fix name and add tests

scilpy/tractograms/streamline_and_mask_operations.py

@@ -337,7 +337,7 @@ def cut_streamlines_with_mask(
 
 def cut_streamlines_between_labels(
     sft, label_data, label_ids=None, min_len=0,
-    keep_in_roi=True, keep_one_point_in_roi=True, processes=1
+    one_point_in_roi=False, no_point_in_roi=False, processes=1
 ):
     """
     Cut streamlines so their segment are going from blob #1 to blob #2 in a
@@ -357,14 +357,10 @@ def cut_streamlines_between_labels(
         in the label map will be used.
     min_len: float
         Minimum length from the resulting streamlines.
-    keep_in_roi: bool
-        If True, the first and last points of the streamline that are in the
-        ROIs will be returned. If False, the var keep_one_point_in_roi will
-        decide which first/last points will be returned.
-    keep_one_point_in_roi: bool
-        If True, the first and last points of the streamline that are in the
-        ROIs will be returned. If False, the first and last points outside of
-        the ROI will be returned.
+    one_point_in_roi: bool
+        If True, one point in each ROI will be kept.
+    no_point_in_roi: bool
+        If True, no point in the ROIs will be kept.
 
     Returns
     -------
@@ -404,7 +400,7 @@ def cut_streamlines_between_labels(
     pool = Pool(processes)
     lists_of_new_strmls = pool.starmap(
         _cut_streamline_with_labels, [(i, s, pt, label_data_1, label_data_2,
-                                       keep_in_roi, keep_one_point_in_roi)
+                                       one_point_in_roi, no_point_in_roi)
                                       for (i, s, pt) in zip(
                                           indices, sft.streamlines,
                                           points_to_idx)])
@@ -427,7 +423,7 @@ def cut_streamlines_between_labels(
 
 def _cut_streamline_with_labels(
     idx, streamline, pts_to_idx, roi_data_1, roi_data_2,
-    keep_in_roi=True, keep_one_point=True
+    one_point_in_roi=False, no_point_in_roi=False
 ):
     """
     Cut streamlines so their segment are going from label mask #1 to label
@@ -446,14 +442,10 @@ def _cut_streamline_with_labels(
         Boolean array representing the region #1.
     roi_data_2: np.ndarray
         Boolean array representing the region #2.
-    keep_in_roi: bool
-        If True, the first and last points of the streamline that are in the
-        ROIs will be returned. If False, the var keep_one_point_in_roi will
-        decide which points will be returned.
-    keep_one_point_in_roi: bool
-        If True, the first and last points of the streamline that are in the
-        ROIs will be returned. If False, the first and last points outside the
-        ROI will.
+    one_point_in_roi: bool
+        If True, one point in each ROI will be kept.
+    no_point_in_roi: bool
+        If True, no point in the ROIs will be kept.
 
     Returns
     -------
@@ -465,8 +457,8 @@ def _cut_streamline_with_labels(
     in_strl_idx, out_strl_idx = _intersects_two_rois(roi_data_1,
                                                      roi_data_2,
                                                      idx,
-                                                     keep_in_roi=keep_in_roi,
-                                                     keep_one_point_in_roi=keep_one_point)
+                                                     one_point_in_roi=one_point_in_roi,
+                                                     no_point_in_roi=no_point_in_roi)
 
     cut_strl = None
     # If the streamline intersects both ROIs
@@ -519,7 +511,7 @@ def _get_longest_streamline_segment_in_roi(all_strl_indices):
 
 
 def _intersects_two_rois(roi_data_1, roi_data_2, strl_indices,
-                         keep_in_roi=True, keep_one_point_in_roi=True):
+                         one_point_in_roi=True, no_point_in_roi=True):
     """ Find the first and last "voxels" of the streamline that are in the
     ROIs.
 
@@ -531,14 +523,10 @@ def _intersects_two_rois(roi_data_1, roi_data_2, strl_indices,
         Boolean array representing the region #2
     strl_indices: list of tuple (N, 3)
         3D indices of the voxels intersected by the streamline
-    keep_in_roi: bool
-        If True, the first and last points of the streamline that are in the
-        ROIs will be returned. If False, the var keep_one_point_in_roi will
-        decide which points will be returned.
-    keep_one_point_in_roi: bool
-        If True, the first and last points of the streamline that are in the
-        ROIs will be returned. If False, the first and last points outside the
-        ROI will.
+    one_point_in_roi: bool
+        If True, one point in each ROI will be kept.
+    no_point_in_roi: bool
+        If True, no point in the ROIs will be kept.
 
     Returns
     -------
@@ -579,13 +567,13 @@ def _intersects_two_rois(roi_data_1, roi_data_2, strl_indices,
 
     # Get the index of the first and last "voxels" of the streamline that are
     # in the ROIs
-    if keep_in_roi:
+    if not one_point_in_roi and not no_point_in_roi:
         in_strl_idx = in_strl_indices[0]
         out_strl_idx = out_strl_indices[-1]
     else:
-        if keep_one_point_in_roi:
+        if one_point_in_roi:
             add_indice = 0
-        else:
+        elif no_point_in_roi:
             add_indice = 1
 
         if in_strl_indices[-1] is not None:

scripts/scil_tractogram_cut_streamlines.py

@@ -21,6 +21,17 @@
 --label: Label containing 2 blobs. Streamlines will be cut so they go from the
 first label region to the second label region. The two blobs must be disjoint.
 
+    Default: Will cut the streamlines according to the mask. New streamlines
+    may be generated if the mask is disjoint.
+
+    --keep_longest: Will keep the longest segment of the streamline that is
+    within the mask. No new streamlines will be generated.
+
+    --trim_endpoints: Will only remove the endpoints of the streamlines that
+    are outside the mask. The middle part of the streamline may go
+    outside the mask, to compensate for hole in the mask for example. No new
+    streamlines will be generated.
+
 Both scenarios will erase data_per_point and data_per_streamline. Streamlines
 will be extended so they reach the boundary of the mask or the two labels,
 therefore won't be equal to the input streamlines.
@@ -96,12 +107,11 @@ def _build_arg_parser():
 
     g1 = p.add_argument_group('Cutting options', 'Options for cutting '
                               'streamlines with --labels.')
-    g1.add_argument('--keep_in_roi', action='store_false',
-                    help='If set, will var keep_one_point will choose whether '
-                    'we keep one point in each label or the point before '
-                    'entering each label.')
-    g1.add_argument('--keep_one_point_in_roi', action='store_true',
+    g3 = g1.add_mutually_exclusive_group()
+    g3.add_argument('--one_point_in_roi', action='store_true',
                     help='If set, will keep one point in each label.')
+    g3.add_argument('--no_point_in_roi', action='store_true',
+                    help='If set, will not keep any point in the labels.')
 
     add_compression_arg(p)
     add_overwrite_arg(p)
@@ -162,8 +172,8 @@ def main():
 
         new_sft = cut_streamlines_between_labels(
             sft, label_data, args.label_ids, min_len=args.min_length,
-            keep_in_roi=args.keep_in_roi,
-            keep_one_point_in_roi=args.keep_one_point_in_roi,
+            one_point_in_roi=args.one_point_in_roi,
+            no_point_in_roi=args.no_point_in_roi,
             processes=args.nbr_processes)
 
     # Saving

scripts/tests/test_tractogram_cut_streamlines.py

@@ -112,3 +112,27 @@ def test_execution_labels_error_trim(script_runner, monkeypatch):
                             '--resample', '0.2', '--compress', '0.1'
                             '--trim_endpoints')
     assert not ret.success
+
+def test_execution_labels_one_points(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_tractogram = os.path.join(SCILPY_HOME, 'connectivity',
+                                 'bundle_all_1mm.trk')
+    in_labels = os.path.join(SCILPY_HOME, 'connectivity',
+                             'endpoints_atlas.nii.gz')
+    ret = script_runner.run('scil_tractogram_cut_streamlines.py',
+                            in_tractogram, '--labels', in_labels,
+                            'out_tractogram_cut.trk', '-f',
+                            '--no_point_in_roi', '--label_ids', '1', '10',)
+    assert ret.success
+
+def test_execution_labels_one_point(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_tractogram = os.path.join(SCILPY_HOME, 'connectivity',
+                                 'bundle_all_1mm.trk')
+    in_labels = os.path.join(SCILPY_HOME, 'connectivity',
+                             'endpoints_atlas.nii.gz')
+    ret = script_runner.run('scil_tractogram_cut_streamlines.py',
+                            in_tractogram, '--labels', in_labels,
+                            'out_tractogram_cut.trk', '-f',
+                            '--one_point_in_roi', '--label_ids', '1', '10',)
+    assert ret.success