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Add support for multiple olfactometers #24

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154ba6d
Update schema to hold multiple olfactometers
bruno-f-cruz Apr 20, 2026
bd71db1
Fix namespace issues
bruno-f-cruz Apr 20, 2026
629f6ee
Refactor logic to support multiple olfactometers
bruno-f-cruz Apr 21, 2026
8e45409
Add qc and data contract
bruno-f-cruz Apr 21, 2026
1f6ea67
Fix example
bruno-f-cruz Apr 21, 2026
9c0c199
Refactor package to simplify task logic and odor definition
bruno-f-cruz Apr 25, 2026
2b7317d
Update example against refactored definition
bruno-f-cruz Apr 25, 2026
40c2d36
Fix the number of channels assignment
bruno-f-cruz Apr 28, 2026
35ed7f9
Align names with VrForaging
bruno-f-cruz Apr 28, 2026
781b1f4
Set the number of olfactometer channels
bruno-f-cruz Apr 28, 2026
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6 changes: 0 additions & 6 deletions examples/clabe.yml
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63 changes: 43 additions & 20 deletions examples/olfactometer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -57,11 +38,53 @@
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",
),
}
)

extra_olf = olf_calibration.model_copy()
extra_olf.channel_config[olf.OlfactometerChannel.Channel3] = olf.OlfactometerChannelConfig(
channel_index=olf.OlfactometerChannel.Channel3,
channel_type=olf.OlfactometerChannelType.ODOR,
flow_rate=100,
odorant="Vanilla",
)


_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),
Expand Down
29 changes: 13 additions & 16 deletions schema/aind_behavior_device_olfactometer.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": "#/$defs/OlfactometerChannel"
},
"title": "Channel Config",
"type": "object"
},
"full_flow_rate": {
"default": 1000,
"description": "Full flow rate of the olfactometer",
Expand Down Expand Up @@ -727,7 +716,7 @@
"OlfactometerCalibrationRig": {
"properties": {
"aind_behavior_services_pkg_version": {
"default": "0.13.6",
"default": "0.13.7",
"pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
"title": "aind_behavior_services package version",
"type": "string"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
},
Expand Down
46 changes: 11 additions & 35 deletions scripts/aind_launcher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
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__)

Expand All @@ -29,9 +29,16 @@ async def calibration_experiment(launcher: Launcher) -> None:
)

session = picker.pick_session(Session)
task_logic = picker.pick_task(OlfactometerCalibrationLogic)

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)

rig = picker.pick_rig(OlfactometerCalibrationRig)
ensure_rig_and_computer_name(rig)

launcher.register_session(session, rig.data_directory)

Expand Down Expand Up @@ -67,7 +74,7 @@ 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?")
Expand All @@ -80,37 +87,6 @@ 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)
Expand Down
3 changes: 2 additions & 1 deletion src/Extensions.csproj
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
55 changes: 29 additions & 26 deletions src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -994,8 +994,6 @@ public partial class OlfactometerCalibrationParameters

private string _aindBehaviorServicesPkgVersion;

private System.Collections.Generic.Dictionary<OlfactometerChannel, OlfactometerChannelConfig> _channelConfig;

private double _fullFlowRate;

private int _nRepeatsPerStimulus;
Expand All @@ -1006,7 +1004,7 @@ public partial class OlfactometerCalibrationParameters

public OlfactometerCalibrationParameters()
{
_aindBehaviorServicesPkgVersion = "0.13.6";
_aindBehaviorServicesPkgVersion = "0.13.7";
_fullFlowRate = 1000D;
_nRepeatsPerStimulus = 1;
_timeOn = 1D;
Expand All @@ -1017,7 +1015,6 @@ protected OlfactometerCalibrationParameters(OlfactometerCalibrationParameters ot
{
_rngSeed = other._rngSeed;
_aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion;
_channelConfig = other._channelConfig;
_fullFlowRate = other._fullFlowRate;
_nRepeatsPerStimulus = other._nRepeatsPerStimulus;
_timeOn = other._timeOn;
Expand Down Expand Up @@ -1054,24 +1051,6 @@ public string AindBehaviorServicesPkgVersion
}
}

/// <summary>
/// Configuration of olfactometer channels
/// </summary>
[System.Xml.Serialization.XmlIgnoreAttribute()]
[Newtonsoft.Json.JsonPropertyAttribute("channel_config")]
[System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")]
public System.Collections.Generic.Dictionary<OlfactometerChannel, OlfactometerChannelConfig> ChannelConfig
{
get
{
return _channelConfig;
}
set
{
_channelConfig = value;
}
}

/// <summary>
/// Full flow rate of the olfactometer
/// </summary>
Expand Down Expand Up @@ -1154,7 +1133,6 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
{
stringBuilder.Append("RngSeed = " + _rngSeed + ", ");
stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", ");
stringBuilder.Append("ChannelConfig = " + _channelConfig + ", ");
stringBuilder.Append("FullFlowRate = " + _fullFlowRate + ", ");
stringBuilder.Append("NRepeatsPerStimulus = " + _nRepeatsPerStimulus + ", ");
stringBuilder.Append("TimeOn = " + _timeOn + ", ");
Expand Down Expand Up @@ -1195,6 +1173,8 @@ public partial class OlfactometerCalibrationRig

private Olfactometer _harpOlfactometer;

private System.Collections.Generic.List<Olfactometer> _harpOlfactometerExtension;

private HarpAnalogInput _harpAnalogInput;

private HarpWhiteRabbit _harpClockGenerator;
Expand All @@ -1205,9 +1185,10 @@ public partial class OlfactometerCalibrationRig

public OlfactometerCalibrationRig()
{
_aindBehaviorServicesPkgVersion = "0.13.6";
_aindBehaviorServicesPkgVersion = "0.13.7";
_version = "0.2.0-rc1";
_harpOlfactometer = new Olfactometer();
_harpOlfactometerExtension = new System.Collections.Generic.List<Olfactometer>();
_harpAnalogInput = new HarpAnalogInput();
_harpClockGenerator = new HarpWhiteRabbit();
_harpManipulator = new AllenNeuralDynamics.AindManipulator.AindManipulator();
Expand All @@ -1221,6 +1202,7 @@ protected OlfactometerCalibrationRig(OlfactometerCalibrationRig other)
_rigName = other._rigName;
_dataDirectory = other._dataDirectory;
_harpOlfactometer = other._harpOlfactometer;
_harpOlfactometerExtension = other._harpOlfactometerExtension;
_harpAnalogInput = other._harpAnalogInput;
_harpClockGenerator = other._harpClockGenerator;
_harpManipulator = other._harpManipulator;
Expand Down Expand Up @@ -1318,6 +1300,26 @@ public Olfactometer HarpOlfactometer
}
}

/// <summary>
/// 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
/// </summary>
[System.Xml.Serialization.XmlIgnoreAttribute()]
[Newtonsoft.Json.JsonPropertyAttribute("harp_olfactometer_extension")]
[System.ComponentModel.DescriptionAttribute("A collection of subordinate olfactometers that can be added to increase the numbe" +
"r of independently delivered odors. The order of the list determines the order b" +
"y which odors are numbered")]
public System.Collections.Generic.List<Olfactometer> HarpOlfactometerExtension
{
get
{
return _harpOlfactometerExtension;
}
set
{
_harpOlfactometerExtension = value;
}
}

[System.Xml.Serialization.XmlIgnoreAttribute()]
[Newtonsoft.Json.JsonPropertyAttribute("harp_analog_input", Required=Newtonsoft.Json.Required.Always)]
public HarpAnalogInput HarpAnalogInput
Expand Down Expand Up @@ -1400,6 +1402,7 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
stringBuilder.Append("RigName = " + _rigName + ", ");
stringBuilder.Append("DataDirectory = " + _dataDirectory + ", ");
stringBuilder.Append("HarpOlfactometer = " + _harpOlfactometer + ", ");
stringBuilder.Append("HarpOlfactometerExtension = " + _harpOlfactometerExtension + ", ");
stringBuilder.Append("HarpAnalogInput = " + _harpAnalogInput + ", ");
stringBuilder.Append("HarpClockGenerator = " + _harpClockGenerator + ", ");
stringBuilder.Append("HarpManipulator = " + _harpManipulator + ", ");
Expand Down Expand Up @@ -1642,8 +1645,8 @@ public partial class Session

public Session()
{
_aindBehaviorServicesPkgVersion = "0.13.6";
_version = "0.13.6";
_aindBehaviorServicesPkgVersion = "0.13.7";
_version = "0.13.7";
_experimenter = new System.Collections.Generic.List<string>();
_allowDirtyRepo = false;
_skipHardwareValidation = false;
Expand Down
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