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import os |
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import nibabel as nb |
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import numpy as np |
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import zipfile |
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TEMP_UNZIP_PATH = '/mnt/EncryptedData1/Users/javier/ext_datasets/LITS17/temp' |
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NII_EXTENSION = '.nii' |
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def save_nifti(data, save_path, header=None, verbose=True): |
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if header is None: |
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data_nifti = nb.Nifti1Image(data, affine=np.eye(4)) |
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else: |
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data_nifti = nb.Nifti1Image(data, affine=None, header=header) |
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data_nifti.header.get_xyzt_units() |
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try: |
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nb.save(data_nifti, save_path) |
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if verbose: |
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print('Saved {}'.format(save_path)) |
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except ValueError: |
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print('Could not save {}'.format(save_path)) |
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def unzip_nii_file(file_path): |
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file_dir, file_name = os.path.split(file_path) |
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file_name = file_name.split('.zip')[0] |
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dest_path = os.path.join(TEMP_UNZIP_PATH, file_name) |
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zipfile.ZipFile(file_path).extractall(TEMP_UNZIP_PATH) |
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if not os.path.exists(dest_path): |
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print('ERR: File {} not unzip-ed!'.format(file_path)) |
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dest_path = None |
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return dest_path |
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def delete_temp(file_path, verbose=False): |
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assert NII_EXTENSION in file_path |
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os.remove(file_path) |
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if verbose: |
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print('Deleted file: ', file_path) |
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