AutoSeg4ETICA / nnunet /postprocessing /consolidate_postprocessing_simple.py

Chris Xiao

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c642393 about 2 years ago

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#    Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
#    Licensed under the Apache License, Version 2.0 (the "License");
#    you may not use this file except in compliance with the License.
#    You may obtain a copy of the License at
#
#        http://www.apache.org/licenses/LICENSE-2.0
#
#    Unless required by applicable law or agreed to in writing, software
#    distributed under the License is distributed on an "AS IS" BASIS,
#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#    See the License for the specific language governing permissions and
#    limitations under the License.


import argparse
from nnunet.postprocessing.consolidate_postprocessing import consolidate_folds
from nnunet.utilities.folder_names import get_output_folder_name
from nnunet.utilities.task_name_id_conversion import convert_id_to_task_name
from nnunet.paths import default_cascade_trainer, default_trainer, default_plans_identifier


def main():
    argparser = argparse.ArgumentParser(usage="Used to determine the postprocessing for a trained model. Useful for "
                                              "when the best configuration (2d, 3d_fullres etc) as selected manually.")
    argparser.add_argument("-m", type=str, required=True, help="U-Net model (2d, 3d_lowres, 3d_fullres or "
                                                               "3d_cascade_fullres)")
    argparser.add_argument("-t", type=str, required=True, help="Task name or id")
    argparser.add_argument("-tr", type=str, required=False, default=None,
                           help="nnUNetTrainer class. Default: %s, unless 3d_cascade_fullres "
                                "(then it's %s)" % (default_trainer, default_cascade_trainer))
    argparser.add_argument("-pl", type=str, required=False, default=default_plans_identifier,
                           help="Plans name, Default=%s" % default_plans_identifier)
    argparser.add_argument("-val", type=str, required=False, default="validation_raw",
                           help="Validation folder name. Default: validation_raw")

    args = argparser.parse_args()
    model = args.m
    task = args.t
    trainer = args.tr
    plans = args.pl
    val = args.val

    if not task.startswith("Task"):
        task_id = int(task)
        task = convert_id_to_task_name(task_id)

    if trainer is None:
        if model == "3d_cascade_fullres":
            trainer = "nnUNetTrainerV2CascadeFullRes"
        else:
            trainer = "nnUNetTrainerV2"

    folder = get_output_folder_name(model, task, trainer, plans, None)

    consolidate_folds(folder, val)


if __name__ == "__main__":
    main()

	# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
	#
	# Licensed under the Apache License, Version 2.0 (the "License");
	# you may not use this file except in compliance with the License.
	# You may obtain a copy of the License at
	#
	# http://www.apache.org/licenses/LICENSE-2.0
	#
	# Unless required by applicable law or agreed to in writing, software
	# distributed under the License is distributed on an "AS IS" BASIS,
	# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	# See the License for the specific language governing permissions and
	# limitations under the License.


	import argparse
	from nnunet.postprocessing.consolidate_postprocessing import consolidate_folds
	from nnunet.utilities.folder_names import get_output_folder_name
	from nnunet.utilities.task_name_id_conversion import convert_id_to_task_name
	from nnunet.paths import default_cascade_trainer, default_trainer, default_plans_identifier


	def main():
	argparser = argparse.ArgumentParser(usage="Used to determine the postprocessing for a trained model. Useful for "
	"when the best configuration (2d, 3d_fullres etc) as selected manually.")
	argparser.add_argument("-m", type=str, required=True, help="U-Net model (2d, 3d_lowres, 3d_fullres or "
	"3d_cascade_fullres)")
	argparser.add_argument("-t", type=str, required=True, help="Task name or id")
	argparser.add_argument("-tr", type=str, required=False, default=None,
	help="nnUNetTrainer class. Default: %s, unless 3d_cascade_fullres "
	"(then it's %s)" % (default_trainer, default_cascade_trainer))
	argparser.add_argument("-pl", type=str, required=False, default=default_plans_identifier,
	help="Plans name, Default=%s" % default_plans_identifier)
	argparser.add_argument("-val", type=str, required=False, default="validation_raw",
	help="Validation folder name. Default: validation_raw")

	args = argparser.parse_args()
	model = args.m
	task = args.t
	trainer = args.tr
	plans = args.pl
	val = args.val

	if not task.startswith("Task"):
	task_id = int(task)
	task = convert_id_to_task_name(task_id)

	if trainer is None:
	if model == "3d_cascade_fullres":
	trainer = "nnUNetTrainerV2CascadeFullRes"
	else:
	trainer = "nnUNetTrainerV2"

	folder = get_output_folder_name(model, task, trainer, plans, None)

	consolidate_folds(folder, val)


	if __name__ == "__main__":
	main()