Add new features total_width, total_height and total_depth (#974)

.gitignore

@@ -3,6 +3,8 @@
 *.pyc
 *~
 .coverage
+.coverage.*
+coverage.xml
 *venv*
 *egg-info*
 .eggs
@@ -16,3 +18,5 @@ dist/*
 .ipynb_checkpoints
 .tox
 pip-wheel-metadata
+morphology-2D.html
+morphology-3D.html

CHANGELOG.rst

@@ -1,6 +1,10 @@
 Changelog
 =========
 
+Version 3.1.0
+-------------
+- Add morphology features total_width, total_height and total_depth
+
 Version 3.0.2
 -------------
 - Fix 'raw' mode in ``neurom stats``.

neurom/features/morphology.py

@@ -55,6 +55,7 @@
 from neurom.core.types import NeuriteType
 from neurom.features import feature, NameSpace, neurite as nf
 
+
 feature = partial(feature, namespace=NameSpace.NEURON)
 
 
@@ -294,3 +295,39 @@ def sholl_frequency(morph, neurite_type=NeuriteType.all, step_size=10, bins=None
         bins = np.arange(min_soma_edge, min_soma_edge + max_radii, step_size)
 
     return sholl_crossings(morph, morph.soma.center, bins, neurite_type)
+
+
+def _extent_along_axis(morph, axis, neurite_type):
+    """Returns the total extent of the morpholog neurites.
+
+    The morphology is filtered by neurite type and the extent is calculated
+    along the coordinate axis direction (e.g. COLS.X).
+    """
+    it_points = (
+            p
+            for n in iter_neurites(morph, filt=is_type(neurite_type))
+            for p in n.points[:, axis]
+    )
+    try:
+        return abs(np.ptp(np.fromiter(it_points, dtype=np.float32)))
+    except ValueError:
+        # a ValueError is thrown when there are no points passed to ptp
+        return 0.0
+
+
+@feature(shape=())
+def total_width(morph, neurite_type=NeuriteType.all):
+    """Extent of morphology along axis x."""
+    return _extent_along_axis(morph, axis=COLS.X, neurite_type=neurite_type)
+
+
+@feature(shape=())
+def total_height(morph, neurite_type=NeuriteType.all):
+    """Extent of morphology along axis y."""
+    return _extent_along_axis(morph, axis=COLS.Y, neurite_type=neurite_type)
+
+
+@feature(shape=())
+def total_depth(morph, neurite_type=NeuriteType.all):
+    """Extent of morphology along axis z."""
+    return _extent_along_axis(morph, axis=COLS.Z, neurite_type=neurite_type)

tests/features/test_get_features.py

@@ -756,3 +756,56 @@ def test_principal_direction_extents():
              346.83281498399697]
     p = features.get('principal_direction_extents', m)
     assert_allclose(p, p_ref, rtol=1e-6)
+
+
+def test_total_width():
+
+    assert_allclose(
+        features.get('total_width', NRN),
+        105.0758
+    )
+
+    assert_allclose(
+        features.get('total_width', NRN, neurite_type=nm.AXON),
+        33.25306
+    )
+
+    assert_allclose(
+        features.get('total_width', NRN, neurite_type=nm.BASAL_DENDRITE),
+        104.57807
+    )
+
+
+def test_total_height():
+
+    assert_allclose(
+        features.get('total_height', NRN),
+        106.11643
+    )
+
+    assert_allclose(
+        features.get('total_height', NRN, neurite_type=nm.AXON),
+        57.60017
+    )
+
+    assert_allclose(
+        features.get('total_height', NRN, neurite_type=nm.BASAL_DENDRITE),
+        48.516262
+    )
+
+def test_total_depth():
+
+    assert_allclose(
+        features.get('total_depth', NRN),
+        54.204086
+    )
+
+    assert_allclose(
+        features.get('total_depth', NRN, neurite_type=nm.AXON),
+        49.70138
+    )
+
+    assert_allclose(
+        features.get('total_depth', NRN, neurite_type=nm.BASAL_DENDRITE),
+        51.64143
+    )

tests/features/test_morphology.py

@@ -278,3 +278,55 @@ def test_sholl_analysis_custom():
                        """)
     assert (list(morphology.sholl_crossings(morph_C, center, radii=radii)) ==
             [2, 2, 2, 2, 2, 2, 10, 10])
+
+
+def test_extent_along_axis():
+    morph = load_swc("""
+        1 1   0  0   0 1. -1
+        2 3   0  -60 0 1.  1
+        3 3  80  0   2 1.  2
+        4 4   0  60  3 1.  1
+        5 4 -80  0.  0 1.  4
+    """)
+    assert_almost_equal(morphology._extent_along_axis(morph, 0, NeuriteType.all), 160.0)
+    assert_almost_equal(morphology._extent_along_axis(morph, 1, NeuriteType.all), 120.0)
+    assert_almost_equal(morphology._extent_along_axis(morph, 2, NeuriteType.all), 3.0)
+
+
+def test_total_width():
+    morph = load_swc("""
+        1 1   0  0   0 1. -1
+        2 3   0  -60 0 1.  1
+        3 3  80  0   2 1.  2
+        4 4   0  60  3 1.  1
+        5 4 -80  0.  0 1.  4
+    """)
+    assert_almost_equal(morphology.total_width(morph, neurite_type=NeuriteType.axon), 0.0)
+    assert_almost_equal(morphology.total_width(morph, neurite_type=NeuriteType.basal_dendrite), 80.0)
+    assert_almost_equal(morphology.total_width(morph, neurite_type=NeuriteType.apical_dendrite), 80.0)
+
+
+def test_total_height():
+    morph = load_swc("""
+        1 1   0  0   0 1. -1
+        2 3   0  -60 0 1.  1
+        3 3  80  0   2 1.  2
+        4 4   0  60  3 1.  1
+        5 4 -80  0.  0 1.  4
+    """)
+    assert_almost_equal(morphology.total_height(morph, neurite_type=NeuriteType.axon), 0.0)
+    assert_almost_equal(morphology.total_height(morph, neurite_type=NeuriteType.basal_dendrite), 60.0)
+    assert_almost_equal(morphology.total_height(morph, neurite_type=NeuriteType.apical_dendrite), 60.0)
+
+
+def test_total_depth():
+    morph = load_swc("""
+        1 1   0  0   0 1. -1
+        2 3   0  -60 0 1.  1
+        3 3  80  0   2 1.  2
+        4 4   0  60  3 1.  1
+        5 4 -80  0.  0 1.  4
+    """)
+    assert_almost_equal(morphology.total_depth(morph, neurite_type=NeuriteType.axon), 0.0)
+    assert_almost_equal(morphology.total_depth(morph, neurite_type=NeuriteType.basal_dendrite), 2.0)
+    assert_almost_equal(morphology.total_depth(morph, neurite_type=NeuriteType.apical_dendrite), 3.0)