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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Manipulate a TRX file internal array to change their data type.
Each instance of --dps, --dpv, --groups require 2 arguments (FILE, DTYPE).
--dpg requires 3 arguments (GROUP, FILE, DTYPE).
The choice of DTYPE are:
- (u)int8, (u)int16, (u)int32, (u)int64
- float16, float32, float64
- bool
Example command:
tff_manipulate_datatype.py input.trx output.trx \
--position float16 --offsets uint64 \
--dpv color_x uint8 --dpv color_y uint8 --dpv color_z uint8 \
--dpv fa float16 --dps algo uint8 --dps clusters_QB uint16 \
--dps commit_colors uint8 --dps commit_weights float16 \
--group CC uint64 --dpg CC mean_fa float64
"""
import argparse
import os
import numpy as np
from trx.workflows import manipulate_trx_datatype
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_tractogram',
help='Input TRX file.')
p.add_argument('out_tractogram',
help='Output filename. Format must be one of\n'
'trk, tck, vtk, fib, dpy, trx.')
p2 = p.add_argument_group(title='Data type options')
p2.add_argument('--positions_dtype',
choices=['float16', 'float32', 'float64'],
help='Specify the datatype for positions for trx. '
'[%(choices)s]')
p2.add_argument('--offsets_dtype',
choices=['uint32', 'uint64'],
help='Specify the datatype for offsets for trx. '
'[%(choices)s]')
p3 = p.add_argument_group(title='Streamlines metadata options')
p3.add_argument('--dpv', metavar=('NAME', 'DTYPE'), nargs=2,
action='append',
help='Specify the datatype for a specific data_per_vertex.')
p3.add_argument('--dps', metavar=('NAME', 'DTYPE'), nargs=2,
action='append',
help='Specify the datatype for a specific data_per_streamline.')
p3.add_argument('--groups', metavar=('NAME', 'DTYPE'), nargs=2,
action='append',
help='Specify the datatype for a specific group.')
p3.add_argument('--dpg', metavar=('GROUP', 'NAME', 'DTYPE'), nargs=3,
action='append',
help='Specify the datatype for a specific data_per_group.')
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))
dtype_dict = {}
if args.positions_dtype:
dtype_dict['positions'] = np.dtype(args.positions_dtype)
if args.offsets_dtype:
dtype_dict['offsets'] = np.dtype(args.offsets_dtype)
if args.dpv:
dtype_dict['dpv'] = {}
for name, dtype in args.dpv:
dtype_dict['dpv'][name] = np.dtype(dtype)
if args.dps:
dtype_dict['dps'] = {}
for name, dtype in args.dps:
dtype_dict['dps'][name] = np.dtype(dtype)
if args.groups:
dtype_dict['groups'] = {}
for name, dtype in args.groups:
dtype_dict['groups'][name] = np.dtype(dtype)
if args.dpg:
dtype_dict['dpg'] = {}
for group, name, dtype in args.dpg:
dtype_dict['dpg'][group] = {name: np.dtype(dtype)}
manipulate_trx_datatype(
args.in_tractogram, args.out_tractogram, dtype_dict)
if __name__ == "__main__":
main()
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