Unit test segment streamlines

src/scilpy/segment/streamlines.py

@@ -17,16 +17,23 @@
 
 def streamlines_in_mask(sft, target_mask, all_in=False):
     """
+    Finds the streamlines that are either touching a mask (if all_in=False) or
+    entirely contained in the mask (if all_in=True).
+
     Parameters
     ----------
     sft : StatefulTractogram
         StatefulTractogram containing the streamlines to segment.
     target_mask : numpy.ndarray
         Binary mask in which the streamlines should pass.
+    all_in: bool
+        If true, finds streamlines satisfying the 'all' criteria. Else, finds
+        streamlines satisfying the 'any' criteria.
+
     Returns
     -------
     ids : list
-        Ids of the streamlines passing through the mask.
+        Ids of the streamlines passing the test.
     """
     sft.to_vox()
     sft.to_corner()
@@ -52,9 +59,11 @@ def streamlines_in_mask(sft, target_mask, all_in=False):
         return np.where(streamlines_case == [0, 1][True])[0].tolist()
 
 
-def filter_grid_roi_both(sft, mask_1, mask_2):
-    """ Filters streamlines with one end in a mask and the other in
-    another mask.
+def filter_grid_roi_both_ends(sft, mask_1, mask_2):
+    """
+    Filters streamlines with one end in a mask and the other in another mask.
+    See also filter_grid_roi, but here we may give two different masks for the
+    endpoints.
 
     Parameters
     ----------
@@ -64,6 +73,7 @@ def filter_grid_roi_both(sft, mask_1, mask_2):
         Binary mask in which the streamlines should start or end.
     mask_2: numpy.ndarray
         Binary mask in which the streamlines should start or end.
+
     Returns
     -------
     new_sft: StatefulTractogram
@@ -108,6 +118,9 @@ def filter_grid_roi_both(sft, mask_1, mask_2):
 def filter_grid_roi(sft, mask, filter_type, is_exclude, filter_distance=0,
                     return_sft=False, return_rejected_sft=False):
     """
+    Filters streamlines based on a given criteria (any, all, either_end,
+    both_ends).
+
     Parameters
     ----------
     sft : StatefulTractogram
@@ -199,8 +212,8 @@ def filter_grid_roi(sft, mask, filter_type, is_exclude, filter_distance=0,
     return line_based_indices
 
 
-def pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
-                                        is_in_vox):
+def _pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
+                                         is_in_vox):
     """
     Parameters
     ----------
@@ -254,14 +267,17 @@ def pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
 def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
                      filter_type, is_exclude, is_in_vox=False):
     """
+    Finds streamlines that respect some criteria in a ROI, where the ROI is
+    a bounding box of ellipsoid type.
+
     Parameters
     ----------
     sft : StatefulTractogram
         Tractogram containing the streamlines to segment.
     ellipsoid_radius : numpy.ndarray (3)
         Size in mm, x/y/z of the ellipsoid.
     ellipsoid_center: numpy.ndarray (3)
-        Center x/y/z of the ellipsoid.
+        Center x/y/z of the ellipsoid, in RASMM space, center origin.
     filter_type: str
         One of the 4 following choices, 'any', 'all', 'either_end', 'both_ends'.
     is_exclude: bool
@@ -280,12 +296,11 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
         return np.array([]), sft
 
     pre_filtered_indices, pre_filtered_sft = \
-        pre_filtering_for_geometrical_shape(sft, ellipsoid_radius,
-                                            ellipsoid_center, filter_type,
-                                            is_in_vox)
+        _pre_filtering_for_geometrical_shape(sft, ellipsoid_radius,
+                                             ellipsoid_center, filter_type,
+                                             is_in_vox)
     pre_filtered_sft.to_rasmm()
     pre_filtered_sft.to_center()
-    pre_filtered_streamlines = pre_filtered_sft.streamlines
     transfo, _, res, _ = sft.space_attributes
 
     if is_in_vox:
@@ -303,7 +318,7 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
     ellipsoid_radius = np.asarray(ellipsoid_radius, dtype=float)
     ellipsoid_center = np.asarray(ellipsoid_center, dtype=float)
 
-    for i, line in enumerate(pre_filtered_streamlines):
+    for i, line in enumerate(pre_filtered_sft.streamlines):
         if filter_type in ['any', 'all']:
             # Resample to 1/10 of the voxel size
             nb_points = max(int(length(line) / np.average(res) * 10), 2)
@@ -360,23 +375,24 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
     return line_based_indices, new_sft
 
 
-def filter_cuboid(sft, cuboid_radius, cuboid_center,
-                  filter_type, is_exclude):
+def filter_cuboid(sft, cuboid_radius, cuboid_center, filter_type, is_exclude):
     """
+    Finds streamlines that respect some criteria in a ROI, where the ROI is
+    a bounding box of cuboid type.
+
     Parameters
     ----------
     sft : StatefulTractogram
         StatefulTractogram containing the streamlines to segment.
     cuboid_radius : numpy.ndarray (3)
         Size in mm, x/y/z of the cuboid.
     cuboid_center: numpy.ndarray (3)
-        Center x/y/z of the cuboid.
+        Center x/y/z of the cuboid, in RASMM space, center origin.
     filter_type: str
         One of the 4 following choices: 'any', 'all', 'either_end', 'both_ends'.
     is_exclude: bool
         Value to indicate if the ROI is an AND (false) or a NOT (true).
-    is_in_vox: bool
-        Value to indicate if the ROI is in voxel space.
+
     Returns
     -------
     ids : list
@@ -388,9 +404,9 @@ def filter_cuboid(sft, cuboid_radius, cuboid_center,
         return np.array([]), sft
 
     pre_filtered_indices, pre_filtered_sft = \
-        pre_filtering_for_geometrical_shape(sft, cuboid_radius,
-                                            cuboid_center, filter_type,
-                                            is_in_vox=False)
+        _pre_filtering_for_geometrical_shape(sft, cuboid_radius,
+                                             cuboid_center, filter_type,
+                                             is_in_vox=False)
     pre_filtered_sft.to_rasmm()
     pre_filtered_sft.to_center()
     pre_filtered_streamlines = pre_filtered_sft.streamlines

src/scilpy/segment/tests/test_bundleseg.py

@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+
+def test_recognize():
+    # todo:
+    # bundleseg = BundleSeg(...)
+    # bundleseg.recognize.
+    pass

src/scilpy/segment/tests/test_streamlines.py

@@ -0,0 +1,138 @@
+# -*- coding: utf-8 -*-
+from dipy.io.stateful_tractogram import StatefulTractogram, Space, Origin
+import nibabel as nib
+import numpy as np
+from scilpy.segment.streamlines import streamlines_in_mask, \
+    filter_grid_roi_both_ends, filter_grid_roi, filter_ellipsoid, filter_cuboid
+
+# Preparing SFT for all tests here.
+# 3 ways to crete ROI, all ~voxels 1 and 2 in x, y, z
+# - mask
+# - bdo_ellipsoid
+# - bdo_cuboid
+
+# Binary mask
+mask = np.zeros((10, 10, 10))
+mask[1:3, 1:3, 1:3] = 1
+
+# bdo.
+# Note. Everything else here is in vox, corner, except bdo_center
+bdo_center_rasmm_centerorigin = np.asarray([1.5, 1.5, 1.5])
+bdo_radius_mm = 1.5
+
+# Preparing streamlines fitting criteria.
+# line 0 'all': entirely in mask.
+line0 = [[1.5, 1.5, 1.5],
+         [1.6, 1.6, 1.6],
+         [1.7, 1.7, 1.7],
+         [2.5, 2.5, 2.5]]
+
+# line 1 'both_ends': both ends in mask but not in the middle.
+line1 = [[1.5, 1.5, 1.5],
+         [9, 9, 9],
+         [1.7, 1.7, 1.7],
+         [2.5, 2.5, 2.5]]
+
+# line 2 'any': Only one end in mask
+line2 = [[1.5, 1.5, 1.5],
+         [1.6, 1.6, 1.6],
+         [1.7, 1.7, 1.7],
+         [9, 9, 9]]
+
+# line 3 'any': Both ends out of mask but touches in the middle
+line3 = [[9, 9, 9],
+         [1.6, 1.6, 1.6],
+         [1.7, 1.7, 1.7],
+         [9, 9, 9]]
+
+# line 4 (exclude): never in mask
+line4 = [[9, 9, 9.0],
+         [8, 8, 8.0],
+         [7, 7, 7.0],
+         [9, 9, 9.0]]
+
+# line 5 'any': passes through, but no real point inside.
+line5 = [[0.1, 0.1, 0.1],
+         [8, 8, 8.0],
+         [7, 7, 7.0],
+         [9, 9, 9.0]]
+
+fake_reference = nib.Nifti1Image(
+    np.zeros((10, 10, 10, 1)), affine=np.eye(4))
+sft = StatefulTractogram([line0, line1, line2, line3, line4, line5],
+                         fake_reference, space=Space.VOXMM,
+                         origin=Origin('corner'))
+
+
+def test_streamlines_in_mask():
+    # Test option 'all'
+    ids = streamlines_in_mask(sft, mask, all_in=True)
+    assert np.array_equal(ids, [0])
+
+    # Test option 'any'
+    ids = streamlines_in_mask(sft, mask, all_in=False)
+    assert np.array_equal(ids, [0, 1, 2, 3, 5])
+
+
+def test_filter_grid_roi_both_ends():
+    # Pretending to have two masks
+    # Test option 'both ends'
+    new_sft, ids = filter_grid_roi_both_ends(sft, mask_1=mask, mask_2=mask)
+    assert np.array_equal(ids, [0, 1])
+    assert len(new_sft) == 2
+
+
+def test_filter_grid_roi():
+    # Note. Distance not tested yet. (toDo)
+    roi_options = (mask,)
+    _test_all_criteria(filter_grid_roi, roi_options, fct_returns_sft=False)
+
+
+def test_filter_ellipsoid():
+    roi_options = (bdo_radius_mm, bdo_center_rasmm_centerorigin)
+    _test_all_criteria(filter_ellipsoid, roi_options, fct_returns_sft=True)
+
+
+def test_filter_cuboid():
+    roi_options = (bdo_radius_mm, bdo_center_rasmm_centerorigin)
+    _test_all_criteria(filter_cuboid, roi_options, fct_returns_sft=True)
+
+
+def _test_all_criteria(fct, roi_args, fct_returns_sft):
+    """
+    The three filtering methods (filter_grid_roi, filter_ellipsoid,
+    filter_cuboid) test the same criteria, but with a different way to treat
+    the ROI. Here are the tests, the roi_args should be different based on fct.
+    """
+    # Parameter is "is_exclude" for all three methods. So:
+    include=False
+    exclude=True
+
+    def get_ids(output):
+        if fct_returns_sft:
+            return output[0]
+        return output
+
+    # Test 'any'
+    ids = get_ids(fct(sft, *roi_args, 'any', include))
+    assert np.array_equal(ids, [0, 1, 2, 3, 5])
+    ids =  get_ids(fct(sft, *roi_args, 'any', exclude))
+    assert np.array_equal(ids, [4])
+
+    # Test 'all'
+    ids =  get_ids(fct(sft, *roi_args, 'all', include))
+    assert np.array_equal(ids, [0])
+    ids =  get_ids(fct(sft, *roi_args, 'all', exclude))
+    assert np.array_equal(ids, [1, 2, 3, 4, 5])
+
+    # Test 'either_end'
+    ids =  get_ids(fct(sft, *roi_args, 'either_end', include))
+    assert np.array_equal(ids, [0, 1, 2])
+    ids =  get_ids(fct(sft, *roi_args, 'either_end', exclude))
+    assert np.array_equal(ids, [3, 4, 5])
+
+    # Test 'both_ends'
+    ids =  get_ids(fct(sft, *roi_args, 'both_ends', include))
+    assert np.array_equal(ids, [0, 1])
+    ids =  get_ids(fct(sft, *roi_args, 'both_ends', exclude))
+    assert np.array_equal(ids, [2, 3, 4, 5])

src/scilpy/segment/tests/test_tractogram_from_roi.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import os
 import tempfile
 import nibabel as nib

src/scilpy/segment/tractogram_from_roi.py

@@ -15,7 +15,7 @@
     split_mask_blobs_kmeans
 from scilpy.io.image import get_data_as_mask
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.segment.streamlines import filter_grid_roi, filter_grid_roi_both
+from scilpy.segment.streamlines import filter_grid_roi, filter_grid_roi_both_ends
 from scilpy.tractograms.streamline_operations import \
     remove_loops_and_sharp_turns
 from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
@@ -363,7 +363,7 @@ def _extract_vb_one_bundle(
             mask_1 = binary_dilation(mask_1, iterations=dilate_endpoints)
             mask_2 = binary_dilation(mask_2, iterations=dilate_endpoints)
 
-        _, vs_ids = filter_grid_roi_both(sft, mask_1, mask_2)
+        _, vs_ids = filter_grid_roi_both_ends(sft, mask_1, mask_2)
     else:
         vs_ids = np.array([])
 
@@ -514,7 +514,7 @@ def _extract_ib_one_bundle(sft, mask_1_filename, mask_2_filename,
             mask_1 = binary_dilation(mask_1, iterations=dilate_endpoints)
             mask_2 = binary_dilation(mask_2, iterations=dilate_endpoints)
 
-        _, fc_ids = filter_grid_roi_both(sft, mask_1, mask_2)
+        _, fc_ids = filter_grid_roi_both_ends(sft, mask_1, mask_2)
     else:
         fc_ids = []
 

src/scilpy/tractograms/tests/test_intersection_finder.py

@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+
+
+def test_find_intersection():
+    # Todo:
+    # finder = IntersectionFinder(...)
+    # finder.find_intersection()
+    pass