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 prep_registration(args):
""" If an atlas is not available, download it.
"""
logging.info("Checking whether the atlas exists")
_, atlas_files_exist = check_atlas_install(args.registration_config)
if not atlas_files_exist:
logging.warning("Atlas does not exist, downloading.")
atlas_download(args.atlas, args.install_path, args.download_path)
amend_cfg(
new_atlas_folder=args.install_path,
atlas=args.atlas,
)
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 main():
args = download_parser().parse_args()
if not args.no_atlas:
atlas_download(args.atlas, args.install_path, args.download_path)
if not args.no_amend_config:
print(f"install: {args.install_path}")
amend_cfg(
new_atlas_folder=args.install_path,
atlas=args.atlas,
)
def main():
args = download_parser().parse_args()
if args.download_path is None:
args.download_path = os.path.join(temp_dir_path, "atlas.tar.gz")
if not args.no_atlas:
atlas.main(args.atlas, args.install_path, args.download_path)
if not args.no_amend_config:
amend_cfg(
new_atlas_folder=args.install_path, atlas=args.atlas,
)