def test_volume_calc(tmpdir):
tmpdir = str(tmpdir)
atlas = Atlas(source_custom_config())
structures_file_path = atlas.get_structures_path()
registration_config = source_custom_config()
volumes_csv_path = os.path.join(tmpdir, "volumes.csv")
calculate_volumes(
registered_atlas_path,
registered_hemispheres_path,
structures_file_path,
registration_config,
volumes_csv_path,
)
volumes_validate = pd.read_csv(
volumes_validate_path, sep=",", header=0, quotechar='"'
)
volumes_test = pd.read_csv(
volumes_csv_path, sep=",", header=0, quotechar='"'
)
assert (volumes_validate == volumes_test).all().all()
def prep_registration(args):
logging.info("Checking whether the atlas exists")
_, atlas_files_exist = check_atlas_install()
if not atlas_files_exist:
logging.warning("Atlas does not exist, downloading.")
if args.download_path is None:
args.download_path = os.path.join(temp_dir_path, "atlas.tar.gz")
atlas_download.main(args.atlas, args.install_path, args.download_path)
amend_cfg(
new_atlas_folder=args.install_path, atlas=args.atlas,
)
if args.registration_config is None:
args.registration_config = source_files.source_custom_config()
logging.debug("Making registration directory")
ensure_directory_exists(args.registration_output_folder)
logging.debug("Copying registration config to output directory")
copy_registration_config(
args.registration_config, args.registration_output_folder
)
additional_images_downsample = {}
if args.downsample_images:
for idx, images in enumerate(args.downsample_images):
name = Path(images).name
additional_images_downsample[name] = images
return args, additional_images_downsample
def amend_cfg(new_atlas_folder=None, atlas=None):
"""
Updates the registration config file to point to the correct atlas path
:param new_atlas_folder:
"""
print("Ensuring custom config file is correct")
original_config = source_files.source_config()
new_config = source_files.source_custom_config()
if new_atlas_folder is not None:
write_atlas_to_cfg(
new_atlas_folder, atlas, original_config, new_config
)
def check_atlas_install():
"""
Checks whether the atlas directory exists, and whether it's empty or not.
:return: Whether the directory exists, and whether the files also exist
"""
dir_exists = False
files_exist = False
cfg_file_path = source_files.source_custom_config()
if os.path.exists(cfg_file_path):
config_obj = get_config_obj(cfg_file_path)
atlas_conf = config_obj["atlas"]
atlas_directory = atlas_conf["base_folder"]
if os.path.exists(atlas_directory):
dir_exists = True
if not os.listdir(atlas_directory) == []:
files_exist = True
return dir_exists, files_exist
def get_atlas_config(self):
if self._atlas_config is None:
self._atlas_config = source_custom_config()