def prep_registration(args, sample_name="amap"):
logging.info("Checking whether the atlas exists")
_, atlas_files_exist = check_atlas_install()
atlas_dir = os.path.join(args.install_path, "atlas")
if not atlas_files_exist:
if args.download_path is None:
atlas_download_path = os.path.join(temp_dir_path, "atlas.tar.gz")
else:
atlas_download_path = os.path.join(args.download_path,
"atlas.tar.gz")
if not args.no_atlas:
logging.warning("Atlas does not exist, downloading.")
atlas_download.main(args.atlas, atlas_dir, atlas_download_path)
amend_cfg(new_atlas_folder=atlas_dir, atlas=args.atlas)
if args.registration_config is None:
args.registration_config = source_files.source_custom_config()
args.target_brain_path = args.background_planes_path[0]
args.sample_name = sample_name
logging.debug("Making registration directory")
ensure_directory_exists(args.paths.registration_output_folder)
additional_images_downsample = {}
for idx, images in enumerate(args.signal_planes_paths):
channel = args.signal_ch_ids[idx]
additional_images_downsample[f"channel_{channel}"] = images
return args, additional_images_downsample
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 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,
)
def main():
args = download_parser().parse_args()
if args.download_path is None:
atlas_download_path = os.path.join(temp_dir_path, "atlas.tar.gz")
else:
atlas_download_path = os.path.join(args.download_path, "atlas.tar.gz")
if not args.no_atlas:
atlas_dir = os.path.join(args.install_path, "atlas")
atlas_download.main(args.atlas, atlas_dir, atlas_download_path)
if not args.no_models:
model_path = models.main(args.model, args.install_path)
amend_cfg(new_atlas_folder=atlas_dir,
atlas=args.atlas,
new_model_path=model_path)