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Various updates to reward and logging #10

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Merged
bruno-f-cruz merged 5 commits into from
May 10, 2025
Merged

Various updates to reward and logging #10

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aa03e46
Update services and regenerate schemas
bruno-f-cruz May 10, 2025
91a4511
Fix bugs and remove monitoring cameras
bruno-f-cruz May 10, 2025
7e3f4e4
Update workflow to latest bonsai packages
bruno-f-cruz May 10, 2025
5caa925
Update examples to latest api
bruno-f-cruz May 10, 2025
269c4d0
Improve logging
bruno-f-cruz May 10, 2025
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35 changes: 16 additions & 19 deletions bonsai/Bonsai.config
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,12 @@
<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="0.8.0" />
<Package id="AllenNeuralDynamics.AindBehaviorServices" version="0.10.2" />
<Package id="AllenNeuralDynamics.AindManipulator" version="0.1.6" />
<Package id="AllenNeuralDynamics.Core" version="0.2.9" />
<Package id="AllenNeuralDynamics.Core.Design" version="0.2.2" />
<Package id="AllenNeuralDynamics.Core" version="0.4.0" />
<Package id="AllenNeuralDynamics.Core.Design" version="0.2.3" />
<Package id="AllenNeuralDynamics.EnvironmentSensor" version="0.2.0" />
<Package id="AllenNeuralDynamics.HarpUtils" version="0.1.9" />
<Package id="AllenNeuralDynamics.HarpUtils" version="0.3.2" />
<Package id="AllenNeuralDynamics.LicketySplit" version="0.2.0" />
<Package id="AllenNeuralDynamics.LicketySplitLickDetector" version="0.1.0-preview20231016" />
<Package id="AllenNeuralDynamics.SniffDetector" version="0.2.0" />
Expand Down Expand Up @@ -49,12 +49,11 @@
<Package id="Bonsai.Windows.Input" version="2.7.0" />
<Package id="Bonsai.ZeroMQ" version="0.2.0" />
<Package id="BonVision" version="0.11.0" />
<Package id="Harp.AnalogInput" version="0.1.0" />
<Package id="Harp.AnalogInput" version="0.2.0" />
<Package id="Harp.Behavior" version="0.1.0" />
<Package id="Harp.LoadCells" version="0.1.0" />
<Package id="Harp.Olfactometer" version="0.1.0-build231127" />
<Package id="Harp.LoadCells" version="0.2.0" />
<Package id="Harp.Olfactometer" version="0.2.0" />
<Package id="Harp.StepperDriver" version="0.3.0" />
<Package id="Harp.TimestampGeneratorGen3" version="0.1.1" />
<Package id="jacobslusser.ScintillaNET" version="3.6.3" />
<Package id="LibGit2Sharp" version="0.27.2" />
<Package id="LibGit2Sharp.NativeBinaries" version="2.0.320" />
Expand Down Expand Up @@ -82,7 +81,7 @@
<Package id="System.Runtime.CompilerServices.Unsafe" version="6.0.0" />
<Package id="System.Threading.Tasks.Extensions" version="4.5.4" />
<Package id="System.ValueTuple" version="4.5.0" />
<Package id="YamlDotNet" version="13.1.1" />
<Package id="YamlDotNet" version="16.0.0" />
<Package id="ZedGraph" version="5.1.7" />
</Packages>
<AssemblyReferences>
Expand Down Expand Up @@ -133,18 +132,17 @@
<AssemblyReference assemblyName="Harp.LoadCells" />
<AssemblyReference assemblyName="Harp.Olfactometer" />
<AssemblyReference assemblyName="Harp.StepperDriver" />
<AssemblyReference assemblyName="Harp.TimestampGeneratorGen3" />
</AssemblyReferences>
<AssemblyLocations>
<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.0.8.0/lib/net472/AllenNeuralDynamics.AindBehaviorServices.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.AindBehaviorServices" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindBehaviorServices.0.10.2/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.0.2.9/lib/net472/AllenNeuralDynamics.Core.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.Core.Design" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.Design.0.2.2/lib/net472/AllenNeuralDynamics.Core.Design.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.Core" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.0.4.0/lib/net472/AllenNeuralDynamics.Core.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.Core.Design" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.Core.Design.0.2.3/lib/net472/AllenNeuralDynamics.Core.Design.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.EnvironmentSensor" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.EnvironmentSensor.0.2.0/lib/net462/AllenNeuralDynamics.EnvironmentSensor.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.HarpUtils" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.HarpUtils.0.1.9/lib/net472/AllenNeuralDynamics.HarpUtils.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" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.LicketySplitLickDetector" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.LicketySplitLickDetector.0.1.0-preview20231016/lib/net462/AllenNeuralDynamics.LicketySplitLickDetector.dll" />
<AssemblyLocation assemblyName="AllenNeuralDynamics.SniffDetector" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.SniffDetector.0.2.0/lib/net462/AllenNeuralDynamics.SniffDetector.dll" />
Expand Down Expand Up @@ -183,12 +181,11 @@
<AssemblyLocation assemblyName="Bonsai.Windows.Input" processorArchitecture="MSIL" location="Packages/Bonsai.Windows.Input.2.7.0/lib/net462/Bonsai.Windows.Input.dll" />
<AssemblyLocation assemblyName="Bonsai.ZeroMQ" processorArchitecture="MSIL" location="Packages/Bonsai.ZeroMQ.0.2.0/lib/net472/Bonsai.ZeroMQ.dll" />
<AssemblyLocation assemblyName="BonVision" processorArchitecture="MSIL" location="Packages/BonVision.0.11.0/lib/net462/BonVision.dll" />
<AssemblyLocation assemblyName="Harp.AnalogInput" processorArchitecture="MSIL" location="Packages/Harp.AnalogInput.0.1.0/lib/net462/Harp.AnalogInput.dll" />
<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.0.1.0/lib/net462/Harp.Behavior.dll" />
<AssemblyLocation assemblyName="Harp.LoadCells" processorArchitecture="MSIL" location="Packages/Harp.LoadCells.0.1.0/lib/net462/Harp.LoadCells.dll" />
<AssemblyLocation assemblyName="Harp.Olfactometer" processorArchitecture="MSIL" location="Packages/Harp.Olfactometer.0.1.0-build231127/lib/net462/Harp.Olfactometer.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.StepperDriver" processorArchitecture="MSIL" location="Packages/Harp.StepperDriver.0.3.0/lib/net462/Harp.StepperDriver.dll" />
<AssemblyLocation assemblyName="Harp.TimestampGeneratorGen3" processorArchitecture="MSIL" location="Packages/Harp.TimestampGeneratorGen3.0.1.1/lib/net462/Harp.TimestampGeneratorGen3.dll" />
<AssemblyLocation assemblyName="LibGit2Sharp" processorArchitecture="MSIL" location="Packages/LibGit2Sharp.0.27.2/lib/net472/LibGit2Sharp.dll" />
<AssemblyLocation assemblyName="Markdig" processorArchitecture="MSIL" location="Packages/Markdig.0.18.1/lib/net40/Markdig.dll" />
<AssemblyLocation assemblyName="MathNet.Numerics" processorArchitecture="MSIL" location="Packages/MathNet.Numerics.4.15.0/lib/net461/MathNet.Numerics.dll" />
Expand Down Expand Up @@ -218,7 +215,7 @@
<AssemblyLocation assemblyName="System.Runtime.CompilerServices.Unsafe" processorArchitecture="MSIL" location="Packages/System.Runtime.CompilerServices.Unsafe.6.0.0/lib/net461/System.Runtime.CompilerServices.Unsafe.dll" />
<AssemblyLocation assemblyName="System.Threading.Tasks.Extensions" processorArchitecture="MSIL" location="Packages/System.Threading.Tasks.Extensions.4.5.4/lib/net461/System.Threading.Tasks.Extensions.dll" />
<AssemblyLocation assemblyName="System.ValueTuple" processorArchitecture="MSIL" location="Packages/System.ValueTuple.4.5.0/lib/net47/System.ValueTuple.dll" />
<AssemblyLocation assemblyName="YamlDotNet" processorArchitecture="MSIL" location="Packages/YamlDotNet.13.1.1/lib/net47/YamlDotNet.dll" />
<AssemblyLocation assemblyName="YamlDotNet" processorArchitecture="MSIL" location="Packages/YamlDotNet.16.0.0/lib/net47/YamlDotNet.dll" />
<AssemblyLocation assemblyName="ZedGraph" processorArchitecture="MSIL" location="Packages/ZedGraph.5.1.7/lib/net35-Client/ZedGraph.dll" />
</AssemblyLocations>
<LibraryFolders>
Expand Down
4 changes: 2 additions & 2 deletions examples/example.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,8 @@ 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.HarpLickometer(port_name="COM8"),
harp_clock_generator=rig.HarpClockGenerator(port_name="COM3"),
harp_lickometer=rig.HarpLicketySplit(port_name="COM8"),
harp_clock_generator=rig.HarpWhiteRabbit(port_name="COM3"),
harp_analog_input=None,
manipulator=AindManipulatorDevice(port_name="COM5", calibration=manipulator_calibration),
calibration=RigCalibration(water_valve=water_valve_calibration),
Expand Down
31 changes: 15 additions & 16 deletions examples/example_w_luts.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
import datetime
import os

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
Expand Down Expand Up @@ -82,29 +81,25 @@ def mock_rig() -> AindTelekinesisRig:
container_extension="avi",
)

load_cells_calibration = lcc.LoadCellsCalibration(
output=lcc.LoadCellsCalibrationOutput(),
input=lcc.LoadCellsCalibrationInput(),
date=datetime.datetime.now(),
)
return AindTelekinesisRig(
rig_name="BCI_Bonsai_i",
triggered_camera_controller=rig.CameraController[rig.SpinnakerCamera](
frame_rate=25,
cameras={
"MainCamera": rig.SpinnakerCamera(
serial_number="SerialNumber",
serial_number="23381093",
binning=2,
exposure=10000,
gain=20,
video_writer=video_writer,
adc_bit_depth=None,
)
},
),
harp_load_cells=lcc.LoadCells(port_name="COM4", calibration=load_cells_calibration),
harp_behavior=rig.HarpBehavior(port_name="COM6"),
harp_lickometer=rig.HarpLickometer(port_name="COM8"),
harp_clock_generator=rig.HarpClockGenerator(port_name="COM3"),
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_analog_input=None,
manipulator=AindManipulatorDevice(port_name="COM5", calibration=manipulator_calibration),
calibration=RigCalibration(water_valve=water_valve_calibration),
Expand Down Expand Up @@ -133,7 +128,7 @@ def mock_task_logic() -> tl.AindTelekinesisTaskLogic:
continuous_feedback=tl.ManipulatorFeedback(converter_lut_input=[0, 1], converter_lut_output=[0, 15]),
),
),
action_source_0=tl.BehaviorAnalogInputActionSource(channel=0),
action_source_0=tl.BehaviorAnalogInputActionSource(channel=1),
lut_reference="linear_normalized_to_1",
)

Expand All @@ -149,7 +144,7 @@ def mock_task_logic() -> tl.AindTelekinesisTaskLogic:
operation_control=tl.OperationControl(
action_luts={
"linear_normalized_to_1": tl.ActionLookUpTableFactory(
path=f"{LOCAL_ASSET_FOLDER}/1d_ramp.tiff",
path=f"../{LOCAL_ASSET_FOLDER}/1d_ramp.tiff",
offset=0,
scale=1,
action0_max=5,
Expand All @@ -158,7 +153,7 @@ def mock_task_logic() -> tl.AindTelekinesisTaskLogic:
action1_min=0,
),
"linear_normalized_to_5": tl.ActionLookUpTableFactory(
path=f"{LOCAL_ASSET_FOLDER}/1d_ramp.tiff",
path=f"../{LOCAL_ASSET_FOLDER}/1d_ramp.tiff",
offset=0,
scale=5,
action0_max=5,
Expand Down Expand Up @@ -206,13 +201,17 @@ def main(path_seed: str = "{LOCAL_ASSET_FOLDER}/{schema}.json"):
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)
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]

for model in models:
with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f:
with open(
path_seed.format(schema=model.__class__.__name__, LOCAL_ASSET_FOLDER=LOCAL_ASSET_FOLDER),
"w",
encoding="utf-8",
) as f:
f.write(model.model_dump_json(indent=2))


Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ readme = "README.md"
dynamic = ["version"]

dependencies = [
"aind_behavior_services>=0.9, <0.10",
"aind_behavior_services<0.11",
"numpy",
"pillow"
]
Expand All @@ -30,7 +30,7 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Telekinesis/re

[project.optional-dependencies]

launcher = ["aind_behavior_experiment_launcher[aind-services]>=0.3, <0.4"]
launcher = ["aind_behavior_experiment_launcher[aind-services]"]

dev = [
"aind_behavior_telekinesis[launcher]",
Expand Down
6 changes: 3 additions & 3 deletions src/DataSchemas/aind_behavior_session_model.json
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
{
"properties": {
"aind_behavior_services_pkg_version": {
"default": "0.9.0",
"default": "0.10.2",
"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"
},
"version": {
"const": "0.3.0",
"default": "0.3.0",
"const": "0.3.1",
"default": "0.3.1",
"title": "Version",
"type": "string"
},
Expand Down
9 changes: 3 additions & 6 deletions src/DataSchemas/aind_behavior_telekinesis/rig.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,13 +78,10 @@ class AindTelekinesisRig(AindBehaviorRigModel):
triggered_camera_controller: rig.CameraController[rig.SpinnakerCamera] = Field(
..., description="Required camera controller to triggered cameras."
)
monitoring_camera_controller: Optional[rig.CameraController[rig.WebCamera]] = Field(
default=None, description="Optional camera controller for monitoring cameras."
)
harp_behavior: rig.HarpBehavior = Field(..., description="Harp behavior")
harp_lickometer: rig.HarpLickometer = Field(..., description="Harp lickometer")
harp_load_cells: Optional[lcc.LoadCells] = Field(..., description="Harp load cells")
harp_clock_generator: rig.HarpClockGenerator = Field(..., description="Harp clock generator")
harp_lickometer: rig.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(
default=None, description="Harp environment sensor"
Expand Down
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