BREAKING CHANGE: Refactoring to CoordinateSystem, Coordinate, and RelativePosition

docs/source/example_workflow/example_workflow.py

@@ -6,7 +6,7 @@
 
 from aind_data_schema.core.data_description import Funding, RawDataDescription
 from aind_data_schema.core.procedures import (
-    NanojectInjection,
+    BrainInjection,
     Perfusion,
     Procedures,
     Surgery,
@@ -99,7 +99,7 @@
                 ethics_review_id=ethics_review_id,
                 experimenters=[experimenter],
                 procedures=[
-                    NanojectInjection(
+                    BrainInjection(
                         protocol_id=protocol,
                         injection_materials=[
                             ViralMaterial(

examples/aibs_smartspim_instrument.py

@@ -18,6 +18,13 @@
 )
 from aind_data_schema_models.modalities import Modality
 from aind_data_schema.core.instrument import Com, Instrument
+from aind_data_schema.components.coordinates import (
+    Axis,
+    AxisName,
+    CoordinateSystem,
+    Direction,
+    Origin,
+)
 
 objective = Objective(
     name="TLX Objective",
@@ -182,6 +189,14 @@
     instrument_id="440_SmartSPIM2_20231004",
     modification_date=datetime.date(2023, 10, 4),
     instrument_type=ImagingInstrumentType.SMARTSPIM,
+    coordinate_system=CoordinateSystem(
+        origin=Origin.BREGMA,
+        axes=[
+            Axis(name=AxisName.AP, direction=Direction.AP),
+            Axis(name=AxisName.ML, direction=Direction.LR),
+            Axis(name=AxisName.SI, direction=Direction.SI),
+        ],
+    ),
     modalities=[Modality.SPIM],
     manufacturer=Organization.LIFECANVAS,
     temperature_control=False,

examples/aind_smartspim_instrument.py

@@ -15,6 +15,13 @@
 )
 from aind_data_schema.core.instrument import Com, Detector, Instrument, Objective
 from aind_data_schema_models.modalities import Modality
+from aind_data_schema.components.coordinates import (
+    Axis,
+    AxisName,
+    CoordinateSystem,
+    Direction,
+    Origin,
+)
 
 objective_1 = Objective(
     name="TLX Objective 1",
@@ -248,6 +255,14 @@
     instrument_type=ImagingInstrumentType.SMARTSPIM,
     manufacturer=Organization.LIFECANVAS,
     modification_date=date(2023, 10, 4),
+    coordinate_system=CoordinateSystem(
+        origin=Origin.BREGMA,
+        axes=[
+            Axis(name=AxisName.AP, direction=Direction.AP),
+            Axis(name=AxisName.ML, direction=Direction.LR),
+            Axis(name=AxisName.SI, direction=Direction.SI),
+        ],
+    ),
     modalities=[Modality.SPIM],
     components=[
         *objectives,

examples/ephys_acquisition.py

@@ -12,17 +12,111 @@
     SubjectDetails,
 )
 from aind_data_schema.components.configs import (
-    CcfCoords,
-    Coordinates3d,
     DomeModule,
-    ManipulatorModule,
+    ManipulatorConfig,
     StimulusModality,
 )
+from aind_data_schema.components.coordinates import Coordinate, FloatAxis, AxisName
 from aind_data_schema.components.stimulus import VisualStimulation
 from aind_data_schema_models.brain_atlas import CCFStructure
 
 bonsai_software = Software(name="Bonsai", version="2.7")
 
+
+ephys_config_a = ManipulatorConfig(
+    rotation_angle=0,
+    arc_angle=5.2,
+    module_angle=8,
+    atlas_coordinates=[
+        Coordinate(
+            position=[
+                FloatAxis(value=8150, axis=AxisName.ML),
+                FloatAxis(value=3250, axis=AxisName.AP),
+                FloatAxis(value=7800, axis=AxisName.SI),
+            ]
+        ),
+    ],
+    device_name="Ephys_assemblyA",
+    coordinate_transform="behavior/calibration_info_np2_2023_04_24.npy",
+    primary_targeted_structure=CCFStructure.LGD,
+    manipulator_axis_position=[
+        Coordinate(
+            position=[
+                FloatAxis(value=8422, axis=AxisName.ML),
+                FloatAxis(value=4205, axis=AxisName.AP),
+                FloatAxis(value=11087.5, axis=AxisName.SI),
+            ]
+        ),
+    ],
+    calibration_date=datetime(year=2023, month=4, day=25, tzinfo=timezone.utc),
+    notes=(
+        "Moved Y to avoid blood vessel, X to avoid edge. Mouse made some noise during the recording"
+        " with a sudden shift in signals. Lots of motion. Maybe some implant motion."
+    ),
+)
+
+ephys_config_b = ManipulatorConfig(
+    rotation_angle=0,
+    arc_angle=25,
+    module_angle=-22,
+    atlas_coordinates=[
+        Coordinate(
+            position=[
+                FloatAxis(value=8150, axis=AxisName.ML),
+                FloatAxis(value=3250, axis=AxisName.AP),
+                FloatAxis(value=7800, axis=AxisName.SI),
+            ]
+        ),
+    ],
+    device_name="Ephys_assemblyB",
+    coordinate_transform="behavior/calibration_info_np2_2023_04_24.py",
+    primary_targeted_structure=CCFStructure.LC,
+    manipulator_axis_position=[
+        Coordinate(
+            position=[
+                FloatAxis(value=8422, axis=AxisName.ML),
+                FloatAxis(value=4205, axis=AxisName.AP),
+                FloatAxis(value=11087.5, axis=AxisName.SI),
+            ]
+        ),
+    ],
+    calibration_date=datetime(year=2023, month=4, day=25, tzinfo=timezone.utc),
+    notes=(
+        "Trouble penetrating. Lots of compression, needed to move probe. Small amount of surface"
+        " bleeding/bruising. Initial Target: X;10070.3\tY:7476.6"
+    ),
+)
+
+
+stick_config_1 = DomeModule(
+    rotation_angle=0,
+    device_name="Stick_assembly_1",
+    arc_angle=-180,
+    module_angle=-180,
+    notes="did not record angles, did not calibrate.",
+)
+stick_config_2 = DomeModule(
+    rotation_angle=0,
+    device_name="Stick_assembly_2",
+    arc_angle=-180,
+    module_angle=-180,
+    notes="Did not record angles, did not calibrate",
+)
+stick_config_3 = DomeModule(
+    rotation_angle=0,
+    device_name="Stick_assembly_3",
+    arc_angle=-180,
+    module_angle=-180,
+    notes="Did not record angles, did not calibrate",
+)
+stick_config_4 = DomeModule(
+    rotation_angle=0,
+    device_name="Stick_assembly_4",
+    arc_angle=-180,
+    module_angle=-180,
+    notes="Did not record angles, did not calibrate",
+)
+
 acquisition = Acquisition(
     experimenters=[Person(name="John Smith")],
     subject_id="664484",
@@ -89,65 +183,12 @@
                 "Ephys_assemblyB",
             ],
             configurations=[
-                DomeModule(
-                    rotation_angle=0,
-                    device_name="Stick_assembly_1",
-                    arc_angle=-180,
-                    module_angle=-180,
-                    notes="did not record angles, did not calibrate.",
-                ),
-                DomeModule(
-                    rotation_angle=0,
-                    device_name="Stick_assembly_2",
-                    arc_angle=-180,
-                    module_angle=-180,
-                    notes="Did not record angles, did not calibrate",
-                ),
-                DomeModule(
-                    rotation_angle=0,
-                    device_name="Stick_assembly_3",
-                    arc_angle=-180,
-                    module_angle=-180,
-                    notes="Did not record angles, did not calibrate",
-                ),
-                DomeModule(
-                    rotation_angle=0,
-                    device_name="Stick_assembly_4",
-                    arc_angle=-180,
-                    module_angle=-180,
-                    notes="Did not record angles, did not calibrate",
-                ),
-                ManipulatorModule(
-                    targeted_ccf_coordinates=[
-                        CcfCoords(ml=8150, ap=3250, dv=7800),
-                    ],
-                    device_name="Ephys_assemblyA",
-                    arc_angle=5.2,
-                    module_angle=8,
-                    coordinate_transform="behavior/calibration_info_np2_2023_04_24.npy",
-                    primary_targeted_structure=CCFStructure.LGD,
-                    manipulator_coordinates=Coordinates3d(x=8422, y=4205, z=11087.5),
-                    calibration_date=datetime(year=2023, month=4, day=25, tzinfo=timezone.utc),
-                    notes=(
-                        "Moved Y to avoid blood vessel, X to avoid edge. Mouse made some noise during the recording"
-                        " with a sudden shift in signals. Lots of motion. Maybe some implant motion."
-                    ),
-                ),
-                ManipulatorModule(
-                    rotation_angle=0,
-                    arc_angle=25,
-                    module_angle=-22,
-                    targeted_ccf_coordinates=[CcfCoords(ml=6637.28, ap=4265.02, dv=10707.35)],
-                    device_name="Ephys_assemblyB",
-                    coordinate_transform="behavior/calibration_info_np2_2023_04_24.py",
-                    primary_targeted_structure=CCFStructure.LC,
-                    manipulator_coordinates=Coordinates3d(x=9015, y=7144, z=13262),
-                    calibration_date=datetime(year=2023, month=4, day=25, tzinfo=timezone.utc),
-                    notes=(
-                        "Trouble penetrating. Lots of compression, needed to move probe. Small amount of surface"
-                        " bleeding/bruising. Initial Target: X;10070.3\tY:7476.6"
-                    ),
-                ),
+                ephys_config_a,
+                ephys_config_b,
+                stick_config_1,
+                stick_config_2,
+                stick_config_3,
+                stick_config_4,
             ],
         ),
         DataStream(
@@ -162,43 +203,7 @@
                 "Ephys_assemblyB",
             ],
             configurations=[
-                DomeModule(
-                    rotation_angle=0,
-                    device_name="Stick_assembly_1",
-                    arc_angle=-180,
-                    module_angle=-180,
-                    notes="did not record angles, did not calibrate.",
-                ),
-                ManipulatorModule(
-                    rotation_angle=0,
-                    arc_angle=5.2,
-                    module_angle=8,
-                    targeted_ccf_coordinates=[CcfCoords(ml=8150, ap=3250, dv=7800)],
-                    device_name="Ephys_assemblyA",
-                    coordinate_transform="behavior/calibration_info_np2_2023_04_24.npy",
-                    primary_targeted_structure=CCFStructure.LGD,
-                    manipulator_coordinates=Coordinates3d(x=8422, y=4205, z=11087.5),
-                    calibration_date=datetime(year=2023, month=4, day=25, tzinfo=timezone.utc),
-                    notes=(
-                        "Moved Y to avoid blood vessel, X to avoid edge. Mouse made some noise during the recording"
-                        " with a sudden shift in signals. Lots of motion. Maybe some implant motion."
-                    ),
-                ),
-                ManipulatorModule(
-                    rotation_angle=0,
-                    arc_angle=25,
-                    module_angle=-22,
-                    targeted_ccf_coordinates=[CcfCoords(ml=6637.28, ap=4265.02, dv=10707.35)],
-                    device_name="Ephys_assemblyB",
-                    coordinate_transform="behavior/calibration_info_np2_2023_04_24.py",
-                    primary_targeted_structure=CCFStructure.LC,
-                    manipulator_coordinates=Coordinates3d(x=9015, y=7144, z=13262),
-                    calibration_date=datetime(year=2023, month=4, day=25, tzinfo=timezone.utc),
-                    notes=(
-                        "Trouble penetrating. Lots of compression, needed to move probe. Small amount of surface"
-                        " bleeding/bruising. Initial Target: X;10070.3\tY:7476.6"
-                    ),
-                ),
+                stick_config_1,
             ],
         ),
     ],

examples/ephys_instrument.py

@@ -6,6 +6,15 @@
 from aind_data_schema_models.modalities import Modality
 from aind_data_schema_models.organizations import Organization
 from aind_data_schema_models.units import FrequencyUnit, SizeUnit
+from aind_data_schema.components.coordinates import (
+    RelativePosition,
+    AnatomicalRelative,
+    CoordinateSystem,
+    Origin,
+    Axis,
+    AxisName,
+    Direction,
+)
 
 from aind_data_schema.components.devices import (
     Calibration,
@@ -149,28 +158,32 @@
 
 microscope_1 = CameraAssembly(
     name="Stick_assembly_1",
-    camera_target=CameraTarget.BRAIN_SURFACE,  # NEEDS TO BE FILLED OUT
+    target=CameraTarget.BRAIN,
+    position=RelativePosition(position=[AnatomicalRelative.SUPERIOR]),
     camera=probe_camera_1,
     lens=stick_lens,
 )
 
 microscope_2 = CameraAssembly(
     name="Stick_assembly_2",
-    camera_target=CameraTarget.BRAIN_SURFACE,  # NEEDS TO BE FILLED OUT
+    target=CameraTarget.BRAIN,
+    position=RelativePosition(position=[AnatomicalRelative.SUPERIOR]),
     camera=probe_camera_2,
     lens=stick_lens,
 )
 
 microscope_3 = CameraAssembly(
     name="Stick_assembly_3",
-    camera_target=CameraTarget.BRAIN_SURFACE,  # NEEDS TO BE FILLED OUT
+    target=CameraTarget.BRAIN,
+    position=RelativePosition(position=[AnatomicalRelative.SUPERIOR]),
     camera=probe_camera_3,
     lens=stick_lens,
 )
 
 microscope_4 = CameraAssembly(
     name="Stick_assembly_4",
-    camera_target=CameraTarget.BRAIN_SURFACE,  # NEEDS TO BE FILLED OUT
+    target=CameraTarget.BRAIN,
+    position=RelativePosition(position=[AnatomicalRelative.SUPERIOR]),
     camera=probe_camera_4,
     lens=stick_lens,
 )
@@ -228,7 +241,8 @@
 camassm1 = CameraAssembly(
     name="Face Camera Assembly",
     camera=face_camera,
-    camera_target="Face side left",
+    target=CameraTarget.FACE,
+    position=RelativePosition(position=[AnatomicalRelative.LEFT]),
     filter=filt,
     lens=lens,
 )
@@ -250,8 +264,9 @@
 
 camassm2 = CameraAssembly(
     name="Body Camera Assembly",
+    target=CameraTarget.BODY,
+    position=RelativePosition(position=[AnatomicalRelative.SUPERIOR]),
     camera=body_camera,
-    camera_target="Body",
     filter=filt,
     lens=lens,
 )
@@ -279,6 +294,14 @@
     instrument_id="323_EPHYS1_20231003",
     modification_date=date(2023, 10, 3),
     modalities=[Modality.ECEPHYS],
+    coordinate_system=CoordinateSystem(
+        origin=Origin.BREGMA,
+        axes=[
+            Axis(name=AxisName.AP, direction=Direction.AP),
+            Axis(name=AxisName.ML, direction=Direction.LR),
+            Axis(name=AxisName.SI, direction=Direction.SI),
+        ],
+    ),
     components=[
         ephys_assemblyA,
         ephys_assemblyB,