def configuration(path_to_folder=None):
config = load_config_file()
control = controller.Controller(config)
try:
control.log({"start": get_date_time()})
yield control
finally:
if path_to_folder is not None:
control.log({"end": get_date_time()})
save_config_file(path_to_folder)
self.domain = domain
self.origin = origin
self.coords_param = coords_param
return
def morph_on_shapemode_shape(self):
self.voxelize_and_parameterize_shapemode_shape()
self.morphed = cytoparam.morph_representation_on_shape(
img=self.domain,
param_img_coords=self.coords_param,
representation=self.aggregated_parameterized_intensity)
self.morphed = np.stack([self.domain, self.morphed])
return
if __name__ == "__main__":
config = general.load_config_file()
control = controller.Controller(config)
parser = argparse.ArgumentParser(description='Batch aggregation.')
parser.add_argument('--csv', help='Path to the dataframe.', required=True)
args = vars(parser.parse_args())
df = pd.read_csv(args['csv'], index_col=0)
aggregator = Aggregator(control)
for index, row in tqdm(df.iterrows(), total=len(df)):
'''Concurrent processes inside. Do not use concurrent here.'''
aggregator.execute(row)