def test_anatomical_implicit(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_multiframe_implicit()
results = convert_philips.dicom_to_nifti(read_dicom_directory(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
settings.enable_validate_multiframe_implicit()
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical_implicit(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_multiframe_implicit()
results = convert_philips.dicom_to_nifti(
read_dicom_directory(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT)[0]) is True
settings.enable_validate_multiframe_implicit()
finally:
shutil.rmtree(tmp_output_dir)
def main():
test_data_directory = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'tests',
'data')
print(test_data_directory)
for root, dir_names, _ in os.walk(test_data_directory):
settings.disable_validate_multiframe_implicit()
# New directory
for dir_name in dir_names:
dir_path = os.path.join(root, dir_name)
if subdir_count(dir_path) > 0:
continue # not processing because not lowest level of directory
logging.info(dir_path)
output_file = dir_path + '_ground_truth.nii.gz'
reoriented_file = dir_path + '_ground_truth_reoriented.nii.gz'
# noinspection PyBroadException
try:
generate_ground_truth(dir_path, output_file, reoriented_file)
except: # explicitly capturing everything here
pass
def main():
for root, dir_names, _ in os.walk(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
'dicom2nifti',
'tests',
'data')):
settings.disable_validate_multiframe_implicit()
# New directory
for dir_name in dir_names:
dir_path = os.path.join(root, dir_name)
if subdir_count(dir_path) > 0:
continue # not processing because not lowest level of directory
print(dir_path)
output_file = dir_path + '_ground_truth.nii.gz'
reoriented_file = dir_path + '_ground_truth_reoriented.nii.gz'
# noinspection PyBroadException
try:
dicom2nifti.dicom_series_to_nifti(dir_path, output_file, False)
image_reorientation.reorient_image(output_file, reoriented_file)
except: # explicitly capturing everything here
pass
def main():
test_data_directory = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
'tests',
'data')
print(test_data_directory)
for root, dir_names, _ in os.walk(test_data_directory):
settings.disable_validate_multiframe_implicit()
# New directory
for dir_name in dir_names:
dir_path = os.path.join(root, dir_name)
if subdir_count(dir_path) > 0:
continue # not processing because not lowest level of directory
logging.info(dir_path)
output_file = dir_path + '_ground_truth.nii.gz'
reoriented_file = dir_path + '_ground_truth_reoriented.nii.gz'
# noinspection PyBroadException
try:
generate_ground_truth(dir_path, output_file, reoriented_file)
except: # explicitly capturing everything here
pass