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cut.py
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import nibabel as nib
import numpy as np
import sys
import argparse
import os
from pathlib import Path
from tqdm import tqdm
def first_nonzero(arr, axis, invalid_val=0):
mask = arr != 0
return np.where(mask.any(axis=axis), mask.argmax(axis=axis), invalid_val)
def last_nonzero(arr, axis, invalid_val=0):
mask = arr != 0
val = arr.shape[axis] - np.flip(mask, axis=axis).argmax(axis=axis) - 1
return np.where(mask.any(axis=axis), val, invalid_val)
def arg_parser():
parser = argparse.ArgumentParser(
description='Extract mask files from directory')
required = parser.add_argument_group('Required')
required.add_argument('-i', '--img-dir', type=str, required=True, nargs='+',
help='path to directory with images to be processed')
required.add_argument('-m', '--mask-dir', type=str, required=True,
help='mask directory')
required.add_argument('-o', '--output', type=str, required=True,
help='output directory')
required.add_argument('-mode', '--mode', type=str, required=False, default='t1',
help='mode')
return parser
def main(args=None):
args = arg_parser().parse_args(args)
try:
Path(args.output).mkdir(parents=True,exist_ok=True)
Path(args.output + '/mask/').mkdir(parents=True,exist_ok=True)
Path(args.output + '/seg/').mkdir(parents=True,exist_ok=True)
Path(args.output + '/' + args.mode).mkdir(parents=True,exist_ok=True)
file_suffix = args.mode
for input_dir in args.img_dir:
if not os.path.isdir(input_dir):
raise ValueError('(-i / --img-dir) argument needs to be a directory of NIfTI images.')
for i, mask_path in tqdm(enumerate(os.listdir(args.mask_dir))):
try:
if mask_path.endswith('_mask.nii.gz') or mask_path.endswith('_mask.nii'):
if not os.path.isfile(args.output + '/' + file_suffix + '/' + mask_path.replace('mask', file_suffix)) or not os.path.isfile(args.output + '/seg/' + mask_path.replace('mask', 'seg')):
# print('Processing file {} of {}'.format(i+1, len(os.listdir(args.mask_dir))))
max_dims = [0, 0, 0]
# Load mask
mask_file = nib.load(os.path.join(args.mask_dir, mask_path))
mask = mask_file.get_fdata()
# Zero axis
zero_min_indices = first_nonzero(mask, 0, 999999).min()
zero_max_indices = last_nonzero(mask, 0).max()
# First axis
first_min_indices = first_nonzero(mask, 1, 999999).min()
first_max_indices = last_nonzero(mask, 1).max()
# Second axis
second_min_indices = first_nonzero(mask, 2, 999999).min()
second_max_indices = last_nonzero(mask, 2).max()
max_dims = np.maximum(max_dims, [zero_max_indices - zero_min_indices,
first_max_indices - first_min_indices,
second_max_indices - second_min_indices])
print(max_dims)
# for k, input_dir in enumerate(args.img_dir):
# Create path if it does not exist yet
# Path(file_suffix + '-cut').mkdir(exist_ok=True)
# Construct new file name
file_name = mask_path.replace('mask', file_suffix)
out_name = args.output + '/' + file_suffix + '/' + mask_path.replace('mask', file_suffix) #
mask_name = args.output + '/mask/' + mask_path
seg_name = args.output + '/seg/' + mask_path.replace('mask', 'seg')
# Load volume
vol = nib.load(os.path.join(input_dir, file_name))
vol_np = vol.get_fdata()
# Slice
new_vol = vol_np[zero_min_indices:zero_max_indices, first_min_indices:first_max_indices,
second_min_indices:second_max_indices]
# Create new nifti file and save it
new_vol_file = nib.Nifti1Image(new_vol, affine=vol.affine, header=vol.header)
nib.save(new_vol_file,out_name)
# Path('mask-cut').mkdir(exist_ok=True)
new_mask_vol = mask[zero_min_indices:zero_max_indices, first_min_indices:first_max_indices,
second_min_indices:second_max_indices]
new_mask_file = nib.Nifti1Image(new_mask_vol, affine=mask_file.affine, header=mask_file.header)
if os.path.isfile((args.mask_dir+mask_path).replace('mask','seg')) and not os.path.isfile(seg_name):
seg_path = os.path.join(args.mask_dir, mask_path).replace('mask','seg')
seg = nib.load(seg_path)
seg_np = seg.get_fdata()
# Slice
new_seg = seg_np[zero_min_indices:zero_max_indices, first_min_indices:first_max_indices,
second_min_indices:second_max_indices]
# Create new nifti file and save it
new_seg_file = nib.Nifti1Image(new_seg, affine=vol.affine, header=vol.header)
nib.save(new_seg_file,seg_name)
# print(mask_name)
if not os.path.isfile(mask_name):
nib.save(new_mask_file, mask_name)
except:
print('error')
print('Maximum dimensions are {}'.format(max_dims))
return 0
except Exception as e:
print(e)
return 1
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))