Release v0.7.0

.config/dotnet-tools.json

@@ -3,7 +3,7 @@
   "isRoot": true,
   "tools": {
     "bonsai.sgen": {
-      "version": "0.6.1",
+      "version": "0.9.0",
       "commands": [
         "bonsai.sgen"
       ]

bonsai/Bonsai.config

@@ -4,10 +4,11 @@
     <Package id="AForge" version="2.2.5" />
     <Package id="AForge.Video" version="2.2.5" />
     <Package id="AForge.Video.DirectShow" version="2.2.5" />
-    <Package id="AllenNeuralDynamics.AindBehaviorServices" version="0.12.0" />
-    <Package id="AllenNeuralDynamics.AindManipulator" version="0.1.6" />
-    <Package id="AllenNeuralDynamics.Core" version="0.4.1" />
-    <Package id="AllenNeuralDynamics.Core.Design" version="0.3.0" />
+    <Package id="AllenNeuralDynamics.AindBehaviorServices" version="0.13.4" />
+    <Package id="AllenNeuralDynamics.AindBehaviorServices.Distributions" version="0.2.0" />
+    <Package id="AllenNeuralDynamics.AindManipulator" version="0.3.0" />
+    <Package id="AllenNeuralDynamics.Core" version="0.3.0" />
+    <Package id="AllenNeuralDynamics.Core.Design" version="0.4.0" />
     <Package id="AllenNeuralDynamics.EnvironmentSensor" version="0.3.0" />
     <Package id="AllenNeuralDynamics.HarpUtils" version="0.3.2" />
     <Package id="AllenNeuralDynamics.LicketySplit" version="0.2.0" />
@@ -30,8 +31,8 @@
     <Package id="Bonsai.Harp.Design" version="3.6.1" />
     <Package id="Bonsai.Numerics" version="0.10.0" />
     <Package id="Bonsai.Player" version="2.8.5" />
-    <Package id="Bonsai.Scripting.Expressions" version="2.9.0" />
-    <Package id="Bonsai.Scripting.Expressions.Design" version="2.9.0" />
+    <Package id="Bonsai.Scripting.Expressions" version="2.10.0" />
+    <Package id="Bonsai.Scripting.Expressions.Design" version="2.10.0" />
     <Package id="Bonsai.Shaders" version="2.9.0" />
     <Package id="Bonsai.Shaders.Design" version="2.9.0" />
     <Package id="Bonsai.Shaders.Rendering" version="2.9.0" />
@@ -50,7 +51,7 @@
     <Package id="Harp.AnalogInput" version="0.2.0" />
     <Package id="Harp.Behavior" version="0.2.0" />
     <Package id="Harp.LoadCells" version="0.2.0" />
-    <Package id="Harp.Olfactometer" version="0.2.0" />
+    <Package id="Harp.Olfactometer" version="0.4.0" />
     <Package id="Harp.StepperDriver" version="0.3.0" />
     <Package id="Hexa.NET.ImGui" version="2.2.8.5" />
     <Package id="Hexa.NET.ImGui.Backends" version="1.0.17.4" />
@@ -74,7 +75,7 @@
     <Package id="SvgNet" version="3.5.0" />
     <Package id="System.Buffers" version="4.6.0" />
     <Package id="System.Collections.Immutable" version="8.0.0" />
-    <Package id="System.Linq.Dynamic" version="1.0.7" />
+    <Package id="System.Linq.Dynamic.Core" version="1.7.1" />
     <Package id="System.Memory" version="4.6.0" />
     <Package id="System.Numerics.Vectors" version="4.6.0" />
     <Package id="System.Resources.Extensions" version="8.0.0" />
@@ -84,6 +85,7 @@
   </Packages>
   <AssemblyReferences>
     <AssemblyReference assemblyName="AllenNeuralDynamics.AindBehaviorServices" />
+    <AssemblyReference assemblyName="AllenNeuralDynamics.AindBehaviorServices.Distributions" />
     <AssemblyReference assemblyName="AllenNeuralDynamics.AindManipulator" />
     <AssemblyReference assemblyName="AllenNeuralDynamics.Core" />
     <AssemblyReference assemblyName="AllenNeuralDynamics.Core.Design" />
@@ -132,10 +134,11 @@
     <AssemblyLocation assemblyName="AForge" processorArchitecture="MSIL" location="Packages/AForge.2.2.5/lib/AForge.dll" />
     <AssemblyLocation assemblyName="AForge.Video" processorArchitecture="MSIL" location="Packages/AForge.Video.2.2.5/lib/AForge.Video.dll" />
     <AssemblyLocation assemblyName="AForge.Video.DirectShow" processorArchitecture="MSIL" location="Packages/AForge.Video.DirectShow.2.2.5/lib/AForge.Video.DirectShow.dll" />
-    <AssemblyLocation assemblyName="AllenNeuralDynamics.AindBehaviorServices" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindBehaviorServices.0.12.0/lib/net472/AllenNeuralDynamics.AindBehaviorServices.dll" />
-    <AssemblyLocation assemblyName="AllenNeuralDynamics.AindManipulator" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindManipulator.0.1.6/lib/net48/AllenNeuralDynamics.AindManipulator.dll" />
-    <AssemblyLocation assemblyName="AllenNeuralDynamics.Core" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.0.4.1/lib/net472/AllenNeuralDynamics.Core.dll" />
-    <AssemblyLocation assemblyName="AllenNeuralDynamics.Core.Design" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.Design.0.3.0/lib/net472/AllenNeuralDynamics.Core.Design.dll" />
+    <AssemblyLocation assemblyName="AllenNeuralDynamics.AindBehaviorServices" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindBehaviorServices.0.13.4/lib/net472/AllenNeuralDynamics.AindBehaviorServices.dll" />
+    <AssemblyLocation assemblyName="AllenNeuralDynamics.AindBehaviorServices.Distributions" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindBehaviorServices.Distributions.0.2.0/lib/net472/AllenNeuralDynamics.AindBehaviorServices.Distributions.dll" />
+    <AssemblyLocation assemblyName="AllenNeuralDynamics.AindManipulator" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindManipulator.0.3.0/lib/net48/AllenNeuralDynamics.AindManipulator.dll" />
+    <AssemblyLocation assemblyName="AllenNeuralDynamics.Core" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.0.3.0/lib/net472/AllenNeuralDynamics.Core.dll" />
+    <AssemblyLocation assemblyName="AllenNeuralDynamics.Core.Design" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.Design.0.4.0/lib/net472/AllenNeuralDynamics.Core.Design.dll" />
     <AssemblyLocation assemblyName="AllenNeuralDynamics.EnvironmentSensor" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.EnvironmentSensor.0.3.0/lib/net462/AllenNeuralDynamics.EnvironmentSensor.dll" />
     <AssemblyLocation assemblyName="AllenNeuralDynamics.HarpUtils" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.HarpUtils.0.3.2/lib/net472/AllenNeuralDynamics.HarpUtils.dll" />
     <AssemblyLocation assemblyName="AllenNeuralDynamics.LicketySplit" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.LicketySplit.0.2.0/lib/net462/AllenNeuralDynamics.LicketySplit.dll" />
@@ -157,8 +160,8 @@
     <AssemblyLocation assemblyName="Bonsai.Harp" processorArchitecture="MSIL" location="Packages/Bonsai.Harp.3.6.1/lib/net462/Bonsai.Harp.dll" />
     <AssemblyLocation assemblyName="Bonsai.Harp.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Harp.Design.3.6.1/lib/net462/Bonsai.Harp.Design.dll" />
     <AssemblyLocation assemblyName="Bonsai.Numerics" processorArchitecture="MSIL" location="Packages/Bonsai.Numerics.0.10.0/lib/net462/Bonsai.Numerics.dll" />
-    <AssemblyLocation assemblyName="Bonsai.Scripting.Expressions" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.2.9.0/lib/net472/Bonsai.Scripting.Expressions.dll" />
-    <AssemblyLocation assemblyName="Bonsai.Scripting.Expressions.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.Design.2.9.0/lib/net472/Bonsai.Scripting.Expressions.Design.dll" />
+    <AssemblyLocation assemblyName="Bonsai.Scripting.Expressions" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.2.10.0/lib/net472/Bonsai.Scripting.Expressions.dll" />
+    <AssemblyLocation assemblyName="Bonsai.Scripting.Expressions.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.Design.2.10.0/lib/net472/Bonsai.Scripting.Expressions.Design.dll" />
     <AssemblyLocation assemblyName="Bonsai.Shaders" processorArchitecture="MSIL" location="Packages/Bonsai.Shaders.2.9.0/lib/net472/Bonsai.Shaders.dll" />
     <AssemblyLocation assemblyName="Bonsai.Shaders.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Shaders.Design.2.9.0/lib/net472/Bonsai.Shaders.Design.dll" />
     <AssemblyLocation assemblyName="Bonsai.Shaders.Rendering" processorArchitecture="MSIL" location="Packages/Bonsai.Shaders.Rendering.2.9.0/lib/net472/Bonsai.Shaders.Rendering.dll" />
@@ -175,7 +178,7 @@
     <AssemblyLocation assemblyName="Harp.AnalogInput" processorArchitecture="MSIL" location="Packages/Harp.AnalogInput.0.2.0/lib/net462/Harp.AnalogInput.dll" />
     <AssemblyLocation assemblyName="Harp.Behavior" processorArchitecture="MSIL" location="Packages/Harp.Behavior.0.2.0/lib/net462/Harp.Behavior.dll" />
     <AssemblyLocation assemblyName="Harp.LoadCells" processorArchitecture="MSIL" location="Packages/Harp.LoadCells.0.2.0/lib/net462/Harp.LoadCells.dll" />
-    <AssemblyLocation assemblyName="Harp.Olfactometer" processorArchitecture="MSIL" location="Packages/Harp.Olfactometer.0.2.0/lib/net462/Harp.Olfactometer.dll" />
+    <AssemblyLocation assemblyName="Harp.Olfactometer" processorArchitecture="MSIL" location="Packages/Harp.Olfactometer.0.4.0/lib/net462/Harp.Olfactometer.dll" />
     <AssemblyLocation assemblyName="Harp.StepperDriver" processorArchitecture="MSIL" location="Packages/Harp.StepperDriver.0.3.0/lib/net462/Harp.StepperDriver.dll" />
     <AssemblyLocation assemblyName="Hexa.NET.ImGui" processorArchitecture="MSIL" location="Packages/Hexa.NET.ImGui.2.2.8.5/lib/netstandard2.0/Hexa.NET.ImGui.dll" />
     <AssemblyLocation assemblyName="Hexa.NET.ImGui.Backends" processorArchitecture="MSIL" location="Packages/Hexa.NET.ImGui.Backends.1.0.17.4/lib/netstandard2.0/Hexa.NET.ImGui.Backends.dll" />
@@ -197,7 +200,7 @@
     <AssemblyLocation assemblyName="SVG" processorArchitecture="MSIL" location="Packages/SvgNet.3.5.0/lib/net462/SVG.dll" />
     <AssemblyLocation assemblyName="System.Buffers" processorArchitecture="MSIL" location="Packages/System.Buffers.4.6.0/lib/net462/System.Buffers.dll" />
     <AssemblyLocation assemblyName="System.Collections.Immutable" processorArchitecture="MSIL" location="Packages/System.Collections.Immutable.8.0.0/lib/net462/System.Collections.Immutable.dll" />
-    <AssemblyLocation assemblyName="System.Linq.Dynamic" processorArchitecture="MSIL" location="Packages/System.Linq.Dynamic.1.0.7/lib/net40/System.Linq.Dynamic.dll" />
+    <AssemblyLocation assemblyName="System.Linq.Dynamic.Core" processorArchitecture="MSIL" location="Packages/System.Linq.Dynamic.Core.1.7.1/lib/net46/System.Linq.Dynamic.Core.dll" />
     <AssemblyLocation assemblyName="System.Memory" processorArchitecture="MSIL" location="Packages/System.Memory.4.6.0/lib/net462/System.Memory.dll" />
     <AssemblyLocation assemblyName="System.Numerics.Vectors" processorArchitecture="MSIL" location="Packages/System.Numerics.Vectors.4.6.0/lib/net462/System.Numerics.Vectors.dll" />
     <AssemblyLocation assemblyName="System.Reactive.Core" processorArchitecture="MSIL" location="Packages/Rx-Core.2.2.5/lib/net45/System.Reactive.Core.dll" />

docs/conf.py

@@ -3,6 +3,8 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from typing import Type
+
 import erdantic as erd
 from pydantic import BaseModel
 
@@ -81,7 +83,7 @@ def linkcode_resolve(domain, info):
 _static_path = "_static"
 
 
-def export_model_diagram(model: BaseModel, root: str = _static_path) -> None:
+def export_model_diagram(model: Type[BaseModel], root: str = _static_path) -> None:
     diagram = erd.create(model)
     diagram.draw(f"{root}/{model.__name__}.svg")
 

examples/rig.py

@@ -1,41 +1,31 @@
 import datetime
 import os
 
-import aind_behavior_services.rig as rig
-from aind_behavior_services.calibration.aind_manipulator import (
+from aind_behavior_services.rig import cameras, visual_stimulation
+from aind_behavior_services.rig.aind_manipulator import (
     AindManipulatorCalibration,
-    AindManipulatorCalibrationInput,
-    AindManipulatorCalibrationOutput,
     Axis,
     AxisConfiguration,
     ManipulatorPosition,
 )
-from aind_behavior_services.calibration.olfactometer import (
+from aind_behavior_services.rig.harp import (
+    HarpBehavior,
+    HarpLicketySplit,
+    HarpSniffDetector,
+    HarpWhiteRabbit,
+)
+from aind_behavior_services.rig.olfactometer import (
     Olfactometer,
     OlfactometerCalibration,
-    OlfactometerCalibrationInput,
-    OlfactometerCalibrationOutput,
     OlfactometerChannel,
     OlfactometerChannelConfig,
     OlfactometerChannelType,
 )
-from aind_behavior_services.calibration.treadmill import (
+from aind_behavior_services.rig.treadmill import (
     Treadmill,
     TreadmillCalibration,
-    TreadmillCalibrationInput,
-    TreadmillCalibrationOutput,
-)
-from aind_behavior_services.calibration.water_valve import (
-    Measurement,
-    WaterValveCalibration,
-    WaterValveCalibrationInput,
-)
-from aind_behavior_services.rig.harp import (
-    HarpBehavior,
-    HarpLicketySplit,
-    HarpSniffDetector,
-    HarpWhiteRabbit,
 )
+from aind_behavior_services.rig.water_valve import Measurement, calibrate_water_valves
 
 from aind_behavior_vr_foraging.rig import (
     AindManipulatorDevice,
@@ -44,85 +34,78 @@
 )
 
 manipulator_calibration = AindManipulatorCalibration(
-    output=AindManipulatorCalibrationOutput(),
-    input=AindManipulatorCalibrationInput(
-        full_step_to_mm=(ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)),
-        axis_configuration=[
-            AxisConfiguration(axis=Axis.Y1, min_limit=-0.01, max_limit=25),
-            AxisConfiguration(axis=Axis.Y2, min_limit=-0.01, max_limit=25),
-            AxisConfiguration(axis=Axis.X, min_limit=-0.01, max_limit=25),
-            AxisConfiguration(axis=Axis.Z, min_limit=-0.01, max_limit=25),
-        ],
-        homing_order=[Axis.Y1, Axis.Y2, Axis.X, Axis.Z],
-        initial_position=ManipulatorPosition(y1=0, y2=0, x=0, z=0),
-    ),
+    full_step_to_mm=(ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)),
+    axis_configuration=[
+        AxisConfiguration(axis=Axis.Y1, min_limit=-0.01, max_limit=25),
+        AxisConfiguration(axis=Axis.Y2, min_limit=-0.01, max_limit=25),
+        AxisConfiguration(axis=Axis.X, min_limit=-0.01, max_limit=25),
+        AxisConfiguration(axis=Axis.Z, min_limit=-0.01, max_limit=25),
+    ],
+    homing_order=[Axis.Y1, Axis.Y2, Axis.X, Axis.Z],
+    initial_position=ManipulatorPosition(y1=0, y2=0, x=0, z=0),
 )
 
 olfactometer_calibration = OlfactometerCalibration(
-    output=OlfactometerCalibrationOutput(),
     date=datetime.datetime.now(),
-    input=OlfactometerCalibrationInput(
-        channel_config={
-            OlfactometerChannel.Channel0: OlfactometerChannelConfig(
-                channel_index=OlfactometerChannel.Channel0,
-                channel_type=OlfactometerChannelType.ODOR,
-                flow_rate_capacity=100,
-                flow_rate=100,
-                odorant="Amyl Acetate",
-                odorant_dilution=1.5,
-            ),
-            OlfactometerChannel.Channel1: OlfactometerChannelConfig(
-                channel_index=OlfactometerChannel.Channel1,
-                channel_type=OlfactometerChannelType.ODOR,
-                flow_rate_capacity=100,
-                flow_rate=100,
-                odorant="Banana",
-                odorant_dilution=1.5,
-            ),
-            OlfactometerChannel.Channel2: OlfactometerChannelConfig(
-                channel_index=OlfactometerChannel.Channel2,
-                channel_type=OlfactometerChannelType.ODOR,
-                flow_rate_capacity=100,
-                flow_rate=100,
-                odorant="Apple",
-                odorant_dilution=1.5,
-            ),
-            OlfactometerChannel.Channel3: OlfactometerChannelConfig(
-                channel_index=OlfactometerChannel.Channel3,
-                channel_type=OlfactometerChannelType.CARRIER,
-                flow_rate_capacity=1000,
-            ),
-        }
-    ),
+    channel_config={
+        OlfactometerChannel.Channel0: OlfactometerChannelConfig(
+            channel_index=OlfactometerChannel.Channel0,
+            channel_type=OlfactometerChannelType.ODOR,
+            flow_rate_capacity=100,
+            flow_rate=100,
+            odorant="Amyl Acetate",
+            odorant_dilution=1.5,
+        ),
+        OlfactometerChannel.Channel1: OlfactometerChannelConfig(
+            channel_index=OlfactometerChannel.Channel1,
+            channel_type=OlfactometerChannelType.ODOR,
+            flow_rate_capacity=100,
+            flow_rate=100,
+            odorant="Banana",
+            odorant_dilution=1.5,
+        ),
+        OlfactometerChannel.Channel2: OlfactometerChannelConfig(
+            channel_index=OlfactometerChannel.Channel2,
+            channel_type=OlfactometerChannelType.ODOR,
+            flow_rate_capacity=100,
+            flow_rate=100,
+            odorant="Apple",
+            odorant_dilution=1.5,
+        ),
+        OlfactometerChannel.Channel3: OlfactometerChannelConfig(
+            channel_index=OlfactometerChannel.Channel3,
+            channel_type=OlfactometerChannelType.CARRIER,
+            flow_rate_capacity=1000,
+        ),
+    },
 )
 
-water_valve_input = WaterValveCalibrationInput(
+water_valve_calibration = calibrate_water_valves(
     measurements=[
         Measurement(valve_open_interval=0.2, valve_open_time=0.01, water_weight=[0.6, 0.6], repeat_count=200),
         Measurement(valve_open_interval=0.2, valve_open_time=0.02, water_weight=[1.2, 1.2], repeat_count=200),
     ]
 )
-water_valve_calibration = WaterValveCalibration(
-    input=water_valve_input, output=water_valve_input.calibrate_output(), date=datetime.datetime.now()
-)
 
-video_writer = rig.cameras.VideoWriterFfmpeg(frame_rate=120, container_extension="mp4")
+video_writer = cameras.VideoWriterFfmpeg(frame_rate=120, container_extension="mp4")
 
 rig = AindVrForagingRig(
+    data_directory=r"C:/data",
+    computer_name="TestRigComputer",
     rig_name="test_rig",
-    triggered_camera_controller=rig.cameras.CameraController[rig.cameras.SpinnakerCamera](
+    triggered_camera_controller=cameras.CameraController[cameras.SpinnakerCamera](
         frame_rate=120,
         cameras={
-            "FaceCamera": rig.cameras.SpinnakerCamera(
+            "FaceCamera": cameras.SpinnakerCamera(
                 serial_number="SerialNumber", binning=1, exposure=5000, gain=0, video_writer=video_writer
             ),
-            "SideCamera": rig.cameras.SpinnakerCamera(
+            "SideCamera": cameras.SpinnakerCamera(
                 serial_number="SerialNumber", binning=1, exposure=5000, gain=0, video_writer=video_writer
             ),
         },
     ),
-    monitoring_camera_controller=rig.cameras.CameraController[rig.cameras.WebCamera](
-        cameras={"WebCam0": rig.cameras.WebCamera(index=0)}
+    monitoring_camera_controller=cameras.CameraController[cameras.WebCamera](
+        cameras={"WebCam0": cameras.WebCamera(index=0)}
     ),
     harp_behavior=HarpBehavior(port_name="COM3"),
     harp_olfactometer=Olfactometer(port_name="COM4", calibration=olfactometer_calibration),
@@ -133,14 +116,11 @@
     harp_treadmill=Treadmill(
         port_name="COM8",
         calibration=TreadmillCalibration(
-            input=TreadmillCalibrationInput(),
-            output=TreadmillCalibrationOutput(
-                wheel_diameter=15, pulses_per_revolution=28800, brake_lookup_calibration=[[0, 0], [1, 65535]]
-            ),
+            wheel_diameter=15, pulses_per_revolution=28800, brake_lookup_calibration=[[0, 0], [1, 65535]]
         ),
     ),
     manipulator=AindManipulatorDevice(port_name="COM9", calibration=manipulator_calibration),
-    screen=rig.visual_stimulation.Screen(display_index=1),
+    screen=visual_stimulation.ScreenAssembly(display_index=1),
     calibration=RigCalibration(water_valve=water_valve_calibration),
 )
 

examples/session.py

@@ -1,15 +1,13 @@
 import datetime
 import os
 
-from aind_behavior_services.session import AindBehaviorSessionModel
+from aind_behavior_services.session import Session
 
-session = AindBehaviorSessionModel(
+session = Session(
     date=datetime.datetime.now(tz=datetime.timezone.utc),
     experiment="AindVrForaging",
-    root_path="c://",
     subject="test",
     notes="test session",
-    experiment_version="0.1.0",
     allow_dirty_repo=True,
     skip_hardware_validation=False,
     experimenter=["Foo", "Bar"],