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gandlf_generateCompetitionMetrics
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gandlf_generateCompetitionMetrics
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#!usr/bin/env python
# -*- coding: utf-8 -*-
import os
import argparse
import ast
import sys
from GANDLF import version
from GANDLF.cli import generate_Competition_metrics, copyrightMessage
if __name__ == "__main__":
parser = argparse.ArgumentParser(
prog="GANDLF_Metrics_Competitions",
formatter_class=argparse.RawTextHelpFormatter,
description="Metrics calculator for the BraTS competition.\n\n" + copyrightMessage,
)
parser.add_argument(
"-c",
"--competition",
"--competition_brats",
metavar="",
type=str,
required=True,
help="Competition Name",
)
parser.add_argument(
"-i",
"--inputdata",
"--data_path",
metavar="",
type=str,
required=True,
help="CSV file that is used to generate the metrics; should contain 3 columns: 'subjectid, prediction, target'",
)
parser.add_argument(
"-o",
"--outputfile",
"--output_path",
metavar="",
type=str,
default=None,
help="Location to save the output dictionary. If not provided, will print to stdout.",
)
parser.add_argument(
"-v",
"--version",
action="version",
version="%(prog)s v{}".format(version) + "\n\n" + copyrightMessage,
help="Show program's version number and exit.",
)
# This is a dummy argument that exists to trigger MLCube mounting requirements.
# Do not remove.
parser.add_argument("-rawinput", "--rawinput", help=argparse.SUPPRESS)
args = parser.parse_args()
assert args.competition is not None, "Missing required parameter: competition"
assert args.inputdata is not None, "Missing required parameter: inputdata"
try:
generate_Competition_metrics.generate_metrics_dict_competition(
args.inputdata,
args.competition,
args.outputfile,
)
except Exception as e:
sys.exit("ERROR: " + str(e))
print("Finished.")