Merge pull request #141 from BlueBrain/morph-utils-tests

Add morphology-utils tests

bluepyemodel/emodel_pipeline/plotting.py

@@ -44,7 +44,7 @@
 from bluepyemodel.evaluation.utils import define_bAP_protocol
 from bluepyemodel.evaluation.utils import define_EPSP_feature
 from bluepyemodel.evaluation.utils import define_EPSP_protocol
-from bluepyemodel.model.morphology_utils import get_basal_and_apical_lengths
+from bluepyemodel.model.morphology_utils import get_basal_and_apical_max_radial_distances
 from bluepyemodel.tools.utils import make_dir
 from bluepyemodel.tools.utils import parse_checkpoint_path
 from bluepyemodel.tools.utils import read_checkpoint
@@ -1103,7 +1103,7 @@ def run_and_plot_bAP(
 
     # get basal and apical lengths
     morph_path = cell_evaluator.cell_model.morphology.morphology_path
-    max_basal_length, max_apical_length = get_basal_and_apical_lengths(morph_path)
+    max_basal_length, max_apical_length = get_basal_and_apical_max_radial_distances(morph_path)
     max_basal_length = int(max_basal_length)
     max_apical_length = int(max_apical_length)
 
@@ -1178,7 +1178,7 @@ def run_and_plot_EPSP(
 
     # get basal and apical lengths
     morph_path = cell_evaluator.cell_model.morphology.morphology_path
-    max_basal_length, max_apical_length = get_basal_and_apical_lengths(morph_path)
+    max_basal_length, max_apical_length = get_basal_and_apical_max_radial_distances(morph_path)
     max_basal_length = int(max_basal_length)
     max_apical_length = int(max_apical_length)
 

bluepyemodel/model/morphology_utils.py

@@ -35,7 +35,7 @@ def get_apical_point_soma_distance(morph_path):
     return neurom.morphmath.point_dist(apical_point, morphio_morph.soma.center)
 
 
-def get_apical_length(morph_path):
+def get_apical_max_radial_distance(morph_path):
     """Returns the max radial distance of the apical dendrites."""
     import neurom
 
@@ -45,8 +45,8 @@ def get_apical_length(morph_path):
     )
 
 
-def get_basal_and_apical_lengths(morph_path):
-    """Returns the max radial distance of the apical and basal dendrites."""
+def get_basal_and_apical_max_radial_distances(morph_path):
+    """Returns the max radial distances of the apical and basal dendrites."""
     import neurom
 
     neurom_morph = neurom.load_morphology(morph_path)
@@ -69,12 +69,12 @@ def get_hotspot_location(morph_path, hotspot_percent=20.0):
 
     Args:
         morph_path (str): path to the morphology
-        hotspot_percent (float): percentage of the radial apical length that is in the hot spot.
-            Here, we assume that the hotspot size is dependent on the apical length.
+        hotspot_percent (float): percentage of the radial apical distance that is in the hot spot.
+            Here, we assume that the hotspot size is dependent on the apical radial distance.
             20% is in accordance with experiments from Larkum and Zhu, 2002
     """
     ap_soma_dist = get_apical_point_soma_distance(morph_path)
-    apical_length = get_apical_length(morph_path)
+    apical_length = get_apical_max_radial_distance(morph_path)
     hotspot_halfsize = apical_length * hotspot_percent / 2.0 / 100.0
 
     return max((0.0, ap_soma_dist - hotspot_halfsize)), ap_soma_dist + hotspot_halfsize

setup.py

@@ -61,7 +61,7 @@
         "gitpython",
         "bluepyopt>=1.14.10",
         "bluepyefe>=2.2.0",
-        "neurom>=3.0,<4.0",
+        "neurom>=3.0",
         "efel>=5.5.5",
         "configparser",
         "neuron>=8.0",

tests/unit_tests/test_morphology_utils.py

@@ -0,0 +1,75 @@
+"""Tests for EModelMetadata methods."""
+
+"""
+Copyright 2024, EPFL/Blue Brain Project
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+import numpy
+import pytest
+
+from bluepyemodel.model.morphology_utils import get_apical_max_radial_distance
+from bluepyemodel.model.morphology_utils import get_apical_point_soma_distance
+from bluepyemodel.model.morphology_utils import get_basal_and_apical_max_radial_distances
+from bluepyemodel.model.morphology_utils import get_hotspot_location
+
+from tests.utils import DATA
+
+
+@pytest.fixture
+def morph_path():
+    return DATA / "morphology" / "C060114A5.asc"
+
+
+def test_get_apical_point_soma_distance(morph_path):
+    """Test get_apical_point_soma_distance function."""
+    soma_dist = get_apical_point_soma_distance(morph_path)
+    numpy.testing.assert_allclose(soma_dist, 624.8454)
+
+
+def test_get_apical_max_radial_distance(morph_path):
+    """Test get_apical_length function."""
+    apical_max_radial_distance =  get_apical_max_radial_distance(morph_path)
+    # increase tolerance because neurom v4 has changed behavior of 'max_radial_distance'
+    numpy.testing.assert_allclose(apical_max_radial_distance, 1044.1445, rtol=0.02)
+
+
+def test_get_basal_and_apical_max_radial_distances(morph_path):
+    """Test get_basal_and_apical_max_radial_distances function."""
+    basal_radial_dist, apical_radial_dist = get_basal_and_apical_max_radial_distances(morph_path)
+    # increase tolerance because neurom v4 has changed behavior of 'max_radial_distance'
+    numpy.testing.assert_allclose(apical_radial_dist, 1044.1445, rtol=0.02)
+    numpy.testing.assert_allclose(basal_radial_dist, 232.56221, rtol=0.1)
+
+
+def test_get_hotspot_location(morph_path):
+    """Test get_hotspot_location function."""
+    hotspot_start, hotspot_end = get_hotspot_location(morph_path)
+    # increase tolerance because neurom v4 has changed behavior of 'max_radial_distance'
+    numpy.testing.assert_allclose(hotspot_start, 520.430945, rtol=0.02)
+    numpy.testing.assert_allclose(hotspot_end, 729.259851, rtol=0.02)
+
+
+def test_morphology_utils(morph_path):
+    """Test that output of morphology_utils functions are consistent with one another."""
+    apical_max_dist_1 =  get_apical_max_radial_distance(morph_path)
+    basal_max_dist, apical_max_dist_2 = get_basal_and_apical_max_radial_distances(morph_path)
+    soma_dist = get_apical_point_soma_distance(morph_path)
+    hotspot_start, hotspot_end = get_hotspot_location(morph_path)
+
+    assert apical_max_dist_1 == apical_max_dist_2
+    assert basal_max_dist < apical_max_dist_2
+    assert soma_dist < apical_max_dist_1
+    assert hotspot_start >= 0
+    assert hotspot_start < soma_dist < hotspot_end