Refactor to latest version of services

bruno-f-cruz · bruno-f-cruz · commit f51184d60af4 · 2025-05-13T11:49:22.000-07:00
diff --git a/examples/example.py b/examples/example.py
@@ -4,7 +4,6 @@
 import aind_behavior_services.calibration.load_cells as lcc
 import aind_behavior_services.rig as rig
 import aind_behavior_telekinesis.task_logic as tl
-from aind_behavior_services import db_utils as db
 from aind_behavior_services.calibration.aind_manipulator import (
     AindManipulatorCalibration,
     AindManipulatorCalibrationInput,
@@ -75,7 +74,7 @@ def mock_rig() -> AindTelekinesisRig:
     )
     water_valve_calibration.output = WaterValveCalibrationOutput(slope=1.0 / 20, offset=0)  # For testing purposes
 
-    video_writer = rig.VideoWriterOpenCv(
+    video_writer = rig.cameras.VideoWriterOpenCv(
         frame_rate=25,
         container_extension="avi",
     )
@@ -87,10 +86,10 @@ def mock_rig() -> AindTelekinesisRig:
     )
     return AindTelekinesisRig(
         rig_name="BCI_Bonsai_i",
-        triggered_camera_controller=rig.CameraController[rig.SpinnakerCamera](
+        triggered_camera_controller=rig.cameras.CameraController[rig.cameras.SpinnakerCamera](
             frame_rate=25,
             cameras={
-                "MainCamera": rig.SpinnakerCamera(
+                "MainCamera": rig.cameras.SpinnakerCamera(
                     serial_number="SerialNumber",
                     binning=2,
                     exposure=10000,
@@ -100,9 +99,9 @@ def mock_rig() -> AindTelekinesisRig:
             },
         ),
         harp_load_cells=lcc.LoadCells(port_name="COM4", calibration=load_cells_calibration),
-        harp_behavior=rig.HarpBehavior(port_name="COM6"),
-        harp_lickometer=rig.HarpLicketySplit(port_name="COM8"),
-        harp_clock_generator=rig.HarpWhiteRabbit(port_name="COM3"),
+        harp_behavior=rig.harp.HarpBehavior(port_name="COM6"),
+        harp_lickometer=rig.harp.HarpLicketySplit(port_name="COM8"),
+        harp_clock_generator=rig.harp.HarpWhiteRabbit(port_name="COM3"),
         harp_analog_input=None,
         manipulator=AindManipulatorDevice(port_name="COM5", calibration=manipulator_calibration),
         calibration=RigCalibration(water_valve=water_valve_calibration),
@@ -165,23 +164,14 @@ def mock_task_logic() -> tl.AindTelekinesisTaskLogic:
     )
 
 
-def mock_subject_database() -> db.SubjectDataBase:
-    """Generates a mock database object"""
-    database = db.SubjectDataBase()
-    database.add_subject("test", db.SubjectEntry(task_logic_target="preward_intercept_stageA"))
-    database.add_subject("test2", db.SubjectEntry(task_logic_target="does_notexist"))
-    return database
-
-
 def main(path_seed: str = "./local/{schema}.json"):
     example_session = mock_session()
     example_rig = mock_rig()
     example_task_logic = mock_task_logic()
-    example_database = mock_subject_database()
 
     os.makedirs(os.path.dirname(path_seed), exist_ok=True)
 
-    models = [example_task_logic, example_session, example_rig, example_database]
+    models = [example_task_logic, example_session, example_rig]
 
     for model in models:
         with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f:
diff --git a/examples/example_w_luts.py b/examples/example_w_luts.py
@@ -3,7 +3,6 @@
 
 import aind_behavior_services.rig as rig
 import aind_behavior_telekinesis.task_logic as tl
-from aind_behavior_services import db_utils as db
 from aind_behavior_services.calibration.aind_manipulator import (
     AindManipulatorCalibration,
     AindManipulatorCalibrationInput,
@@ -76,17 +75,17 @@ def mock_rig() -> AindTelekinesisRig:
     )
     water_valve_calibration.output = WaterValveCalibrationOutput(slope=1.0 / 20, offset=0)  # For testing purposes
 
-    video_writer = rig.VideoWriterOpenCv(
+    video_writer = rig.cameras.VideoWriterOpenCv(
         frame_rate=25,
         container_extension="avi",
     )
 
     return AindTelekinesisRig(
         rig_name="BCI_Bonsai_i",
-        triggered_camera_controller=rig.CameraController[rig.SpinnakerCamera](
+        triggered_camera_controller=rig.cameras.CameraController[rig.cameras.SpinnakerCamera](
             frame_rate=25,
             cameras={
-                "MainCamera": rig.SpinnakerCamera(
+                "MainCamera": rig.cameras.SpinnakerCamera(
                     serial_number="23381093",
                     binning=2,
                     exposure=10000,
@@ -97,9 +96,9 @@ def mock_rig() -> AindTelekinesisRig:
             },
         ),
         harp_load_cells=None,
-        harp_behavior=rig.HarpBehavior(port_name="COM4"),
-        harp_lickometer=rig.HarpLicketySplit(port_name="COM6"),
-        harp_clock_generator=rig.HarpWhiteRabbit(port_name="COM7"),
+        harp_behavior=rig.harp.HarpBehavior(port_name="COM4"),
+        harp_lickometer=rig.harp.HarpLicketySplit(port_name="COM6"),
+        harp_clock_generator=rig.harp.HarpWhiteRabbit(port_name="COM7"),
         harp_analog_input=None,
         manipulator=AindManipulatorDevice(port_name="COM5", calibration=manipulator_calibration),
         calibration=RigCalibration(water_valve=water_valve_calibration),
@@ -170,14 +169,6 @@ def mock_task_logic() -> tl.AindTelekinesisTaskLogic:
     )
 
 
-def mock_subject_database() -> db.SubjectDataBase:
-    """Generates a mock database object"""
-    database = db.SubjectDataBase()
-    database.add_subject("test", db.SubjectEntry(task_logic_target="preward_intercept_stageA"))
-    database.add_subject("test2", db.SubjectEntry(task_logic_target="does_notexist"))
-    return database
-
-
 def generate_luts() -> None:
     import numpy as np
     from PIL import Image
@@ -200,11 +191,10 @@ def main(path_seed: str = "{LOCAL_ASSET_FOLDER}/{schema}.json"):
     example_session = mock_session()
     example_rig = mock_rig()
     example_task_logic = mock_task_logic()
-    example_database = mock_subject_database()
     os.makedirs(os.path.dirname(path_seed).format(LOCAL_ASSET_FOLDER=LOCAL_ASSET_FOLDER, schema=""), exist_ok=True)
     generate_luts()
 
-    models = [example_task_logic, example_session, example_rig, example_database]
+    models = [example_task_logic, example_session, example_rig]
 
     for model in models:
         with open(
diff --git a/src/DataSchemas/aind_behavior_session_model.json b/src/DataSchemas/aind_behavior_session_model.json
@@ -1,7 +1,7 @@
 {
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.10.2",
+      "default": "0.11.0",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"
diff --git a/src/DataSchemas/aind_behavior_telekinesis/rig.py b/src/DataSchemas/aind_behavior_telekinesis/rig.py
@@ -75,15 +75,15 @@ class Slap2pInterface(_OphysInterfaceBase):
 
 class AindTelekinesisRig(AindBehaviorRigModel):
     version: Literal[__version__] = __version__
-    triggered_camera_controller: rig.CameraController[rig.SpinnakerCamera] = Field(
+    triggered_camera_controller: rig.cameras.CameraController[rig.cameras.SpinnakerCamera] = Field(
         ..., description="Required camera controller to triggered cameras."
     )
-    harp_behavior: rig.HarpBehavior = Field(..., description="Harp behavior")
-    harp_lickometer: rig.HarpLicketySplit = Field(..., description="Harp lickometer")
+    harp_behavior: rig.harp.HarpBehavior = Field(..., description="Harp behavior")
+    harp_lickometer: rig.harp.HarpLicketySplit = Field(..., description="Harp lickometer")
     harp_load_cells: Optional[lcc.LoadCells] = Field(default=None, description="Harp load cells")
-    harp_clock_generator: rig.HarpWhiteRabbit = Field(..., description="Harp clock generator")
-    harp_analog_input: Optional[rig.HarpAnalogInput] = Field(default=None, description="Harp analog input")
-    harp_environment_sensor: Optional[rig.HarpEnvironmentSensor] = Field(
+    harp_clock_generator: rig.harp.HarpWhiteRabbit = Field(..., description="Harp clock generator")
+    harp_analog_input: Optional[rig.harp.HarpAnalogInput] = Field(default=None, description="Harp analog input")
+    harp_environment_sensor: Optional[rig.harp.HarpEnvironmentSensor] = Field(
         default=None, description="Harp environment sensor"
     )
     manipulator: AindManipulatorDevice = Field(..., description="Manipulator")
diff --git a/src/DataSchemas/aind_telekinesis_rig.json b/src/DataSchemas/aind_telekinesis_rig.json
@@ -169,6 +169,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "$ref": "#/definitions/AindManipulatorAdditionalSettings",
           "default": {
@@ -327,6 +340,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -416,6 +442,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -479,6 +518,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -542,6 +594,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -605,6 +670,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -668,6 +746,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -814,6 +905,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -1217,6 +1321,19 @@
           "title": "Device Type",
           "type": "string"
         },
+        "device_name": {
+          "default": null,
+          "description": "Device name",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "title": "Device Name"
+        },
         "additional_settings": {
           "default": null,
           "description": "Additional settings",
@@ -1900,7 +2017,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.10.2",
+      "default": "0.11.0",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"
diff --git a/src/DataSchemas/aind_telekinesis_task_logic.json b/src/DataSchemas/aind_telekinesis_task_logic.json
@@ -199,7 +199,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.10.2",
+          "default": "0.11.0",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
diff --git a/src/Extensions/AindBehaviorSessionModel.cs b/src/Extensions/AindBehaviorSessionModel.cs
@@ -15,7 +15,7 @@ namespace AindTelekinesisDataSchema.Session
     public partial class AindBehaviorSessionModel
     {
     
-        private string _aindBehaviorServicesPkgVersion = "0.10.2";
+        private string _aindBehaviorServicesPkgVersion = "0.11.0";
     
         private string _version = "0.3.1";
     
diff --git a/src/Extensions/AindTelekinesisRig.cs b/src/Extensions/AindTelekinesisRig.cs
diff --git a/src/Extensions/AindTelekinesisTaskLogic.cs b/src/Extensions/AindTelekinesisTaskLogic.cs

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"properties": {`
`3`	`3`	`"aind_behavior_services_pkg_version": {`
`4`		`- "default": "0.10.2",`
	`4`	`+ "default": "0.11.0",`
`5`	`5`	`"pattern": "^(0\|[1-9]\\d)\\.(0\|[1-9]\\d)\\.(0\|[1-9]\\d)(?:-((?:0\|[1-9]\\d\|\\d[a-zA-Z-][0-9a-zA-Z-])(?:\\.(?:0\|[1-9]\\d\|\\d[a-zA-Z-][0-9a-zA-Z-]))))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",`
`6`	`6`	`"title": "aind_behavior_services package version",`
`7`	`7`	`"type": "string"`
Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,7 @@ namespace AindTelekinesisDataSchema.Session`
`15`	`15`	`public partial class AindBehaviorSessionModel`
`16`	`16`	`{`
`17`	`17`
`18`		`- private string _aindBehaviorServicesPkgVersion = "0.10.2";`
	`18`	`+ private string _aindBehaviorServicesPkgVersion = "0.11.0";`
`19`	`19`
`20`	`20`	`private string _version = "0.3.1";`
`21`	`21`