Introduce NeuronModelsHelper, an analog of MorphHelper (#123)

It is used to access neuron models

bluepysnap/morph.py

@@ -17,7 +17,7 @@
 
 """Morphology access."""
 
-import os
+from pathlib import Path
 
 import numpy as np
 import neurom as nm
@@ -61,10 +61,10 @@ def get_filepath(self, node_id):
         Args:
             node_id (int/CircuitNodeId): could be a int or CircuitNodeId.
         """
+        if not isinstance(node_id, (int, CircuitNodeId)):
+            raise BluepySnapError("node_id must be a int or a CircuitNodeId")
         name = self._population.get(node_id, Node.MORPHOLOGY)
-        if isinstance(node_id, (int, CircuitNodeId)):
-            return os.path.join(self._morph_dir, "%s.swc" % name)
-        raise BluepySnapError("node_id must be a int or a CircuitNodeId")
+        return Path(self._morph_dir, f"{name}.swc")
 
     def get(self, node_id, transform=False):
         """Return NeuroM morphology object corresponding to `node_id`.

bluepysnap/neuron_models.py

@@ -0,0 +1,76 @@
+# Copyright (c) 2019, EPFL/Blue Brain Project
+
+# This file is part of BlueBrain SNAP library <https://github.com/BlueBrain/snap>
+
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License version 3.0 as published
+# by the Free Software Foundation.
+
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+"""Neuron models access."""
+
+from pathlib import Path
+
+from bluepysnap.circuit_ids import CircuitNodeId
+from bluepysnap.exceptions import BluepySnapError
+from bluepysnap.sonata_constants import Node
+
+
+class NeuronModelsHelper:
+    """Collection of neuron models related methods."""
+
+    def __init__(self, config_components, population):
+        """Constructor.
+
+        Args:
+            config_components (dict): 'components' part of circuit's config
+            population (NodePopulation): NodePopulation object used to query the nodes.
+
+        Returns:
+            NeuronModelsHelper: A NeuronModelsHelper object.
+        """
+        # all nodes from a population must have the same model type
+        if population.get(0, Node.MODEL_TYPE) not in {"biophysical", "point_neuron"}:
+            raise BluepySnapError(
+                "Neuron models can be only in biophysical or point node population.")
+
+        self._config_components = config_components
+        self._population = population
+
+    def get_filepath(self, node_id):
+        """Return path to model file corresponding to `node_id`.
+
+        Args:
+            node_id (int|CircuitNodeId): node id
+
+        Returns:
+            Path: path to the model file of neuron
+        """
+        if not isinstance(node_id, (int, CircuitNodeId)):
+            raise BluepySnapError("node_id must be a int or a CircuitNodeId")
+        node = self._population.get(node_id, [Node.MODEL_TYPE, Node.MODEL_TEMPLATE])
+        if node[Node.MODEL_TYPE] == "biophysical":
+            models_dir = self._config_components.get("biophysical_neuron_models_dir")
+            if models_dir is None:
+                raise BluepySnapError(
+                    "Missing 'biophysical_neuron_models_dir' in Sonata config")
+        else:
+            models_dir = self._config_components.get("point_neuron_models_dir")
+            if models_dir is None:
+                raise BluepySnapError("Missing 'point_neuron_models_dir' in Sonata config")
+
+        template = node[Node.MODEL_TEMPLATE]
+        assert ':' in template, "Format of 'model_template' must be <schema>:<resource>."
+        schema, resource = template.split(':', 1)
+        resource = Path(resource).with_suffix(f'.{schema}')
+        if resource.is_absolute():
+            return resource
+        return Path(models_dir, resource)

bluepysnap/nodes.py

@@ -734,3 +734,9 @@ def morph(self):
             self._node_storage.circuit.config['components']['morphologies_dir'],
             self
         )
+
+    @cached_property
+    def models(self):
+        """Access to node neuron models."""
+        from bluepysnap.neuron_models import NeuronModelsHelper
+        return NeuronModelsHelper(self._node_storage.circuit.config['components'], self)

tests/data/point_neuron_models/empty_bio.nml

@@ -0,0 +1 @@
+{}

tests/test_edges.py

@@ -554,6 +554,7 @@ def create_edge_population(filepath, pop_name):
             'edge_types_file': None,
         }
         circuit = Mock()
+        circuit.config = {}
         create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default", circuit=circuit,
                                node_sets=NodeSets(str(TEST_DATA_DIR / 'node_sets.json')))
         storage = test_module.EdgeStorage(config, circuit)

tests/test_morph.py

@@ -62,7 +62,7 @@ def test_get_filepath(self):
         node_id = 0
         assert self.nodes.get(node_id, properties="morphology") == "morph-A"
         actual = self.test_obj.get_filepath(node_id)
-        expected = str(self.morph_path / 'morph-A.swc')
+        expected = self.morph_path / 'morph-A.swc'
         assert actual == expected
         node_id = CircuitNodeId("default", 0)
         assert self.nodes.get(node_id, properties="morphology") == "morph-A"

tests/test_neuron_models.py

@@ -0,0 +1,105 @@
+from pathlib import Path
+import h5py
+import bluepysnap.neuron_models as test_module
+from bluepysnap.circuit import Circuit, Config
+from bluepysnap.circuit_ids import CircuitNodeId
+from bluepysnap.sonata_constants import Node
+from bluepysnap.exceptions import BluepySnapError
+
+import pytest
+
+from utils import TEST_DATA_DIR, copy_circuit, copy_config, edit_config, create_node_population
+
+
+def test_invalid_model_type():
+    """test that model type, other than 'biophysical' or 'point_neuron', throws an error"""
+    with copy_circuit() as (circuit_copy_path, config_copy_path):
+        config = Config(config_copy_path).resolve()
+        nodes_file = config["networks"]["nodes"][0]["nodes_file"]
+        with h5py.File(nodes_file, 'r+') as h5f:
+            grp_name = 'nodes/default/0/model_type'
+            data = h5f[grp_name][:]
+            del h5f[grp_name]
+            h5f.create_dataset(grp_name,
+                               data=["virtual"] * data.shape[0],
+                               dtype=h5py.string_dtype())
+        nodes = create_node_population(nodes_file, "default")
+        with pytest.raises(BluepySnapError) as e:
+            test_module.NeuronModelsHelper({}, nodes)
+        assert 'biophysical or point node population' in e.value.args[0]
+
+
+def test_get_invalid_node_id():
+    nodes = create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default")
+    config = Config(TEST_DATA_DIR / 'circuit_config.json').resolve()
+    test_obj = test_module.NeuronModelsHelper(config['components'], nodes)
+
+    with pytest.raises(BluepySnapError) as e:
+        test_obj.get_filepath('1')
+    assert "node_id must be a int or a CircuitNodeId" in e.value.args[0]
+
+
+def test_get_filepath_biophysical():
+    nodes = create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default")
+    config = Config(TEST_DATA_DIR / 'circuit_config.json').resolve()
+    test_obj = test_module.NeuronModelsHelper(config['components'], nodes)
+
+    node_id = 0
+    assert nodes.get(node_id, properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-A"
+    actual = test_obj.get_filepath(node_id)
+    expected = Path(config['components']['biophysical_neuron_models_dir'], 'small_bio-A.hoc')
+    assert actual == expected
+
+    node_id = CircuitNodeId('default', 0)
+    assert nodes.get(node_id, properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-A"
+    actual = test_obj.get_filepath(node_id)
+    assert actual == expected
+
+    node_id = CircuitNodeId('default', 2)
+    assert nodes.get(node_id, properties=Node.MODEL_TEMPLATE) == "hoc:small_bio-C"
+    actual = test_obj.get_filepath(node_id)
+    expected = Path(config['components']['biophysical_neuron_models_dir'], 'small_bio-C.hoc')
+    assert actual == expected
+
+
+def test_no_biophysical_dir():
+    nodes = create_node_population(str(TEST_DATA_DIR / 'nodes.h5'), "default")
+    config = Config(TEST_DATA_DIR / 'circuit_config.json').resolve()
+    del config['components']['biophysical_neuron_models_dir']
+    test_obj = test_module.NeuronModelsHelper(config['components'], nodes)
+
+    with pytest.raises(BluepySnapError) as e:
+        test_obj.get_filepath(0)
+    assert "Missing 'biophysical_neuron_models_dir'" in e.value.args[0]
+
+
+def test_get_filepath_point():
+    with copy_config() as config_copy_path:
+        with edit_config(config_copy_path) as config:
+            config['components']['point_neuron_models_dir'] = "$COMPONENT_DIR/point_neuron_models"
+
+        circuit = Circuit(config_copy_path)
+        nodes = create_node_population(str(TEST_DATA_DIR / 'nodes_points.h5'), "default", circuit)
+        test_obj = test_module.NeuronModelsHelper(circuit.config['components'], nodes)
+
+        node_id = 0
+        assert nodes.get(node_id, properties=Node.MODEL_TEMPLATE) == "nml:empty_bio"
+        actual = test_obj.get_filepath(node_id)
+        expected = Path(circuit.config['components']['point_neuron_models_dir'], 'empty_bio.nml')
+        assert actual == expected
+
+        node_id = 1
+        assert nodes.get(node_id, properties=Node.MODEL_TEMPLATE) == "nml:/abs/path/empty_bio"
+        actual = test_obj.get_filepath(node_id)
+        expected = Path('/abs/path/empty_bio.nml')
+        assert actual == expected
+
+
+def test_no_point_dir():
+    nodes = create_node_population(str(TEST_DATA_DIR / 'nodes_points.h5'), "default")
+    config = Config(TEST_DATA_DIR / 'circuit_config.json').resolve()
+    test_obj = test_module.NeuronModelsHelper(config['components'], nodes)
+
+    with pytest.raises(BluepySnapError) as e:
+        test_obj.get_filepath(0)
+    assert "Missing 'point_neuron_models_dir'" in e.value.args[0]

tests/test_nodes.py

@@ -419,6 +419,7 @@ def _mock_edge(name, source, target):
             return edges
 
         circuit = Mock()
+        circuit.config = {}
         circuit.edges = {"edge1": _mock_edge('edge1', "default", "nodeother"),
                          "edge2": _mock_edge('edge2', "nodeother", "default"),
                          "edge3": _mock_edge('edge3', "default", "nodeother")}
@@ -869,3 +870,10 @@ def test_morph(self):
             }
         }
         assert isinstance(self.test_obj.morph, MorphHelper)
+
+    def test_models(self):
+        from bluepysnap.neuron_models import NeuronModelsHelper
+        self.test_obj._node_storage.circuit.config = {
+            'components': {}
+        }
+        assert isinstance(self.test_obj.models, NeuronModelsHelper)

tests/utils.py

@@ -91,9 +91,10 @@ def create_node_population(filepath, pop_name, circuit=None, node_sets=None):
     }
     if circuit is None:
         circuit = mock.Mock()
+        circuit.config = {}
+    circuit.config.update({"networks": {"nodes": [config]}})
     if node_sets is not None:
         circuit.node_sets = node_sets
     node_pop = NodeStorage(config, circuit).population(pop_name)
-    circuit.config = {"networks": {"nodes": [config]}}
     circuit.nodes = Nodes(circuit)
     return node_pop