From 4df37a00ef35f127084b3b8cc2391dcbbb9f9b72 Mon Sep 17 00:00:00 2001
From: jtyoung84 <104453205+jtyoung84@users.noreply.github.com>
Date: Tue, 6 Aug 2024 09:17:42 -0700
Subject: [PATCH] feat: adds optional anatomical coordinates and reference
 fields to Manipulator Module

---
 examples/ephys_session.json          | 8 ++++++++
 src/aind_data_schema/core/session.py | 6 +++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/examples/ephys_session.json b/examples/ephys_session.json
index d77f2697f..291d6f26b 100644
--- a/examples/ephys_session.json
+++ b/examples/ephys_session.json
@@ -54,6 +54,8 @@
                   "z": "11087.5",
                   "unit": "micrometer"
                },
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "bregma_coordinates": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
@@ -86,6 +88,8 @@
                   "z": "13262",
                   "unit": "micrometer"
                },
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "bregma_coordinates": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
@@ -187,6 +191,8 @@
                   "z": "11087.5",
                   "unit": "micrometer"
                },
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "bregma_coordinates": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
@@ -219,6 +225,8 @@
                   "z": "13262",
                   "unit": "micrometer"
                },
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "bregma_coordinates": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
diff --git a/src/aind_data_schema/core/session.py b/src/aind_data_schema/core/session.py
index 423da591b..bbcd4c9ef 100644
--- a/src/aind_data_schema/core/session.py
+++ b/src/aind_data_schema/core/session.py
@@ -39,7 +39,7 @@
     VisualStimulation,
 )
 from aind_data_schema.components.tile import Channel
-from aind_data_schema.core.procedures import Anaesthetic
+from aind_data_schema.core.procedures import Anaesthetic, CoordinateReferenceLocation
 
 
 class StimulusModality(str, Enum):
@@ -217,6 +217,10 @@ class ManipulatorModule(DomeModule):
         ...,
         title="Manipulator coordinates",
     )
+    anatomical_coordinates: Optional[Coordinates3d] = Field(default=None, title="Anatomical coordinates")
+    anatomical_reference: Optional[
+        Literal[CoordinateReferenceLocation.BREGMA, CoordinateReferenceLocation.LAMBDA]
+    ] = Field(default=None, title="Anatomical coordinate reference")
     bregma_coordinates: Optional[Coordinates3d] = Field(default=None, title="Bregma coordinates")
     surface_z: Optional[Decimal] = Field(default=None, title="Surface z")
     surface_z_unit: SizeUnit = Field(SizeUnit.UM, title="Surface z unit")