Support morphology containers (#274)

* MorphIO supports "containers"; this uses a file system layout or an h5 file containing many morphologies

Author: mgeplf

CHANGELOG.rst

@@ -20,6 +20,7 @@ Improvements
 - Update simulation validation to conform to the SONATA spec
 
   - ``synapse_replay.source`` and ``.dat`` spike input files are no longer supported
+- Support morphology containers
 
 
 Version v3.0.1

bluepysnap/morph.py

@@ -20,8 +20,8 @@
 from pathlib import Path
 
 import morph_tool.transform as transformations
+import morphio
 import numpy as np
-from morphio.mut import Morphology
 
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap.sonata_constants import Node
@@ -51,8 +51,8 @@ def __init__(self, morph_dir, population, alternate_morphologies=None):
         self._alternate_morphologies = alternate_morphologies or {}
         self._population = population
 
-    def get_morphology_dir(self, extension):
-        """Return morphology directory based on a given extension."""
+    def _get_morphology_base(self, extension):
+        """Get morphology base path; this will be a directory unless it's a morphology container."""
         if extension == "swc":
             if not self._morph_dir:
                 raise BluepySnapError("'morphologies_dir' is not defined in config")
@@ -68,16 +68,33 @@ def get_morphology_dir(self, extension):
 
         return morph_dir
 
+    def get_morphology_dir(self, extension="swc"):
+        """Return morphology directory based on a given extension."""
+        morph_dir = self._get_morphology_base(extension)
+
+        if extension == "h5" and Path(morph_dir).is_file():
+            raise BluepySnapError(
+                f"'{morph_dir}' is a morphology container, so a directory does not exist"
+            )
+
+        return morph_dir
+
+    def get_name(self, node_id):
+        """Get the morphology name for a `node_id`."""
+        if not is_node_id(node_id):
+            raise BluepySnapError("node_id must be a int or a CircuitNodeId")
+
+        name = self._population.get(node_id, Node.MORPHOLOGY)
+        return name
+
     def get_filepath(self, node_id, extension="swc"):
         """Return path to SWC morphology file corresponding to `node_id`.
 
         Args:
             node_id (int/CircuitNodeId): could be a int or CircuitNodeId.
             extension (str): expected filetype extension of the morph file.
         """
-        if not is_node_id(node_id):
-            raise BluepySnapError("node_id must be a int or a CircuitNodeId")
-        name = self._population.get(node_id, Node.MORPHOLOGY)
+        name = self.get_name(node_id)
 
         return Path(self.get_morphology_dir(extension), f"{name}.{extension}")
 
@@ -90,11 +107,19 @@ def get(self, node_id, transform=False, extension="swc"):
                 according to `node_id` position in the circuit.
             extension (str): expected filetype extension of the morph file.
         """
-        filepath = self.get_filepath(node_id, extension=extension)
-        result = Morphology(filepath)
+        collection = morphio.Collection(
+            self._get_morphology_base(extension),
+            [
+                f".{extension}",
+            ],
+        )
+        name = self.get_name(node_id)
+        result = collection.load(name, mutable=True)
+
         if transform:
             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()

setup.py

@@ -49,7 +49,7 @@ def __init__(self, *args, **kwargs):
         "importlib_resources>=5.0.0",
         "jsonschema>=4.0.0,<5.0.0",
         "libsonata>=0.1.24,<1.0.0",
-        "morphio>=3.0.0,<4.0.0",
+        "morphio>=3.3.5,<4.0.0",
         "morph-tool>=2.4.3,<3.0.0",
         "numpy>=1.8",
         "pandas>=1.0.0",

tests/data/morphologies/container-morphs.h5

@@ -126,6 +126,25 @@ def test_get_morphology(self):
         with pytest.raises(BluepySnapError, match="node_id must be a int or a CircuitNodeId"):
             self.test_obj.get([0, 1])
 
+    def test_get_alternate_morphology_collection(self):
+        morph_path = TEST_DATA_DIR / "morphologies/container-morphs.h5"
+        alternate_morphs = {"h5v1": str(morph_path)}
+
+        test_obj = test_module.MorphHelper(
+            None, self.nodes, alternate_morphologies=alternate_morphs
+        )
+
+        node_id = 0
+
+        with pytest.raises(BluepySnapError):
+            test_obj.get_morphology_dir(extension="h5")
+
+        with pytest.raises(BluepySnapError):
+            test_obj.get_filepath(node_id, extension="h5")
+
+        morph_A = test_obj.get(node_id, extension="h5")
+        assert len(morph_A.points) == 13
+
     def test_get_alternate_morphology(self):
         alternate_morphs = {"h5v1": str(self.morph_path)}
         test_obj = test_module.MorphHelper(