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| import argparse | |
| import sys | |
| from Utils.fileconverter import itk_to_nrrd | |
| from Engine.train import initiate as train_initiate | |
| from Engine.evaluate import initiate as evaluate_initiate | |
| from Utils.MSD_utilities import generate_training_data | |
| from Utils.plot import plot_train_data | |
| from Utils.PETCT_LungDx_utilities import convert_nsclc_petct | |
| class Parser(object): | |
| def __init__(self): | |
| parser = argparse.ArgumentParser( | |
| description='Interface for utilities', | |
| usage='''interface <command> [<args>] | |
| Available commands: | |
| itk_to_nrrd Converts files in folder from other ITK formats to .nrrd format | |
| train Initiates training | |
| evaluate Initiates evaluation | |
| plot Generates and shows plot based on specified metric file | |
| msd_generate_data_file Generates a datafile for training on MSD dataset | |
| format_petct_dataset Converts the the LUNGPTCT dataset to nifti files and generates segboxes for each scan | |
| ''') | |
| parser.add_argument('command', help='Subcommand to run') | |
| args = parser.parse_args(sys.argv[1:2]) | |
| if(not hasattr(self, args.command)): | |
| print('Unrecognized command') | |
| parser.print_help() | |
| exit(1) | |
| getattr(self, args.command)() | |
| def itk_to_nrrd(self): | |
| parser = argparse.ArgumentParser( | |
| description='Converts files in folder from other ITK formats to .nrrd format') | |
| parser.add_argument("source") | |
| parser.add_argument("destination") | |
| args = parser.parse_args(sys.argv[2:]) | |
| itk_to_nrrd(args.source, args.destination) | |
| def train(self): | |
| parser = argparse.ArgumentParser( | |
| description='Initiates training of model based on specified config file') | |
| parser.add_argument("config") | |
| args = parser.parse_args(sys.argv[2:]) | |
| train_initiate(args.config) | |
| def evaluate(self): | |
| parser = argparse.ArgumentParser( | |
| description='Initiates evaluation of model based on specified config file') | |
| parser.add_argument("config") | |
| args = parser.parse_args(sys.argv[2:]) | |
| evaluate_initiate(args.config) | |
| def plot(self): | |
| parser = argparse.ArgumentParser( | |
| description='Generates and shows plot based on specified metric file') | |
| parser.add_argument("metric_file") | |
| parser.add_argument("-store_file") | |
| parser.add_argument("--dont_show", "-d", default=False) | |
| parser.add_argument("-steps_per_epoch", default=-1) | |
| args = parser.parse_args(sys.argv[2:]) | |
| plot_train_data(args.metric_file, args.store_file, not args.dont_show, steps_in_epoch=int(args.steps_per_epoch)) | |
| def msd_generate_data_file(self): | |
| parser = argparse.ArgumentParser( | |
| description='Generates a datafile for training on MSD dataset') | |
| parser.add_argument("datafile_save_path") | |
| parser.add_argument("msd_directory") | |
| parser.add_argument("target_platform") | |
| args = parser.parse_args(sys.argv[2:]) | |
| generate_training_data(args.datafile_save_path, args.msd_directory, args.target_platform) | |
| def format_petct_dataset(self): | |
| parser = argparse.ArgumentParser( | |
| description='Converts the the LUNGPTCT dataset to nifti files and generates segboxes for each scan') | |
| parser.add_argument("annotation_folder") | |
| parser.add_argument("dataset_folder") | |
| parser.add_argument("label_folder") | |
| parser.add_argument("input_folder") | |
| args = parser.parse_args(sys.argv[2:]) | |
| convert_nsclc_petct(args.annotation_folder, args.dataset_folder, args.label_folder, args.input_folder) | |
| if __name__ == '__main__': | |
| Parser() |