Add support for multiple olfactometers

bonsai/Bonsai.config

@@ -3,7 +3,7 @@
   <Packages>
     <Package id="AllenNeuralDynamics.AindBehaviorServices" version="0.13.4" />
     <Package id="AllenNeuralDynamics.AindBehaviorServices.Distributions" version="0.2.0" />
-    <Package id="AllenNeuralDynamics.AindManipulator" version="0.4.0" />
+    <Package id="AllenNeuralDynamics.AindManipulator" version="0.4.1" />
     <Package id="AllenNeuralDynamics.AlicatFlowmeter" version="0.1.0" />
     <Package id="AllenNeuralDynamics.Core" version="0.4.1" />
     <Package id="AllenNeuralDynamics.Core.Design" version="0.4.0" />
@@ -114,7 +114,7 @@
   <AssemblyLocations>
     <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.0.4.0/lib/net48/AllenNeuralDynamics.AindManipulator.dll" />
+    <AssemblyLocation assemblyName="AllenNeuralDynamics.AindManipulator" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AindManipulator.0.4.1/lib/net48/AllenNeuralDynamics.AindManipulator.dll" />
     <AssemblyLocation assemblyName="AllenNeuralDynamics.AlicatFlowmeter" processorArchitecture="MSIL" location="Packages/AllenNeuralDynamics.AlicatFlowmeter.0.1.0/lib/net472/AllenNeuralDynamics.AlicatFlowmeter.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.0.4.0/lib/net472/AllenNeuralDynamics.Core.Design.dll" />

examples/olfactometer.py

@@ -9,27 +9,8 @@
 from aind_behavior_device_olfactometer import rig, task_logic
 from aind_behavior_device_olfactometer.rig import AlicatFlowmeter
 
-olf_calibration = olf.OlfactometerCalibration(
-    channel_config={
-        olf.OlfactometerChannel.Channel0: olf.OlfactometerChannelConfig(
-            channel_index=olf.OlfactometerChannel.Channel0,
-            channel_type=olf.OlfactometerChannelType.ODOR,
-            flow_rate=100,
-            odorant="Banana",
-            odorant_dilution=0.1,
-        ),
-        olf.OlfactometerChannel.Channel3: olf.OlfactometerChannelConfig(
-            channel_index=olf.OlfactometerChannel.Channel3,
-            channel_type=olf.OlfactometerChannelType.CARRIER,
-            odorant="Air",
-        ),
-    }
-)
-
-
 calibration_logic = task_logic.OlfactometerCalibrationLogic(
     task_parameters=task_logic.OlfactometerCalibrationParameters(
-        channel_config=olf_calibration.channel_config,
         full_flow_rate=1000,
         n_repeats_per_stimulus=10,
         time_on=2,
@@ -57,11 +38,54 @@
     initial_position=man.ManipulatorPosition(y1=0, y2=0, x=0, z=0),
 )
 
+
+olf_calibration = olf.OlfactometerCalibration(
+    channel_config={
+        olf.OlfactometerChannel.Channel0: olf.OlfactometerChannelConfig(
+            channel_index=olf.OlfactometerChannel.Channel0,
+            channel_type=olf.OlfactometerChannelType.ODOR,
+            flow_rate=100,
+            odorant="Banana",
+            odorant_dilution=0.1,
+        ),
+        olf.OlfactometerChannel.Channel1: olf.OlfactometerChannelConfig(
+            channel_index=olf.OlfactometerChannel.Channel1,
+            channel_type=olf.OlfactometerChannelType.ODOR,
+            flow_rate=100,
+            odorant="None",
+            odorant_dilution=0.0,
+        ),
+        olf.OlfactometerChannel.Channel2: olf.OlfactometerChannelConfig(
+            channel_index=olf.OlfactometerChannel.Channel2,
+            channel_type=olf.OlfactometerChannelType.ODOR,
+            flow_rate=100,
+            odorant="None",
+            odorant_dilution=0.0,
+        ),
+        olf.OlfactometerChannel.Channel3: olf.OlfactometerChannelConfig(
+            channel_index=olf.OlfactometerChannel.Channel3,
+            channel_type=olf.OlfactometerChannelType.CARRIER,
+            odorant="Air",
+            flow_rate_capacity=1000,
+        ),
+    }
+)
+
+extra_olf = olf_calibration.model_copy(deep=True)
+extra_olf.channel_config[olf.OlfactometerChannel.Channel3] = olf.OlfactometerChannelConfig(
+    channel_index=olf.OlfactometerChannel.Channel3,
+    channel_type=olf.OlfactometerChannelType.ODOR,
+    flow_rate=100,
+    odorant="Vanilla",
+)
+
+print(olf_calibration)
 _rig = rig.OlfactometerCalibrationRig(
     computer_name="TestPC",
-    data_directory="c:/data",
+    data_directory=r"C:/data",
     rig_name="OlfactometerRig",
     harp_olfactometer=olf.Olfactometer(port_name="COM10", calibration=olf_calibration),
+    harp_olfactometer_extension=[olf.Olfactometer(port_name="COM11", calibration=extra_olf)],
     harp_analog_input=HarpAnalogInput(port_name="COM8"),
     harp_clock_generator=HarpWhiteRabbit(port_name="COM9"),
     harp_manipulator=man.AindManipulator(port_name="COM7", calibration=manipulator_calibration),

schema/aind_behavior_device_olfactometer.json

@@ -675,22 +675,11 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.13.6",
+          "default": "0.13.7",
           "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-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
         },
-        "channel_config": {
-          "additionalProperties": {
-            "$ref": "#/$defs/OlfactometerChannelConfig"
-          },
-          "description": "Configuration of olfactometer channels",
-          "propertyNames": {
-            "$ref": "#/$defs/OlfactometerChannel"
-          },
-          "title": "Channel Config",
-          "type": "object"
-        },
         "full_flow_rate": {
           "default": 1000,
           "description": "Full flow rate of the olfactometer",
@@ -727,7 +716,7 @@
     "OlfactometerCalibrationRig": {
       "properties": {
         "aind_behavior_services_pkg_version": {
-          "default": "0.13.6",
+          "default": "0.13.7",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
@@ -758,6 +747,14 @@
           "$ref": "#/$defs/Olfactometer",
           "title": "Olfactometer device"
         },
+        "harp_olfactometer_extension": {
+          "description": "A collection of subordinate olfactometers that can be added to increase the number of independently delivered odors. The order of the list determines the order by which odors are numbered",
+          "items": {
+            "$ref": "#/$defs/Olfactometer"
+          },
+          "title": "Harp Olfactometer Extension",
+          "type": "array"
+        },
         "harp_analog_input": {
           "$ref": "#/$defs/HarpAnalogInput",
           "title": "Analog input device"
@@ -882,14 +879,14 @@
     "Session": {
       "properties": {
         "aind_behavior_services_pkg_version": {
-          "default": "0.13.6",
+          "default": "0.13.7",
           "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": "0.13.6",
-          "default": "0.13.6",
+          "const": "0.13.7",
+          "default": "0.13.7",
           "title": "Version",
           "type": "string"
         },

scripts/aind_launcher.py → scripts/aind-launcher.py

@@ -9,10 +9,11 @@
 from clabe.data_transfer.robocopy import RobocopyService, RobocopySettings
 from clabe.launcher import Launcher, LauncherCliArgs, experiment
 from clabe.pickers import DefaultBehaviorPicker, DefaultBehaviorPickerSettings
+from clabe.utils import utcnow
 from pydantic_settings import CliApp
 
 from aind_behavior_device_olfactometer.rig import OlfactometerCalibrationRig
-from aind_behavior_device_olfactometer.task_logic import OlfactometerCalibrationLogic
+from aind_behavior_device_olfactometer.task_logic import OlfactometerCalibrationLogic, OlfactometerCalibrationParameters
 
 logger = logging.getLogger(__name__)
 
@@ -25,13 +26,30 @@ async def calibration_experiment(launcher: Launcher) -> None:
         settings=DefaultBehaviorPickerSettings(
             config_library_dir=r"\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceOlfactometer",
         ),
-        experimenter_validator=None,
     )
+    experimenter = picker.prompt_experimenter()
+    assert experimenter is not None and len(experimenter) > 0, (
+        "Experimenter selection is required to proceed with the experiment setup."
+    )
+    # Pick and register session
+    session = Session(
+        subject="CALIBRATION",
+        experiment="CALIBRATION",
+        date=utcnow(),
+        allow_dirty_repo=False,
+        experimenter=experimenter,
+        notes="Session for rig calibration. No actual experiment data will be recorded.",
+    )
+
+    task_logic = OlfactometerCalibrationLogic(task_parameters=OlfactometerCalibrationParameters())
+    launcher.ui_helper.print(f"Loading task logic with default parameters: {task_logic.task_parameters}")
+    skip_manual_task = launcher.ui_helper.prompt_yes_no_question(
+        "Skip manual task parameter configuration and use defaults?"
+    )
+    if not skip_manual_task:
+        task_logic = picker.pick_task(OlfactometerCalibrationLogic)
 
-    session = picker.pick_session(Session)
-    task_logic = picker.pick_task(OlfactometerCalibrationLogic)
     rig = picker.pick_rig(OlfactometerCalibrationRig)
-    ensure_rig_and_computer_name(rig)
 
     launcher.register_session(session, rig.data_directory)
 
@@ -67,7 +85,7 @@ async def calibration_experiment(launcher: Launcher) -> None:
             runner.run_all_with_progress(reporter=reporter)
             webbrowser.open(qc_path.as_uri(), new=2)
         except Exception as e:
-            logger.error(f"Failed to run data QC: {e}")
+            logger.error("Failed to run data QC: %s", e)
 
     # Transfer data
     is_transfer = picker.ui_helper.prompt_yes_no_question("Would you like to transfer data?")
@@ -80,37 +98,6 @@ async def calibration_experiment(launcher: Launcher) -> None:
     return
 
 
-def ensure_rig_and_computer_name(rig: OlfactometerCalibrationRig) -> None:
-    """Ensures rig and computer name are set from environment variables if available, otherwise defaults to rig configuration values."""
-
-    import os
-
-    rig_name = os.environ.get("aibs_comp_id", None)
-    computer_name = os.environ.get("hostname", None)
-
-    if rig_name is None:
-        logger.warning(
-            "'aibs_comp_id' environment variable not set. Defaulting to rig name from configuration. %s", rig.rig_name
-        )
-        rig_name = rig.rig_name
-    if computer_name is None:
-        computer_name = rig.computer_name
-        logger.warning(
-            "'hostname' environment variable not set. Defaulting to computer name from configuration. %s",
-            rig.computer_name,
-        )
-
-    if rig_name != rig.rig_name or computer_name != rig.computer_name:
-        logger.warning(
-            "Rig name or computer name from environment variables do not match the rig configuration. "
-            "Forcing rig name: %s and computer name: %s from environment variables.",
-            rig_name,
-            computer_name,
-        )
-        rig.rig_name = rig_name
-        rig.computer_name = computer_name
-
-
 class ClabeCli(LauncherCliArgs):
     def cli_cmd(self):
         launcher = Launcher(settings=self)

src/Extensions.csproj

@@ -5,12 +5,13 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Bonsai.Core" Version="2.8.1" />
+    <PackageReference Include="Bonsai.Core" Version="2.9.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
     <PackageReference Include="Bonsai.Harp" Version="3.6.1" />
     <PackageReference Include="AllenNeuralDynamics.AindBehaviorServices" Version="0.13.4" />
     <PackageReference Include="AllenNeuralDynamics.AindBehaviorServices.Distributions" Version="0.2.0" />
     <PackageReference Include="AllenNeuralDynamics.AindManipulator" Version="0.3.0" />
+    <PackageReference Include="Harp.Olfactometer" Version="0.4.0" />
   </ItemGroup>
 
 </Project>