Merge pull request #605 from AllenNeuralDynamics/feat_239_acquistion-medium

dyf · web-flow · commit 529ae6bf6166 · 2023-11-15T12:14:18.000-08:00
immersion medium
diff --git a/examples/aibs_smartspim_instrument.json b/examples/aibs_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
-   "schema_version": "0.9.4",
+   "schema_version": "0.9.5",
    "instrument_id": "SmartSPIM2-2",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",
diff --git a/examples/aind_smartspim_instrument.json b/examples/aind_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
-   "schema_version": "0.9.4",
+   "schema_version": "0.9.5",
    "instrument_id": "SmartSPIM1-3",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",
diff --git a/examples/bergamo_ophys_session.json b/examples/bergamo_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
-   "schema_version": "0.0.7",
+   "schema_version": "0.0.8",
    "experimenter_full_name": [
       "John Doe"
    ],
diff --git a/examples/ephys_rig.json b/examples/ephys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",
-   "schema_version": "0.1.6",
+   "schema_version": "0.1.7",
    "rig_id": "323_EPHYS1",
    "modification_date": "2023-10-03",
    "modalities": [
diff --git a/examples/ephys_session.json b/examples/ephys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
-   "schema_version": "0.0.7",
+   "schema_version": "0.0.8",
    "experimenter_full_name": [
       "Jane Doe"
    ],
diff --git a/examples/exaspim_acquisition.json b/examples/exaspim_acquisition.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/acquisition.py",
-   "schema_version": "0.5.3",
+   "schema_version": "0.5.4",
    "experimenter_full_name": [
       "###"
    ],
diff --git a/examples/exaspim_instrument.json b/examples/exaspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
-   "schema_version": "0.9.4",
+   "schema_version": "0.9.5",
    "instrument_id": "exaSPIM1-1",
    "modification_date": "2023-10-04",
    "instrument_type": "exaSPIM",
diff --git a/examples/fip_ophys_rig.json b/examples/fip_ophys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",
-   "schema_version": "0.1.6",
+   "schema_version": "0.1.7",
    "rig_id": "428_FIP1_2",
    "modification_date": "2023-10-03",
    "modalities": [
diff --git a/examples/ophys_session.json b/examples/ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
-   "schema_version": "0.0.7",
+   "schema_version": "0.0.8",
    "experimenter_full_name": [
       "John Doe"
    ],
diff --git a/src/aind_data_schema/behavior/behavior_rig.py b/src/aind_data_schema/behavior/behavior_rig.py
@@ -26,7 +26,7 @@
 class BehaviorRig(AindCoreModel):
     """Description of an behavior rig. This is being deprecated after 2023-11-01. Use Rig class instead."""
 
-    schema_version: str = Field("0.1.20", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.1.21", description="schema version", title="Version", const=True)
 
     rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
     mouse_platform: Annotated[
diff --git a/src/aind_data_schema/behavior/behavior_session.py b/src/aind_data_schema/behavior/behavior_session.py
@@ -55,7 +55,7 @@ class BehaviorSession(AindCoreModel):
     """Description of a behavior session. This is being deprecated after 2023-11-01. Use Session class instead."""
 
     schema_version: str = Field(
-        "0.0.13",
+        "0.0.14",
         description="Schema version",
         title="Schema Version",
         const=True,
diff --git a/src/aind_data_schema/device.py b/src/aind_data_schema/device.py
@@ -238,12 +238,13 @@ class MotorizedStage(Device):
     firmware: Optional[str] = Field(None, title="Firmware")
 
 
-class Immersion(Enum):
-    """Immersion media name"""
+class ImmersionMedium(Enum):
+    """Immersion medium name"""
 
     AIR = "air"
     MULTI = "multi"
     OIL = "oil"
+    PBS = "PBS"
     WATER = "water"
     OTHER = "other"
 
@@ -261,7 +262,7 @@ class Objective(Device):
     device_type: Literal["Objective"] = Field("Objective", const=True, readOnly=True)
     numerical_aperture: Decimal = Field(..., title="Numerical aperture (in air)")
     magnification: Decimal = Field(..., title="Magnification")
-    immersion: Immersion = Field(..., title="Immersion")
+    immersion: ImmersionMedium = Field(..., title="Immersion")
     objective_type: Optional[ObjectiveType] = Field(None, title="Objective type")
 
 
@@ -547,7 +548,7 @@ class Detector(Device):
     detector_type: DetectorType = Field(..., title="Detector Type")
     data_interface: DataInterface = Field(..., title="Data interface")
     cooling: Cooling = Field(..., title="Cooling")
-    immersion: Optional[Immersion] = Field(None, title="Immersion")
+    immersion: Optional[ImmersionMedium] = Field(None, title="Immersion")
     chroma: Optional[CameraChroma] = Field(None, title="Camera chroma")
     sensor_width: Optional[int] = Field(None, title="Width of the sensor in pixels")
     sensor_height: Optional[int] = Field(None, title="Height of the sensor in pixels")
diff --git a/src/aind_data_schema/ephys/ephys_rig.py b/src/aind_data_schema/ephys/ephys_rig.py
@@ -111,7 +111,7 @@ class EphysAssembly(AindModel):
 class EphysRig(AindCoreModel):
     """Description of an ephys rig. This is being deprecated after 2023-11-01. Use Rig class instead."""
 
-    schema_version: str = Field("0.7.19", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.7.20", description="schema version", title="Version", const=True)
     rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
     ephys_assemblies: Optional[List[EphysAssembly]] = Field(None, title="Ephys probes", unique_items=True)
     stick_microscopes: Optional[List[StickMicroscopeAssembly]] = Field(None, title="Stick microscopes")
diff --git a/src/aind_data_schema/imaging/acquisition.py b/src/aind_data_schema/imaging/acquisition.py
@@ -10,7 +10,7 @@
 from pydantic import Field
 
 from aind_data_schema.base import AindCoreModel, AindModel, EnumSubset
-from aind_data_schema.device import Calibration, Maintenance
+from aind_data_schema.device import Calibration, ImmersionMedium, Maintenance
 from aind_data_schema.imaging.tile import AcquisitionTile
 from aind_data_schema.processing import ProcessName
 from aind_data_schema.utils.units import SizeUnit
@@ -74,9 +74,9 @@ def from_direction_code(code) -> List[Axis]:
 
 
 class Immersion(AindModel):
-    """Description of immersion media"""
+    """Description of immersion medium"""
 
-    medium: str = Field(..., title="Immersion medium")
+    medium: ImmersionMedium = Field(..., title="Immersion medium")
     refractive_index: Decimal = Field(..., title="Index of refraction")
 
 
@@ -102,7 +102,7 @@ class ProcessingSteps(AindModel):
 class Acquisition(AindCoreModel):
     """Description of an imaging acquisition session"""
 
-    schema_version: str = Field("0.5.3", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.5.4", description="schema version", title="Version", const=True)
     experimenter_full_name: List[str] = Field(
         ...,
         description="First and last name of the experimenter(s).",
diff --git a/src/aind_data_schema/imaging/instrument.py b/src/aind_data_schema/imaging/instrument.py
@@ -108,7 +108,7 @@ class OpticalTable(Device):
 class Instrument(AindCoreModel):
     """Description of an instrument, which is a collection of devices"""
 
-    schema_version: str = Field("0.9.4", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.9.5", description="schema version", title="Version", const=True)
     instrument_id: Optional[str] = Field(
         None,
         description="Unique identifier for this instrument. Naming convention: <room>-<apparatus>-<version>",
diff --git a/src/aind_data_schema/imaging/mri_session.py b/src/aind_data_schema/imaging/mri_session.py
@@ -98,7 +98,7 @@ def validate_other(cls, v):
 class MriSession(AindCoreModel):
     """Description of an MRI scan"""
 
-    schema_version: str = Field("0.1.14", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.1.15", description="schema version", title="Version", const=True)
     subject_id: str = Field(
         ...,
         description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",
diff --git a/src/aind_data_schema/metadata.py b/src/aind_data_schema/metadata.py
@@ -42,7 +42,7 @@ class Metadata(AindCoreModel):
     # default
     _DEFAULT_FILE_EXTENSION = ".nd.json"
 
-    schema_version: str = Field("0.0.10", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.0.11", description="schema version", title="Version", const=True)
     id: UUID = Field(
         default_factory=uuid4,
         alias="_id",
diff --git a/src/aind_data_schema/ophys/ophys_rig.py b/src/aind_data_schema/ophys/ophys_rig.py
@@ -20,7 +20,7 @@
     Disc,
     Filter,
     HarpDevice,
-    Immersion,
+    ImmersionMedium,
     Laser,
     Lens,
     LightEmittingDiode,
@@ -63,7 +63,7 @@ class Detector(Device):
     detector_type: DetectorType = Field(..., title="Detector Type")
     data_interface: DataInterface = Field(..., title="Data interface")
     cooling: Cooling = Field(..., title="Cooling")
-    immersion: Optional[Immersion] = Field(None, title="Immersion")
+    immersion: Optional[ImmersionMedium] = Field(None, title="Immersion")
 
     chroma: Optional[CameraChroma] = Field(None, title="Camera chroma")
     bit_depth: Optional[int] = Field(None, title="Bit depth")
@@ -89,7 +89,7 @@ class OphysRig(AindCoreModel):
     """Description of an optical physiology rig. This is being deprecated after 2023-11-01. Use Rig class instead."""
 
     schema_version: str = Field(
-        "0.7.9",
+        "0.7.10",
         description="schema version",
         title="Schema Version",
         const=True,
diff --git a/src/aind_data_schema/rig.py b/src/aind_data_schema/rig.py
@@ -48,7 +48,7 @@
 class Rig(AindCoreModel):
     """Description of a rig"""
 
-    schema_version: str = Field("0.1.6", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.1.7", description="schema version", title="Version", const=True)
     rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
     modification_date: date = Field(..., title="Date of modification")
     modalities: List[Modality] = Field(..., title="Modalities", unique_items=True)
diff --git a/src/aind_data_schema/session.py b/src/aind_data_schema/session.py
@@ -315,7 +315,7 @@ class Session(AindCoreModel):
     """Description of a physiology and/or behavior session"""
 
     schema_version: str = Field(
-        "0.0.7",
+        "0.0.8",
         description="schema version",
         title="Schema Version",
         const=True,

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",`
`3`		`- "schema_version": "0.9.4",`
	`3`	`+ "schema_version": "0.9.5",`
`4`	`4`	`"instrument_id": "SmartSPIM2-2",`
`5`	`5`	`"modification_date": "2023-10-04",`
`6`	`6`	`"instrument_type": "SmartSPIM",`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",`
`3`		`- "schema_version": "0.0.7",`
	`3`	`+ "schema_version": "0.0.8",`
`4`	`4`	`"experimenter_full_name": [`
`5`	`5`	`"John Doe"`
`6`	`6`	`],`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",`
`3`		`- "schema_version": "0.1.6",`
	`3`	`+ "schema_version": "0.1.7",`
`4`	`4`	`"rig_id": "323_EPHYS1",`
`5`	`5`	`"modification_date": "2023-10-03",`
`6`	`6`	`"modalities": [`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/acquisition.py",`
`3`		`- "schema_version": "0.5.3",`
	`3`	`+ "schema_version": "0.5.4",`
`4`	`4`	`"experimenter_full_name": [`
`5`	`5`	`"###"`
`6`	`6`	`],`