doc and test fix

scilpy/tractanalysis/fibertube_scoring.py

@@ -20,10 +20,12 @@ def fibertube_density(sft, samples_per_voxel_axis, verbose=False):
     Estimates the per-voxel volumetric density of a set of fibertubes. In other
     words, how much space is occupied by fibertubes and how much is emptiness.
 
-    Works by building a binary mask segmenting voxels that contain at least
-    a single fibertube. Then, valid voxels are finely sampled and we count the
-    number of samples that landed within a fibertube. For each voxel, this
-    number is then divided by its total amount of samples.
+    1. Segments voxels that contain at least a single fibertube.
+    2. Valid voxels are finely sampled and we count the number of samples that
+    landed within a fibertube. For each voxel, this number is then divided by
+    its total amount of samples.
+    3. By doing the same steps for samples that landed within 2 or more
+    fibertubes, we can create a density map of the fibertube collisions.
 
     Parameters
     ----------

scripts/scil_fibertube_compute_density.py

@@ -5,10 +5,12 @@
 Estimates the per-voxel volumetric density of a set of fibertubes. In other
 words, how much space is occupied by fibertubes and how much is emptiness.
 
-Works by building a binary mask segmenting voxels that contain at least
-a single fibertube. Then, valid voxels are finely sampled and we count the
-number of samples that landed within a fibertube. For each voxel, this
-number is then divided by its total amount of samples.
+1. Segments voxels that contain at least a single fibertube.
+2. Valid voxels are finely sampled and we count the number of samples that
+landed within a fibertube. For each voxel, this number is then divided by
+its total amount of samples.
+3. By doing the same steps for samples that landed within 2 or more
+fibertubes, we can create a density map of the fibertube collisions.
 
 See also:
     - docs/source/documentation/fibertube_tracking.rst

scripts/tests/test_fibertube_compute_density.py

@@ -42,14 +42,23 @@ def test_help_option(script_runner):
     assert ret.success
 
 
-def test_execution(script_runner, monkeypatch):
+def test_execution_density(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     init_data()
     ret = script_runner.run('scil_fibertube_compute_density.py',
                             'fibertubes.trk',
                             '--out_density_map', 'density_map.nii.gz',
                             '--out_density_measures',
                             'density_measures.json',
+                            '-f')
+    assert ret.success
+
+
+def test_execution_collisions(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    init_data()
+    ret = script_runner.run('scil_fibertube_compute_density.py',
+                            'fibertubes.trk',
                             '--out_collision_map', 'collision_map.nii.gz',
                             '--out_collision_measures',
                             'collision_measures.json',