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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Conversion of '.tck', '.trk', '.fib', '.vtk', '.trx' and 'dpy' files using
updated file format standard. TCK file always needs a reference file, a NIFTI,
for conversion. The FIB file format is in fact a VTK, MITK Diffusion supports
it.
"""
import argparse
import os
from trx.workflows import convert_tractogram
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_tractogram', metavar='IN_TRACTOGRAM',
help='Tractogram filename. Format must be one of \n'
'trk, tck, vtk, fib, dpy, trx.')
p.add_argument('out_tractogram', metavar='OUT_TRACTOGRAM',
help='Output filename. Format must be one of \n'
'trk, tck, vtk, fib, dpy, trx.')
p.add_argument('--reference',
help='Reference anatomy for tck/vtk/fib/dpy file\n'
'support (.nii or .nii.gz).')
p2 = p.add_argument_group(title='Data type options')
p2.add_argument('--positions_dtype', default='float32',
choices=['float16', 'float32', 'float64'],
help='Specify the datatype for positions for trx. [%(default)s]')
p2.add_argument('--offsets_dtype', default='uint64',
choices=['uint32', 'uint64'],
help='Specify the datatype for offsets for trx. [%(default)s]')
p.add_argument('-f', dest='overwrite', action='store_true',
help='Force overwriting of the output files.')
return p
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if os.path.isfile(args.out_tractogram) and not args.overwrite:
raise IOError('{} already exists, use -f to overwrite.'.format(
args.out_tractogram))
convert_tractogram(args.in_tractogram, args.out_tractogram, args.reference,
pos_dtype=args.positions_dtype,
offsets_dtype=args.offsets_dtype)
if __name__ == "__main__":
main()
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