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import os
import nibabel
import numpy as np
from misc import crop_and_pad, viewVolume, MRIread, make_dir
test_flag = False
directory = '/autofs/space/yogurt_004/users/pl629/ASNR-MICCAI-BraTS2023-Local-Synthesis-Challenge-Training'
new_directory = make_dir('/autofs/space/yogurt_004/users/pl629/ASNR-MICCAI-BraTS2023-Local-Synthesis-Challenge-Training_CropPad')
database = []
mask_vis = []
pad_size = [224, 224, 224]
for root, dirs, files in os.walk(directory):
dirs_sorted = sorted(dirs)
for dir_id in dirs_sorted:
datapoint = dict()
sli_dict = dict()
for ro, di, fi in os.walk(root + "/" + str(dir_id)):
fi_sorted = sorted(fi)
assert os.path.isfile(os.path.join(root, dir_id, dir_id + '-t1n.nii.gz'))
new_dir = make_dir(os.path.join(new_directory, dir_id))
print('Create new case dir:', new_dir)
'''try:
to_crop, aff = MRIread(os.path.join(root, dir_id, dir_id + '-t1n.nii.gz'), im_only=False, dtype='float')
_, crop_idx = crop_and_pad(to_crop, pad_size = pad_size, to_print = True)
print('-- crop_idx:', crop_idx)
except:
raise NotImplementedError
for f in fi_sorted:
seqtype = f.split("-")[-1].split(".")[0]
datapoint[seqtype] = os.path.join(root, dir_id, f)
print('-- current filename:', f)
print('-- current seqtype:', seqtype)
print('-- to save in new_dir:', os.path.join(new_dir, f.split('.')[0] + '.nii.gz'))
curr_nda, _ = MRIread(os.path.join(root, dir_id, f), im_only=False, dtype='float')
new_curr_nda, _ = crop_and_pad(curr_nda, crop_idx, pad_size = pad_size, to_print = False)
viewVolume(new_curr_nda, aff, names = [f.split('.')[0]], save_dir = new_dir)'''
nda, aff = MRIread(os.path.join(new_dir, dir_id + '-t1n.nii.gz'), im_only=False, dtype='float')
mask, _ = MRIread(os.path.join(new_dir, dir_id + '-mask-healthy.nii.gz'), im_only=False, dtype='float')
viewVolume(nda * (1 - mask), aff, names = [dir_id + '-t1n-healthyvoided'], save_dir = new_dir)
database.append(datapoint)
#exit()
break
print('Total num of cases:', len(database)) |