/usr/bin/nipy_3dto4d is in python-nipy 0.3.0-1ubuntu2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
DESCRIP = 'Read 3D image files and write a 4D file'
EPILOG = \
'''nipy_3dto4d will take a series of 3D nifti images in any format readable by
nibabel and concatenate them into a 4D image, and write the image with format
guessed from the output image filename. You can set the filename with the
``--out-4d`` parameter, or we make a filename from the input names.
'''
import os
from os.path import join as pjoin
from nipy.externals.argparse import (ArgumentParser,
RawDescriptionHelpFormatter)
import nibabel as nib
def do_3d_to_4d(filenames, check_affines=True):
imgs = []
for fname in filenames:
img = nib.load(fname)
imgs.append(img)
return nib.concat_images(imgs, check_affines=check_affines)
def main():
parser = ArgumentParser(description=DESCRIP,
epilog=EPILOG,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('in_filenames', type=str,
nargs='+',
help='3D image filenames')
parser.add_argument('--out-4d', type=str,
help='4D output image name')
parser.add_argument('--check-affines', type=bool,
default=True,
help='False if you want to ignore differences '
'in affines between the 3D images, True if you '
'want to raise an error for significant '
'differences (default is True)')
# parse the command line
args = parser.parse_args()
# get input 3ds
filenames = args.in_filenames
# affine check
check_affines = args.check_affines
# get output name
out_fname = args.out_4d
if out_fname is None:
pth, fname = os.path.split(filenames[0])
froot, ext = os.path.splitext(fname)
if ext in ('.gz', '.bz2'):
gz = ext
froot, ext = os.path.splitext(froot)
else:
gz = ''
out_fname = pjoin(pth, froot + '_4d' + ext + gz)
img4d = do_3d_to_4d(filenames, check_affines=check_affines)
nib.save(img4d, out_fname)
if __name__ == '__main__':
main()
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