Remove invalid streamlines (out of bbox)

scilpy/io/utils.py

@@ -23,7 +23,8 @@ def load_tractogram_with_reference(parser, args, filepath,
                                    bbox_check=True):
     _, ext = os.path.splitext(filepath)
     if ext == '.trk':
-        sft = load_tractogram(filepath, 'same')
+        sft = load_tractogram(filepath, 'same',
+                              bbox_valid_check=bbox_check)
     elif ext in ['.tck', '.fib', '.vtk', '.dpy']:
         if args.reference is None:
             parser.error('--reference is required for this file format '

scripts/scil_remove_invalid_streamlines.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+
+from dipy.io.streamline import save_tractogram
+
+from scilpy.io.utils import (add_overwrite_arg, add_reference,
+                             assert_inputs_exist, assert_outputs_exist,
+                             load_tractogram_with_reference)
+
+DESCRIPTION = """
+Removal of streamlines that are out of the volume bounding box. In voxel space
+no negative coordinate and no above volume dimension coordinate are possible.
+Any streamlines that do not respect these two conditions are removed.
+"""
+
+
+def _build_args_parser():
+    p = argparse.ArgumentParser(description=DESCRIPTION,
+                                formatter_class=argparse.RawTextHelpFormatter)
+
+    p.add_argument('in_tractogram', metavar='IN_TRACTOGRAM',
+                   help='Tractogram filename. Format must be one of \n'
+                        'trk, tck, vtk, fib, dpy.')
+
+    p.add_argument('output_name', metavar='OUTPUT_NAME',
+                   help='Output filename. Format must be one of \n'
+                        'trk, tck, vtk, fib, dpy.')
+
+    add_reference(p)
+
+    add_overwrite_arg(p)
+
+    return p
+
+
+def main():
+    parser = _build_args_parser()
+    args = parser.parse_args()
+
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
+    assert_outputs_exist(parser, args, args.output_name)
+
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram,
+                                         bbox_check=False)
+    sft.remove_invalid_streamlines()
+    save_tractogram(sft, args.output_name)
+
+
+if __name__ == "__main__":
+    main()