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']
