Use morphio for the morphologies (#134)

* removing the MORPH_CACHE_SIZE
* removing neurom as the main reader for morphologies
* adding morphio as the main reader for morphologies
* remove the self._load

CHANGELOG.rst

@@ -1,12 +1,14 @@
 Changelog
 =========
 
-Version v0.11.1
+Version v0.12.0
 ---------------
 
 Improvements
 ~~~~~~~~~~~~~~
-- Pinned major versions of neurom to >=2.0.0.
+- removing the MORPH_CACHE_SIZE
+- removing neurom as the main reader for morphologies
+- adding morphio as the main reader for the morphologies
 
 
 Version v0.11.0

bluepysnap/morph.py

@@ -20,9 +20,10 @@
 from pathlib import Path
 
 import numpy as np
-import neurom as nm
+from morphio.mut import Morphology
+import morph_tool.transform as transformations
+
 
-from bluepysnap.settings import MORPH_CACHE_SIZE
 from bluepysnap.sonata_constants import Node
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.circuit_ids import CircuitNodeId
@@ -47,10 +48,6 @@ def __init__(self, morph_dir, population):
         # all nodes from a population must have the same model type
         if not self._is_biophysical(0):
             raise BluepySnapError("Node population does not contain biophysical nodes.")
-        self._load = nm.load_neuron
-        if MORPH_CACHE_SIZE is not None:
-            from functools import lru_cache
-            self._load = lru_cache(maxsize=MORPH_CACHE_SIZE)(self._load)
 
     def _is_biophysical(self, node_id):
         return self._population.get(node_id, Node.MODEL_TYPE) == "biophysical"
@@ -75,9 +72,10 @@ def get(self, node_id, transform=False):
                 according to `node_id` position in the circuit.
         """
         filepath = self.get_filepath(node_id)
-        result = self._load(filepath)
+        result = Morphology(filepath)
         if transform:
-            A_t = self._population.orientations(node_id).transpose()
-            B = self._population.positions(node_id).values
-            result = result.transform(lambda p: np.dot(p, A_t) + B)
-        return result
+            T = np.eye(4)
+            T[:3, :3] = self._population.orientations(node_id)  # rotations
+            T[:3, 3] = self._population.positions(node_id).values  # translations
+            transformations.transform(result, T)
+        return result.as_immutable()

bluepysnap/settings.py

@@ -19,9 +19,6 @@
 
 import os
 
-# NeuroM morphology loader cache size
-MORPH_CACHE_SIZE = None
-
 # All possible checks enabled / deprecated methods disallowed
 STRICT_MODE = False
 
@@ -37,9 +34,6 @@ def str2bool(value):
 def load_env():
     """Load settings from environment variables."""
     # pylint: disable=global-statement
-    if 'BLUESNAP_MORPH_CACHE_SIZE' in os.environ:
-        global MORPH_CACHE_SIZE
-        MORPH_CACHE_SIZE = int(os.environ['BLUESNAP_MORPH_CACHE_SIZE'])
     if 'BLUESNAP_STRICT_MODE' in os.environ:
         global STRICT_MODE
         STRICT_MODE = str2bool(os.environ['BLUESNAP_STRICT_MODE'])

setup.py

@@ -44,7 +44,8 @@ def __init__(self, *args, **kwargs):
         'cached_property>=1.0',
         'h5py>=3.0.1,<4.0.0',
         'libsonata>=0.1.6,<1.0.0',
-        'neurom>=2.0.0,<3.0.0',
+        'morphio>=3.0.0,<4.0.0',
+        'morph-tool>=2.4.3,<3.0.0',
         'numpy>=1.8,<2.0.0',
         'pandas>=1.0.0,<2.0.0',
         'click>=7.0,<8.0.0',

tests/test_morph.py

@@ -3,7 +3,6 @@
 import numpy.testing as npt
 import pandas as pd
 
-from mock import Mock, patch
 import pandas.testing as pdt
 import pytest
 
@@ -76,13 +75,14 @@ def test_get_filepath(self):
             self.test_obj.get_filepath([0, 1])
 
     def test_get_morphology(self):
-        actual = self.test_obj.get(0).points
-        assert len(actual) == 13
+        actual = self.test_obj.get(0)
+        assert len(actual.points) == 13
         expected = [
-            [0., 5., 0., 1.],
-            [2., 9., 0., 1.],
+            [0., 5., 0.],
+            [2., 9., 0.],
         ]
-        npt.assert_almost_equal(expected, actual[:2])
+        npt.assert_almost_equal(expected, actual.points[:2])
+        npt.assert_almost_equal([2., 2.], actual.diameters[:2])
 
         with pytest.raises(BluepySnapError):
             self.test_obj.get([0, 1])
@@ -103,19 +103,20 @@ def test_get_morphology_simple_rotation(self):
             decimal=6
         )
 
-        actual = self.test_obj.get(node_id, transform=True).points
-        assert len(actual) == 13
+        actual = self.test_obj.get(node_id, transform=True)
+        assert len(actual.points) == 13
         # swc file
         # index       type         X            Y            Z       radius       parent
         #   22           2     0.000000     5.000000     0.000000     1.000000           1
         #   23           2     2.000000     9.000000     0.000000     1.000000          22
         # rotation around the x axis 90 degrees counter clockwise (swap Y and Z)
         # x = X + 101, y = Z + 102, z = Y + 103, radius does not change
         expected = [
-            [101., 102., 108.,   1.],
-            [103., 102., 112.,   1.]
+            [101., 102., 108.],
+            [103., 102., 112.]
         ]
-        npt.assert_almost_equal(actual[:2], expected)
+        npt.assert_almost_equal(actual.points[:2], expected)
+        npt.assert_almost_equal(actual.diameters[:2], [2., 2.])
 
     def test_get_morphology_standard_rotation(self):
         nodes = create_node_population(
@@ -142,37 +143,7 @@ def test_get_morphology_standard_rotation(self):
 
         assert len(actual) == 13
         expected = [
-            [101., 107., 103., 1.],
-            [102.47644, 111., 101.65088, 1.]
+            [101., 107., 103.],
+            [102.47644, 111., 101.65088]
         ]
         npt.assert_almost_equal(actual[:2], expected, decimal=6)
-
-
-@patch(test_module.__name__ + '.MORPH_CACHE_SIZE', 1)
-@patch('neurom.load_neuron')
-def test_MorphHelper_cache_1(nm_load):
-    nodes = Mock()
-    nodes.get.side_effect = ['morph-A', 'morph-A', 'morph-B', 'morph-A']
-    with patch.object(test_module.MorphHelper, '_is_biophysical', return_value=True):
-        test_obj = test_module.MorphHelper('morph-dir', nodes)
-        nm_load.side_effect = Mock
-        morph0 = test_obj.get(0)
-        # should get cached object for 'morph-A'
-        assert test_obj.get(1) is morph0
-        # should get new object ('morph-B')
-        assert test_obj.get(2) is not morph0
-        # 'morph-A' was evicted from cache
-        assert test_obj.get(3) is not morph0
-
-
-@patch(test_module.__name__ + '.MORPH_CACHE_SIZE', None)
-@patch('neurom.load_neuron')
-def test_MorphHelper_cache_2(nm_load):
-    nodes = Mock()
-    nodes.get.side_effect = ['morph-A', 'morph-A']
-    with patch.object(test_module.MorphHelper, '_is_biophysical', return_value=True):
-        test_obj = test_module.MorphHelper('morph-dir', nodes)
-        nm_load.side_effect = Mock
-        morph1 = test_obj.get(0)
-        # same morphology, but no caching
-        assert test_obj.get(1) is not morph1

tests/test_settings.py

@@ -15,12 +15,6 @@ def test_str2bool():
     assert not test_module.str2bool(None)
 
 
-def test_MORPH_CACHE_SIZE():
-    with patch.dict(os.environ, {'BLUESNAP_MORPH_CACHE_SIZE': '42'}):
-        test_module.load_env()
-    assert test_module.MORPH_CACHE_SIZE == 42
-
-
 def test_STRICT_MODE():
     with patch.dict(os.environ, {'BLUESNAP_STRICT_MODE': '1'}):
         test_module.load_env()