0].SequenceName))
elif 'ProtocolName' in dicom_input[0]:
base_filename = _remove_accents('%s_%s' % (base_filename,
dicom_input[0].ProtocolName))
else:
base_filename = _remove_accents(dicom_input[0].SeriesInstanceUID)
logger.info('--------------------------------------------')
logger.info('Start converting %s' % base_filename)
if compression:
nifti_file = os.path.join(output_folder, base_filename + '.nii.gz')
else:
nifti_file = os.path.join(output_folder, base_filename + '.nii')
convert_dicom.dicom_array_to_nifti(dicom_input, nifti_file, reorient)
gc.collect()
except: # Explicitly capturing app exceptions here to be able to continue processing
logger.info("Unable to convert: %s" % base_filename)
traceback.print_exc()