Merge pull request #101 from CAVEconnectome/spine-annotation

Add Spine class with volume attribute

Author: bdpedigo

emannotationschemas/__init__.py

@@ -48,14 +48,22 @@
     V1DDFunctionalUnitCoregistration,
 )
 from emannotationschemas.schemas.functional_props import (
-    FunctionalPropertiesBCM,
     DigitalTwinPropertiesBCM,
+    FunctionalPropertiesBCM,
 )
 from emannotationschemas.schemas.glia_contact import GliaContact
 from emannotationschemas.schemas.groups import SimpleGroup, SimpleGroupIndexed
+from emannotationschemas.schemas.matching import (
+    CellMatch,
+    CellMatchReference,
+    CellSimilarity,
+)
 from emannotationschemas.schemas.neuropil import FlyNeuropil
 from emannotationschemas.schemas.nucleus_detection import NucleusDetection
-from emannotationschemas.schemas.postsynaptic_compartment import PostsynapticCompartment
+from emannotationschemas.schemas.postsynaptic_compartment import (
+    PostsynapticCompartment,
+    SpineWithInfo,
+)
 from emannotationschemas.schemas.presynaptic_bouton_type import PresynapticBoutonType
 from emannotationschemas.schemas.proofreading import (
     CompartmentProofreadStatus,
@@ -66,11 +74,6 @@
 from emannotationschemas.schemas.reference_text_float import (
     ReferenceTagFloat,
 )
-from emannotationschemas.schemas.matching import (
-    CellMatch,
-    CellSimilarity,
-    CellMatchReference,
-)
 from emannotationschemas.schemas.synapse import (
     BuhmannEcksteinSynapseSchema,
     BuhmannSynapseSchema,
@@ -92,6 +95,7 @@
     "bouton_shape": BoutonShape,
     "presynaptic_bouton_type": PresynapticBoutonType,
     "postsynaptic_compartment": PostsynapticCompartment,
+    "spine_with_info": SpineWithInfo,
     "microns_func_coreg": FunctionalCoregistration,
     "microns_func_unit_coreg": FunctionalUnitCoregistration,
     "v1dd_func_unit_coreg": V1DDFunctionalUnitCoregistration,

emannotationschemas/schemas/postsynaptic_compartment.py

@@ -1,7 +1,8 @@
 import marshmallow as mm
-from emannotationschemas.schemas.base import ReferenceAnnotation
 from marshmallow.validate import OneOf
 
+from emannotationschemas.schemas.base import BoundSpatialPoint, ReferenceAnnotation
+
 allowed_compartments = [
     "soma",
     "dendrite",
@@ -12,7 +13,6 @@
 
 
 class PostsynapticCompartment(ReferenceAnnotation):
-
     compartment = mm.fields.Str(
         required=True,
         validate=OneOf(allowed_compartments),
@@ -30,3 +30,14 @@ class PostsynapticCompartment(ReferenceAnnotation):
         validate=OneOf(allowed_dendrite_classes),
         description="Type of dendritic branch, e.g. basal or apical",
     )
+
+
+class SpineWithInfo(BoundSpatialPoint):
+    volume = mm.fields.Float(
+        required=False, description="Estimated volume of the spine"
+    )
+
+    n_inputs = mm.fields.Int(
+        required=False,
+        description="Number of synaptic inputs (unique root IDs) onto the spine",
+    )

tests/test_spine.py

@@ -0,0 +1,35 @@
+from emannotationschemas.schemas.postsynaptic_compartment import SpineWithInfo
+
+good_spine_with_info = {
+    "position": [100, 200, 300],
+    "supervoxel_id": 50,
+    "root_id": 10,
+    "volume": 1.5,
+    "n_inputs": 3,
+}
+
+
+def test_spine_with_info_schema():
+    schema = SpineWithInfo()
+    result = schema.load(good_spine_with_info)
+    assert result["position"] == [100, 200, 300]
+    assert result["supervoxel_id"] == 50
+    assert result["root_id"] == 10
+    assert result["volume"] == 1.5
+    assert result["n_inputs"] == 3
+
+
+def test_spine_with_info_optional():
+    schema = SpineWithInfo()
+    result = schema.load(
+        {
+            "position": [100, 200, 300],
+            "supervoxel_id": 50,
+            "root_id": 10,
+        }
+    )
+    assert result["position"] == [100, 200, 300]
+    assert result["supervoxel_id"] == 50
+    assert result["root_id"] == 10
+    assert "volume" not in result
+    assert "n_inputs" not in result