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