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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Concatenate multiple tractograms into one.
If the data_per_point or data_per_streamline is not the same for all
tractograms, the data must be deleted first.
"""
import argparse
import os
from trx.io import load, save
from trx.trx_file_memmap import TrxFile, concatenate
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_tractograms', nargs='+',
help='Tractogram filename. Format must be one of \n'
'trk, tck, vtk, fib, dpy, trx.')
p.add_argument('out_tractogram',
help='Filename of the concatenated tractogram.')
p.add_argument('--delete_dpv', action='store_true',
help='Delete the dpv if it exists. '
'Required if not all input has the same metadata.')
p.add_argument('--delete_dps', action='store_true',
help='Delete the dps if it exists. '
'Required if not all input has the same metadata.')
p.add_argument('--delete_groups', action='store_true',
help='Delete the groups if it exists. '
'Required if not all input has the same metadata.')
p.add_argument('--reference',
help='Reference anatomy for tck/vtk/fib/dpy file\n'
'support (.nii or .nii.gz).')
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))
trx_list = []
has_group = False
for filename in args.in_tractograms:
tractogram_obj = load(filename, args.reference)
if not isinstance(tractogram_obj, TrxFile):
tractogram_obj = TrxFile.from_sft(tractogram_obj)
elif len(tractogram_obj.groups):
has_group = True
trx_list.append(tractogram_obj)
trx = concatenate(trx_list, delete_dpv=args.delete_dpv,
delete_dps=args.delete_dps,
delete_groups=args.delete_groups or not has_group,
check_space_attributes=True,
preallocation=False)
save(trx, args.out_tractogram)
if __name__ == "__main__":
main()
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