diff --git a/examples/clabe.yml b/examples/clabe.yml deleted file mode 100644 index dcf0b5e..0000000 --- a/examples/clabe.yml +++ /dev/null @@ -1,6 +0,0 @@ -# In order to get picked up, move this file to the root of the project or ./local - -data_dir: C:/Data - -default_behavior_picker: - config_library_dir: '\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceOlfactometer' diff --git a/examples/olfactometer.py b/examples/olfactometer.py index b65968b..9d6ca5f 100644 --- a/examples/olfactometer.py +++ b/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 +38,53 @@ 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), diff --git a/schema/aind_behavior_device_olfactometer.json b/schema/aind_behavior_device_olfactometer.json index 114a46b..498bf6f 100644 --- a/schema/aind_behavior_device_olfactometer.json +++ b/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" }, diff --git a/scripts/aind_launcher.py b/scripts/aind_launcher.py index ae41fe8..d552aae 100644 --- a/scripts/aind_launcher.py +++ b/scripts/aind_launcher.py @@ -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__) @@ -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) @@ -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?") @@ -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) diff --git a/src/Extensions.csproj b/src/Extensions.csproj index 19ffa04..f73c758 100644 --- a/src/Extensions.csproj +++ b/src/Extensions.csproj @@ -5,12 +5,13 @@ - + + \ No newline at end of file diff --git a/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs b/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs index cd773da..8c86af0 100644 --- a/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs +++ b/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs @@ -994,8 +994,6 @@ public partial class OlfactometerCalibrationParameters private string _aindBehaviorServicesPkgVersion; - private System.Collections.Generic.Dictionary _channelConfig; - private double _fullFlowRate; private int _nRepeatsPerStimulus; @@ -1006,7 +1004,7 @@ public partial class OlfactometerCalibrationParameters public OlfactometerCalibrationParameters() { - _aindBehaviorServicesPkgVersion = "0.13.6"; + _aindBehaviorServicesPkgVersion = "0.13.7"; _fullFlowRate = 1000D; _nRepeatsPerStimulus = 1; _timeOn = 1D; @@ -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; @@ -1054,24 +1051,6 @@ public string AindBehaviorServicesPkgVersion } } - /// - /// Configuration of olfactometer channels - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] - [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] - public System.Collections.Generic.Dictionary ChannelConfig - { - get - { - return _channelConfig; - } - set - { - _channelConfig = value; - } - } - /// /// Full flow rate of the olfactometer /// @@ -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 + ", "); @@ -1195,6 +1173,8 @@ public partial class OlfactometerCalibrationRig private Olfactometer _harpOlfactometer; + private System.Collections.Generic.List _harpOlfactometerExtension; + private HarpAnalogInput _harpAnalogInput; private HarpWhiteRabbit _harpClockGenerator; @@ -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(); _harpAnalogInput = new HarpAnalogInput(); _harpClockGenerator = new HarpWhiteRabbit(); _harpManipulator = new AllenNeuralDynamics.AindManipulator.AindManipulator(); @@ -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; @@ -1318,6 +1300,26 @@ public Olfactometer HarpOlfactometer } } + /// + /// 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 + /// + [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 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 @@ -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 + ", "); @@ -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(); _allowDirtyRepo = false; _skipHardwareValidation = false; diff --git a/src/Extensions/CalibrationLogic.bonsai b/src/Extensions/CalibrationLogic.bonsai index a3741d4..f0ddf03 100644 --- a/src/Extensions/CalibrationLogic.bonsai +++ b/src/Extensions/CalibrationLogic.bonsai @@ -1,11 +1,9 @@  - @@ -14,10 +12,49 @@ - TaskLogicParameters + RigSchema - ChannelConfig + HarpOlfactometer + + + RigSchema + + + HarpOlfactometerExtension + + + + + + + + + + + + Value.Calibration.ChannelConfig + + + + + + Value + + + + + + Item2.Index,Item1 + + + + + + ChannelsToCalibrate + + + ChannelsToCalibrate @@ -29,16 +66,19 @@ Source1 - - Key - 1 - OdorChannel + thisOdor + + + thisOdor + + + CurrentOdorBeingCalibrated @@ -49,31 +89,7 @@ OdorEndValveState - TaskLogicParameters - - - ChannelConfig - - - OdorChannel - - - - - - - - - 0 - - - - - 1 - - - - ThisOdorChannel + thisOdor @@ -101,24 +117,22 @@ - Channel3AsCarrier - - - - - + thisOdor - ThisOdorChannel - - - FlowRate + olfactometerChannelCount - + + + + 12 + 1 + + TaskLogicParameters @@ -131,176 +145,54 @@ - OdorChannel - - - - 0 - - - - it ? 1.0 : 0.0 - it ? 1.0 : 0.0 + olfactometerChannelCount - + - OdorChannel - - - - 1 - + thisOdor - - it ? 1.0 : 0.0 - it ? 1.0 : 0.0 - - - - - - - - OdorChannel - - - - 2 - - - - it ? 1.0 : 0.0 - it ? 1.0 : 0.0 + + Item2.FlowRate - + - - true - 1 - 0 - 0 - NaN - true - 100 + + 100 1000 + 3 - - ChannelsTargetFlow - - - OdorValveState - - - - - HarpOlfactometerCommands + SetOdorMix - - - - - + + + + + - - - + + + - + - - - - - - - - - - - - - - - - - IsCarrierChannel? - - - - TaskLogicParameters - - - ChannelConfig - - - OdorChannel - - - - - - - - - 0 - - - - ChannelType - - - IsCarrier - - - - Source1 - - - - Carrier - - - - - - - - - - - - - - - - - - - - - - - false - - TaskLogicParameters @@ -318,7 +210,6 @@ PT5S - PT0S @@ -376,9 +267,6 @@ true - - - 1 @@ -394,52 +282,40 @@ - - - - + + + - + - - + + - + - + - + - - + + - + - - - - - - - - - TaskLogicParameters - - - ChannelConfig + ChannelsToCalibrate @@ -451,43 +327,22 @@ Source1 - - Key - 1 - OdorChannel + thisOdor - TaskLogicParameters + thisOdor - - ChannelConfig + + CurrentOdorBeingCalibrated - OdorChannel - - - - - - - - - 3 - - - - - 1 - - - - ThisOdorChannel + thisOdor @@ -519,58 +374,66 @@ - Channel3AsCarrier + thisOdor + + + olfactometerChannelCount - + + + + 12 + 0 + + - ThisOdorChannel + TaskLogicParameters - FlowRate + FullFlowRate - + - TaskLogicParameters + olfactometerChannelCount + + + + + + + + thisOdor - FullFlowRate + Item2.FlowRate - + - - true - 0 - 0 - 0 - NaN - true - 100 + + 100 1000 + 3 - - ChannelsTargetFlow - - - OdorValveState + + SetOdorMix - - - - HarpOlfactometerCommands + + PT0.03S + @@ -583,89 +446,26 @@ - - - - - + + + + + - - - - - - - + + + + + + + + - - IsCarrierChannel? - - - - TaskLogicParameters - - - ChannelConfig - - - OdorChannel - - - - - - - - - 3 - - - - ChannelType - - - IsCarrier - - - - Source1 - - - - Carrier - - - - - - - - - - - - - - - - - - - - - - - - - - false - - TaskLogicParameters @@ -683,7 +483,6 @@ PT5S - PT0S @@ -691,24 +490,22 @@ - Channel3AsCarrier - - - - - + thisOdor - ThisOdorChannel - - - FlowRate + olfactometerChannelCount - + + + + 12 + 1 + + TaskLogicParameters @@ -721,79 +518,33 @@ - OdorChannel - - - - 0 - - - - it ? 1.0 : 0.0 - it ? 1.0 : 0.0 + olfactometerChannelCount - + - OdorChannel - - - - 1 - - - - it ? 1.0 : 0.0 - it ? 1.0 : 0.0 - - - - - - - - OdorChannel - - - - 2 - + thisOdor - - it ? 1.0 : 0.0 - it ? 1.0 : 0.0 + + Item2.FlowRate - + - - true - 1 - 0 - 0 - NaN - true - 100 + + 100 1000 + 3 - - ChannelsTargetFlow - - - OdorValveState - - - - - HarpOlfactometerCommands + SetOdorMix @@ -801,33 +552,21 @@ - - - - - + + + + + - - - + + + - + - - - - - - - - - - - - @@ -855,78 +594,77 @@ - Channel3AsCarrier + thisOdor + + + olfactometerChannelCount - + + + + 12 + 0 + + - ThisOdorChannel + TaskLogicParameters - FlowRate + FullFlowRate - + - TaskLogicParameters - - - FullFlowRate + olfactometerChannelCount - + - - - true - 0 - 0 - 0 - NaN - true - 100 - 1000 - + + thisOdor - ChannelsTargetFlow + Item2.FlowRate - - OdorValveState + + + + - + + 100 + 1000 + 3 + - HarpOlfactometerCommands - - - + SetOdorMix - - - - - + + + + + - - - - - - - + + + + + + @@ -956,9 +694,6 @@ true - - - 1 @@ -974,42 +709,33 @@ - - - + + - + - - + - - + + + - + - - + + - + - + - + - - - - - - - - @@ -1026,16 +752,28 @@ - + - - + + - + + + + + + + + + + + + + diff --git a/src/Extensions/CreateHubOdorMixture.cs b/src/Extensions/CreateHubOdorMixture.cs new file mode 100644 index 0000000..4e61a97 --- /dev/null +++ b/src/Extensions/CreateHubOdorMixture.cs @@ -0,0 +1,105 @@ +using System; +using System.Collections.Generic; +using System.ComponentModel; +using System.Linq; +using System.Reactive.Linq; +using Bonsai; +using Bonsai.Harp; +using Harp.Olfactometer; + + +[Description("Returns a list of pairs of Harp messages necessary to configure all olfactometers in a hub to deliver a given odor mixture.")] +public class CreateHubOdorMixture : Transform, IList> +{ + private int perOdorFlow = 100; + [Range(0, 900)] + [Editor(DesignTypes.SliderEditor, DesignTypes.UITypeEditor)] + [Description("The total desired flow of the odor mixture. This value will be used to automatically calculate the carrier(s) flow based on the total flow.")] + public int PerOdorFlow + { + get { return perOdorFlow; } + set { perOdorFlow = value; } + } + + + private int totalFlow = 1000; + [Range(100, 1000)] + [Editor(DesignTypes.SliderEditor, DesignTypes.UITypeEditor)] + [Description("The total desired flow at the end of the manifold. This value will be used to automatically calculate the carrier(s) flow.")] + public int TotalFlow + { + get { return totalFlow; } + set { totalFlow = value; } + } + + private int olfactometerChannelCount = 3; + public int OlfactometerChannelCount + { + get { return olfactometerChannelCount; } + set { olfactometerChannelCount = value; } + } + + private const int _MINIMUM_CARRIER_FLOW = 100; + + private IList ConstructMessage(IList channelConcentrations) + { + int nChannels = OlfactometerChannelCount; + if (channelConcentrations.Count > nChannels) + { + throw new ArgumentException("The number of channel concentrations provided " + channelConcentrations.Count + " does not match the expected number based on the olfactometer count " + nChannels + "."); + } + // We make sure all odors sum to 1 and then calculate the "real" flow for each channel based on the target odor flow + var adjustedFlow = channelConcentrations.Select(c => (int)(PerOdorFlow * c)) + .Concat(Enumerable.Repeat(0, nChannels - channelConcentrations.Count)); // We pad with zeros if there are fewer concentrations than channels + var carrierFlow = totalFlow - adjustedFlow.Sum(); + if (carrierFlow < _MINIMUM_CARRIER_FLOW) + { + throw new InvalidOperationException("The total odor flow exceeds the total flow minus the minimum carrier flow. Reduce the total target odor flow or the concentrations."); + } + var indexedConcentrations = Enumerable.Range(0, nChannels).Select(i => i < 3 ? 0 : ((i - 3) / 4) + 1).Zip(adjustedFlow, (index, flow) => Tuple.Create(index, flow)).ToList(); + + List messages = new List(); + foreach (var group in indexedConcentrations.GroupBy(x => x.Item1)) // Group by olfactometer index + { + var concentrationList = group.Select(x => x.Item2); + var olfactometerIndex = group.Key; + var channel3Flow = olfactometerIndex > 0 ? concentrationList.ElementAtOrDefault(3) : totalFlow; // for the first olfactometer we use it as a carrier for the blank, + var flows = Enumerable.Range(0, 4).Select(i => i < 3 ? concentrationList.ElementAtOrDefault(i) : channel3Flow).ToList(); + + var channelsTargetFlow = ChannelsTargetFlow.FromPayload(MessageType.Write, new ChannelsTargetFlowPayload( + flows[0], + flows[1], + flows[2], + flows[3], + olfactometerIndex == 0 ? carrierFlow : 0 // We explicitly turn off the air supply to the extension olfactometers since it should never be used + )); + OdorValves valves = OdorValves.None; + for (int i = 0; i < flows.Count; i++) + { + if (flows[i] > 0) + valves |= (OdorValves)(1 << i); + } + var odorValveState = OdorValveState.FromPayload(MessageType.Write, valves); + messages.Add(new OdorMixMessages() + { + ChannelsTargetFlow = channelsTargetFlow, + OdorValveState = odorValveState, + OlfactometerIndex = olfactometerIndex + }); + } + return messages; + } + + public override IObservable> Process(IObservable> source) + { + return source.Select(value => ConstructMessage(value)); + } +} + +public class OdorMixMessages +{ + public HarpMessage ChannelsTargetFlow { get; set; } + public HarpMessage OdorValveState { get; set; } + + public int OlfactometerIndex { get; set; } +} diff --git a/src/Extensions/CreateOneHotConcentrationArray.cs b/src/Extensions/CreateOneHotConcentrationArray.cs new file mode 100644 index 0000000..681c161 --- /dev/null +++ b/src/Extensions/CreateOneHotConcentrationArray.cs @@ -0,0 +1,45 @@ +using Bonsai; +using System; +using System.ComponentModel; +using System.Collections.Generic; +using System.Linq; +using System.Reactive.Linq; +using AindBehaviorDeviceOlfactometerDataSchema; + +[Combinator] +[Description("Creates an array of one-hot encoded concentration values for each olfactometer channel.")] +[WorkflowElementCategory(ElementCategory.Transform)] +public class CreateOneHotConcentrationArray +{ + private int olfactometerChannelsCount = 12; + public int OlfactometerChannelsCount + { + get { return olfactometerChannelsCount; } + set { olfactometerChannelsCount = value; } + } + + private double concentration = 1.0; + public double Concentration + { + get { return concentration; } + set { concentration = value; } + } + + public IObservable> Process(IObservable> source) + { + return source.Select(value => + { + var olfactometerIndex = value.Item1; + var channelConfig = value.Item2; + var numberOfChannels = olfactometerChannelsCount; // 3 channels for the first olfactometer, 4 channels for each additional olfactometer + var oneHotArray = new List(new double[numberOfChannels]); + var globalChannelIndex = olfactometerIndex == 0 ? channelConfig.ChannelIndex : (3 + (olfactometerIndex-1) * 4) + channelConfig.ChannelIndex; + if (globalChannelIndex >= oneHotArray.Count) + { + throw new ArgumentOutOfRangeException("Calculated global channel index " + globalChannelIndex + " exceeds the one-hot array size."); + } + oneHotArray[globalChannelIndex] = concentration; + return oneHotArray; + }); + } +} diff --git a/src/Extensions/Hardware.bonsai b/src/Extensions/Hardware.bonsai index fc4f0b3..b40cef7 100644 --- a/src/Extensions/Hardware.bonsai +++ b/src/Extensions/Hardware.bonsai @@ -1,12 +1,11 @@  @@ -14,55 +13,33 @@ HarpDevices - - TaskLogicParameters - - - ChannelConfig - - - - 3 - - - - ChannelType - - - - Carrier - + + + true + Channel3AsCarrier - - Channel3AsCarrier - - - - - - RigSchema HarpOlfactometer + + RigSchema + - PortName + HarpOlfactometerExtension - - - - + + - - COM10 - TriggerHarpReadDump - true + + + RigSchema @@ -108,8 +85,8 @@ Event - - + + Seconds @@ -146,35 +123,31 @@ - - + - - - + + + - - + + - + - + - + + - - - - - + @@ -204,7 +177,7 @@ PoolingPeriod - + @@ -218,7 +191,7 @@ PT0.2S - + HarpTimestampSource diff --git a/src/Extensions/HardwareValidation.bonsai b/src/Extensions/HardwareValidation.bonsai index 1858b94..d4a9b9c 100644 --- a/src/Extensions/HardwareValidation.bonsai +++ b/src/Extensions/HardwareValidation.bonsai @@ -1,5 +1,5 @@  - - HarpOlfactometerEvents + OlfactometerHubEventsGroupedBy + + + it.Key == 0 + + + + + + Item2 @@ -118,14 +127,17 @@ - + - - - - - + + + + + + + + diff --git a/src/Extensions/HarpOlfactometerExtensionManager.bonsai b/src/Extensions/HarpOlfactometerExtensionManager.bonsai new file mode 100644 index 0000000..ebcce22 --- /dev/null +++ b/src/Extensions/HarpOlfactometerExtensionManager.bonsai @@ -0,0 +1,294 @@ + + + + + + Source1 + + + + + + InstantiateOlfactometer + + + + Source1 + + + + 1 + + + + thisOlfactometer + + + OlfactometerHubCommandsGroupedBy + + + thisOlfactometer + + + Index + + + + + + isThisOlfactometer? + it.Item1.Key == it.Item2 + + + + 1 + + + + Item1 + + + + + + Item2 + + + thisHarpOlfactometerCommands + + + thisHarpOlfactometerEvents + + + thisOlfactometer + + + Index + + + + + + Item2,Item1 + + + OlfactometerHubEvents + + + thisHarpOlfactometerCommands + + + thisOlfactometer + + + Value.PortName + + + + + + + + + Active + On + true + On + Enabled + false + COM6 + + + + thisHarpOlfactometerEvents + + + + + + TriggerHarpReadDump + + + Write + + Active + true + false + On + On + Enabled + + + + thisHarpOlfactometerCommands + + + thisOlfactometer + + + Index + + + Channel3Range + FlowRate1000 + + + Channel3Range + FlowRate100 + + + + + + it.Item1 == 0 ? it.Item2 : it.Item3 + + + Write + + + + thisHarpOlfactometerCommands + + + + PT0.05S + + + + Write + + Flowmeter DI0Trigger ChannelActualFlow + + + + thisHarpOlfactometerCommands + + + + PT0.05S + + + + Write + + Enabled + + + + thisHarpOlfactometerCommands + + + + PT0.05S + + + + Write + + None + + + + thisHarpOlfactometerCommands + + + thisHarpOlfactometerEvents + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MultiplexIO + + + + OlfactometerHubCommands + + + Item1 + + + OlfactometerHubCommandsGroupedBy + + + + OlfactometerHubEvents + + + Item1 + + + OlfactometerHubEventsGroupedBy + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/Logging.bonsai b/src/Extensions/Logging.bonsai index bb2b5c2..731a122 100644 --- a/src/Extensions/Logging.bonsai +++ b/src/Extensions/Logging.bonsai @@ -5,6 +5,7 @@ xmlns:p1="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:sys="clr-namespace:System;assembly=mscorlib" xmlns:p2="clr-namespace:Harp.Olfactometer;assembly=Harp.Olfactometer" + xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:p3="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" xmlns:p4="clr-namespace:Harp.AnalogInput;assembly=Harp.AnalogInput" xmlns:p5="clr-namespace:Harp.StepperDriver;assembly=Harp.StepperDriver" @@ -43,28 +44,88 @@ - HarpOlfactometerEvents + OlfactometerHubEventsGroupedBy - - Modality - - - - - + + LogOlfactometerHub + + + + Source1 + + + + 1 + + + + thisOlfactometer + + + + thisOlfactometer + + + + + + Item2 + + + Modality + + + + + + + + + + + + + + + + thisOlfactometer + + + Key + + + it > 0 ? "OlfactometerExtension" + it.ToString() : "Olfactometer" + + + + + + + + + Behavior + Olfactometer + + + + + + + + + + + + + + + + + + - - - - - - - - - - Behavior - Olfactometer + HarpWhiteRabbitEvents @@ -140,26 +201,23 @@ - + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -174,40 +232,108 @@ HarpSeconds - HarpOlfactometerCommands - - - HarpSeconds - - - - - - - - - - - - Modality + OlfactometerHubCommandsGroupedBy - - - - + + LogOlfactometerHub + + + + Source1 + + + + 1 + + + + thisOlfactometer + + + + thisOlfactometer + + + + + + Item2 + + + HarpTimestampSource + + + + + + + + + + + + Modality + + + + + + + + + + + + + + + + thisOlfactometer + + + Key + + + it > 0 ? "OlfactometerExtension" + it.ToString() : "Olfactometer" + + + HarpCommands/{0} + it + + + + + + + + + Behavior + Olfactometer + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - Behavior - HarpCommands/Olfactometer + HarpAnalogInputCommands @@ -320,38 +446,32 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/Extensions/OdorControl.bonsai b/src/Extensions/OdorControl.bonsai new file mode 100644 index 0000000..2e6fb3d --- /dev/null +++ b/src/Extensions/OdorControl.bonsai @@ -0,0 +1,528 @@ + + + + + + EndValveControl + + + + OlfactometerHubEvents + + + RigSchema + + + HarpOlfactometerExtension + + + Count + + + + 1 + + + + + + + + + + 1 + + + + + false + + + + OdorEndValveState + + + OdorEndValveState + + + OdorPath + + + + Source1 + + + + + + + + + + EndValvesState + EndValve0 + + + + CarrierPath + + + + Source1 + + + + + + + + + + EndValvesState + None + + + + + + Write + + + + + 0 + + + + + + + OlfactometerHubCommands + + + + + + + + + + + + + + + + + + + + + + + + + + + + InitialState + + + + OlfactometerHubEvents + + + RigSchema + + + HarpOlfactometerExtension + + + Count + + + + 1 + + + + + + + + + + 1 + + + + olfactometerChannelCount + + + + + + + + + 0 + 0 + + + + + 0 + + + + + + + + + + Item2 + + + olfactometerChannelCount + + + + + + + + TaskLogicParameters + + + FullFlowRate + + + + + + + + + 100 + 1000 + 3 + + + + SetOdorMix + + + + + + + + + + + + + + + + + + + + + + + + + + + + RigSchema + + + HarpOlfactometerExtension + + + CountChannels + 3 + (it.Count * 4) + + + olfactometerChannelCount + + + SetOdorMix + + + + + + BroadcastToOlfactometerHub + + + + Source1 + + + + 1 + + + + thisBundle + + + SetChannelsTargetFlow + + + + thisBundle + + + OlfactometerIndex,ChannelsTargetFlow + + + OlfactometerHubCommands + + + OlfactometerHubEventsGroupedBy + + + thisBundle + + + OlfactometerIndex + + + + + + it.Item1.Key == it.Item2 + + + Item1 + + + + + + Item2 + + + + Include + Write + + + + thisBundle + + + ChannelsTargetFlow + + + Address + + + + + + + + Include + + + + + + + + PT0.01S + + + + + + + + + 1 + + + + thisBundle + + + + + + Item2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + SetOdorValveState + + + + thisBundle + + + OlfactometerIndex,OdorValveState + + + OlfactometerHubCommands + + + OlfactometerHubEventsGroupedBy + + + thisBundle + + + OlfactometerIndex + + + + + + it.Item1.Key == it.Item2 + + + Item1 + + + + + + Item2 + + + + Include + Write + + + + thisBundle + + + OdorValveState + + + Address + + + + + + + + Include + + + + + + + + PT0.01S + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/UserInterface.bonsai b/src/Extensions/UserInterface.bonsai index 62f4032..aab3b69 100644 --- a/src/Extensions/UserInterface.bonsai +++ b/src/Extensions/UserInterface.bonsai @@ -1,12 +1,12 @@  - - HarpAnalogInputEvents - - - - - - Seconds - Value.Channel0 - None - 3 - - - PID - Black - - - - - - - - - - - HarpOlfactometerEvents - - - - - - Seconds - Value - None - 1 - - - Channel0 - Blue - - - - - - - - - - - HarpOlfactometerEvents - - - - - - Seconds - Value - None - 1 - - - Channel1 - Blue - - - - - - - - - - - HarpOlfactometerEvents - - - - - - Seconds - Value - None - 1 - - - Channel2 - Blue - - - - - - - - - - - HarpOlfactometerEvents - - - - - - Seconds - Value - None - 1 - - - Blank - #C04000 - - - - - - - - - - - HarpOlfactometerEvents - - - - - - Seconds - Value - None - 1 - - - Carrier - Gray - - - - - - - - - - - HarpOlfactometerEvents - - - - - + + UserInterface - - Source1 + + HarpAnalogInputEvents + + + + + + Seconds + Value.Channel0 + None + 3 + + + PID + Black + + + + + + + + + + + CurrentOdorBeingCalibrated - - - EndValve0 - + + GetFlowFromCurrentChannel + + + + Source1 + + + + 1 + + + + thisOdor + + + thisOdor + + + Item1 + + + thisOlfactometerIndex + + + thisOdor + + + Item2 + + + thisChannelIndex + + + + 48 + + + + thisChannelIndex + + + ChannelIndex + + + + + + + + 1 + + + + ActualFlowAddress + + + OlfactometerHubEventsGroupedBy + + + + + + Source1 + + + Key + + + thisOlfactometerIndex + + + + + + + + + + + + + + + + + + + 1 + + + + + + + Item2 + + + ActualFlowAddress + + + + + + + + Include + + + + + + + TimestampedFloat + false + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Seconds + Value + None + 1 + + + Blank + #C04000 + + + + + + + + + + + OlfactometerHubEventsGroupedBy + + + it.Key == 0 + + + + + + Item2 + + + + + + Seconds + Value + None + 1 + + + Blank + #C04000 + + + + + + + + + + + OlfactometerHubEventsGroupedBy + + + it.Key == 0 + + + + + + Item2 + + + + + + Seconds + Value + None + 1 + + + Carrier + Gray + + + + + + + + + + + OlfactometerHubEventsGroupedBy + + + it.Key == 0 + + + + + + Item2 + + + + + + + + + Source1 + + + + EndValve0 + + + + + + + + 1000 + + + + + + + Item1 ? Item2 : 0 + + + + + + + + + + + + + + + + Seconds + Value + Circle + 0 + + + EndValveState + Orange + + + + + + + + - + + + + Olfactometer + false + false + 10 + + X + Cluster + + + + + + + + SoftwareEvent + + + + + + + true + + + + + 1 + + + + StartExperimentTrigger + + + + false + - - 1000 + + 1 - + + + + + + + + + false + true + Microsoft Sans Serif, 16pt + Start! + + + StartButton + + + + + + CurrentOdorBeingCalibrated + + + Olfactometer {0} , OdorConfig {1} + Item1, Item2 + + + + + + + + false + true + Microsoft Sans Serif, 16pt - - Item1 ? Item2 : 0 + + + OlfactometerCalibration + true + true + 1 + 2 + + + + + + + OlfactometerCalibration + true + true + 2 + 1 + + + Percent + 0.8 + + + Percent + 0.2 + + + + + + + + OlfactometerCalibration + 1 + 2 + + + + Percent + 0.7 + + + Percent + 0.3 + + + + + + + + + + + + + AlicatFlowmeterEvents + + + Seconds + Value.VolumetricFlowRate,Value.MassFlowRate,Value.MassFlowTotal + None + 2 + + + EndValveState + Orange + + + 200 + + + + + + + + Seconds + Value.AbsolutePressure,Value.Temperature + None + 2 + + + EndValveState + Orange + + + 200 + + + + + + + + AlicatFlowmeter + true + true + 1 + 2 + + + + + + + + + UserInterface + true + true + + + OlfactometerCalibration + true + + + Minimized + + StartButton + + + + 1 + + + + + StartExperimentTrigger + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - Seconds - Value - Circle - 0 - - - EndValveState - Orange - - - - - - - - - - - - - - Olfactometer - false - false - 10 - - X - Cluster - - - - - - - - SoftwareEvent - - - - - - - true - - - - - 1 - - - - StartExperimentTrigger - - - - false - - - - - 1 - - - - - - - - - - - - false - true - Microsoft Sans Serif, 16pt - Start! - - - StartButton - - - - - - OlfactometerCalibration - true - true - 2 - 1 - - - Percent - 0.8 - - - Percent - 0.2 - - - - - - - - OlfactometerCalibration - 1 - 2 - - - - Percent - 0.7 - - - Percent - 0.3 - - - - - - - - - - - - - AlicatFlowmeterEvents - - - Seconds - Value.VolumetricFlowRate,Value.MassFlowRate,Value.MassFlowTotal - None - 2 - - - EndValveState - Orange - - - 200 - - - - - - - - Seconds - Value.AbsolutePressure,Value.Temperature - None - 2 - - - EndValveState - Orange - - - 200 - - - - - - - - AlicatFlowmeter - true - true - 1 - 2 - - - - - - - - - UserInterface - true - true - - - OlfactometerCalibration - true - - - Minimized - - - StartButton - - - - 1 - - - - - StartExperimentTrigger - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/aind_behavior_device_olfactometer/data_contract/__init__.py b/src/aind_behavior_device_olfactometer/data_contract/__init__.py index af54785..32e73f2 100644 --- a/src/aind_behavior_device_olfactometer/data_contract/__init__.py +++ b/src/aind_behavior_device_olfactometer/data_contract/__init__.py @@ -13,6 +13,8 @@ def _dataset_lookup_helper(version: str) -> t.Callable[[Path], contraqctor.contr parsed_version = semver.Version.parse(version) if semver.Version.parse("0.3.0") <= parsed_version < semver.Version.parse("0.4.0"): from .v0_3_0 import dataset as _dataset + elif semver.Version.parse("0.4.0") <= parsed_version: + from .v0_4_0 import dataset as _dataset else: raise ValueError(f"Unsupported version: {version}") return partial(_dataset, version=version) diff --git a/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py b/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py index 2dd8328..05e86fb 100644 --- a/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py +++ b/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py @@ -1,17 +1,13 @@ from pathlib import Path -from aind_behavior_services.session import AindBehaviorSessionModel from contraqctor.contract import Dataset, DataStreamCollection from contraqctor.contract.harp import ( DeviceYmlByFile, HarpDevice, ) -from contraqctor.contract.json import PydanticModel, SoftwareEvents +from contraqctor.contract.json import Json, SoftwareEvents from contraqctor.contract.text import Text -from ..rig import OlfactometerCalibrationRig -from ..task_logic import OlfactometerCalibrationLogic - def dataset( root_path: Path, @@ -138,24 +134,21 @@ def dataset( name="InputSchemas", description="Configuration files for the behavior rig, task_logic and session.", data_streams=[ - PydanticModel( + Json( name="Rig", - reader_params=PydanticModel.make_params( - model=OlfactometerCalibrationRig, + reader_params=Json.make_params( path=root_path / "behavior/Logs/rig_input.json", ), ), - PydanticModel( + Json( name="TaskLogic", - reader_params=PydanticModel.make_params( - model=OlfactometerCalibrationLogic, + reader_params=Json.make_params( path=root_path / "behavior/Logs/tasklogic_input.json", ), ), - PydanticModel( + Json( name="Session", - reader_params=PydanticModel.make_params( - model=AindBehaviorSessionModel, + reader_params=Json.make_params( path=root_path / "behavior/Logs/session_input.json", ), ), diff --git a/src/aind_behavior_device_olfactometer/data_contract/v0_4_0.py b/src/aind_behavior_device_olfactometer/data_contract/v0_4_0.py new file mode 100644 index 0000000..7675165 --- /dev/null +++ b/src/aind_behavior_device_olfactometer/data_contract/v0_4_0.py @@ -0,0 +1,194 @@ +from pathlib import Path + +from aind_behavior_services.session import Session +from contraqctor.contract import Dataset, DataStreamCollection +from contraqctor.contract.harp import ( + DeviceYmlByFile, + HarpDevice, +) +from contraqctor.contract.json import PydanticModel, SoftwareEvents +from contraqctor.contract.mux import MapFromPaths +from contraqctor.contract.text import Text + +from ..rig import OlfactometerCalibrationRig +from ..task_logic import OlfactometerCalibrationLogic + + +def dataset( + root_path: Path, + name: str = "OlfactometerCalibrationDataset", + description: str = "A Olfactometer Calibration dataset", + version: str = "0.4.0", +) -> Dataset: + """ + Creates a Dataset object for the Olfactometer calibration procedure. + """ + + root_path = Path(root_path) + return Dataset( + name=name, + version=version, + description=description, + data_streams=[ + DataStreamCollection( + name="Behavior", + description="Data from the Behavior modality", + data_streams=[ + HarpDevice( + name="HarpOlfactometer", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/Olfactometer.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpClockGenerator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/WhiteRabbit.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpAnalogInput", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/AnalogInput.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpManipulator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/StepperDriver.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + MapFromPaths( + name="HarpOlfactometerExtension", + description="Data from any additional Harp Olfactometer devices that were added as extensions to the main olfactometer. The number of these devices can vary between sessions, but they will always be named sequentially as OlfactometerExtension1, OlfactometerExtension2, etc.", + reader_params=MapFromPaths.make_params( + paths=[root_path / "behavior"], + include_glob_pattern=["OlfactometerExtension*.harp"], + inner_data_stream=HarpDevice, + inner_param_factory=lambda device_name: HarpDevice.make_params( + path=root_path / "behavior" / device_name, + device_yml_hint=DeviceYmlByFile(), + ), + ), + ), + DataStreamCollection( + name="HarpCommands", + description="Commands sent to Harp devices", + data_streams=[ + HarpDevice( + name="HarpOlfactometer", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/Olfactometer.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpManipulator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/StepperDriver.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpClockGenerator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/WhiteRabbit.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpAnalogInput", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/AnalogInput.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + MapFromPaths( + name="HarpOlfactometerExtension", + description="Data from any additional Harp Olfactometer devices that were added as extensions to the main olfactometer. The number of these devices can vary between sessions, but they will always be named sequentially as OlfactometerExtension1, OlfactometerExtension2, etc.", + reader_params=MapFromPaths.make_params( + paths=[root_path / "behavior/HarpCommands"], + include_glob_pattern=["OlfactometerExtension*.harp"], + inner_data_stream=HarpDevice, + inner_param_factory=lambda device_name: HarpDevice.make_params( + path=root_path / "behavior/HarpCommands" / device_name, + device_yml_hint=DeviceYmlByFile(), + ), + ), + ), + ], + ), + DataStreamCollection( + name="SoftwareEvents", + description="Software events generated by the workflow. The timestamps of these events are low precision and should not be used to align to physiology data.", + data_streams=[ + SoftwareEvents( + name="OdorChannel", + description="The OdorChannel currently being used.", + reader_params=SoftwareEvents.make_params( + root_path / "behavior/SoftwareEvents/OdorChannel.json" + ), + ), + SoftwareEvents( + name="IsEndValveCalibration", + description="Whether the calibration is running in end-valve mode or not.", + reader_params=SoftwareEvents.make_params( + root_path / "behavior/SoftwareEvents/IsEndValveCalibration.json" + ), + ), + ], + ), + DataStreamCollection( + name="Logs", + data_streams=[ + Text( + name="Launcher", + description="Contains the console log of the launcher process.", + reader_params=Text.make_params( + path=root_path / "behavior/Logs/.launcher/launcher.log", + ), + ), + SoftwareEvents( + name="EndSession", + description="A file that determines the end of the session. If the file is empty, the session is still running or it was not closed properly.", + reader_params=SoftwareEvents.make_params( + path=root_path / "behavior/SoftwareEvents/EndSession.json", + ), + ), + ], + ), + DataStreamCollection( + name="InputSchemas", + description="Configuration files for the behavior rig, task_logic and session.", + data_streams=[ + PydanticModel( + name="Rig", + reader_params=PydanticModel.make_params( + model=OlfactometerCalibrationRig, + path=root_path / "behavior/Logs/rig_input.json", + ), + ), + PydanticModel( + name="TaskLogic", + reader_params=PydanticModel.make_params( + model=OlfactometerCalibrationLogic, + path=root_path / "behavior/Logs/tasklogic_input.json", + ), + ), + PydanticModel( + name="Session", + reader_params=PydanticModel.make_params( + model=Session, + path=root_path / "behavior/Logs/session_input.json", + ), + ), + ], + ), + ], + ), + ], + ) diff --git a/src/aind_behavior_device_olfactometer/data_qc/data_qc.py b/src/aind_behavior_device_olfactometer/data_qc/data_qc.py index 8935868..90a8fbd 100644 --- a/src/aind_behavior_device_olfactometer/data_qc/data_qc.py +++ b/src/aind_behavior_device_olfactometer/data_qc/data_qc.py @@ -71,14 +71,32 @@ def make_qc_runner(dataset: contract.Dataset) -> qc.Runner: commands = t.cast(HarpDevice, _r["HarpCommands"][stream.name]) _runner.add_suite(qc.harp.HarpDeviceTestSuite(stream, commands), stream.name) + # Also add the HarpOlfactometerExtension if it exists, as it may not be present in all sessions and is not a HarpDevice itself but contains them + dataset["Behavior"]["HarpOlfactometerExtension"].load() + dataset["Behavior"]["HarpCommands"]["HarpOlfactometerExtension"].load() + + for stream in dataset["Behavior"]["HarpOlfactometerExtension"]: + if isinstance(stream, HarpDevice): + commands = t.cast(HarpDevice, dataset["Behavior"]["HarpCommands"]["HarpOlfactometerExtension"][stream.name]) + _runner.add_suite(qc.harp.HarpDeviceTestSuite(stream, commands), stream.name) + # Add Harp Hub tests + all_harp_devices = [harp_device for harp_device in dataset["Behavior"] if isinstance(harp_device, HarpDevice)] + all_harp_devices.extend( + [ + harp_device + for harp_device in dataset["Behavior"]["HarpOlfactometerExtension"] + if isinstance(harp_device, HarpDevice) + ] + ) _runner.add_suite( qc.harp.HarpHubTestSuite( dataset["Behavior"]["HarpClockGenerator"], - [harp_device for harp_device in dataset["Behavior"] if isinstance(harp_device, HarpDevice)], + all_harp_devices, ), "HarpHub", ) + # Add Csv tests csv_streams = [stream for stream in dataset.iter_all() if isinstance(stream, contract.csv.Csv)] for stream in csv_streams: diff --git a/src/aind_behavior_device_olfactometer/rig.py b/src/aind_behavior_device_olfactometer/rig.py index b8e1542..3f1716c 100644 --- a/src/aind_behavior_device_olfactometer/rig.py +++ b/src/aind_behavior_device_olfactometer/rig.py @@ -3,7 +3,7 @@ import aind_behavior_services.rig.aind_manipulator as man from aind_behavior_services import rig from aind_behavior_services.rig import harp -from aind_behavior_services.rig import olfactometer as olf +from aind_behavior_services.rig import olfactometer as oc from pydantic import Field from . import __semver__ @@ -18,7 +18,11 @@ class AlicatFlowmeter(rig.Device): class OlfactometerCalibrationRig(rig.Rig): version: Literal[__semver__] = __semver__ - harp_olfactometer: olf.Olfactometer = Field(title="Olfactometer device") + harp_olfactometer: oc.Olfactometer = Field(title="Olfactometer device") + harp_olfactometer_extension: list[oc.Olfactometer] = Field( + default_factory=list, + 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", + ) harp_analog_input: harp.HarpAnalogInput = Field(title="Analog input device") harp_clock_generator: harp.HarpWhiteRabbit = Field(title="Clock generator device") harp_manipulator: man.AindManipulator = Field(description="Manipulator") diff --git a/src/aind_behavior_device_olfactometer/task_logic.py b/src/aind_behavior_device_olfactometer/task_logic.py index 2b81577..0ea9da0 100644 --- a/src/aind_behavior_device_olfactometer/task_logic.py +++ b/src/aind_behavior_device_olfactometer/task_logic.py @@ -1,6 +1,5 @@ -from typing import Dict, Literal +from typing import Literal -from aind_behavior_services.rig import olfactometer as olf from aind_behavior_services.task import Task, TaskParameters from pydantic import Field @@ -8,9 +7,6 @@ class OlfactometerCalibrationParameters(TaskParameters): - channel_config: Dict[olf.OlfactometerChannel, olf.OlfactometerChannelConfig] = Field( - default_factory=dict, description="Configuration of olfactometer channels" - ) full_flow_rate: float = Field(default=1000, ge=0, le=1000, description="Full flow rate of the olfactometer") n_repeats_per_stimulus: int = Field(default=1, ge=1, description="Number of repeats per stimulus") time_on: float = Field(default=1, ge=0, description="Time (s) the valve is open during calibration") diff --git a/src/main.bonsai b/src/main.bonsai index e324140..cc35fbf 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -2,29 +2,27 @@ - + - C:\git\AllenNeuralDynamics\Aind.Behavior.Device.Olfactometer\local\olfactometer_calibration_logic.json - C:\git\AllenNeuralDynamics\Aind.Behavior.Device.Olfactometer\local\olfactometer_rig.json - C:\git\AllenNeuralDynamics\Aind.Behavior.Device.Olfactometer\local\olfactometer_session.json + + + - - 10 - + @@ -50,171 +48,7 @@ - - OdorControl - - - - EndValveControl - - - - HarpOlfactometerEvents - - - - 1 - - - - - false - - - - OdorEndValveState - - - OdorEndValveState - - - OdorPath - - - - Source1 - - - - - - - - - - EndValvesState - EndValve0 - - - - CarrierPath - - - - Source1 - - - - - - - - - - EndValvesState - None - - - - - - Write - - - - HarpOlfactometerCommands - - - - - - - - - - - - - - - - - - - - InitialState - - - - Channel3AsCarrier - - - - - - - - TaskLogicParameters - - - FullFlowRate - - - - - - - - - true - 0 - 0 - 0 - NaN - true - 100 - 1000 - - - - ChannelsTargetFlow - - - OdorValveState - - - - - - HarpOlfactometerCommands - - - HarpOlfactometerEvents - - - - - - - - - - - - - - - - - - - - - - - - - + Init @@ -244,14 +78,17 @@ LoggingRootPath - - ../. + + ../. 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