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Merge pull request #606 from MarcCote/enh_conversion_scripts
ENH: adding TRK <=> TCK streamlines conversion scripts
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‎bin/nib-tck2trk

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#!python
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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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#
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# See COPYING file distributed along with the NiBabel package for the
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# copyright and license terms.
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#
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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"""
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Convert tractograms (TCK -> TRK).
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"""
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from nibabel.cmdline.tck2trk import main
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if __name__ == '__main__':
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main()

‎bin/nib-trk2tck

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#!python
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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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#
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# See COPYING file distributed along with the NiBabel package for the
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# copyright and license terms.
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#
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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"""
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Convert tractograms (TRK -> TCK).
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"""
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from nibabel.cmdline.trk2tck import main
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if __name__ == '__main__':
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main()

‎nibabel/cmdline/tck2trk.py

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"""
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Convert tractograms (TCK -> TRK).
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"""
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import os
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import argparse
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import nibabel as nib
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from nibabel.streamlines import Field
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from nibabel.orientations import aff2axcodes
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def parse_args():
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DESCRIPTION = "Convert tractograms (TCK -> TRK)."
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parser = argparse.ArgumentParser(description=DESCRIPTION)
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parser.add_argument("anatomy",
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help="reference anatomical image (.nii|.nii.gz.")
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parser.add_argument("tractograms", metavar="tractogram", nargs="+",
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help="list of tractograms (.tck).")
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parser.add_argument("-f", "--force", action="store_true",
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help="overwrite existing output files.")
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args = parser.parse_args()
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return args, parser
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def main():
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args, parser = parse_args()
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try:
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nii = nib.load(args.anatomy)
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except Exception:
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parser.error("Expecting anatomical image as first agument.")
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for tractogram in args.tractograms:
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tractogram_format = nib.streamlines.detect_format(tractogram)
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if tractogram_format is not nib.streamlines.TckFile:
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print("Skipping non TCK file: '{}'".format(tractogram))
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continue
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filename, _ = os.path.splitext(tractogram)
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output_filename = filename + '.trk'
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if os.path.isfile(output_filename) and not args.force:
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msg = "Skipping existing file: '{}'. Use -f to overwrite."
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print(msg.format(output_filename))
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continue
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# Build header using infos from the anatomical image.
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header = {}
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header[Field.VOXEL_TO_RASMM] = nii.affine.copy()
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header[Field.VOXEL_SIZES] = nii.header.get_zooms()[:3]
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header[Field.DIMENSIONS] = nii.shape[:3]
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header[Field.VOXEL_ORDER] = "".join(aff2axcodes(nii.affine))
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tck = nib.streamlines.load(tractogram)
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nib.streamlines.save(tck.tractogram, output_filename, header=header)

‎nibabel/cmdline/trk2tck.py

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"""
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Convert tractograms (TRK -> TCK).
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"""
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import os
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import argparse
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import nibabel as nib
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def parse_args():
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DESCRIPTION = "Convert tractograms (TRK -> TCK)."
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parser = argparse.ArgumentParser(description=DESCRIPTION)
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parser.add_argument("tractograms", metavar="tractogram", nargs="+",
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help="list of tractograms (.trk).")
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parser.add_argument("-f", "--force", action="store_true",
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help="overwrite existing output files.")
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args = parser.parse_args()
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return args, parser
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def main():
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args, parser = parse_args()
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for tractogram in args.tractograms:
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tractogram_format = nib.streamlines.detect_format(tractogram)
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if tractogram_format is not nib.streamlines.TrkFile:
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print("Skipping non TRK file: '{}'".format(tractogram))
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continue
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filename, _ = os.path.splitext(tractogram)
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output_filename = filename + '.tck'
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if os.path.isfile(output_filename) and not args.force:
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msg = "Skipping existing file: '{}'. Use -f to overwrite."
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print(msg.format(output_filename))
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continue
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trk = nib.streamlines.load(tractogram)
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nib.streamlines.save(trk.tractogram, output_filename)

‎nibabel/tests/test_scripts.py

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import sys
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import os
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import shutil
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from os.path import (dirname, join as pjoin, abspath, splitext, basename,
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exists)
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import csv
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from glob import glob
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import numpy as np
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import nibabel as nib
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from ..tmpdirs import InTemporaryDirectory
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from ..loadsave import load
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from ..orientations import flip_axis, aff2axcodes, inv_ornt_aff
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from nose.tools import assert_true, assert_false, assert_equal
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from nose import SkipTest
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from numpy.testing import assert_almost_equal
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from numpy.testing import assert_almost_equal, assert_array_equal
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from .scriptrunner import ScriptRunner
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from .nibabel_data import needs_nibabel_data
@@ -357,3 +359,92 @@ def test_parrec2nii_with_data():
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assert_equal(sorted(csv_keys), ['diffusion b value number',
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'gradient orientation number'])
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assert_equal(nlines, 8) # 8 volumes present in DTI.PAR
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@script_test
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def test_nib_trk2tck():
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simple_trk = pjoin(DATA_PATH, "simple.trk")
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standard_trk = pjoin(DATA_PATH, "standard.trk")
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with InTemporaryDirectory() as tmpdir:
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# Copy input files to convert.
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shutil.copy(simple_trk, tmpdir)
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shutil.copy(standard_trk, tmpdir)
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simple_trk = pjoin(tmpdir, "simple.trk")
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standard_trk = pjoin(tmpdir, "standard.trk")
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simple_tck = pjoin(tmpdir, "simple.tck")
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standard_tck = pjoin(tmpdir, "standard.tck")
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# Convert one file.
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cmd = ["nib-trk2tck", simple_trk]
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code, stdout, stderr = run_command(cmd)
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assert_equal(len(stdout), 0)
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assert_true(os.path.isfile(simple_tck))
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trk = nib.streamlines.load(simple_trk)
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tck = nib.streamlines.load(simple_tck)
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assert_array_equal(tck.streamlines.data, trk.streamlines.data)
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assert_true(isinstance(tck, nib.streamlines.TckFile))
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# Skip non TRK files.
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cmd = ["nib-trk2tck", simple_tck]
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code, stdout, stderr = run_command(cmd)
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assert_true("Skipping non TRK file" in stdout)
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# By default, refuse to overwrite existing output files.
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cmd = ["nib-trk2tck", simple_trk]
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code, stdout, stderr = run_command(cmd)
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assert_true("Skipping existing file" in stdout)
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# Convert multiple files and with --force.
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cmd = ["nib-trk2tck", "--force", simple_trk, standard_trk]
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code, stdout, stderr = run_command(cmd)
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assert_equal(len(stdout), 0)
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trk = nib.streamlines.load(standard_trk)
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tck = nib.streamlines.load(standard_tck)
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assert_array_equal(tck.streamlines.data, trk.streamlines.data)
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@script_test
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def test_nib_tck2trk():
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anat = pjoin(DATA_PATH, "standard.nii.gz")
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standard_tck = pjoin(DATA_PATH, "standard.tck")
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with InTemporaryDirectory() as tmpdir:
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# Copy input file to convert.
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shutil.copy(standard_tck, tmpdir)
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standard_trk = pjoin(tmpdir, "standard.trk")
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standard_tck = pjoin(tmpdir, "standard.tck")
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# Anatomical image not found as first argument.
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cmd = ["nib-tck2trk", standard_tck, anat]
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code, stdout, stderr = run_command(cmd, check_code=False)
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assert_equal(code, 2) # Parser error.
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assert_true("Expecting anatomical image as first agument" in stderr)
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# Convert one file.
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cmd = ["nib-tck2trk", anat, standard_tck]
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code, stdout, stderr = run_command(cmd)
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assert_equal(len(stdout), 0)
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assert_true(os.path.isfile(standard_trk))
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tck = nib.streamlines.load(standard_tck)
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trk = nib.streamlines.load(standard_trk)
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assert_array_equal(trk.streamlines.data, tck.streamlines.data)
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assert_true(isinstance(trk, nib.streamlines.TrkFile))
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# Skip non TCK files.
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cmd = ["nib-tck2trk", anat, standard_trk]
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code, stdout, stderr = run_command(cmd)
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assert_true("Skipping non TCK file" in stdout)
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# By default, refuse to overwrite existing output files.
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cmd = ["nib-tck2trk", anat, standard_tck]
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code, stdout, stderr = run_command(cmd)
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assert_true("Skipping existing file" in stdout)
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# Convert multiple files and with --force.
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cmd = ["nib-tck2trk", "--force", anat, standard_tck, standard_tck]
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code, stdout, stderr = run_command(cmd)
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assert_equal(len(stdout), 0)
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tck = nib.streamlines.load(standard_tck)
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trk = nib.streamlines.load(standard_trk)
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assert_array_equal(tck.streamlines.data, trk.streamlines.data)

‎setup.py

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@@ -117,6 +117,8 @@ def main(**extra_args):
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pjoin('bin', 'nib-ls'),
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pjoin('bin', 'nib-dicomfs'),
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pjoin('bin', 'nib-nifti-dx'),
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pjoin('bin', 'nib-tck2trk'),
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pjoin('bin', 'nib-trk2tck'),
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],
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cmdclass = cmdclass,
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**extra_args

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