Merge pull request #121 from AllenNeuralDynamics/feat-add-new-harp-de…

…vices

Implement clock output mapping from clock generator devices

src/Extensions/AindBehaviorSession.cs

@@ -15,7 +15,7 @@ namespace AindBehaviorServices.AindBehaviorSession
     public partial class AindBehaviorSessionModel
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private string _version = "0.3.0";
 

src/Extensions/AindManipulatorCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         public CalibrationParameters()
         {

src/Extensions/AindManipulatorCalibrationRig.cs

@@ -897,7 +897,7 @@ public enum MotorOperationMode
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private string _version = "0.1.0";
 

src/Extensions/LoadCellsCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private System.Collections.Generic.List<int> _channels = new System.Collections.Generic.List<int>();
 

src/Extensions/LoadCellsCalibrationRig.cs

@@ -892,7 +892,7 @@ public override string ToString()
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private string _version = "0.0.0";
 

src/Extensions/OlfactometerCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private System.Collections.Generic.IDictionary<string, OlfactometerChannelConfig> _channelConfig;
 

src/Extensions/OlfactometerCalibrationRig.cs

@@ -53,6 +53,92 @@ public override string ToString()
     }
 
 
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")]
+    [Bonsai.CombinatorAttribute()]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+    public partial class ConnectedClockOutput
+    {
+
+        private string _targetDevice;
+
+        private int _outputChannel;
+
+        public ConnectedClockOutput()
+        {
+        }
+
+        protected ConnectedClockOutput(ConnectedClockOutput other)
+        {
+            _targetDevice = other._targetDevice;
+            _outputChannel = other._outputChannel;
+        }
+
+        /// <summary>
+        /// Optional device name to provide user additional information
+        /// </summary>
+        [Newtonsoft.Json.JsonPropertyAttribute("target_device")]
+        [System.ComponentModel.DescriptionAttribute("Optional device name to provide user additional information")]
+        public string TargetDevice
+        {
+            get
+            {
+                return _targetDevice;
+            }
+            set
+            {
+                _targetDevice = value;
+            }
+        }
+
+        /// <summary>
+        /// Output channel
+        /// </summary>
+        [Newtonsoft.Json.JsonPropertyAttribute("output_channel", Required=Newtonsoft.Json.Required.Always)]
+        [System.ComponentModel.DescriptionAttribute("Output channel")]
+        public int OutputChannel
+        {
+            get
+            {
+                return _outputChannel;
+            }
+            set
+            {
+                _outputChannel = value;
+            }
+        }
+
+        public System.IObservable<ConnectedClockOutput> Process()
+        {
+            return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ConnectedClockOutput(this)));
+        }
+
+        public System.IObservable<ConnectedClockOutput> Process<TSource>(System.IObservable<TSource> source)
+        {
+            return System.Reactive.Linq.Observable.Select(source, _ => new ConnectedClockOutput(this));
+        }
+
+        protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+        {
+            stringBuilder.Append("target_device = " + _targetDevice + ", ");
+            stringBuilder.Append("output_channel = " + _outputChannel);
+            return true;
+        }
+
+        public override string ToString()
+        {
+            System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder();
+            stringBuilder.Append(GetType().Name);
+            stringBuilder.Append(" { ");
+            if (PrintMembers(stringBuilder))
+            {
+                stringBuilder.Append(" ");
+            }
+            stringBuilder.Append("}");
+            return stringBuilder.ToString();
+        }
+    }
+
+
     [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")]
     [Bonsai.CombinatorAttribute()]
     [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
@@ -235,6 +321,8 @@ public partial class HarpClockGenerator
 
         private string _portName;
 
+        private System.Collections.Generic.List<ConnectedClockOutput> _connectedClockOutputs = new System.Collections.Generic.List<ConnectedClockOutput>();
+
         public HarpClockGenerator()
         {
         }
@@ -247,6 +335,7 @@ protected HarpClockGenerator(HarpClockGenerator other)
             _whoAmI = other._whoAmI;
             _serialNumber = other._serialNumber;
             _portName = other._portName;
+            _connectedClockOutputs = other._connectedClockOutputs;
         }
 
         [Newtonsoft.Json.JsonPropertyAttribute("device_type")]
@@ -345,6 +434,24 @@ public string PortName
             }
         }
 
+        /// <summary>
+        /// Connected clock outputs
+        /// </summary>
+        [System.Xml.Serialization.XmlIgnoreAttribute()]
+        [Newtonsoft.Json.JsonPropertyAttribute("connected_clock_outputs")]
+        [System.ComponentModel.DescriptionAttribute("Connected clock outputs")]
+        public System.Collections.Generic.List<ConnectedClockOutput> ConnectedClockOutputs
+        {
+            get
+            {
+                return _connectedClockOutputs;
+            }
+            set
+            {
+                _connectedClockOutputs = value;
+            }
+        }
+
         public System.IObservable<HarpClockGenerator> Process()
         {
             return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpClockGenerator(this)));
@@ -362,7 +469,8 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
             stringBuilder.Append("calibration = " + _calibration + ", ");
             stringBuilder.Append("who_am_i = " + _whoAmI + ", ");
             stringBuilder.Append("serial_number = " + _serialNumber + ", ");
-            stringBuilder.Append("port_name = " + _portName);
+            stringBuilder.Append("port_name = " + _portName + ", ");
+            stringBuilder.Append("connected_clock_outputs = " + _connectedClockOutputs);
             return true;
         }
 
@@ -979,7 +1087,7 @@ public enum OlfactometerChannelType
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private string _version = "0.0.0";
 
@@ -1179,6 +1287,11 @@ public System.IObservable<string> Process(System.IObservable<BaseModel> source)
             return Process<BaseModel>(source);
         }
 
+        public System.IObservable<string> Process(System.IObservable<ConnectedClockOutput> source)
+        {
+            return Process<ConnectedClockOutput>(source);
+        }
+
         public System.IObservable<string> Process(System.IObservable<HarpAnalogInput> source)
         {
             return Process<HarpAnalogInput>(source);
@@ -1229,6 +1342,7 @@ public System.IObservable<string> Process(System.IObservable<CalibrationRig> sou
     [System.ComponentModel.DefaultPropertyAttribute("Type")]
     [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)]
     [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<BaseModel>))]
+    [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<ConnectedClockOutput>))]
     [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<HarpAnalogInput>))]
     [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<HarpClockGenerator>))]
     [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Olfactometer>))]

src/Extensions/TreadmillCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         public CalibrationParameters()
         {

src/Extensions/TreadmillCalibrationRig.cs

@@ -550,7 +550,7 @@ public override string ToString()
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private string _version = "0.0.0";
 

src/Extensions/WaterValveCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private System.Collections.Generic.List<double> _valveOpenTime = new System.Collections.Generic.List<double>();
 

src/Extensions/WaterValveCalibrationRig.cs

@@ -15,7 +15,7 @@ namespace AindBehaviorServices.WaterValveCalibrationRig
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.5";
+        private string _aindBehaviorServicesPkgVersion = "0.8.6";
 
         private string _version = "0.0.0";
 

src/aind_behavior_services/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.8.5"
+__version__ = "0.8.6"
 
 from .rig import AindBehaviorRigModel  # noqa: F401
 from .session import AindBehaviorSessionModel  # noqa: F401

src/aind_behavior_services/rig/__init__.py

@@ -2,7 +2,7 @@
 
 import os
 from enum import Enum
-from typing import Annotated, Dict, Generic, Literal, Optional, TypeVar, Union
+from typing import Annotated, Dict, Generic, List, Literal, Optional, TypeVar, Union
 
 from pydantic import BaseModel, Field, field_validator
 from typing_extensions import TypeAliasType
@@ -99,6 +99,7 @@ class CameraController(Device, Generic[TCamera]):
 
 
 class HarpDeviceType(str, Enum):
+    GENERIC = "generic"
     LOADCELLS = "loadcells"
     BEHAVIOR = "behavior"
     OLFACTOMETER = "olfactometer"
@@ -111,7 +112,8 @@ class HarpDeviceType(str, Enum):
     SNIFFDETECTOR = "sniffdetector"
     CUTTLEFISH = "cuttlefish"
     STEPPERDRIVER = "stepperdriver"
-    GENERIC = "generic"
+    ENVIRONMENTSENSOR = "environmentsensor"
+    WHITERABBIT = "whiterabbit"
 
 
 class HarpDeviceGeneric(Device):
@@ -121,6 +123,53 @@ class HarpDeviceGeneric(Device):
     port_name: str = Field(..., description="Device port name")
 
 
+class ConnectedClockOutput(BaseModel):
+    target_device: Optional[str] = Field(
+        default=None, description="Optional device name to provide user additional information"
+    )
+    output_channel: int = Field(..., ge=0, description="Output channel")
+
+
+def _assert_unique_output_channels(outputs: List[ConnectedClockOutput]) -> List[ConnectedClockOutput]:
+    channels = set([ch.output_channel for ch in outputs])
+    if len(channels) != len(outputs):
+        raise ValueError("Output channels must be unique")
+    return outputs
+
+
+class HarpClockGenerator(HarpDeviceGeneric):
+    device_type: Literal[HarpDeviceType.CLOCKGENERATOR] = HarpDeviceType.CLOCKGENERATOR
+    who_am_i: Literal[1158] = 1158
+    connected_clock_outputs: List[ConnectedClockOutput] = Field(default=[], description="Connected clock outputs")
+
+    @field_validator("connected_clock_outputs")
+    @classmethod
+    def validate_connected_clock_outputs(cls, v: List[ConnectedClockOutput]) -> List[ConnectedClockOutput]:
+        return _assert_unique_output_channels(v)
+
+
+class HarpWhiteRabbit(HarpDeviceGeneric):
+    device_type: Literal[HarpDeviceType.WHITERABBIT] = HarpDeviceType.WHITERABBIT
+    who_am_i: Literal[1404] = 1404
+    connected_clock_outputs: List[ConnectedClockOutput] = Field(default=[], description="Connected clock outputs")
+
+    @field_validator("connected_clock_outputs")
+    @classmethod
+    def validate_connected_clock_outputs(cls, v: List[ConnectedClockOutput]) -> List[ConnectedClockOutput]:
+        return _assert_unique_output_channels(v)
+
+
+class HarpClockSynchronizer(HarpDeviceGeneric):
+    device_type: Literal[HarpDeviceType.CLOCKSYNCHRONIZER] = HarpDeviceType.CLOCKSYNCHRONIZER
+    who_am_i: Literal[1152] = 1152
+    connected_clock_outputs: List[ConnectedClockOutput] = Field(default=[], description="Connected clock outputs")
+
+    @field_validator("connected_clock_outputs")
+    @classmethod
+    def validate_connected_clock_outputs(cls, v: List[ConnectedClockOutput]) -> List[ConnectedClockOutput]:
+        return _assert_unique_output_channels(v)
+
+
 class HarpBehavior(HarpDeviceGeneric):
     device_type: Literal[HarpDeviceType.BEHAVIOR] = HarpDeviceType.BEHAVIOR
     who_am_i: Literal[1216] = 1216
@@ -141,16 +190,6 @@ class HarpOlfactometer(HarpDeviceGeneric):
     who_am_i: Literal[1140] = 1140
 
 
-class HarpClockGenerator(HarpDeviceGeneric):
-    device_type: Literal[HarpDeviceType.CLOCKGENERATOR] = HarpDeviceType.CLOCKGENERATOR
-    who_am_i: Literal[1158] = 1158
-
-
-class HarpClockSynchronizer(HarpDeviceGeneric):
-    device_type: Literal[HarpDeviceType.CLOCKSYNCHRONIZER] = HarpDeviceType.CLOCKSYNCHRONIZER
-    who_am_i: Literal[1152] = 1152
-
-
 class HarpAnalogInput(HarpDeviceGeneric):
     device_type: Literal[HarpDeviceType.ANALOGINPUT] = HarpDeviceType.ANALOGINPUT
     who_am_i: Literal[1236] = 1236
@@ -181,6 +220,11 @@ class HarpStepperDriver(HarpDeviceGeneric):
     who_am_i: Literal[1130] = 1130
 
 
+class HarpEnvironmentSensor(HarpDeviceGeneric):
+    device_type: Literal[HarpDeviceType.ENVIRONMENTSENSOR] = HarpDeviceType.ENVIRONMENTSENSOR
+    who_am_i: Literal[1405] = 1405
+
+
 HarpDevice = TypeAliasType(
     "HarpDevice",
     Annotated[
@@ -197,6 +241,8 @@ class HarpStepperDriver(HarpDeviceGeneric):
             HarpSniffDetector,
             HarpClockSynchronizer,
             HarpStepperDriver,
+            HarpEnvironmentSensor,
+            HarpWhiteRabbit,
         ],
         Field(discriminator="device_type"),
     ],

src/schemas/aind_behavior_data_types.json

@@ -162,7 +162,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.5",
+      "default": "0.8.6",
       "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"