def main():
import argparse
parser = argparse.ArgumentParser(
description=
"The MSD provides data as 4D Niftis with the modality being the first"
" dimension. We think this may be cumbersome for some users and "
"therefore expect 3D niftixs instead, with one file per modality. "
"This utility will convert 4D MSD data into the format nnU-Net "
"expects")
parser.add_argument(
"-i",
help=
"Input folder. Must point to a TaskXX_TASKNAME folder as downloaded from the MSD "
"website",
default=
"C:/Research/IMA_on_segmentation/nnUnet/nnUNet/rawData/nnUNet_raw_data/Task05_Prostate"
)
parser.add_argument(
"-p",
required=False,
default=default_num_threads,
type=int,
help=
"Use this to specify how many processes are used to run the script. "
"Default is %d" % default_num_threads)
parser.add_argument(
"-output_task_id",
required=False,
default=None,
type=int,
help=
"If specified, this will overwrite the task id in the output folder. If unspecified, the "
"task id of the input folder will be used.")
args = parser.parse_args()
crawl_and_remove_hidden_from_decathlon(args.i)
split_4d(args.i, args.p, args.output_task_id)
raise ValueError("only 0 or 1 allowed for override")
if no_preprocessing == 0:
no_preprocessing = False
elif no_preprocessing == 1:
no_preprocessing = True
else:
raise ValueError("only 0 or 1 allowed for override")
if use_splitted == 0:
use_splitted = False
elif use_splitted == 1:
use_splitted = True
else:
raise ValueError("only 0 or 1 allowed for use_splitted")
if task == "all":
all_tasks = subdirs(nnUNet_raw_data, prefix="Task", join=False)
for t in all_tasks:
crop(t, override=override, num_threads=processes_lowres)
analyze_dataset(t, override=override, collect_intensityproperties=True, num_processes=processes_lowres)
plan_and_preprocess(t, processes_lowres, processes_fullres, no_preprocessing)
else:
if not use_splitted or not isdir(join(nnUNet_raw_data, task)):
print("splitting task ", task)
split_4d(task)
crop(task, override=override, num_threads=processes_lowres)
analyze_dataset(task, override, collect_intensityproperties=True, num_processes=processes_lowres)
plan_and_preprocess(task, processes_lowres, processes_fullres, no_preprocessing)