def main():
LC.configure()
logger = logging.getLogger(__name__)
input_path = "C://Users//Agnieszka//Documents//Out"
output_path = "C://Users//Agnieszka//Documents//Out"
csv_names = ['Cells.csv', 'Cytoplasm.csv', 'ExpandedNucleiLess.csv', 'ExpandedNucleiMore.csv', 'Image.csv', 'Nuclei.csv', 'RingCytoplasm.csv', 'ShrinkedNuclei.csv']
#'Experiment.csv' was not icluded in 'csv_names' list of files, because of different structure
subdir_list = FM.get_dir_names(input_path) # getting the subdirectories' list (1 subdir = 1 well data) of the given directory
for csv_name in csv_names: # merging data file (type) by file
csv.merge(csv_name, subdir_list, input_path, output_path)
def main():
#Logging section.
PP_path = os.path.abspath('..')
LC.configure(PP_path)
logger = logging.getLogger(__name__)
logger.info("Starting program...")
#Arg parse section.
parser = argparse.ArgumentParser( description='\n (...Example description...)' )
parser.add_argument( '-s',
metavar='<settingspath>',
type=str,
required=True,
nargs=1,
help='Input_settings path' )
args = parser.parse_args()
#Setting up pipeline.
logger.debug("Input settings source: %s", args.s[0])
pipeline, config_dict = p.parse(args.s[0])
"""Default input_settings path.
input_path= (os.path.join(PP_path, "input_output", "settings.xml").replace("\\", "//")) # setting up path to input settings (in xml format)
logger.debug("Input settings source: %s", input_path)
pipeline, config_dict = p.parse(input_path)"""
pipeline.execute(config_dict)