Add more missing tests

scilpy/tractanalysis/connectivity_segmentation.py

@@ -15,7 +15,7 @@
     compute_streamline_segment
 from scilpy.tractograms.streamline_operations import \
     (remove_loops as perform_remove_loops,
-     remove_shap_turns_qb,
+     remove_sharp_turns_qb,
      remove_streamlines_with_overlapping_points, filter_streamlines_by_length)
 
 
@@ -341,7 +341,7 @@ def construct_hdf5_from_connectivity(
         if remove_curv_dev:
             logging.debug("- Step 4: Removing sharp turns (Qb threshold: {})"
                           .format(curv_qb_distance))
-            no_qb_curv_ids = remove_shap_turns_qb(
+            no_qb_curv_ids = remove_sharp_turns_qb(
                 current_sft.streamlines, qb_threshold=curv_qb_distance)
             qb_curv_ids = np.setdiff1d(np.arange(len(current_sft)),
                                        no_qb_curv_ids)

scilpy/tractograms/streamline_operations.py

@@ -335,7 +335,8 @@ def remove_single_point_streamlines(sft):
 
 def remove_overlapping_points_streamlines(sft, threshold=0.001):
     """
-    Remove overlapping points from streamlines in a StatefulTractogram.
+    Remove overlapping points from streamlines in a StatefulTractogram, i.e.
+    points forming a segment of length < threshold in a given streamline.
 
     Parameters
     ----------
@@ -844,7 +845,7 @@ def remove_loops(streamlines, max_angle, num_processes=1):
     return ids, streamlines_clean
 
 
-def remove_shap_turns_qb(streamlines, qb_threshold=15.0, qb_seed=0):
+def remove_sharp_turns_qb(streamlines, qb_threshold=15.0, qb_seed=0):
     """
     Remove sharp turns from a list of streamlines. Should only be used on
     bundled streamlines, not on whole-brain tractograms.
@@ -918,7 +919,7 @@ def remove_loops_and_sharp_turns(streamlines, max_angle, qb_threshold=None,
                                           num_processes)
 
     if qb_threshold is not None:
-        ids = remove_shap_turns_qb(streamlines_clean, qb_threshold, qb_seed)
+        ids = remove_sharp_turns_qb(streamlines_clean, qb_threshold, qb_seed)
     return ids
 
 

scilpy/tractograms/tests/test_streamline_operations.py

@@ -2,7 +2,6 @@
 import os
 import tempfile
 
-import nibabel as nib
 import numpy as np
 from numpy.testing import assert_array_almost_equal
 import pytest
@@ -12,17 +11,21 @@
 from scilpy import SCILPY_HOME
 from scilpy.io.fetcher import fetch_data, get_testing_files_dict
 from scilpy.tractograms.streamline_operations import (
+    compress_sft,
+    cut_invalid_streamlines,
     filter_streamlines_by_length,
     filter_streamlines_by_total_length_per_dim,
+    get_angles,
+    get_streamlines_as_linspaces,
     resample_streamlines_num_points,
     resample_streamlines_step_size,
     smooth_line_gaussian,
     smooth_line_spline,
-    parallel_transport_streamline, get_angles, get_streamlines_as_linspaces,
-    compress_sft, cut_invalid_streamlines)
+    parallel_transport_streamline,
+    remove_overlapping_points_streamlines,
+    remove_single_point_streamlines)
 from scilpy.tractograms.tractogram_operations import concatenate_sft
 
-
 fetch_data(get_testing_files_dict(), keys=['tractograms.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
@@ -100,6 +103,30 @@ def test_cut_invalid_streamlines():
     assert nb == 1
 
 
+def test_remove_single_point_streamlines():
+    sft = load_tractogram(in_short_sft, in_ref)
+
+    # Adding a one-point streamline
+    sft.streamlines.append([[7, 7, 7]])
+    new_sft = remove_single_point_streamlines(sft)
+    assert len(new_sft) == len(sft) - 1
+
+
+def test_remove_overlapping_points_streamlines():
+    sft = load_tractogram(in_short_sft, in_ref)
+
+    fake_line = np.asarray([[3, 3, 3],
+                            [4, 4, 4],
+                            [5, 5, 5],
+                            [5, 5, 5.00000001]], dtype=float)
+    sft.streamlines.append(fake_line)
+
+    new_sft = remove_overlapping_points_streamlines(sft)
+    assert len(new_sft.streamlines[-1]) == len(sft.streamlines[-1]) - 1
+    assert np.all([len(new_sft.streamlines[i]) == len(sft.streamlines[i]) for
+                   i in range(len(sft) - 1)])
+
+
 def test_filter_streamlines_by_length():
     long_sft = load_tractogram(in_long_sft, in_ref)
     mid_sft = load_tractogram(in_mid_sft, in_ref)
@@ -382,3 +409,19 @@ def test_parallel_transport_streamline():
                               decimal=4)
     assert [len(s) for s in pt_streamlines] == [130] * 20
     assert len(pt_streamlines) == 20
+
+
+def test_remove_loops():
+    # toDO
+    # Coverage will not work: uses multi-processing
+    pass
+
+
+def test_remove_sharp_turns_qb():
+    # toDO
+    pass
+
+
+def test_remove_loops_and_sharp_turns():
+    # ok. Just a combination of the two previous functions.
+    pass