Merge pull request #1011 from arnaudbore/add_script_normalise_bvec

[ENH] Add script normalize bvec

scripts/scil_gradients_normalize_bvecs.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Script to normalize gradients bvecs.
+"""
+
+import argparse
+import logging
+
+import numpy as np
+
+from scilpy.io.utils import (assert_inputs_exist, assert_outputs_exist,
+                             add_overwrite_arg, add_verbose_arg)
+from scilpy.gradients.bvec_bval_tools import normalize_bvecs
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
+                                description=__doc__)
+
+    p.add_argument('in_bvec',
+                   help='Path to the gradient file (.bvec).')
+
+    p.add_argument('out_bvec',
+                   help='Output bvec file.')
+
+    add_overwrite_arg(p)
+    add_verbose_arg(p)
+
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
+
+    assert_inputs_exist(parser, args.in_bvec)
+    assert_outputs_exist(parser, args, args.out_bvec)
+
+    bvecs = np.loadtxt(args.in_bvec)
+    np.savetxt(args.out_bvec, normalize_bvecs(bvecs))
+
+
+if __name__ == "__main__":
+    main()

scripts/tests/test_gradients_normalize_bvecs.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import tempfile
+
+from scilpy import SCILPY_HOME
+from scilpy.io.fetcher import fetch_data, get_testing_files_dict
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_gradients_normalize_bvecs.py',
+                            '--help')
+    assert ret.success
+
+
+def test_execution_processing_fsl(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+    ret = script_runner.run('scil_gradients_normalize_bvecs.py',
+                            in_bvec, '1000_norm.bvec')
+    assert ret.success