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#!python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
DESCRIP = 'Read 4D image file and write 3D nifti file for each volume'
EPILOG = \
'''nipy_4dto3d will generate a series of 3D nifti images for each volume a 4D
image series in any format readable by `nibabel`.
'''
from os.path import splitext, join as pjoin, split as psplit
import nibabel as nib
from nipy.externals.argparse import (ArgumentParser,
RawDescriptionHelpFormatter)
def main():
parser = ArgumentParser(description=DESCRIP,
epilog=EPILOG,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('filename', type=str,
help='4D image filename')
parser.add_argument('--out-path', type=str,
help='path for output image files')
args = parser.parse_args()
out_path = args.out_path
img = nib.load(args.filename)
imgs = nib.four_to_three(img)
froot, ext = splitext(args.filename)
if ext in ('.gz', '.bz2'):
froot, ext = splitext(froot)
if out_path is not None:
pth, fname = psplit(froot)
froot = pjoin(out_path, fname)
for i, img3d in enumerate(imgs):
fname3d = '%s_%04d.nii' % (froot, i)
nib.save(img3d, fname3d)
if __name__ == '__main__':
main()
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