Merge pull request #696 from karanphil/apply_transform_to_bvecs

(WIP) Adding script to apply transform to bvecs

scripts/scil_apply_transform_to_bvecs.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Transform bvecs using an affine/rigid transformation.
+"""
+
+import argparse
+
+import numpy as np
+
+from dipy.io.gradients import read_bvals_bvecs
+
+from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
+                             assert_outputs_exist, load_matrix_in_any_format)
+from scilpy.utils.filenames import split_name_with_nii
+from scilpy.utils.image import transform_anatomy
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
+                                description=__doc__)
+
+    p.add_argument('in_bvecs',
+                   help='Path of the bvec file, in FSL format')
+    p.add_argument('in_transfo',
+                   help='Path of the file containing the 4x4 \n'
+                        'transformation, matrix (.txt, .npy or .mat).')
+    p.add_argument('out_bvecs',
+                   help='Output filename of the transformed bvecs.')
+
+    p.add_argument('--inverse', action='store_true',
+                   help='Apply the inverse transformation.')
+
+    add_overwrite_arg(p)
+
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    assert_inputs_exist(parser, [args.in_bvecs, args.in_transfo])
+    assert_outputs_exist(parser, args, args.out_bvecs)
+
+    transfo = load_matrix_in_any_format(args.in_transfo)[:3, :3]
+
+    if args.inverse:
+        transfo = np.linalg.inv(transfo)
+
+    _, bvecs = read_bvals_bvecs(None, args.in_bvecs)
+
+    bvecs = bvecs @ transfo
+
+    np.savetxt(str(args.out_bvecs), bvecs.T)
+
+
+if __name__ == "__main__":
+    main()

scripts/tests/test_apply_transform_to_bvecs.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import tempfile
+
+from scilpy.io.fetcher import get_testing_files_dict, fetch_data, get_home
+
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['bst.zip'])
+fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_apply_transform_to_bvecs.py', '--help')
+    assert ret.success
+
+
+def test_execution_bst(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_bvecs = os.path.join(get_home(), 'processing',
+                           'dwi.bvec')
+    in_aff = os.path.join(get_home(), 'bst',
+                          'output0GenericAffine.mat')
+    ret = script_runner.run('scil_apply_transform_to_bvecs.py',
+                            in_bvecs, in_aff,
+                            'bvecs_transformed.bvec', '--inverse')
+    assert ret.success