parser.add_argument("input_spec", type=str, help="input specifier. ini") parser.add_argument("--op", type=str, help="operation id") args = parser.parse_args() print('args', args) input_spec = load_ini(args.input_spec) stack = input_spec['stack'] sqlController = SqlController() fileLocationManager = FileLocationManager(stack) execute_command('python align_v3.py %s --op %s' % (args.input_spec, args.op)) # execute_command('python compose_v3.py %s --op %s' % (args.input_spec, args.op)) #image_name_list = input_spec['image_name_list'] image_name_list = sqlController.get_image_list(stack, 'destination') #if image_name_list == 'all': # #image_name_list = DataManager.load_sorted_filenames(stack=stack)[0].keys() # image_name_list = map(lambda x: x[0], sorted(DataManager.load_sorted_filenames(stack=input_spec['stack'])[0].items(), key=lambda x: x[1])) #op = load_ini(os.path.join(DATA_ROOTDIR, 'CSHL_data_processed', input_spec['stack'], 'operation_configs', args.op + '.ini')) op = load_ini( os.path.join(fileLocationManager.operation_configs, args.op + '.ini')) assert op['type'] == 'warp', "Op type must be warp." assert op['base_prep_id'] == input_spec[ 'prep_id'], "Op requires %s, but input has prep %s." % ( op['base_prep_id'], input_spec['prep_id']) elastix_output_dir = fileLocationManager.elastix_dir custom_output_dir = fileLocationManager.custom_output toanchor_transforms_fp = op['transforms_csv']
parser.add_argument("stack", type=str, help="stack name") args = parser.parse_args() stack = args.stack from metadata import load_ini #from preprocess_utilities import * #from data_manager import DataManager sqlController = SqlController() fileLocationManager = FileLocationManager(stack) input_spec = load_ini(args.input_spec) #image_name_list = input_spec['image_name_list'] image_name_list = sqlController.get_image_list(stack, 'source') #if image_name_list == 'all': # #image_name_list = DataManager.load_sorted_filenames(stack=stack)[0].keys() # image_name_list = map(lambda x: x[0], sorted(DataManager.load_sorted_filenames(stack=input_spec['stack'])[0].items(), key=lambda x: x[1])) #op = load_ini(os.path.join(DATA_ROOTDIR, 'CSHL_data_processed', input_spec['stack'], 'operation_configs', args.op + '.ini')) op = load_ini(os.path.join(fileLocationManager.operation_configs, args.op + '.ini')) assert op['type'] == 'warp', "Op type must be warp." assert op['base_prep_id'] == input_spec['prep_id'], "Op requires %s, but input has prep %s." % (op['base_prep_id'], input_spec['prep_id']) elastix_output_dir = fileLocationManager.elastix_dir custom_output_dir = fileLocationManager.custom_output toanchor_transforms_fp = op['transforms_csv'] anchor_img_name = op['anchor_image_name'] base_prep_id = op['base_prep_id']