From 784224d8c301179622f3360d4f9e06b04cbc1aa7 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 13:29:53 +0000 Subject: [PATCH 01/17] Add rig specific arduino device and data format + parser --- .bonsai/Bonsai.config | 12 +- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 97 ++- examples/rig.py | 9 +- local_packages/UclOpen.Core.0.1.2-dev0.nupkg | Bin 10256 -> 12950 bytes local_packages/UclOpen.Core.0.1.3-dev0.nupkg | Bin 12942 -> 0 bytes .../UclOpen.Devices.0.1.1-dev0.nupkg | Bin 7651 -> 0 bytes .../UclOpen.Devices.0.1.2-dev0.nupkg | Bin 7668 -> 7589 bytes .../UclOpen.Devices.0.1.3-dev0.nupkg | Bin 7664 -> 0 bytes .../UclOpen.Logging.0.1.0-dev0.nupkg | Bin 8090 -> 0 bytes .../UclOpen.Logging.0.1.2-dev0.nupkg | Bin 8109 -> 8039 bytes .../UclOpen.Logging.0.1.3-dev0.nupkg | Bin 8028 -> 0 bytes pyproject.toml | 2 +- src/DataSchemas/ucl_open_hf_visual.json | 199 +++-- src/Extensions/ParseMatrixSerialDevice.cs | 26 + src/Extensions/UclOpenHfVisual.Generated.cs | 812 ++++++++++-------- src/main.bonsai | 51 +- src/ucl_open_hf_visual/data_types.py | 9 + src/ucl_open_hf_visual/regenerate.py | 2 + src/ucl_open_hf_visual/rig.py | 4 +- src/ucl_open_hf_visual/visual_stimulation.py | 2 +- uv.lock | 4 +- 22 files changed, 744 insertions(+), 487 deletions(-) delete mode 100644 local_packages/UclOpen.Core.0.1.3-dev0.nupkg delete mode 100644 local_packages/UclOpen.Devices.0.1.1-dev0.nupkg delete mode 100644 local_packages/UclOpen.Devices.0.1.3-dev0.nupkg delete mode 100644 local_packages/UclOpen.Logging.0.1.0-dev0.nupkg delete mode 100644 local_packages/UclOpen.Logging.0.1.3-dev0.nupkg create mode 100644 src/Extensions/ParseMatrixSerialDevice.cs create mode 100644 src/ucl_open_hf_visual/data_types.py diff --git a/.bonsai/Bonsai.config b/.bonsai/Bonsai.config index bd63aed..88a88e9 100644 --- a/.bonsai/Bonsai.config +++ b/.bonsai/Bonsai.config @@ -40,9 +40,9 @@ - - - + + + @@ -108,9 +108,9 @@ - - - + + + diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 998d34c..144fd97 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index 0829d87..9f0e399 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -1,2 +1,97 @@  - \ No newline at end of file + + + + + + 344 + 310 + + + 334 + 64 + + Bonsai.Design.ObjectTextVisualizer + + + + + + false + + 361 + 396 + + + 334 + 64 + + Bonsai.Design.ObjectTextVisualizer + + + + + + + + + 511 + 236 + + + 334 + 64 + + Bonsai.Design.ObjectTextVisualizer + + + + + + + 500 + 144 + + + 334 + 64 + + Bonsai.Design.ObjectTextVisualizer + + + + + + + + + + false + + 640 + 283 + + + 334 + 184 + + Bonsai.Design.ObjectTextVisualizer + + + + + + + 174 + 146 + + + 837 + 213 + + Bonsai.Design.ObjectTextVisualizer + + + + + \ No newline at end of file diff --git a/examples/rig.py b/examples/rig.py index 76fb67f..6bbbc66 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -3,8 +3,8 @@ from ucl_open_hf_visual.rig import ( UclOpenHfVisualRig ) -from ucl_open.rigs.device import ( - SerialDeviceModule +from ucl_open_hf_visual.rig import ( + MatrixArduino ) from ucl_open.rigs.device import ( Screen, @@ -14,11 +14,10 @@ screen=Screen( texture_assets_directory="../textures" ), - arduino=SerialDeviceModule( + arduino=MatrixArduino( port_name="COM10", baud_rate=1000000, - new_line="\n", - pattern="%d" + new_line="\n" ) ) diff --git a/local_packages/UclOpen.Core.0.1.2-dev0.nupkg b/local_packages/UclOpen.Core.0.1.2-dev0.nupkg index acb92234ef9ef573371f10daf027abd9df8d6810..b31e0928b2d2569d16aab8d802bc64617452b0b8 100644 GIT binary patch delta 11325 zcmaiaV|3s>&~I&bYumPMZEf2&{k`SQN^e!9uYBr}*3j9B*p^LelD-+{?G&OO<28;zI z{0iPb;)gGnOtmj{T~VEAJ)8-V(WK(?cUR)5`5u4p)`ApKU!KW#qU{;^48h5tuTR#Kht`LX+7|3z z$a;dH$paz{`(zdzI^h25`uQDAPG&my057H{Afjza)bn;m%!?s= 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z8k=zQa+(>N8FPK$HREAr=P_gF<@{j6!|dQ}3o>=EO%$;&cxUm9;l#g|mxddKPPa(7 zNNq*HCMo8-Wt-*zNoiF&=qSJb+*QC$9P<6+2aL|0-fT<&~vpv`{X7ey`&u)Qx&leg~gfML4l=;p->6C z)XV}cW(J5;R8(8LYX-vDp${ZKFY)tVYFaGlS?#6mvX)ba5)Pw;m-4B}niB4=tWU5T zd_xe-RGA7e5Au{0q|RuXwov|xlP7fxo9y!sd8zQCa@vmKa?X-2q%|R6jGyWkPO>*Zy^y)r??BTx*47MhAfO+vZ}Qa z$=1C_@rcDlfyqIO!u$V#Ml06}ore|0rPkDfmSdkI4J;$r+bq#1_?GRfM$ag%~ zE#yR5BW&+jE6Dl6g$9_j`0T$fAt`8vR3h`*HM&WxBnJ+G1@`~fPTzy#U$%cyQvY`R zTQmH}OXNMk{?>#3kAnC&#@~X{KNuG8O5}epFa3@6cf$GyOAY_O#d=@+|BCgW63stY z`|nu)FYWxR+keV3|F{7N{$tMh8{qHd`40d+;s3&7Rg!~-`SS?a_Z{gyBk&Rbx%w|5 CJ&YOv diff --git a/pyproject.toml b/pyproject.toml index 59d11aa..e107add 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,4 +62,4 @@ default-groups = ['dev'] required-version = '>=0.8.4' [tool.uv.sources] -ucl-open-rigs = {git = "https://github.com/ucl-open/ucl_open_rigs/", branch = "visual-displays"} \ No newline at end of file +ucl-open-rigs = {git = "https://github.com/ucl-open/ucl_open_rigs/", branch = "test_build"} \ No newline at end of file diff --git a/src/DataSchemas/ucl_open_hf_visual.json b/src/DataSchemas/ucl_open_hf_visual.json index 428f52a..8049347 100644 --- a/src/DataSchemas/ucl_open_hf_visual.json +++ b/src/DataSchemas/ucl_open_hf_visual.json @@ -121,81 +121,11 @@ "title": "Experiment", "type": "object" }, - "Screen": { + "MatrixArduino": { "properties": { "deviceType": { - "const": "Screen", - "default": "Screen", - "description": "Device type", - "title": "DeviceType", - "type": "string" - }, - "displayIndex": { - "default": 1, - "description": "Display index", - "title": "DisplayIndex", - "type": "integer" - }, - "targetRenderFrequency": { - "default": 60, - "description": "Target render frequency", - "title": "TargetRenderFrequency", - "type": "number" - }, - "targetUpdateFrequency": { - "default": 120, - "description": "Target update frequency", - "title": "TargetUpdateFrequency", - "type": "number" - }, - "textureAssetsDirectory": { - "default": "Textures", - "description": "Calibration directory", - "title": "TextureAssetsDirectory", - "type": "string" - }, - "calibration": { - "default": null, - "description": "Calibration parameters for a set of named display monitors for visual stimuli", - "oneOf": [ - { - "additionalProperties": { - "$ref": "#/$defs/DisplayCalibration" - }, - "type": "object" - }, - { - "type": "null" - } - ], - "title": "Calibration" - }, - "brightness": { - "default": 0, - "description": "Brightness", - "maximum": 1, - "minimum": -1, - "title": "Brightness", - "type": "number" - }, - "contrast": { - "default": 1, - "description": "Contrast", - "maximum": 1, - "minimum": -1, - "title": "Contrast", - "type": "number" - } - }, - "title": "Screen", - "type": "object" - }, - "SerialDeviceModule": { - "description": "Represents the SerialDevice workflow module.\n\nMirrors all externalized properties of SerialDevice.bonsai, including\nport configuration, framing, buffer settings, and parsing pattern.", - "properties": { - "deviceType": { - "const": "SerialDevice", - "default": "SerialDevice", + "const": "MatrixArduino", + "default": "MatrixArduino", "title": "DeviceType", "type": "string" }, @@ -213,12 +143,6 @@ "title": "BaudRate", "type": "integer" }, - "pattern": { - "default": "", - "description": "Pattern used to parse each incoming serial line (same syntax as Bonsai Parse/ScanPattern).", - "title": "Pattern", - "type": "string" - }, "encoding": { "default": null, "description": "Optional text encoding for interpreting incoming bytes.", @@ -314,7 +238,114 @@ "required": [ "portName" ], - "title": "SerialDeviceModule", + "title": "MatrixArduino", + "type": "object" + }, + "MatrixArduinoData": { + "properties": { + "encoderCount": { + "title": "EncoderCount", + "type": "integer" + }, + "lickCountLeft": { + "title": "LickCountLeft", + "type": "integer" + }, + "lickCountRight": { + "title": "LickCountRight", + "type": "integer" + }, + "lastSyncPulseTime": { + "title": "LastSyncPulseTime", + "type": "integer" + }, + "photodiodeVal": { + "title": "PhotodiodeVal", + "type": "integer" + }, + "currentMs": { + "title": "CurrentMs", + "type": "integer" + } + }, + "required": [ + "encoderCount", + "lickCountLeft", + "lickCountRight", + "lastSyncPulseTime", + "photodiodeVal", + "currentMs" + ], + "title": "MatrixArduinoData", + "type": "object" + }, + "Screen": { + "properties": { + "deviceType": { + "const": "Screen", + "default": "Screen", + "description": "Device type", + "title": "DeviceType", + "type": "string" + }, + "displayIndex": { + "default": 1, + "description": "Display index", + "title": "DisplayIndex", + "type": "integer" + }, + "targetRenderFrequency": { + "default": 60, + "description": "Target render frequency", + "title": "TargetRenderFrequency", + "type": "number" + }, + "targetUpdateFrequency": { + "default": 120, + "description": "Target update frequency", + "title": "TargetUpdateFrequency", + "type": "number" + }, + "textureAssetsDirectory": { + "default": "Textures", + "description": "Calibration directory", + "title": "TextureAssetsDirectory", + "type": "string" + }, + "calibration": { + "default": null, + "description": "Calibration parameters for a set of named display monitors for visual stimuli", + "oneOf": [ + { + "additionalProperties": { + "$ref": "#/$defs/DisplayCalibration" + }, + "type": "object" + }, + { + "type": "null" + } + ], + "title": "Calibration" + }, + "brightness": { + "default": 0, + "description": "Brightness", + "maximum": 1, + "minimum": -1, + "title": "Brightness", + "type": "number" + }, + "contrast": { + "default": 1, + "description": "Contrast", + "maximum": 1, + "minimum": -1, + "title": "Contrast", + "type": "number" + } + }, + "title": "Screen", "type": "object" }, "UclOpenHfVisualRig": { @@ -329,7 +360,7 @@ "$ref": "#/$defs/Screen" }, "arduino": { - "$ref": "#/$defs/SerialDeviceModule", + "$ref": "#/$defs/MatrixArduino", "title": "Arduino" } }, @@ -414,17 +445,17 @@ "Vector3": { "properties": { "x": { - "description": "X coordinate of the point", + "description": "X coordinate of the point.", "title": "X", "type": "number" }, "y": { - "description": "Y coordinate of the point", + "description": "Y coordinate of the point.", "title": "Y", "type": "number" }, "z": { - "description": "Z coordinate of the point", + "description": "Z coordinate of the point.", "title": "Z", "type": "number" } diff --git a/src/Extensions/ParseMatrixSerialDevice.cs b/src/Extensions/ParseMatrixSerialDevice.cs new file mode 100644 index 0000000..f4134d1 --- /dev/null +++ b/src/Extensions/ParseMatrixSerialDevice.cs @@ -0,0 +1,26 @@ +using System; +using System.Reactive.Linq; +using Bonsai; +using Bonsai.Harp; +using UclOpenHfVisualDataSchema; + +public class ParseMatrixSerialDevice : Transform> +{ + public override IObservable> Process(IObservable source) + { + return source.Select(value => + { + var values = value.Split(','); + var matrixArduinoData = new MatrixArduinoData + { + EncoderCount = Convert.ToInt32(values[0]), + LickCountLeft = Convert.ToInt32(values[1]), + LickCountRight = Convert.ToInt32(values[2]), + LastSyncPulseTime = Convert.ToInt32(values[3]), + PhotodiodeVal = Convert.ToInt32(values[4]), + CurrentMs = Convert.ToInt32(values[5]), + }; + return new Timestamped(matrixArduinoData, matrixArduinoData.CurrentMs / 1000d); + }); + } +} \ No newline at end of file diff --git a/src/Extensions/UclOpenHfVisual.Generated.cs b/src/Extensions/UclOpenHfVisual.Generated.cs index 39afd30..6f418c9 100644 --- a/src/Extensions/UclOpenHfVisual.Generated.cs +++ b/src/Extensions/UclOpenHfVisual.Generated.cs @@ -435,53 +435,84 @@ public override string ToString() [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class Screen + public partial class MatrixArduino { private string _deviceType; - private int _displayIndex; + private string _portName; - private double _targetRenderFrequency; + private int _baudRate; - private double _targetUpdateFrequency; + private string _encoding; - private string _textureAssetsDirectory; + private string _newLine; - private System.Collections.Generic.Dictionary _calibration; + private string _parity; - private double _brightness; + private int _parityReplace; - private double _contrast; + private int _dataBits; - public Screen() + private string _stopBits; + + private string _handshake; + + private bool _discardNull; + + private bool _dtrEnable; + + private bool _rtsEnable; + + private int _readBufferSize; + + private int _writeBufferSize; + + private int _receivedBytesThreshold; + + private string _serialMessageSubjectName; + + public MatrixArduino() { - _deviceType = "Screen"; - _displayIndex = 1; - _targetRenderFrequency = 60D; - _targetUpdateFrequency = 120D; - _textureAssetsDirectory = "Textures"; - _brightness = 0D; - _contrast = 1D; + _deviceType = "MatrixArduino"; + _baudRate = 9600; + _newLine = "\r\n"; + _parity = "None"; + _parityReplace = 63; + _dataBits = 8; + _stopBits = "One"; + _handshake = "None"; + _discardNull = false; + _dtrEnable = false; + _rtsEnable = false; + _readBufferSize = 4096; + _writeBufferSize = 2048; + _receivedBytesThreshold = 1; + _serialMessageSubjectName = "SerialMessages"; } - protected Screen(Screen other) + protected MatrixArduino(MatrixArduino other) { _deviceType = other._deviceType; - _displayIndex = other._displayIndex; - _targetRenderFrequency = other._targetRenderFrequency; - _targetUpdateFrequency = other._targetUpdateFrequency; - _textureAssetsDirectory = other._textureAssetsDirectory; - _calibration = other._calibration; - _brightness = other._brightness; - _contrast = other._contrast; + _portName = other._portName; + _baudRate = other._baudRate; + _encoding = other._encoding; + _newLine = other._newLine; + _parity = other._parity; + _parityReplace = other._parityReplace; + _dataBits = other._dataBits; + _stopBits = other._stopBits; + _handshake = other._handshake; + _discardNull = other._discardNull; + _dtrEnable = other._dtrEnable; + _rtsEnable = other._rtsEnable; + _readBufferSize = other._readBufferSize; + _writeBufferSize = other._writeBufferSize; + _receivedBytesThreshold = other._receivedBytesThreshold; + _serialMessageSubjectName = other._serialMessageSubjectName; } - ///

- /// Device type - /// [Newtonsoft.Json.JsonPropertyAttribute("deviceType")] - [System.ComponentModel.DescriptionAttribute("Device type")] public string DeviceType { get @@ -495,145 +526,306 @@ public string DeviceType } /// - /// Display index + /// The name of the device serial port. /// - [Newtonsoft.Json.JsonPropertyAttribute("displayIndex")] - [System.ComponentModel.DescriptionAttribute("Display index")] - public int DisplayIndex + [Newtonsoft.Json.JsonPropertyAttribute("portName", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The name of the device serial port.")] + public string PortName { get { - return _displayIndex; + return _portName; } set { - _displayIndex = value; + _portName = value; } } /// - /// Target render frequency + /// Baud rate for serial communication. /// - [Newtonsoft.Json.JsonPropertyAttribute("targetRenderFrequency")] - [System.ComponentModel.DescriptionAttribute("Target render frequency")] - public double TargetRenderFrequency + [Newtonsoft.Json.JsonPropertyAttribute("baudRate")] + [System.ComponentModel.DescriptionAttribute("Baud rate for serial communication.")] + public int BaudRate { get { - return _targetRenderFrequency; + return _baudRate; } set { - _targetRenderFrequency = value; + _baudRate = value; } } /// - /// Target update frequency + /// Optional text encoding for interpreting incoming bytes. /// - [Newtonsoft.Json.JsonPropertyAttribute("targetUpdateFrequency")] - [System.ComponentModel.DescriptionAttribute("Target update frequency")] - public double TargetUpdateFrequency + [Newtonsoft.Json.JsonPropertyAttribute("encoding")] + [System.ComponentModel.DescriptionAttribute("Optional text encoding for interpreting incoming bytes.")] + public string Encoding { get { - return _targetUpdateFrequency; + return _encoding; } set { - _targetUpdateFrequency = value; + _encoding = value; } } /// - /// Calibration directory + /// Line termination sequence used to delimit incoming messages. /// - [Newtonsoft.Json.JsonPropertyAttribute("textureAssetsDirectory")] - [System.ComponentModel.DescriptionAttribute("Calibration directory")] - public string TextureAssetsDirectory + [Newtonsoft.Json.JsonPropertyAttribute("newLine")] + [System.ComponentModel.DescriptionAttribute("Line termination sequence used to delimit incoming messages.")] + public string NewLine { get { - return _textureAssetsDirectory; + return _newLine; } set { - _textureAssetsDirectory = value; + _newLine = value; } } /// - /// Calibration parameters for a set of named display monitors for visual stimuli + /// Parity checking mode for the serial port. /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration parameters for a set of named display monitors for visual stimuli")] - public System.Collections.Generic.Dictionary Calibration + [Newtonsoft.Json.JsonPropertyAttribute("parity")] + [System.ComponentModel.DescriptionAttribute("Parity checking mode for the serial port.")] + public string Parity { get { - return _calibration; + return _parity; } set { - _calibration = value; + _parity = value; } } /// - /// Brightness + /// Byte used to replace invalid bytes detected by a parity error. /// - [Newtonsoft.Json.JsonPropertyAttribute("brightness")] - [System.ComponentModel.DescriptionAttribute("Brightness")] - public double Brightness + [Newtonsoft.Json.JsonPropertyAttribute("parityReplace")] + [System.ComponentModel.DescriptionAttribute("Byte used to replace invalid bytes detected by a parity error.")] + public int ParityReplace { get { - return _brightness; + return _parityReplace; } set { - _brightness = value; + _parityReplace = value; } } /// - /// Contrast + /// Number of data bits per serial frame. /// - [Newtonsoft.Json.JsonPropertyAttribute("contrast")] - [System.ComponentModel.DescriptionAttribute("Contrast")] - public double Contrast + [Newtonsoft.Json.JsonPropertyAttribute("dataBits")] + [System.ComponentModel.DescriptionAttribute("Number of data bits per serial frame.")] + public int DataBits { get { - return _contrast; + return _dataBits; } set { - _contrast = value; + _dataBits = value; } } - public System.IObservable Generate() + /// + /// Number of stop bits per serial frame. + /// + [Newtonsoft.Json.JsonPropertyAttribute("stopBits")] + [System.ComponentModel.DescriptionAttribute("Number of stop bits per serial frame.")] + public string StopBits { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Screen(this))); + get + { + return _stopBits; + } + set + { + _stopBits = value; + } } - public System.IObservable Generate(System.IObservable source) + /// + /// Hardware or software handshaking mode. + /// + [Newtonsoft.Json.JsonPropertyAttribute("handshake")] + [System.ComponentModel.DescriptionAttribute("Hardware or software handshaking mode.")] + public string Handshake { - return System.Reactive.Linq.Observable.Select(source, _ => new Screen(this)); + get + { + return _handshake; + } + set + { + _handshake = value; + } + } + + /// + /// Whether to discard null bytes appearing in the serial stream. + /// + [Newtonsoft.Json.JsonPropertyAttribute("discardNull")] + [System.ComponentModel.DescriptionAttribute("Whether to discard null bytes appearing in the serial stream.")] + public bool DiscardNull + { + get + { + return _discardNull; + } + set + { + _discardNull = value; + } + } + + /// + /// Whether to enable Data Terminal Ready (DTR) control line. + /// + [Newtonsoft.Json.JsonPropertyAttribute("dtrEnable")] + [System.ComponentModel.DescriptionAttribute("Whether to enable Data Terminal Ready (DTR) control line.")] + public bool DtrEnable + { + get + { + return _dtrEnable; + } + set + { + _dtrEnable = value; + } + } + + /// + /// Whether to enable Request To Send (RTS) control line. + /// + [Newtonsoft.Json.JsonPropertyAttribute("rtsEnable")] + [System.ComponentModel.DescriptionAttribute("Whether to enable Request To Send (RTS) control line.")] + public bool RtsEnable + { + get + { + return _rtsEnable; + } + set + { + _rtsEnable = value; + } + } + + /// + /// Size, in bytes, of the read buffer. + /// + [Newtonsoft.Json.JsonPropertyAttribute("readBufferSize")] + [System.ComponentModel.DescriptionAttribute("Size, in bytes, of the read buffer.")] + public int ReadBufferSize + { + get + { + return _readBufferSize; + } + set + { + _readBufferSize = value; + } + } + + /// + /// Size, in bytes, of the write buffer. + /// + [Newtonsoft.Json.JsonPropertyAttribute("writeBufferSize")] + [System.ComponentModel.DescriptionAttribute("Size, in bytes, of the write buffer.")] + public int WriteBufferSize + { + get + { + return _writeBufferSize; + } + set + { + _writeBufferSize = value; + } + } + + /// + /// Minimum number of bytes in the buffer that triggers a read event. + /// + [Newtonsoft.Json.JsonPropertyAttribute("receivedBytesThreshold")] + [System.ComponentModel.DescriptionAttribute("Minimum number of bytes in the buffer that triggers a read event.")] + public int ReceivedBytesThreshold + { + get + { + return _receivedBytesThreshold; + } + set + { + _receivedBytesThreshold = value; + } + } + + /// + /// Name of the subject to which parsed serial messages are published. + /// + [Newtonsoft.Json.JsonPropertyAttribute("serialMessageSubjectName")] + [System.ComponentModel.DescriptionAttribute("Name of the subject to which parsed serial messages are published.")] + public string SerialMessageSubjectName + { + get + { + return _serialMessageSubjectName; + } + set + { + _serialMessageSubjectName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new MatrixArduino(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new MatrixArduino(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("DisplayIndex = " + _displayIndex + ", "); - stringBuilder.Append("TargetRenderFrequency = " + _targetRenderFrequency + ", "); - stringBuilder.Append("TargetUpdateFrequency = " + _targetUpdateFrequency + ", "); - stringBuilder.Append("TextureAssetsDirectory = " + _textureAssetsDirectory + ", "); - stringBuilder.Append("Calibration = " + _calibration + ", "); - stringBuilder.Append("Brightness = " + _brightness + ", "); - stringBuilder.Append("Contrast = " + _contrast); + stringBuilder.Append("PortName = " + _portName + ", "); + stringBuilder.Append("BaudRate = " + _baudRate + ", "); + stringBuilder.Append("Encoding = " + _encoding + ", "); + stringBuilder.Append("NewLine = " + _newLine + ", "); + stringBuilder.Append("Parity = " + _parity + ", "); + stringBuilder.Append("ParityReplace = " + _parityReplace + ", "); + stringBuilder.Append("DataBits = " + _dataBits + ", "); + stringBuilder.Append("StopBits = " + _stopBits + ", "); + stringBuilder.Append("Handshake = " + _handshake + ", "); + stringBuilder.Append("DiscardNull = " + _discardNull + ", "); + stringBuilder.Append("DtrEnable = " + _dtrEnable + ", "); + stringBuilder.Append("RtsEnable = " + _rtsEnable + ", "); + stringBuilder.Append("ReadBufferSize = " + _readBufferSize + ", "); + stringBuilder.Append("WriteBufferSize = " + _writeBufferSize + ", "); + stringBuilder.Append("ReceivedBytesThreshold = " + _receivedBytesThreshold + ", "); + stringBuilder.Append("SerialMessageSubjectName = " + _serialMessageSubjectName); return true; } @@ -652,432 +844,354 @@ public override string ToString() } - /// - /// Represents the SerialDevice workflow module. - /// - ///Mirrors all externalized properties of SerialDevice.bonsai, including - ///port configuration, framing, buffer settings, and parsing pattern. - /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Represents the SerialDevice workflow module.\n\nMirrors all externalized properties" + - " of SerialDevice.bonsai, including\nport configuration, framing, buffer settings," + - " and parsing pattern.")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class SerialDeviceModule + public partial class MatrixArduinoData { - private string _deviceType; - - private string _portName; - - private int _baudRate; - - private string _pattern; - - private string _encoding; - - private string _newLine; - - private string _parity; - - private int _parityReplace; - - private int _dataBits; - - private string _stopBits; - - private string _handshake; + private int _encoderCount; - private bool _discardNull; - - private bool _dtrEnable; + private int _lickCountLeft; - private bool _rtsEnable; + private int _lickCountRight; - private int _readBufferSize; - - private int _writeBufferSize; + private int _lastSyncPulseTime; - private int _receivedBytesThreshold; + private int _photodiodeVal; - private string _serialMessageSubjectName; + private int _currentMs; - public SerialDeviceModule() + public MatrixArduinoData() { - _deviceType = "SerialDevice"; - _baudRate = 9600; - _pattern = ""; - _newLine = "\r\n"; - _parity = "None"; - _parityReplace = 63; - _dataBits = 8; - _stopBits = "One"; - _handshake = "None"; - _discardNull = false; - _dtrEnable = false; - _rtsEnable = false; - _readBufferSize = 4096; - _writeBufferSize = 2048; - _receivedBytesThreshold = 1; - _serialMessageSubjectName = "SerialMessages"; } - protected SerialDeviceModule(SerialDeviceModule other) + protected MatrixArduinoData(MatrixArduinoData other) { - _deviceType = other._deviceType; - _portName = other._portName; - _baudRate = other._baudRate; - _pattern = other._pattern; - _encoding = other._encoding; - _newLine = other._newLine; - _parity = other._parity; - _parityReplace = other._parityReplace; - _dataBits = other._dataBits; - _stopBits = other._stopBits; - _handshake = other._handshake; - _discardNull = other._discardNull; - _dtrEnable = other._dtrEnable; - _rtsEnable = other._rtsEnable; - _readBufferSize = other._readBufferSize; - _writeBufferSize = other._writeBufferSize; - _receivedBytesThreshold = other._receivedBytesThreshold; - _serialMessageSubjectName = other._serialMessageSubjectName; + _encoderCount = other._encoderCount; + _lickCountLeft = other._lickCountLeft; + _lickCountRight = other._lickCountRight; + _lastSyncPulseTime = other._lastSyncPulseTime; + _photodiodeVal = other._photodiodeVal; + _currentMs = other._currentMs; } - [Newtonsoft.Json.JsonPropertyAttribute("deviceType")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } - - /// - /// The name of the device serial port. - /// - [Newtonsoft.Json.JsonPropertyAttribute("portName", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("The name of the device serial port.")] - public string PortName - { - get - { - return _portName; - } - set - { - _portName = value; - } - } - - /// - /// Baud rate for serial communication. - /// - [Newtonsoft.Json.JsonPropertyAttribute("baudRate")] - [System.ComponentModel.DescriptionAttribute("Baud rate for serial communication.")] - public int BaudRate + [Newtonsoft.Json.JsonPropertyAttribute("encoderCount", Required=Newtonsoft.Json.Required.Always)] + public int EncoderCount { get { - return _baudRate; + return _encoderCount; } set { - _baudRate = value; + _encoderCount = value; } } - /// - /// Pattern used to parse each incoming serial line (same syntax as Bonsai Parse/ScanPattern). - /// - [Newtonsoft.Json.JsonPropertyAttribute("pattern")] - [System.ComponentModel.DescriptionAttribute("Pattern used to parse each incoming serial line (same syntax as Bonsai Parse/Scan" + - "Pattern).")] - public string Pattern + [Newtonsoft.Json.JsonPropertyAttribute("lickCountLeft", Required=Newtonsoft.Json.Required.Always)] + public int LickCountLeft { get { - return _pattern; + return _lickCountLeft; } set { - _pattern = value; + _lickCountLeft = value; } } - /// - /// Optional text encoding for interpreting incoming bytes. - /// - [Newtonsoft.Json.JsonPropertyAttribute("encoding")] - [System.ComponentModel.DescriptionAttribute("Optional text encoding for interpreting incoming bytes.")] - public string Encoding + [Newtonsoft.Json.JsonPropertyAttribute("lickCountRight", Required=Newtonsoft.Json.Required.Always)] + public int LickCountRight { get { - return _encoding; + return _lickCountRight; } set { - _encoding = value; + _lickCountRight = value; } } - /// - /// Line termination sequence used to delimit incoming messages. - /// - [Newtonsoft.Json.JsonPropertyAttribute("newLine")] - [System.ComponentModel.DescriptionAttribute("Line termination sequence used to delimit incoming messages.")] - public string NewLine + [Newtonsoft.Json.JsonPropertyAttribute("lastSyncPulseTime", Required=Newtonsoft.Json.Required.Always)] + public int LastSyncPulseTime { get { - return _newLine; + return _lastSyncPulseTime; } set { - _newLine = value; + _lastSyncPulseTime = value; } } - /// - /// Parity checking mode for the serial port. - /// - [Newtonsoft.Json.JsonPropertyAttribute("parity")] - [System.ComponentModel.DescriptionAttribute("Parity checking mode for the serial port.")] - public string Parity + [Newtonsoft.Json.JsonPropertyAttribute("photodiodeVal", Required=Newtonsoft.Json.Required.Always)] + public int PhotodiodeVal { get { - return _parity; + return _photodiodeVal; } set { - _parity = value; + _photodiodeVal = value; } } - /// - /// Byte used to replace invalid bytes detected by a parity error. - /// - [Newtonsoft.Json.JsonPropertyAttribute("parityReplace")] - [System.ComponentModel.DescriptionAttribute("Byte used to replace invalid bytes detected by a parity error.")] - public int ParityReplace + [Newtonsoft.Json.JsonPropertyAttribute("currentMs", Required=Newtonsoft.Json.Required.Always)] + public int CurrentMs { get { - return _parityReplace; + return _currentMs; } set { - _parityReplace = value; + _currentMs = value; } } - /// - /// Number of data bits per serial frame. - /// - [Newtonsoft.Json.JsonPropertyAttribute("dataBits")] - [System.ComponentModel.DescriptionAttribute("Number of data bits per serial frame.")] - public int DataBits + public System.IObservable Generate() { - get - { - return _dataBits; - } - set - { - _dataBits = value; - } + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new MatrixArduinoData(this))); } - /// - /// Number of stop bits per serial frame. - /// - [Newtonsoft.Json.JsonPropertyAttribute("stopBits")] - [System.ComponentModel.DescriptionAttribute("Number of stop bits per serial frame.")] - public string StopBits + public System.IObservable Generate(System.IObservable source) { - get - { - return _stopBits; - } - set + return System.Reactive.Linq.Observable.Select(source, _ => new MatrixArduinoData(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("EncoderCount = " + _encoderCount + ", "); + stringBuilder.Append("LickCountLeft = " + _lickCountLeft + ", "); + stringBuilder.Append("LickCountRight = " + _lickCountRight + ", "); + stringBuilder.Append("LastSyncPulseTime = " + _lastSyncPulseTime + ", "); + stringBuilder.Append("PhotodiodeVal = " + _photodiodeVal + ", "); + stringBuilder.Append("CurrentMs = " + _currentMs); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) { - _stopBits = value; + stringBuilder.Append(" "); } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class Screen + { + + private string _deviceType; + + private int _displayIndex; + + private double _targetRenderFrequency; + + private double _targetUpdateFrequency; + + private string _textureAssetsDirectory; + + private System.Collections.Generic.Dictionary _calibration; + + private double _brightness; + + private double _contrast; + + public Screen() + { + _deviceType = "Screen"; + _displayIndex = 1; + _targetRenderFrequency = 60D; + _targetUpdateFrequency = 120D; + _textureAssetsDirectory = "Textures"; + _brightness = 0D; + _contrast = 1D; + } + + protected Screen(Screen other) + { + _deviceType = other._deviceType; + _displayIndex = other._displayIndex; + _targetRenderFrequency = other._targetRenderFrequency; + _targetUpdateFrequency = other._targetUpdateFrequency; + _textureAssetsDirectory = other._textureAssetsDirectory; + _calibration = other._calibration; + _brightness = other._brightness; + _contrast = other._contrast; } /// - /// Hardware or software handshaking mode. + /// Device type /// - [Newtonsoft.Json.JsonPropertyAttribute("handshake")] - [System.ComponentModel.DescriptionAttribute("Hardware or software handshaking mode.")] - public string Handshake + [Newtonsoft.Json.JsonPropertyAttribute("deviceType")] + [System.ComponentModel.DescriptionAttribute("Device type")] + public string DeviceType { get { - return _handshake; + return _deviceType; } set { - _handshake = value; + _deviceType = value; } } /// - /// Whether to discard null bytes appearing in the serial stream. + /// Display index /// - [Newtonsoft.Json.JsonPropertyAttribute("discardNull")] - [System.ComponentModel.DescriptionAttribute("Whether to discard null bytes appearing in the serial stream.")] - public bool DiscardNull + [Newtonsoft.Json.JsonPropertyAttribute("displayIndex")] + [System.ComponentModel.DescriptionAttribute("Display index")] + public int DisplayIndex { get { - return _discardNull; + return _displayIndex; } set { - _discardNull = value; + _displayIndex = value; } } /// - /// Whether to enable Data Terminal Ready (DTR) control line. + /// Target render frequency /// - [Newtonsoft.Json.JsonPropertyAttribute("dtrEnable")] - [System.ComponentModel.DescriptionAttribute("Whether to enable Data Terminal Ready (DTR) control line.")] - public bool DtrEnable + [Newtonsoft.Json.JsonPropertyAttribute("targetRenderFrequency")] + [System.ComponentModel.DescriptionAttribute("Target render frequency")] + public double TargetRenderFrequency { get { - return _dtrEnable; + return _targetRenderFrequency; } set { - _dtrEnable = value; + _targetRenderFrequency = value; } } /// - /// Whether to enable Request To Send (RTS) control line. + /// Target update frequency /// - [Newtonsoft.Json.JsonPropertyAttribute("rtsEnable")] - [System.ComponentModel.DescriptionAttribute("Whether to enable Request To Send (RTS) control line.")] - public bool RtsEnable + [Newtonsoft.Json.JsonPropertyAttribute("targetUpdateFrequency")] + [System.ComponentModel.DescriptionAttribute("Target update frequency")] + public double TargetUpdateFrequency { get { - return _rtsEnable; + return _targetUpdateFrequency; } set { - _rtsEnable = value; + _targetUpdateFrequency = value; } } /// - /// Size, in bytes, of the read buffer. + /// Calibration directory /// - [Newtonsoft.Json.JsonPropertyAttribute("readBufferSize")] - [System.ComponentModel.DescriptionAttribute("Size, in bytes, of the read buffer.")] - public int ReadBufferSize + [Newtonsoft.Json.JsonPropertyAttribute("textureAssetsDirectory")] + [System.ComponentModel.DescriptionAttribute("Calibration directory")] + public string TextureAssetsDirectory { get { - return _readBufferSize; + return _textureAssetsDirectory; } set { - _readBufferSize = value; + _textureAssetsDirectory = value; } } /// - /// Size, in bytes, of the write buffer. + /// Calibration parameters for a set of named display monitors for visual stimuli /// - [Newtonsoft.Json.JsonPropertyAttribute("writeBufferSize")] - [System.ComponentModel.DescriptionAttribute("Size, in bytes, of the write buffer.")] - public int WriteBufferSize + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration parameters for a set of named display monitors for visual stimuli")] + public System.Collections.Generic.Dictionary Calibration { get { - return _writeBufferSize; + return _calibration; } set { - _writeBufferSize = value; + _calibration = value; } } /// - /// Minimum number of bytes in the buffer that triggers a read event. + /// Brightness /// - [Newtonsoft.Json.JsonPropertyAttribute("receivedBytesThreshold")] - [System.ComponentModel.DescriptionAttribute("Minimum number of bytes in the buffer that triggers a read event.")] - public int ReceivedBytesThreshold + [Newtonsoft.Json.JsonPropertyAttribute("brightness")] + [System.ComponentModel.DescriptionAttribute("Brightness")] + public double Brightness { get { - return _receivedBytesThreshold; + return _brightness; } set { - _receivedBytesThreshold = value; + _brightness = value; } } /// - /// Name of the subject to which parsed serial messages are published. + /// Contrast /// - [Newtonsoft.Json.JsonPropertyAttribute("serialMessageSubjectName")] - [System.ComponentModel.DescriptionAttribute("Name of the subject to which parsed serial messages are published.")] - public string SerialMessageSubjectName + [Newtonsoft.Json.JsonPropertyAttribute("contrast")] + [System.ComponentModel.DescriptionAttribute("Contrast")] + public double Contrast { get { - return _serialMessageSubjectName; + return _contrast; } set { - _serialMessageSubjectName = value; + _contrast = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SerialDeviceModule(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Screen(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new SerialDeviceModule(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new Screen(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("PortName = " + _portName + ", "); - stringBuilder.Append("BaudRate = " + _baudRate + ", "); - stringBuilder.Append("Pattern = " + _pattern + ", "); - stringBuilder.Append("Encoding = " + _encoding + ", "); - stringBuilder.Append("NewLine = " + _newLine + ", "); - stringBuilder.Append("Parity = " + _parity + ", "); - stringBuilder.Append("ParityReplace = " + _parityReplace + ", "); - stringBuilder.Append("DataBits = " + _dataBits + ", "); - stringBuilder.Append("StopBits = " + _stopBits + ", "); - stringBuilder.Append("Handshake = " + _handshake + ", "); - stringBuilder.Append("DiscardNull = " + _discardNull + ", "); - stringBuilder.Append("DtrEnable = " + _dtrEnable + ", "); - stringBuilder.Append("RtsEnable = " + _rtsEnable + ", "); - stringBuilder.Append("ReadBufferSize = " + _readBufferSize + ", "); - stringBuilder.Append("WriteBufferSize = " + _writeBufferSize + ", "); - stringBuilder.Append("ReceivedBytesThreshold = " + _receivedBytesThreshold + ", "); - stringBuilder.Append("SerialMessageSubjectName = " + _serialMessageSubjectName); + stringBuilder.Append("DisplayIndex = " + _displayIndex + ", "); + stringBuilder.Append("TargetRenderFrequency = " + _targetRenderFrequency + ", "); + stringBuilder.Append("TargetUpdateFrequency = " + _targetUpdateFrequency + ", "); + stringBuilder.Append("TextureAssetsDirectory = " + _textureAssetsDirectory + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("Brightness = " + _brightness + ", "); + stringBuilder.Append("Contrast = " + _contrast); return true; } @@ -1106,13 +1220,13 @@ public partial class UclOpenHfVisualRig private Screen _screen; - private SerialDeviceModule _arduino; + private MatrixArduino _arduino; public UclOpenHfVisualRig() { _version = "0.0.0-rc1"; _screen = new Screen(); - _arduino = new SerialDeviceModule(); + _arduino = new MatrixArduino(); } protected UclOpenHfVisualRig(UclOpenHfVisualRig other) @@ -1151,7 +1265,7 @@ public Screen Screen [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("arduino", Required=Newtonsoft.Json.Required.Always)] - public SerialDeviceModule Arduino + public MatrixArduino Arduino { get { @@ -1463,10 +1577,10 @@ protected Vector3(Vector3 other) } /// - /// X coordinate of the point + /// X coordinate of the point. /// [Newtonsoft.Json.JsonPropertyAttribute("x", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("X coordinate of the point")] + [System.ComponentModel.DescriptionAttribute("X coordinate of the point.")] public double X { get @@ -1480,10 +1594,10 @@ public double X } /// - /// Y coordinate of the point + /// Y coordinate of the point. /// [Newtonsoft.Json.JsonPropertyAttribute("y", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Y coordinate of the point")] + [System.ComponentModel.DescriptionAttribute("Y coordinate of the point.")] public double Y { get @@ -1497,10 +1611,10 @@ public double Y } /// - /// Z coordinate of the point + /// Z coordinate of the point. /// [Newtonsoft.Json.JsonPropertyAttribute("z", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Z coordinate of the point")] + [System.ComponentModel.DescriptionAttribute("Z coordinate of the point.")] public double Z { get @@ -1584,14 +1698,19 @@ public System.IObservable Process(System.IObservable source) return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -1627,8 +1746,9 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] diff --git a/src/main.bonsai b/src/main.bonsai index be11309..ef02b17 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -8,8 +8,8 @@ xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System" xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" - xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" - xmlns:p2="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" + xmlns:p2="clr-namespace:;assembly=Extensions" + xmlns:p3="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -153,7 +153,6 @@ - @@ -174,8 +173,6 @@ 2048 1 Arduino - %d - , SerialMessages @@ -424,7 +421,7 @@ - SN_1_1 + SynthIm_1_1 @@ -557,33 +554,14 @@ SerialMessages - - new( - it[0] as EncoderCount, - it[1] as LickCountLeft, - it[2] as LickCountRight, - it[3] as LastSyncPulseTime, - it[4] as PhotodiodeVal, - it[5] as ArduinoMilliseconds -) - - - ArduinoMilliseconds - - - - 1000 - - - + - - - - - TODO - + + + TODO + + LogData @@ -621,7 +599,7 @@ - + @@ -716,13 +694,8 @@ - - - - - - - + + \ No newline at end of file diff --git a/src/ucl_open_hf_visual/data_types.py b/src/ucl_open_hf_visual/data_types.py new file mode 100644 index 0000000..06933f7 --- /dev/null +++ b/src/ucl_open_hf_visual/data_types.py @@ -0,0 +1,9 @@ +from ucl_open.rigs.base import BaseSchema + +class MatrixArduinoData(BaseSchema): + encoder_count: int + lick_count_left: int + lick_count_right: int + last_sync_pulse_time: int + photodiode_val: int + current_ms: int \ No newline at end of file diff --git a/src/ucl_open_hf_visual/regenerate.py b/src/ucl_open_hf_visual/regenerate.py index 7099b92..e52e27a 100644 --- a/src/ucl_open_hf_visual/regenerate.py +++ b/src/ucl_open_hf_visual/regenerate.py @@ -7,6 +7,7 @@ import ucl_open_hf_visual.rig import ucl_open_hf_visual.task +import ucl_open_hf_visual.data_types SCHEMA_ROOT = Path("./src/DataSchemas/") EXTENSIONS_ROOT = Path("./src/Extensions/") @@ -18,6 +19,7 @@ def main(): ucl_open_hf_visual.task.UclOpenHfVisualTaskLogic, ucl_open_hf_visual.rig.UclOpenHfVisualRig, Experiment, + ucl_open_hf_visual.data_types.MatrixArduinoData ] model = pydantic.RootModel[Union[tuple(models)]] diff --git a/src/ucl_open_hf_visual/rig.py b/src/ucl_open_hf_visual/rig.py index 5398565..072bb7c 100644 --- a/src/ucl_open_hf_visual/rig.py +++ b/src/ucl_open_hf_visual/rig.py @@ -8,9 +8,11 @@ from ucl_open_hf_visual import __semver__ +class MatrixArduino(SerialDeviceModule): + device_type: Literal["MatrixArduino"] = "MatrixArduino" class UclOpenHfVisualRig(BaseSchema): version: Literal[__semver__] = __semver__ # type: ignore screen: Screen - arduino: SerialDeviceModule + arduino: MatrixArduino ... \ No newline at end of file diff --git a/src/ucl_open_hf_visual/visual_stimulation.py b/src/ucl_open_hf_visual/visual_stimulation.py index cb138ef..a8c9945 100644 --- a/src/ucl_open_hf_visual/visual_stimulation.py +++ b/src/ucl_open_hf_visual/visual_stimulation.py @@ -4,7 +4,7 @@ from typing import Literal from pydantic import Field -from swc.aeon.schema import BaseSchema, Device +from ucl_open.rigs.base import BaseSchema, Device class Vector3(BaseSchema): x: float = Field(default=0, description="X coordinate of the point") diff --git a/uv.lock b/uv.lock index 18f5a83..8894d56 100644 --- a/uv.lock +++ b/uv.lock @@ -775,7 +775,7 @@ requires-dist = [ { name = "contraqctor", marker = "extra == 'data'", specifier = "<0.5.0" }, { name = "pydantic-settings" }, { name = "swc-aeon", specifier = ">=0.1.0" }, - { name = "ucl-open-rigs", git = "https://github.com/ucl-open/ucl_open_rigs/?branch=visual-displays" }, + { name = "ucl-open-rigs", git = "https://github.com/ucl-open/ucl_open_rigs/?branch=test_build" }, ] provides-extras = ["data"] @@ -790,7 +790,7 @@ dev = [ [[package]] name = "ucl-open-rigs" version = "0.1.0" -source = { git = "https://github.com/ucl-open/ucl_open_rigs/?branch=visual-displays#1bdf5495e28d3dc764657a146ee020625ea7daa1" } +source = { git = "https://github.com/ucl-open/ucl_open_rigs/?branch=test_build#5cabc5b4d596747a60cf74431f5b76c4bdbfe019" } dependencies = [ { name = "pydantic" }, { name = "pydantic-yaml" }, From 245ecfb3fc0c0659ad6da71124ac271c1f14d846 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 13:38:17 +0000 Subject: [PATCH 02/17] Add blank textures --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 8 ++++-- examples/task.py | 2 +- src/main.bonsai | 48 ++++++++++++++++++++----------- textures/blankStim_1.tif | Bin 0 -> 4550 bytes textures/blankStim_2.tif | Bin 0 -> 4550 bytes 6 files changed, 39 insertions(+), 21 deletions(-) create mode 100644 textures/blankStim_1.tif create mode 100644 textures/blankStim_2.tif diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 144fd97..998d34c 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index 9f0e399..bbe8b83 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -3,6 +3,7 @@ + false 344 310 @@ -34,6 +35,7 @@ + false 511 236 @@ -48,6 +50,7 @@ + false 500 144 @@ -65,7 +68,7 @@ - + false 640 @@ -80,7 +83,8 @@ - + + false 174 146 diff --git a/examples/task.py b/examples/task.py index d396aba..cb12854 100644 --- a/examples/task.py +++ b/examples/task.py @@ -8,7 +8,7 @@ task_logic = UclOpenHfVisualTaskLogic( task_parameters=UclOpenHfVisualTaskParameters( available_textures=["SN_1_1", "SynthIm_1_1"], - inter_presentation_texture="SN_1_2", + inter_presentation_texture="blankStim_1", presentation_time=1, inter_presentation_time=0.5 ), diff --git a/src/main.bonsai b/src/main.bonsai index ef02b17..af4dff9 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -199,7 +199,7 @@ true Resizable - Fullscreen + Normal Second 60 120 @@ -375,6 +375,21 @@ 0 0 + + DrawCall + + + 0.1 + 0.1 + 1 + 1 + 0 + 0 + 1 + 1 + 1 + 1 + TaskLogicParameters @@ -421,7 +436,7 @@ - SynthIm_1_1 + SN_1_1 @@ -473,7 +488,7 @@ - SN_1_2 + blankStim_1 @@ -557,11 +572,9 @@ - - - TODO - - + + TODO + LogData @@ -648,7 +661,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-10T17-50-17\Arduino\Arduino.csv + C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T13-36-07\Arduino\Arduino.csv false false None @@ -686,16 +699,17 @@ - - - - - + + + + - - - + + + + + \ No newline at end of file diff --git a/textures/blankStim_1.tif b/textures/blankStim_1.tif new file mode 100644 index 0000000000000000000000000000000000000000..0979dc9e4c8b8553b195df1825cbe5d529e9e5cb GIT binary patch literal 4550 zcmeI0OA5j;6h&X`$Lrq;DyRd8;zGpks?M?^hYnqrrzJvmAjoSuy|L73&j#D4=ii(hLN(0$q#sj%(NEdfOX@6b*zO$rdB54we@X8qf>=}p pvCs%ANKi?FDiTzapfL&J1ranMK~oYmBSCW#v>-uzt_WI@@B#m@D7gRt literal 0 HcmV?d00001 diff --git a/textures/blankStim_2.tif b/textures/blankStim_2.tif new file mode 100644 index 0000000000000000000000000000000000000000..0979dc9e4c8b8553b195df1825cbe5d529e9e5cb GIT binary patch literal 4550 zcmeI0OA5j;6h&X`$Lrq;DyRd8;zGpks?M?^hYnqrrzJvmAjoSuy|L73&j#D4=ii(hLN(0$q#sj%(NEdfOX@6b*zO$rdB54we@X8qf>=}p pvCs%ANKi?FDiTzapfL&J1ranMK~oYmBSCW#v>-uzt_WI@@B#m@D7gRt literal 0 HcmV?d00001 From 1983476f15845e75850c8b5e0208fd748711b9a5 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 13:42:37 +0000 Subject: [PATCH 03/17] Reverse order of blank and texture presentation --- .bonsai/Settings/src/main.layout | 4 +- src/main.bonsai | 71 ++++++++++++++++++-------------- 2 files changed, 42 insertions(+), 33 deletions(-) diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index bbe8b83..d327e18 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -68,7 +68,7 @@ - + false 640 @@ -83,7 +83,7 @@ - + false 174 diff --git a/src/main.bonsai b/src/main.bonsai index af4dff9..d7cd4a1 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -390,6 +390,14 @@ 1 1 + + + false + + + + SynchQuadColor + TaskLogicParameters @@ -427,7 +435,10 @@ TextureBank - TextureName + TaskLogicParameters + + + InterPresentationTexture @@ -436,7 +447,7 @@ - SN_1_1 + blankStim_1 @@ -451,7 +462,7 @@ TaskLogicParameters - PresentationTime + InterPresentationTime TimeSpan.FromSeconds(it) @@ -463,7 +474,7 @@ - PT1S + PT0.5S @@ -476,10 +487,7 @@ Item2 - TaskLogicParameters - - - InterPresentationTexture + TextureName @@ -488,7 +496,7 @@ - blankStim_1 + SynthIm_1_1 @@ -503,7 +511,7 @@ TaskLogicParameters - InterPresentationTime + PresentationTime TimeSpan.FromSeconds(it) @@ -515,7 +523,7 @@ - PT0.5S + PT1S @@ -528,20 +536,20 @@ - + - - - - + + + + - - - - - - + + + + + + @@ -661,7 +669,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T13-36-07\Arduino\Arduino.csv + C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T13-42-17\Arduino\Arduino.csv false false None @@ -700,16 +708,17 @@ - - - - - + + + + - - - + + + + + \ No newline at end of file From e2a9a116550c90b9a678a488ca8f281ac001b7ec Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 13:50:05 +0000 Subject: [PATCH 04/17] Add sync quad --- .bonsai/Settings/src/main.layout | 6 +- src/main.bonsai | 146 ++++++++++++++++++++++++------- 2 files changed, 118 insertions(+), 34 deletions(-) diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index d327e18..ee920a0 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -1,6 +1,6 @@  - + false @@ -68,7 +68,7 @@ - + false 640 @@ -83,7 +83,7 @@ - + false 174 diff --git a/src/main.bonsai b/src/main.bonsai index d7cd4a1..8ba3530 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -6,8 +6,8 @@ xmlns:p1="clr-namespace:UclOpenHfVisualDataSchema;assembly=Extensions" xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders" xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System" - xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" + xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics" xmlns:p2="clr-namespace:;assembly=Extensions" xmlns:p3="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -18,6 +18,10 @@ + + TODO + + ReadSchemas @@ -378,6 +382,23 @@ DrawCall + + SyncQuadColor + + + it ? 1.0 : 0.0 + + + + + + + + + + + Item1 + 0.1 0.1 @@ -396,7 +417,7 @@ - SynchQuadColor + SyncQuadColor TaskLogicParameters @@ -458,6 +479,34 @@ Texture2D + + UpdateSyncQuad + + + + Source1 + + + + + + + false + + + + SyncQuadColor + + + + + + + + + + + TaskLogicParameters @@ -507,6 +556,34 @@ Texture2D + + UpdateSyncQuad + + + + Source1 + + + + + + + true + + + + SyncQuadColor + + + + + + + + + + + TaskLogicParameters @@ -541,25 +618,27 @@ - - + + - - - - - - - - - + + + + + + + + + - + - + - + + + @@ -669,7 +748,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T13-42-17\Arduino\Arduino.csv + C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T13-48-46\Arduino\Arduino.csv false false None @@ -690,35 +769,40 @@ - - + + - + - + - - - + + + - - + + + + - - - + + + - - + + + + + \ No newline at end of file From a64940d9377d53906bf719448a83eb69833de782 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 14:04:12 +0000 Subject: [PATCH 05/17] Clean up workflow --- .bonsai/Settings/src/main.layout | 110 +- examples/rig.py | 9 +- src/DataSchemas/ucl_open_hf_visual.json | 32 + src/Extensions/UclOpenHfVisual.Generated.cs | 137 +++ src/main.bonsai | 1136 ++++++++++--------- src/ucl_open_hf_visual/rig.py | 9 + 6 files changed, 839 insertions(+), 594 deletions(-) diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index ee920a0..bab0b8c 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -1,44 +1,14 @@  - + - - false - - 344 - 310 - - - 334 - 64 - - Bonsai.Design.ObjectTextVisualizer - - - - - - false - - 361 - 396 - - - 334 - 64 - - Bonsai.Design.ObjectTextVisualizer - - - - - + - + false - 511 - 236 + 344 + 310 334 @@ -49,11 +19,11 @@ - + false - 500 - 144 + 361 + 396 334 @@ -64,38 +34,42 @@ + + + + false + + 511 + 236 + + + 334 + 64 + + Bonsai.Design.ObjectTextVisualizer + + + + + + false + + 500 + 144 + + + 334 + 64 + + Bonsai.Design.ObjectTextVisualizer + + + + + + - - false - - 640 - 283 - - - 334 - 184 - - Bonsai.Design.ObjectTextVisualizer - - - - - - false - - 174 - 146 - - - 837 - 213 - - Bonsai.Design.ObjectTextVisualizer - - - - \ No newline at end of file diff --git a/examples/rig.py b/examples/rig.py index 6bbbc66..28dfe77 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -4,7 +4,8 @@ UclOpenHfVisualRig ) from ucl_open_hf_visual.rig import ( - MatrixArduino + MatrixArduino, + SyncQuad ) from ucl_open.rigs.device import ( Screen, @@ -14,6 +15,12 @@ screen=Screen( texture_assets_directory="../textures" ), + sync_quad=SyncQuad( + extent_x=0.1, + extent_y=0.1, + location_x=1, + location_y=1 + ), arduino=MatrixArduino( port_name="COM10", baud_rate=1000000, diff --git a/src/DataSchemas/ucl_open_hf_visual.json b/src/DataSchemas/ucl_open_hf_visual.json index 8049347..36306d2 100644 --- a/src/DataSchemas/ucl_open_hf_visual.json +++ b/src/DataSchemas/ucl_open_hf_visual.json @@ -348,6 +348,34 @@ "title": "Screen", "type": "object" }, + "SyncQuad": { + "properties": { + "extentX": { + "title": "ExtentX", + "type": "number" + }, + "extentY": { + "title": "ExtentY", + "type": "number" + }, + "locationX": { + "title": "LocationX", + "type": "number" + }, + "locationY": { + "title": "LocationY", + "type": "number" + } + }, + "required": [ + "extentX", + "extentY", + "locationX", + "locationY" + ], + "title": "SyncQuad", + "type": "object" + }, "UclOpenHfVisualRig": { "properties": { "version": { @@ -359,6 +387,9 @@ "screen": { "$ref": "#/$defs/Screen" }, + "syncQuad": { + "$ref": "#/$defs/SyncQuad" + }, "arduino": { "$ref": "#/$defs/MatrixArduino", "title": "Arduino" @@ -366,6 +397,7 @@ }, "required": [ "screen", + "syncQuad", "arduino" ], "title": "UclOpenHfVisualRig", diff --git a/src/Extensions/UclOpenHfVisual.Generated.cs b/src/Extensions/UclOpenHfVisual.Generated.cs index 6f418c9..6aec3f2 100644 --- a/src/Extensions/UclOpenHfVisual.Generated.cs +++ b/src/Extensions/UclOpenHfVisual.Generated.cs @@ -1210,6 +1210,118 @@ public override string ToString() } + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SyncQuad + { + + private double _extentX; + + private double _extentY; + + private double _locationX; + + private double _locationY; + + public SyncQuad() + { + } + + protected SyncQuad(SyncQuad other) + { + _extentX = other._extentX; + _extentY = other._extentY; + _locationX = other._locationX; + _locationY = other._locationY; + } + + [Newtonsoft.Json.JsonPropertyAttribute("extentX", Required=Newtonsoft.Json.Required.Always)] + public double ExtentX + { + get + { + return _extentX; + } + set + { + _extentX = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("extentY", Required=Newtonsoft.Json.Required.Always)] + public double ExtentY + { + get + { + return _extentY; + } + set + { + _extentY = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("locationX", Required=Newtonsoft.Json.Required.Always)] + public double LocationX + { + get + { + return _locationX; + } + set + { + _locationX = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("locationY", Required=Newtonsoft.Json.Required.Always)] + public double LocationY + { + get + { + return _locationY; + } + set + { + _locationY = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SyncQuad(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SyncQuad(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("ExtentX = " + _extentX + ", "); + stringBuilder.Append("ExtentY = " + _extentY + ", "); + stringBuilder.Append("LocationX = " + _locationX + ", "); + stringBuilder.Append("LocationY = " + _locationY); + 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -1220,12 +1332,15 @@ public partial class UclOpenHfVisualRig private Screen _screen; + private SyncQuad _syncQuad; + private MatrixArduino _arduino; public UclOpenHfVisualRig() { _version = "0.0.0-rc1"; _screen = new Screen(); + _syncQuad = new SyncQuad(); _arduino = new MatrixArduino(); } @@ -1233,6 +1348,7 @@ protected UclOpenHfVisualRig(UclOpenHfVisualRig other) { _version = other._version; _screen = other._screen; + _syncQuad = other._syncQuad; _arduino = other._arduino; } @@ -1263,6 +1379,20 @@ public Screen Screen } } + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("syncQuad", Required=Newtonsoft.Json.Required.Always)] + public SyncQuad SyncQuad + { + get + { + return _syncQuad; + } + set + { + _syncQuad = value; + } + } + [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("arduino", Required=Newtonsoft.Json.Required.Always)] public MatrixArduino Arduino @@ -1291,6 +1421,7 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("Version = " + _version + ", "); stringBuilder.Append("Screen = " + _screen + ", "); + stringBuilder.Append("SyncQuad = " + _syncQuad + ", "); stringBuilder.Append("Arduino = " + _arduino); return true; } @@ -1713,6 +1844,11 @@ public System.IObservable Process(System.IObservable source) return Process(source); } + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + public System.IObservable Process(System.IObservable source) { return Process(source); @@ -1749,6 +1885,7 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] diff --git a/src/main.bonsai b/src/main.bonsai index 8ba3530..5c0da02 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -4,12 +4,13 @@ xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System" xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:p1="clr-namespace:UclOpenHfVisualDataSchema;assembly=Extensions" + xmlns:p2="clr-namespace:System.Reactive;assembly=System.Reactive.Core" xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders" xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics" - xmlns:p2="clr-namespace:;assembly=Extensions" - xmlns:p3="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" + xmlns:p3="clr-namespace:;assembly=Extensions" + xmlns:p4="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -146,624 +147,737 @@ - - RigSchema - - - Arduino - - - - - - - - - - COM10 - 1000000 - - - - None - 63 - 8 - One - None - false - false - false - 4096 - 2048 - 1 - Arduino - SerialMessages - - - RigSchema - - - Screen - - - - - - - - - - - 640 - 480 - On - false - Black - DepthBufferBit ColorBufferBit - true - - Resizable - Normal - Second - 60 - 120 - - - - 8 - 8 - 8 - 8 - - 16 - 0 - 0 - - 0 - 0 - 0 - 0 - - 2 - false - - - - - - - - - RigSchema - - - Screen.TextureAssetsDirectory - - - - - - - - TODO - + + Initialization + + + + StartExperiment + + + StopExperiment + + + + - LoadTextureBank + Hardware - - - + + RigSchema - - - ../textures - *.tif - TopDirectoryOnly - + + Arduino - - + + + + + + - - LoadTexture + + COM10 + 1000000 + + + + None + 63 + 8 + One + None + false + false + false + 4096 + 2048 + 1 + Arduino + SerialMessages + + + Display - - Source1 + + RigSchema + + + Screen + + + + + + + - - 1 + + 640 + 480 + On + false + Black + DepthBufferBit ColorBufferBit + true + + Resizable + Normal + Second + 60 + 120 + + + + 8 + 8 + 8 + 8 + + 16 + 0 + 0 + + 0 + 0 + 0 + 0 + + 2 + false + - - TexturePath + + + + + + RigSchema + + + Screen.TextureAssetsDirectory + + + + + + + + TODO + + + + LoadTextureBank + + + + + + + + + ../textures + *.tif + TopDirectoryOnly + + + + + + + LoadTexture + + + + Source1 + + + + 1 + + + + TexturePath + + + TexturePath + + + + + + TexturePath + + + + + + + + + + + Rgba + Repeat + Repeat + Linear + Linear + ../textures\SynthIm_42_5.tif + Unchanged + Vertical + + + + + + + + + + + + + + + + + + + + + + + + Item1 + Item2 + + + + + + TextureBank + + + + + + + + + + + + + + + + + + -1 + 1 + -1 + 1 + + + DrawCall - TexturePath + DrawCall + + + + 2 + 2 + 0 + 0 + 0 + 0 + 1 + 1 + 0 + 0 + + + DrawCall + + + SyncQuadColor + + + it ? 1.0 : 0.0 - + + + + + + + + + Item1 - TexturePath + RigSchema + + + SyncQuad - + + + + + + 0.1 + 0.1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 1 + - - - - Rgba - Repeat - Repeat - Linear - Linear - ../textures\SynthIm_42_5.tif - Unchanged - Vertical + + false - - + + SyncQuadColor - + - - + - - + + + + + + + + + + + + + + + - - - - - Item1 - Item2 - - - - - - TextureBank - - - - - - - - - - -1 - 1 - -1 - 1 - - - DrawCall - - - DrawCall - - - - 2 - 2 - 0 - 0 - 0 - 0 - 1 - 1 - 0 - 0 - - - DrawCall - - - SyncQuadColor - - - it ? 1.0 : 0.0 - - - - - - - - - - - Item1 - - - 0.1 - 0.1 - 1 - 1 - 0 - 0 - 1 - 1 - 1 - 1 - - - - false - - - - SyncQuadColor - - - TaskLogicParameters - - - AvailableTextures - - - - - - - - - TextureBank - - - - - - PresentationSequence + + TaskLogic - - Source1 - - - - 1 - - - - TextureName - - - TextureBank - TaskLogicParameters - InterPresentationTexture + AvailableTextures - - - - + + + + + - - - blankStim_1 - + + TextureBank - - Texture0 - Image - - Texture2D - + - - UpdateSyncQuad + + PresentationSequence Source1 - - + + + 1 + + + + TextureName + + + TextureBank + + + TaskLogicParameters + + + InterPresentationTexture + + + + + + + + + blankStim_1 + - - false + + Texture0 + Image + + Texture2D - - SyncQuadColor + + UpdateSyncQuad + + + + Source1 + + + + + + + false + + + + SyncQuadColor + + + + + + + + + + - - - - - - - - - - - - TaskLogicParameters - - - InterPresentationTime - - - TimeSpan.FromSeconds(it) - - - - - - - - - PT0.5S - - - - TextureBank - - - - - - Item2 - - - TextureName - - - - - - - - - SynthIm_1_1 - - - - - Texture0 - Image - - Texture2D - - - - UpdateSyncQuad - - - - Source1 + + TaskLogicParameters - - + + InterPresentationTime + + + TimeSpan.FromSeconds(it) + + + + + - - true + + PT0.5S - - SyncQuadColor + + TextureBank + + + + + + Item2 + + + TextureName + + + + + + + + + SN_1_1 + + + + + Texture0 + Image + + Texture2D + + + + UpdateSyncQuad + + + + Source1 + + + + + + + true + + + + SyncQuadColor + + + + + + + + + + + + + TaskLogicParameters + + + PresentationTime + + + TimeSpan.FromSeconds(it) + + + + + + + + + PT1S + + + + + 1 + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - TaskLogicParameters - - - PresentationTime - - - TimeSpan.FromSeconds(it) - - - - - - - - PT1S - + - - 1 - + - - + + + - + - - - - - - - - - - - - - - - - - - - - - - + + StartExperiment - - - - Algernon - 001 - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data + - SerialMessages + StopExperiment - - - - TODO - + - LogData + Logging - - Source1 + + Algernon + 001 + C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data - - - + + SerialMessages + + + + + + TODO + - FormatFileName - Generates a log filename based on the input timestamp. + LogData - - PathPrefix - Source1 - + + - - - Arduino - + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + Arduino + + + + + 1 + + + + + + + + + + + csv + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + - - - 1 - - - - + + + + - - - - - csv - - - - - 1 - - - - + - - {0}\{1}\{2}.{3} - Item1,Item2,Item3,Item4 + + C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T14-00-42\Arduino\Arduino.csv + false + false + None + true + it - - - - - - - - - - - - + + + + + + - - - - - - - - - - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T13-48-46\Arduino\Arduino.csv - false - false - None - true - it - - - - - - - + + @@ -771,38 +885,10 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + \ No newline at end of file diff --git a/src/ucl_open_hf_visual/rig.py b/src/ucl_open_hf_visual/rig.py index 072bb7c..bbb252e 100644 --- a/src/ucl_open_hf_visual/rig.py +++ b/src/ucl_open_hf_visual/rig.py @@ -8,11 +8,20 @@ from ucl_open_hf_visual import __semver__ +# TODO - should be part of main package? +# TODO - should be able to define generic number of sync quads (e.g. for different screens) +class SyncQuad(BaseSchema): + extent_x: float + extent_y: float + location_x: float + location_y: float + class MatrixArduino(SerialDeviceModule): device_type: Literal["MatrixArduino"] = "MatrixArduino" class UclOpenHfVisualRig(BaseSchema): version: Literal[__semver__] = __semver__ # type: ignore screen: Screen + sync_quad: SyncQuad arduino: MatrixArduino ... \ No newline at end of file From beb78ba4a00d554f12d8fc56bdc3c453865a6d67 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 14:53:05 +0000 Subject: [PATCH 06/17] Add visualizer --- .bonsai/Bonsai.config | 24 ++- .bonsai/Settings/src/main.editor | 3 +- .bonsai/Settings/src/main.layout | 103 ++++++++++++ src/main.bonsai | 271 ++++++++++++++++++++++++++++--- 4 files changed, 377 insertions(+), 24 deletions(-) diff --git a/.bonsai/Bonsai.config b/.bonsai/Bonsai.config index 88a88e9..27a19c4 100644 --- a/.bonsai/Bonsai.config +++ b/.bonsai/Bonsai.config @@ -5,8 +5,11 @@ - + + + + @@ -16,7 +19,8 @@ - + + @@ -29,6 +33,7 @@ + @@ -44,13 +49,17 @@ + + + + @@ -61,6 +70,7 @@ + @@ -73,8 +83,11 @@ - + + + + @@ -84,7 +97,8 @@ - + + @@ -96,6 +110,7 @@ + @@ -114,6 +129,7 @@ + diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 998d34c..227521a 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -13,8 +13,9 @@ - + + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index bab0b8c..4ef5947 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -72,4 +72,107 @@ + + + 120 + 130 + + + 418 + 377 + + Bonsai.Gui.TableLayoutPanelVisualizer + + + + Bonsai.Gui.GroupBoxVisualizer + + + + Bonsai.Gui.TableLayoutPanelVisualizer + + + + Bonsai.Gui.ButtonVisualizer + + + + + + Bonsai.Gui.ButtonVisualizer + + + + + + + + + + + + Bonsai.Gui.GroupBoxVisualizer + + + + Bonsai.Design.ObjectTextVisualizer + + + + + + + + + Bonsai.Gui.GroupBoxVisualizer + + + + Bonsai.Gui.ZedGraph.RollingGraphVisualizer + + + 0 + -1 + 1 + true + + + + + + + + Bonsai.Gui.GroupBoxVisualizer + + + + Bonsai.Gui.ZedGraph.RollingGraphVisualizer + + + 0 + 0 + 1.1 + true + + + + + + + + Bonsai.Gui.GroupBoxVisualizer + + + + Bonsai.Vision.Design.IplImageVisualizer + + + + + + + + + + \ No newline at end of file diff --git a/src/main.bonsai b/src/main.bonsai index 5c0da02..500ffaa 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -5,11 +5,13 @@ xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:p1="clr-namespace:UclOpenHfVisualDataSchema;assembly=Extensions" xmlns:p2="clr-namespace:System.Reactive;assembly=System.Reactive.Core" + xmlns:p3="clr-namespace:;assembly=Extensions" xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders" xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics" - xmlns:p3="clr-namespace:;assembly=Extensions" + xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" + xmlns:zg="clr-namespace:Bonsai.Gui.ZedGraph;assembly=Bonsai.Gui.ZedGraph" xmlns:p4="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -198,6 +200,15 @@ Arduino SerialMessages + + SerialMessages + + + + + + MatrixArduino + Display @@ -386,6 +397,20 @@ DrawCall + + + + + + + + + + + + + DebugView + DrawCall @@ -443,9 +468,9 @@ 1 0 0 - 0 - 0 - 0 + 1 + 1 + 1 1 @@ -469,16 +494,19 @@ + - + - - - - + + + - + + + + @@ -487,6 +515,8 @@ + + @@ -620,7 +650,7 @@ - SN_1_1 + SynthIm_1_1 @@ -750,6 +780,213 @@ + + Visualizer + + + + StartButton + true + true + Start + + + StartExperiment + + + + Source1 + + + + StartExperiment + + + + + + + + + + + + + StopButton + true + true + Stop + + + StopExperiment + + + + Source1 + + + + StopExperiment + + + + + + + + + + + + + ExperimentControls + true + true + 2 + 1 + + + + + + + ExperimentControls + true + true + Experiment Controls + + + + MatrixArduino + + + + Matrix Arduino + true + true + MatrixArduino + + + + MatrixArduino + + + Value.EncoderCount + + + None + 2 + + + + + + + + Encoder + true + true + Encoder + + + + MatrixArduino + + + Value.LastSyncPulseTime + + + + + + + 1 + + + + + + 2 + + + + None + 2 + + + + + + + + SyncPulse + true + true + Sync Pulse + + + + DebugView + + + + Displau + true + true + Display + + + + ExperimentPanel + true + true + 2 + 3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Logging @@ -760,10 +997,7 @@ C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data - SerialMessages - - - + MatrixArduino TODO @@ -854,7 +1088,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T14-00-42\Arduino\Arduino.csv + C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T14-52-00\Arduino\Arduino.csv false false None @@ -875,9 +1109,8 @@ - - - + + From c45d12555e27e2d813829ac834f81e40d6cd40b0 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 15:04:04 +0000 Subject: [PATCH 07/17] Add spinnaker settings --- examples/rig.py | 9 + src/DataSchemas/ucl_open_hf_visual.json | 61 +++++- src/Extensions/UclOpenHfVisual.Generated.cs | 202 +++++++++++++++++++- src/ucl_open_hf_visual/rig.py | 2 + 4 files changed, 272 insertions(+), 2 deletions(-) diff --git a/examples/rig.py b/examples/rig.py index 28dfe77..ae027af 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -10,6 +10,9 @@ from ucl_open.rigs.device import ( Screen, ) +from ucl_open.rigs.video import ( + SpinnakerCamera +) rig = UclOpenHfVisualRig( screen=Screen( @@ -25,6 +28,12 @@ port_name="COM10", baud_rate=1000000, new_line="\n" + ), + eye_camera=SpinnakerCamera( + exposure_time=5000, + serial_number="00000", + gain=0, + binning=1 ) ) diff --git a/src/DataSchemas/ucl_open_hf_visual.json b/src/DataSchemas/ucl_open_hf_visual.json index 36306d2..26e0046 100644 --- a/src/DataSchemas/ucl_open_hf_visual.json +++ b/src/DataSchemas/ucl_open_hf_visual.json @@ -348,6 +348,60 @@ "title": "Screen", "type": "object" }, + "SpinnakerCamera": { + "properties": { + "cameraType": { + "const": "Spinnaker", + "default": "Spinnaker", + "description": "Camera type discriminator for Spinnaker devices.", + "title": "CameraType", + "type": "string" + }, + "triggerFrequency": { + "default": 50, + "description": "The frequency at which the camera is triggered (in Hz).", + "minimum": 1, + "title": "TriggerFrequency", + "type": "number" + }, + "exposureTime": { + "default": 15000, + "description": "The exposure time for the camera (in microseconds).", + "minimum": 0, + "title": "ExposureTime", + "type": "number" + }, + "serialNumber": { + "default": "00000", + "description": "The serial number of the camera.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "SerialNumber" + }, + "gain": { + "default": 1, + "description": "The camera gain.", + "minimum": 0, + "title": "Gain", + "type": "number" + }, + "binning": { + "default": 1, + "description": "The binning setting for the camera.", + "minimum": 1, + "title": "Binning", + "type": "integer" + } + }, + "title": "SpinnakerCamera", + "type": "object" + }, "SyncQuad": { "properties": { "extentX": { @@ -393,12 +447,17 @@ "arduino": { "$ref": "#/$defs/MatrixArduino", "title": "Arduino" + }, + "eyeCamera": { + "$ref": "#/$defs/SpinnakerCamera", + "title": "EyeCamera" } }, "required": [ "screen", "syncQuad", - "arduino" + "arduino", + "eyeCamera" ], "title": "UclOpenHfVisualRig", "type": "object" diff --git a/src/Extensions/UclOpenHfVisual.Generated.cs b/src/Extensions/UclOpenHfVisual.Generated.cs index 6aec3f2..452e124 100644 --- a/src/Extensions/UclOpenHfVisual.Generated.cs +++ b/src/Extensions/UclOpenHfVisual.Generated.cs @@ -1210,6 +1210,181 @@ public override string ToString() } + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SpinnakerCamera + { + + private string _cameraType; + + private double _triggerFrequency; + + private double _exposureTime; + + private string _serialNumber; + + private double _gain; + + private int _binning; + + public SpinnakerCamera() + { + _cameraType = "Spinnaker"; + _triggerFrequency = 50D; + _exposureTime = 15000D; + _gain = 1D; + _binning = 1; + } + + protected SpinnakerCamera(SpinnakerCamera other) + { + _cameraType = other._cameraType; + _triggerFrequency = other._triggerFrequency; + _exposureTime = other._exposureTime; + _serialNumber = other._serialNumber; + _gain = other._gain; + _binning = other._binning; + } + + /// + /// Camera type discriminator for Spinnaker devices. + /// + [Newtonsoft.Json.JsonPropertyAttribute("cameraType")] + [System.ComponentModel.DescriptionAttribute("Camera type discriminator for Spinnaker devices.")] + public string CameraType + { + get + { + return _cameraType; + } + set + { + _cameraType = value; + } + } + + /// + /// The frequency at which the camera is triggered (in Hz). + /// + [Newtonsoft.Json.JsonPropertyAttribute("triggerFrequency")] + [System.ComponentModel.DescriptionAttribute("The frequency at which the camera is triggered (in Hz).")] + public double TriggerFrequency + { + get + { + return _triggerFrequency; + } + set + { + _triggerFrequency = value; + } + } + + /// + /// The exposure time for the camera (in microseconds). + /// + [Newtonsoft.Json.JsonPropertyAttribute("exposureTime")] + [System.ComponentModel.DescriptionAttribute("The exposure time for the camera (in microseconds).")] + public double ExposureTime + { + get + { + return _exposureTime; + } + set + { + _exposureTime = value; + } + } + + /// + /// The serial number of the camera. + /// + [Newtonsoft.Json.JsonPropertyAttribute("serialNumber")] + [System.ComponentModel.DescriptionAttribute("The serial number of the camera.")] + public string SerialNumber + { + get + { + return _serialNumber; + } + set + { + _serialNumber = value; + } + } + + /// + /// The camera gain. + /// + [Newtonsoft.Json.JsonPropertyAttribute("gain")] + [System.ComponentModel.DescriptionAttribute("The camera gain.")] + public double Gain + { + get + { + return _gain; + } + set + { + _gain = value; + } + } + + /// + /// The binning setting for the camera. + /// + [Newtonsoft.Json.JsonPropertyAttribute("binning")] + [System.ComponentModel.DescriptionAttribute("The binning setting for the camera.")] + public int Binning + { + get + { + return _binning; + } + set + { + _binning = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SpinnakerCamera(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SpinnakerCamera(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("CameraType = " + _cameraType + ", "); + stringBuilder.Append("TriggerFrequency = " + _triggerFrequency + ", "); + stringBuilder.Append("ExposureTime = " + _exposureTime + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("Gain = " + _gain + ", "); + stringBuilder.Append("Binning = " + _binning); + 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -1336,12 +1511,15 @@ public partial class UclOpenHfVisualRig private MatrixArduino _arduino; + private SpinnakerCamera _eyeCamera; + public UclOpenHfVisualRig() { _version = "0.0.0-rc1"; _screen = new Screen(); _syncQuad = new SyncQuad(); _arduino = new MatrixArduino(); + _eyeCamera = new SpinnakerCamera(); } protected UclOpenHfVisualRig(UclOpenHfVisualRig other) @@ -1350,6 +1528,7 @@ protected UclOpenHfVisualRig(UclOpenHfVisualRig other) _screen = other._screen; _syncQuad = other._syncQuad; _arduino = other._arduino; + _eyeCamera = other._eyeCamera; } [Newtonsoft.Json.JsonPropertyAttribute("version")] @@ -1407,6 +1586,20 @@ public MatrixArduino Arduino } } + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("eyeCamera", Required=Newtonsoft.Json.Required.Always)] + public SpinnakerCamera EyeCamera + { + get + { + return _eyeCamera; + } + set + { + _eyeCamera = value; + } + } + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new UclOpenHfVisualRig(this))); @@ -1422,7 +1615,8 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("Version = " + _version + ", "); stringBuilder.Append("Screen = " + _screen + ", "); stringBuilder.Append("SyncQuad = " + _syncQuad + ", "); - stringBuilder.Append("Arduino = " + _arduino); + stringBuilder.Append("Arduino = " + _arduino + ", "); + stringBuilder.Append("EyeCamera = " + _eyeCamera); return true; } @@ -1844,6 +2038,11 @@ public System.IObservable Process(System.IObservable source) return Process(source); } + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + public System.IObservable Process(System.IObservable source) { return Process(source); @@ -1885,6 +2084,7 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] diff --git a/src/ucl_open_hf_visual/rig.py b/src/ucl_open_hf_visual/rig.py index bbb252e..23ce0d2 100644 --- a/src/ucl_open_hf_visual/rig.py +++ b/src/ucl_open_hf_visual/rig.py @@ -5,6 +5,7 @@ from ucl_open.rigs.base import BaseSchema from ucl_open.rigs.device import Screen # TODO - change to ucl rigs from ucl_open.rigs.device import SerialDeviceModule +from ucl_open.rigs.video import SpinnakerCamera from ucl_open_hf_visual import __semver__ @@ -24,4 +25,5 @@ class UclOpenHfVisualRig(BaseSchema): screen: Screen sync_quad: SyncQuad arduino: MatrixArduino + eye_camera: SpinnakerCamera ... \ No newline at end of file From af194befd5432d5cfdef76537cfb176f2433d5d1 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 15:19:42 +0000 Subject: [PATCH 08/17] Add current texture monitor --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 18 ++ examples/session.py | 8 +- src/DataSchemas/ucl_open_hf_visual.json | 58 ++--- src/Extensions/UclOpenHfVisual.Generated.cs | 247 ++++++++++---------- src/main.bonsai | 163 ++++++++++--- src/ucl_open_hf_visual/regenerate.py | 3 +- src/ucl_open_hf_visual/session.py | 5 + 8 files changed, 325 insertions(+), 179 deletions(-) create mode 100644 src/ucl_open_hf_visual/session.py diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 227521a..6a5f4af 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index 4ef5947..f5b1eed 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -172,6 +172,24 @@ + + Bonsai.Gui.GroupBoxVisualizer + + + + Bonsai.Design.Visualizers.TimeSeriesVisualizer + + + 640 + 930 + 955 + true + + + + + + diff --git a/examples/session.py b/examples/session.py index 2874664..67f0d23 100644 --- a/examples/session.py +++ b/examples/session.py @@ -1,13 +1,15 @@ import datetime import os -from ucl_open.rigs.experiment import Experiment +from ucl_open_hf_visual.session import UclOpenSession # TODO - autofill experiment fields -session = Experiment( +# TODO - versions, repo configs etc. +session = UclOpenSession( workflow="main.bonsai", commit="", - repository_url="https://github.com/ucl-open/hf-visual" + repository_url="https://github.com/ucl-open/hf-visual", + logging_root_path="C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data" ) def main(path_seed: str = "./local/{schema}.json"): diff --git a/src/DataSchemas/ucl_open_hf_visual.json b/src/DataSchemas/ucl_open_hf_visual.json index 26e0046..04e1fbc 100644 --- a/src/DataSchemas/ucl_open_hf_visual.json +++ b/src/DataSchemas/ucl_open_hf_visual.json @@ -94,33 +94,6 @@ "title": "DisplayIntrinsics", "type": "object" }, - "Experiment": { - "description": "The base class for creating ucl-open experiment models.", - "properties": { - "workflow": { - "description": "Path to the workflow running the experiment.", - "title": "Workflow", - "type": "string" - }, - "commit": { - "description": "Commit hash of the experiment/rig repo.", - "title": "Commit", - "type": "string" - }, - "repositoryUrl": { - "description": "The URL of the git repository used to version experiment source code.", - "title": "RepositoryUrl", - "type": "string" - } - }, - "required": [ - "workflow", - "commit", - "repositoryUrl" - ], - "title": "Experiment", - "type": "object" - }, "MatrixArduino": { "properties": { "deviceType": { @@ -533,6 +506,37 @@ "title": "UclOpenHfVisualTaskParameters", "type": "object" }, + "UclOpenSession": { + "properties": { + "workflow": { + "description": "Path to the workflow running the experiment.", + "title": "Workflow", + "type": "string" + }, + "commit": { + "description": "Commit hash of the experiment/rig repo.", + "title": "Commit", + "type": "string" + }, + "repositoryUrl": { + "description": "The URL of the git repository used to version experiment source code.", + "title": "RepositoryUrl", + "type": "string" + }, + "loggingRootPath": { + "title": "LoggingRootPath", + "type": "string" + } + }, + "required": [ + "workflow", + "commit", + "repositoryUrl", + "loggingRootPath" + ], + "title": "UclOpenSession", + "type": "object" + }, "Vector3": { "properties": { "x": { diff --git a/src/Extensions/UclOpenHfVisual.Generated.cs b/src/Extensions/UclOpenHfVisual.Generated.cs index 452e124..4d7bcf8 100644 --- a/src/Extensions/UclOpenHfVisual.Generated.cs +++ b/src/Extensions/UclOpenHfVisual.Generated.cs @@ -321,117 +321,6 @@ public override string ToString() } - /// - /// The base class for creating ucl-open experiment models. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("The base class for creating ucl-open experiment models.")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class Experiment - { - - private string _workflow; - - private string _commit; - - private string _repositoryUrl; - - public Experiment() - { - } - - protected Experiment(Experiment other) - { - _workflow = other._workflow; - _commit = other._commit; - _repositoryUrl = other._repositoryUrl; - } - - /// - /// Path to the workflow running the experiment. - /// - [Newtonsoft.Json.JsonPropertyAttribute("workflow", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Path to the workflow running the experiment.")] - public string Workflow - { - get - { - return _workflow; - } - set - { - _workflow = value; - } - } - - /// - /// Commit hash of the experiment/rig repo. - /// - [Newtonsoft.Json.JsonPropertyAttribute("commit", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Commit hash of the experiment/rig repo.")] - public string Commit - { - get - { - return _commit; - } - set - { - _commit = value; - } - } - - /// - /// The URL of the git repository used to version experiment source code. - /// - [Newtonsoft.Json.JsonPropertyAttribute("repositoryUrl", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("The URL of the git repository used to version experiment source code.")] - public string RepositoryUrl - { - get - { - return _repositoryUrl; - } - set - { - _repositoryUrl = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Experiment(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new Experiment(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("Workflow = " + _workflow + ", "); - stringBuilder.Append("Commit = " + _commit + ", "); - stringBuilder.Append("RepositoryUrl = " + _repositoryUrl); - 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -1878,6 +1767,130 @@ public override string ToString() } + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class UclOpenSession + { + + private string _workflow; + + private string _commit; + + private string _repositoryUrl; + + private string _loggingRootPath; + + public UclOpenSession() + { + } + + protected UclOpenSession(UclOpenSession other) + { + _workflow = other._workflow; + _commit = other._commit; + _repositoryUrl = other._repositoryUrl; + _loggingRootPath = other._loggingRootPath; + } + + /// + /// Path to the workflow running the experiment. + /// + [Newtonsoft.Json.JsonPropertyAttribute("workflow", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Path to the workflow running the experiment.")] + public string Workflow + { + get + { + return _workflow; + } + set + { + _workflow = value; + } + } + + /// + /// Commit hash of the experiment/rig repo. + /// + [Newtonsoft.Json.JsonPropertyAttribute("commit", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Commit hash of the experiment/rig repo.")] + public string Commit + { + get + { + return _commit; + } + set + { + _commit = value; + } + } + + /// + /// The URL of the git repository used to version experiment source code. + /// + [Newtonsoft.Json.JsonPropertyAttribute("repositoryUrl", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The URL of the git repository used to version experiment source code.")] + public string RepositoryUrl + { + get + { + return _repositoryUrl; + } + set + { + _repositoryUrl = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("loggingRootPath", Required=Newtonsoft.Json.Required.Always)] + public string LoggingRootPath + { + get + { + return _loggingRootPath; + } + set + { + _loggingRootPath = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new UclOpenSession(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new UclOpenSession(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Workflow = " + _workflow + ", "); + stringBuilder.Append("Commit = " + _commit + ", "); + stringBuilder.Append("RepositoryUrl = " + _repositoryUrl + ", "); + stringBuilder.Append("LoggingRootPath = " + _loggingRootPath); + 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -2018,11 +2031,6 @@ public System.IObservable Process(System.IObservable return Process(source); } - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - public System.IObservable Process(System.IObservable source) { return Process(source); @@ -2063,6 +2071,11 @@ public System.IObservable Process(System.IObservable(source); } + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + public System.IObservable Process(System.IObservable source) { return Process(source); @@ -2080,7 +2093,6 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] @@ -2089,6 +2101,7 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder { diff --git a/src/main.bonsai b/src/main.bonsai index 500ffaa..91ea96c 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -5,6 +5,7 @@ xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:p1="clr-namespace:UclOpenHfVisualDataSchema;assembly=Extensions" xmlns:p2="clr-namespace:System.Reactive;assembly=System.Reactive.Core" + xmlns:sys="clr-namespace:System;assembly=mscorlib" xmlns:p3="clr-namespace:;assembly=Extensions" xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders" xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System" @@ -34,7 +35,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\local\Experiment.json + C:\Users\neurogears\source\repos\ucl-open\hf-visual\local\UclOpenSession.json @@ -89,7 +90,7 @@ RawSessionSchema - + @@ -97,7 +98,7 @@ - SubjectSchema + SessionSchema RawRigSchema @@ -159,6 +160,9 @@ StopExperiment + + CurrentTexture + @@ -612,6 +616,40 @@ + + UpdateCurrentTexture + + + + Source1 + + + TaskLogicParameters + + + InterPresentationTexture + + + + + + Item2 + + + CurrentTexture + + + + + + + + + + + + + TaskLogicParameters @@ -689,6 +727,36 @@ + + UpdateCurrentTexture + + + + Source1 + + + TextureName + + + + + + Item2 + + + CurrentTexture + + + + + + + + + + + + TaskLogicParameters @@ -724,26 +792,28 @@ - - + + - - - - - - - - + + + + + + + + - + - + - + - + + + @@ -857,14 +927,14 @@ - MatrixArduino + CurrentTexture - Matrix Arduino + CurrentTexture true true - MatrixArduino + Current Texture @@ -930,12 +1000,26 @@ - Displau + Display true true Display + + MatrixArduino + + + Value.PhotodiodeVal + + + + Photodiode + true + true + Photodiode + + ExperimentPanel true @@ -958,17 +1042,17 @@ - + - + - + @@ -978,12 +1062,17 @@ - + - + + + + + + @@ -991,10 +1080,21 @@ Logging + + SessionSchema + + + LoggingRootPath + + + + + + Algernon 001 - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data MatrixArduino @@ -1088,7 +1188,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\temp_data\sub-Algernon\ses-001_date-2025-12-11T14-52-00\Arduino\Arduino.csv + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Algernon\ses-001_date-2025-12-11T15-19-14\Arduino\Arduino.csv false false None @@ -1109,8 +1209,11 @@ - - + + + + + diff --git a/src/ucl_open_hf_visual/regenerate.py b/src/ucl_open_hf_visual/regenerate.py index e52e27a..a5853a1 100644 --- a/src/ucl_open_hf_visual/regenerate.py +++ b/src/ucl_open_hf_visual/regenerate.py @@ -8,6 +8,7 @@ import ucl_open_hf_visual.rig import ucl_open_hf_visual.task import ucl_open_hf_visual.data_types +import ucl_open_hf_visual.session SCHEMA_ROOT = Path("./src/DataSchemas/") EXTENSIONS_ROOT = Path("./src/Extensions/") @@ -18,7 +19,7 @@ def main(): models = [ ucl_open_hf_visual.task.UclOpenHfVisualTaskLogic, ucl_open_hf_visual.rig.UclOpenHfVisualRig, - Experiment, + ucl_open_hf_visual.session.UclOpenSession, ucl_open_hf_visual.data_types.MatrixArduinoData ] model = pydantic.RootModel[Union[tuple(models)]] diff --git a/src/ucl_open_hf_visual/session.py b/src/ucl_open_hf_visual/session.py new file mode 100644 index 0000000..9a259cf --- /dev/null +++ b/src/ucl_open_hf_visual/session.py @@ -0,0 +1,5 @@ +from ucl_open.rigs.experiment import Experiment + +# TODO - should be part of ucl open rigs +class UclOpenSession(Experiment): + logging_root_path: str \ No newline at end of file From c358f7983b1a84daca4769b4bd7ea6749b6da3cb Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 15:26:58 +0000 Subject: [PATCH 09/17] Add other logging session variables --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 4 +- examples/session.py | 4 +- src/DataSchemas/ucl_open_hf_visual.json | 12 +- src/Extensions/UclOpenHfVisual.Generated.cs | 36 ++++- src/main.bonsai | 164 +++++++++++++++++++- src/ucl_open_hf_visual/session.py | 4 +- 7 files changed, 213 insertions(+), 13 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 6a5f4af..f4e3c7d 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index f5b1eed..3e769ea 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -181,8 +181,8 @@ 640 - 930 - 955 + 935 + 960 true diff --git a/examples/session.py b/examples/session.py index 67f0d23..b9b7aad 100644 --- a/examples/session.py +++ b/examples/session.py @@ -9,7 +9,9 @@ workflow="main.bonsai", commit="", repository_url="https://github.com/ucl-open/hf-visual", - logging_root_path="C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data" + logging_root_path="C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data", + animal_id="Plimbo", + session_id="001" ) def main(path_seed: str = "./local/{schema}.json"): diff --git a/src/DataSchemas/ucl_open_hf_visual.json b/src/DataSchemas/ucl_open_hf_visual.json index 04e1fbc..c50f3b1 100644 --- a/src/DataSchemas/ucl_open_hf_visual.json +++ b/src/DataSchemas/ucl_open_hf_visual.json @@ -526,13 +526,23 @@ "loggingRootPath": { "title": "LoggingRootPath", "type": "string" + }, + "animalId": { + "title": "AnimalId", + "type": "string" + }, + "sessionId": { + "title": "SessionId", + "type": "string" } }, "required": [ "workflow", "commit", "repositoryUrl", - "loggingRootPath" + "loggingRootPath", + "animalId", + "sessionId" ], "title": "UclOpenSession", "type": "object" diff --git a/src/Extensions/UclOpenHfVisual.Generated.cs b/src/Extensions/UclOpenHfVisual.Generated.cs index 4d7bcf8..8651dc5 100644 --- a/src/Extensions/UclOpenHfVisual.Generated.cs +++ b/src/Extensions/UclOpenHfVisual.Generated.cs @@ -1781,6 +1781,10 @@ public partial class UclOpenSession private string _loggingRootPath; + private string _animalId; + + private string _sessionId; + public UclOpenSession() { } @@ -1791,6 +1795,8 @@ protected UclOpenSession(UclOpenSession other) _commit = other._commit; _repositoryUrl = other._repositoryUrl; _loggingRootPath = other._loggingRootPath; + _animalId = other._animalId; + _sessionId = other._sessionId; } /// @@ -1857,6 +1863,32 @@ public string LoggingRootPath } } + [Newtonsoft.Json.JsonPropertyAttribute("animalId", Required=Newtonsoft.Json.Required.Always)] + public string AnimalId + { + get + { + return _animalId; + } + set + { + _animalId = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("sessionId", Required=Newtonsoft.Json.Required.Always)] + public string SessionId + { + get + { + return _sessionId; + } + set + { + _sessionId = value; + } + } + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new UclOpenSession(this))); @@ -1872,7 +1904,9 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("Workflow = " + _workflow + ", "); stringBuilder.Append("Commit = " + _commit + ", "); stringBuilder.Append("RepositoryUrl = " + _repositoryUrl + ", "); - stringBuilder.Append("LoggingRootPath = " + _loggingRootPath); + stringBuilder.Append("LoggingRootPath = " + _loggingRootPath + ", "); + stringBuilder.Append("AnimalId = " + _animalId + ", "); + stringBuilder.Append("SessionId = " + _sessionId); return true; } diff --git a/src/main.bonsai b/src/main.bonsai index 91ea96c..62334bb 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -14,6 +14,7 @@ xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" xmlns:zg="clr-namespace:Bonsai.Gui.ZedGraph;assembly=Bonsai.Gui.ZedGraph" xmlns:p4="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" + xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -188,8 +189,7 @@ COM10 1000000 - - + None 63 8 @@ -1091,6 +1091,28 @@ + + SessionSchema + + + AnimalId + + + + + + + + SessionSchema + + + SessionId + + + + + + Algernon 001 @@ -1188,7 +1210,126 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Algernon\ses-001_date-2025-12-11T15-19-14\Arduino\Arduino.csv + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Algernon\ses-001_date-2025-12-11T15-21-56\Arduino\Arduino.csv + false + false + None + true + it + + + + + + + + + + + + + + + CurrentTexture + + + MatrixArduino + + + Seconds + + + + + + + + + LogData + + + + Source1 + + + + + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + Texture + + + + + 1 + + + + + + + + + + + csv + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Algernon\ses-001_date-2025-12-11T15-21-56\Texture\Texture.csv false false None @@ -1211,9 +1352,20 @@ - - - + + + + + + + + + + + + + + diff --git a/src/ucl_open_hf_visual/session.py b/src/ucl_open_hf_visual/session.py index 9a259cf..e3d6ae1 100644 --- a/src/ucl_open_hf_visual/session.py +++ b/src/ucl_open_hf_visual/session.py @@ -2,4 +2,6 @@ # TODO - should be part of ucl open rigs class UclOpenSession(Experiment): - logging_root_path: str \ No newline at end of file + logging_root_path: str + animal_id: str + session_id: str \ No newline at end of file From 7cac29bd3067e8cea9e84da5c8be7d0472e02416 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 15:40:25 +0000 Subject: [PATCH 10/17] Add display intrinsics --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 4 +- examples/rig.py | 12 ++++- src/main.bonsai | 83 +++++++++++++++++++++++++------- 4 files changed, 80 insertions(+), 21 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index f4e3c7d..5250c8c 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index 3e769ea..aec044d 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -181,8 +181,8 @@ 640 - 935 - 960 + 876 + 882 true diff --git a/examples/rig.py b/examples/rig.py index ae027af..a075221 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -13,10 +13,20 @@ from ucl_open.rigs.video import ( SpinnakerCamera ) +from ucl_open.rigs.displays import ( + DisplayCalibration, + DisplayIntrinsics +) rig = UclOpenHfVisualRig( screen=Screen( - texture_assets_directory="../textures" + texture_assets_directory="../textures", + calibration={"main": DisplayCalibration( + intrinsics=DisplayIntrinsics( + frame_width=640, + frame_height=480 + ) + )} ), sync_quad=SyncQuad( extent_x=0.1, diff --git a/src/main.bonsai b/src/main.bonsai index 62334bb..d975035 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -189,7 +189,8 @@ COM10 1000000 - + + None 63 8 @@ -230,6 +231,44 @@ + + RigSchema + + + Screen.Calibration + + + + main + + + + Intrinsics.FrameWidth + + + + + + + + RigSchema + + + Screen.Calibration + + + + main + + + + Intrinsics.FrameHeight + + + + + + 640 @@ -489,28 +528,38 @@ - + + - - - + + + + - + - + - - - + + + - + - - + + + + + + + + + + @@ -688,7 +737,7 @@ - SynthIm_1_1 + SN_1_1 @@ -1114,7 +1163,7 @@ - Algernon + Plimbo 001 C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data @@ -1210,7 +1259,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Algernon\ses-001_date-2025-12-11T15-21-56\Arduino\Arduino.csv + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T15-34-28\Arduino\Arduino.csv false false None @@ -1329,7 +1378,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Algernon\ses-001_date-2025-12-11T15-21-56\Texture\Texture.csv + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T15-34-28\Texture\Texture.csv false false None From 25b073d10bfe974a9abf59bc56e92f7ce44a8db3 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 16:12:09 +0000 Subject: [PATCH 11/17] Add schema logging --- .bonsai/Bonsai.config | 4 +- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 27 +- .../UclOpen.Logging.0.1.3-dev0.nupkg | Bin 0 -> 8614 bytes src/main.bonsai | 358 +++++++++++++++++- 5 files changed, 379 insertions(+), 12 deletions(-) create mode 100644 local_packages/UclOpen.Logging.0.1.3-dev0.nupkg diff --git a/.bonsai/Bonsai.config b/.bonsai/Bonsai.config index 27a19c4..446a0e4 100644 --- a/.bonsai/Bonsai.config +++ b/.bonsai/Bonsai.config @@ -47,7 +47,7 @@ - + @@ -125,7 +125,7 @@ - + diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 5250c8c..227521a 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index aec044d..b93b276 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -150,8 +150,8 @@ 0 - 0 - 1.1 + 0.95 + 1.05 true @@ -181,8 +181,8 @@ 640 - 876 - 882 + 934 + 948 true @@ -193,4 +193,23 @@ + + + + false + + 144 + 156 + + + 994 + 196 + + Bonsai.Design.ObjectTextVisualizer + + + + + + \ No newline at end of file diff --git a/local_packages/UclOpen.Logging.0.1.3-dev0.nupkg b/local_packages/UclOpen.Logging.0.1.3-dev0.nupkg new file mode 100644 index 0000000000000000000000000000000000000000..22c2e6845783655b412b67e509aa06492d0fafe1 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zKP0LmY!v~IC#RhnPZLME{N+M3JE9brDn>;`YvsCG70Cg+H}PRXMC42tGHYbB^J$x- zlrDsL03)b^?LpI0eA-yyjXQrP-*ChP zg>n21$!gbABn5AR7UR%bNXjGgEHlJNYKK*myZ!(}@oWV;pHAeOH7fPV=w0DknmwHO zvh=9UX#q{I3#tZ=cBuu?Jf{=G0v?PN;F=pX;P* zO7Ji6;Qs$E{Bu(L>-d)^|99Zu-t#|EQqKwYx2^bJPW0a#fBTaEaM(UO+W)gl`8U_! z1?wNKEaLx>>v`?}o9jOnnt!;sNd8rJ{vGz8s?0xOcF$q|q2~Ne@b~ikhrpHe|6sAI VDIp^LdBn@-6aBd&1e5>i{XcKLv#9_8 literal 0 HcmV?d00001 diff --git a/src/main.bonsai b/src/main.bonsai index d975035..cdfd568 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -15,6 +15,7 @@ xmlns:zg="clr-namespace:Bonsai.Gui.ZedGraph;assembly=Bonsai.Gui.ZedGraph" xmlns:p4="clr-namespace:UclOpen.Core;assembly=UclOpen.Core" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" + xmlns:p5="clr-namespace:UclOpen.Logging;assembly=UclOpen.Logging" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -511,9 +512,9 @@ 1 0 0 - 1 - 1 - 1 + 0 + 0 + 0 1 @@ -1259,7 +1260,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T15-34-28\Arduino\Arduino.csv + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\Arduino\Arduino.csv false false None @@ -1378,7 +1379,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T15-34-28\Texture\Texture.csv + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\Texture\Texture.csv false false None @@ -1397,6 +1398,343 @@ + + RigSchema + + + + None + + + + + PT1S + + + + LogDataSchema + + + + Source1 + + + + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + RigSchema + + + + + 1 + + + + + + + + + + + json + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\RigSchema\RigSchema.json + None + false + + + + + + + + + + + + + + + TaskLogicSchema + + + + None + + + + + PT1S + + + + LogDataSchema + + + + Source1 + + + + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + TaskLogicSchema + + + + + 1 + + + + + + + + + + + json + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\TaskLogicSchema\TaskLogicSchema.json + None + false + + + + + + + + + + + + + + + SessionSchema + + + + None + + + + + PT1S + + + + TODO + + + + LogDataSchema + + + + Source1 + + + + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + SessionSchema + + + + + 1 + + + + + + + + + + + json + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\SessionSchema\SessionSchema.json + None + false + + + + + + + + + + + + + @@ -1415,6 +1753,16 @@ + + + + + + + + + + From 904647a836fa343358a284514ccb3a2dfacd9182 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 16:31:44 +0000 Subject: [PATCH 12/17] Modify for extra arduino --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 2 +- examples/rig.py | 10 +- src/DataSchemas/ucl_open_hf_visual.json | 200 +++-- .../ParseMatrixPhotodiodeSerialDevice.cs | 22 + src/Extensions/UclOpenHfVisual.Generated.cs | 697 +++++++++++++----- src/main.bonsai | 189 ++++- src/ucl_open_hf_visual/data_types.py | 6 +- src/ucl_open_hf_visual/regenerate.py | 3 +- src/ucl_open_hf_visual/rig.py | 7 +- 10 files changed, 871 insertions(+), 267 deletions(-) create mode 100644 src/Extensions/ParseMatrixPhotodiodeSerialDevice.cs diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 227521a..f4e3c7d 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index b93b276..f476e24 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -195,7 +195,7 @@ - + false 144 diff --git a/examples/rig.py b/examples/rig.py index a075221..54afa08 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -5,6 +5,7 @@ ) from ucl_open_hf_visual.rig import ( MatrixArduino, + MatrixArduinoPhotodiode, SyncQuad ) from ucl_open.rigs.device import ( @@ -39,11 +40,10 @@ baud_rate=1000000, new_line="\n" ), - eye_camera=SpinnakerCamera( - exposure_time=5000, - serial_number="00000", - gain=0, - binning=1 + arduino_photodiode=MatrixArduinoPhotodiode( + port_name="COM11", + baud_rate=250000, + new_line="\n" ) ) diff --git a/src/DataSchemas/ucl_open_hf_visual.json b/src/DataSchemas/ucl_open_hf_visual.json index c50f3b1..5e1939c 100644 --- a/src/DataSchemas/ucl_open_hf_visual.json +++ b/src/DataSchemas/ucl_open_hf_visual.json @@ -252,6 +252,144 @@ "title": "MatrixArduinoData", "type": "object" }, + "MatrixArduinoPhotodiode": { + "properties": { + "deviceType": { + "const": "MatrixArduinoPhotodiode", + "default": "MatrixArduinoPhotodiode", + "title": "DeviceType", + "type": "string" + }, + "portName": { + "description": "The name of the device serial port.", + "examples": [ + "COMx" + ], + "title": "PortName", + "type": "string" + }, + "baudRate": { + "default": 9600, + "description": "Baud rate for serial communication.", + "title": "BaudRate", + "type": "integer" + }, + "encoding": { + "default": null, + "description": "Optional text encoding for interpreting incoming bytes.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Encoding" + }, + "newLine": { + "default": "\r\n", + "description": "Line termination sequence used to delimit incoming messages.", + "title": "NewLine", + "type": "string" + }, + "parity": { + "default": "None", + "description": "Parity checking mode for the serial port.", + "title": "Parity", + "type": "string" + }, + "parityReplace": { + "default": 63, + "description": "Byte used to replace invalid bytes detected by a parity error.", + "title": "ParityReplace", + "type": "integer" + }, + "dataBits": { + "default": 8, + "description": "Number of data bits per serial frame.", + "title": "DataBits", + "type": "integer" + }, + "stopBits": { + "default": "One", + "description": "Number of stop bits per serial frame.", + "title": "StopBits", + "type": "string" + }, + "handshake": { + "default": "None", + "description": "Hardware or software handshaking mode.", + "title": "Handshake", + "type": "string" + }, + "discardNull": { + "default": false, + "description": "Whether to discard null bytes appearing in the serial stream.", + "title": "DiscardNull", + "type": "boolean" + }, + "dtrEnable": { + "default": false, + "description": "Whether to enable Data Terminal Ready (DTR) control line.", + "title": "DtrEnable", + "type": "boolean" + }, + "rtsEnable": { + "default": false, + "description": "Whether to enable Request To Send (RTS) control line.", + "title": "RtsEnable", + "type": "boolean" + }, + "readBufferSize": { + "default": 4096, + "description": "Size, in bytes, of the read buffer.", + "title": "ReadBufferSize", + "type": "integer" + }, + "writeBufferSize": { + "default": 2048, + "description": "Size, in bytes, of the write buffer.", + "title": "WriteBufferSize", + "type": "integer" + }, + "receivedBytesThreshold": { + "default": 1, + "description": "Minimum number of bytes in the buffer that triggers a read event.", + "title": "ReceivedBytesThreshold", + "type": "integer" + }, + "serialMessageSubjectName": { + "default": "SerialMessages", + "description": "Name of the subject to which parsed serial messages are published.", + "title": "SerialMessageSubjectName", + "type": "string" + } + }, + "required": [ + "portName" + ], + "title": "MatrixArduinoPhotodiode", + "type": "object" + }, + "MatrixArduinoPhotodiodeData": { + "properties": { + "photodiodeVal": { + "title": "PhotodiodeVal", + "type": "integer" + }, + "syncVal": { + "title": "SyncVal", + "type": "integer" + } + }, + "required": [ + "photodiodeVal", + "syncVal" + ], + "title": "MatrixArduinoPhotodiodeData", + "type": "object" + }, "Screen": { "properties": { "deviceType": { @@ -321,60 +459,6 @@ "title": "Screen", "type": "object" }, - "SpinnakerCamera": { - "properties": { - "cameraType": { - "const": "Spinnaker", - "default": "Spinnaker", - "description": "Camera type discriminator for Spinnaker devices.", - "title": "CameraType", - "type": "string" - }, - "triggerFrequency": { - "default": 50, - "description": "The frequency at which the camera is triggered (in Hz).", - "minimum": 1, - "title": "TriggerFrequency", - "type": "number" - }, - "exposureTime": { - "default": 15000, - "description": "The exposure time for the camera (in microseconds).", - "minimum": 0, - "title": "ExposureTime", - "type": "number" - }, - "serialNumber": { - "default": "00000", - "description": "The serial number of the camera.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "SerialNumber" - }, - "gain": { - "default": 1, - "description": "The camera gain.", - "minimum": 0, - "title": "Gain", - "type": "number" - }, - "binning": { - "default": 1, - "description": "The binning setting for the camera.", - "minimum": 1, - "title": "Binning", - "type": "integer" - } - }, - "title": "SpinnakerCamera", - "type": "object" - }, "SyncQuad": { "properties": { "extentX": { @@ -421,16 +505,16 @@ "$ref": "#/$defs/MatrixArduino", "title": "Arduino" }, - "eyeCamera": { - "$ref": "#/$defs/SpinnakerCamera", - "title": "EyeCamera" + "arduinoPhotodiode": { + "$ref": "#/$defs/MatrixArduinoPhotodiode", + "title": "ArduinoPhotodiode" } }, "required": [ "screen", "syncQuad", "arduino", - "eyeCamera" + "arduinoPhotodiode" ], "title": "UclOpenHfVisualRig", "type": "object" diff --git a/src/Extensions/ParseMatrixPhotodiodeSerialDevice.cs b/src/Extensions/ParseMatrixPhotodiodeSerialDevice.cs new file mode 100644 index 0000000..49594bc --- /dev/null +++ b/src/Extensions/ParseMatrixPhotodiodeSerialDevice.cs @@ -0,0 +1,22 @@ +using System; +using System.Reactive.Linq; +using Bonsai; +using Bonsai.Harp; +using UclOpenHfVisualDataSchema; + +public class ParseMatrixPhotodiodeSerialDevice : Transform +{ + public override IObservable Process(IObservable source) + { + return source.Select(value => + { + var values = value.Split(','); + var matrixArduinoData = new MatrixArduinoPhotodiodeData + { + PhotodiodeVal = Convert.ToInt32(values[0]), + SyncVal = Convert.ToInt32(values[0]) + }; + return matrixArduinoData; + }); + } +} \ No newline at end of file diff --git a/src/Extensions/UclOpenHfVisual.Generated.cs b/src/Extensions/UclOpenHfVisual.Generated.cs index 8651dc5..1412428 100644 --- a/src/Extensions/UclOpenHfVisual.Generated.cs +++ b/src/Extensions/UclOpenHfVisual.Generated.cs @@ -879,6 +879,496 @@ public override string ToString() } + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class MatrixArduinoPhotodiode + { + + private string _deviceType; + + private string _portName; + + private int _baudRate; + + private string _encoding; + + private string _newLine; + + private string _parity; + + private int _parityReplace; + + private int _dataBits; + + private string _stopBits; + + private string _handshake; + + private bool _discardNull; + + private bool _dtrEnable; + + private bool _rtsEnable; + + private int _readBufferSize; + + private int _writeBufferSize; + + private int _receivedBytesThreshold; + + private string _serialMessageSubjectName; + + public MatrixArduinoPhotodiode() + { + _deviceType = "MatrixArduinoPhotodiode"; + _baudRate = 9600; + _newLine = "\r\n"; + _parity = "None"; + _parityReplace = 63; + _dataBits = 8; + _stopBits = "One"; + _handshake = "None"; + _discardNull = false; + _dtrEnable = false; + _rtsEnable = false; + _readBufferSize = 4096; + _writeBufferSize = 2048; + _receivedBytesThreshold = 1; + _serialMessageSubjectName = "SerialMessages"; + } + + protected MatrixArduinoPhotodiode(MatrixArduinoPhotodiode other) + { + _deviceType = other._deviceType; + _portName = other._portName; + _baudRate = other._baudRate; + _encoding = other._encoding; + _newLine = other._newLine; + _parity = other._parity; + _parityReplace = other._parityReplace; + _dataBits = other._dataBits; + _stopBits = other._stopBits; + _handshake = other._handshake; + _discardNull = other._discardNull; + _dtrEnable = other._dtrEnable; + _rtsEnable = other._rtsEnable; + _readBufferSize = other._readBufferSize; + _writeBufferSize = other._writeBufferSize; + _receivedBytesThreshold = other._receivedBytesThreshold; + _serialMessageSubjectName = other._serialMessageSubjectName; + } + + [Newtonsoft.Json.JsonPropertyAttribute("deviceType")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// The name of the device serial port. + /// + [Newtonsoft.Json.JsonPropertyAttribute("portName", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The name of the device serial port.")] + public string PortName + { + get + { + return _portName; + } + set + { + _portName = value; + } + } + + /// + /// Baud rate for serial communication. + /// + [Newtonsoft.Json.JsonPropertyAttribute("baudRate")] + [System.ComponentModel.DescriptionAttribute("Baud rate for serial communication.")] + public int BaudRate + { + get + { + return _baudRate; + } + set + { + _baudRate = value; + } + } + + /// + /// Optional text encoding for interpreting incoming bytes. + /// + [Newtonsoft.Json.JsonPropertyAttribute("encoding")] + [System.ComponentModel.DescriptionAttribute("Optional text encoding for interpreting incoming bytes.")] + public string Encoding + { + get + { + return _encoding; + } + set + { + _encoding = value; + } + } + + /// + /// Line termination sequence used to delimit incoming messages. + /// + [Newtonsoft.Json.JsonPropertyAttribute("newLine")] + [System.ComponentModel.DescriptionAttribute("Line termination sequence used to delimit incoming messages.")] + public string NewLine + { + get + { + return _newLine; + } + set + { + _newLine = value; + } + } + + /// + /// Parity checking mode for the serial port. + /// + [Newtonsoft.Json.JsonPropertyAttribute("parity")] + [System.ComponentModel.DescriptionAttribute("Parity checking mode for the serial port.")] + public string Parity + { + get + { + return _parity; + } + set + { + _parity = value; + } + } + + /// + /// Byte used to replace invalid bytes detected by a parity error. + /// + [Newtonsoft.Json.JsonPropertyAttribute("parityReplace")] + [System.ComponentModel.DescriptionAttribute("Byte used to replace invalid bytes detected by a parity error.")] + public int ParityReplace + { + get + { + return _parityReplace; + } + set + { + _parityReplace = value; + } + } + + /// + /// Number of data bits per serial frame. + /// + [Newtonsoft.Json.JsonPropertyAttribute("dataBits")] + [System.ComponentModel.DescriptionAttribute("Number of data bits per serial frame.")] + public int DataBits + { + get + { + return _dataBits; + } + set + { + _dataBits = value; + } + } + + /// + /// Number of stop bits per serial frame. + /// + [Newtonsoft.Json.JsonPropertyAttribute("stopBits")] + [System.ComponentModel.DescriptionAttribute("Number of stop bits per serial frame.")] + public string StopBits + { + get + { + return _stopBits; + } + set + { + _stopBits = value; + } + } + + /// + /// Hardware or software handshaking mode. + /// + [Newtonsoft.Json.JsonPropertyAttribute("handshake")] + [System.ComponentModel.DescriptionAttribute("Hardware or software handshaking mode.")] + public string Handshake + { + get + { + return _handshake; + } + set + { + _handshake = value; + } + } + + /// + /// Whether to discard null bytes appearing in the serial stream. + /// + [Newtonsoft.Json.JsonPropertyAttribute("discardNull")] + [System.ComponentModel.DescriptionAttribute("Whether to discard null bytes appearing in the serial stream.")] + public bool DiscardNull + { + get + { + return _discardNull; + } + set + { + _discardNull = value; + } + } + + /// + /// Whether to enable Data Terminal Ready (DTR) control line. + /// + [Newtonsoft.Json.JsonPropertyAttribute("dtrEnable")] + [System.ComponentModel.DescriptionAttribute("Whether to enable Data Terminal Ready (DTR) control line.")] + public bool DtrEnable + { + get + { + return _dtrEnable; + } + set + { + _dtrEnable = value; + } + } + + /// + /// Whether to enable Request To Send (RTS) control line. + /// + [Newtonsoft.Json.JsonPropertyAttribute("rtsEnable")] + [System.ComponentModel.DescriptionAttribute("Whether to enable Request To Send (RTS) control line.")] + public bool RtsEnable + { + get + { + return _rtsEnable; + } + set + { + _rtsEnable = value; + } + } + + /// + /// Size, in bytes, of the read buffer. + /// + [Newtonsoft.Json.JsonPropertyAttribute("readBufferSize")] + [System.ComponentModel.DescriptionAttribute("Size, in bytes, of the read buffer.")] + public int ReadBufferSize + { + get + { + return _readBufferSize; + } + set + { + _readBufferSize = value; + } + } + + /// + /// Size, in bytes, of the write buffer. + /// + [Newtonsoft.Json.JsonPropertyAttribute("writeBufferSize")] + [System.ComponentModel.DescriptionAttribute("Size, in bytes, of the write buffer.")] + public int WriteBufferSize + { + get + { + return _writeBufferSize; + } + set + { + _writeBufferSize = value; + } + } + + /// + /// Minimum number of bytes in the buffer that triggers a read event. + /// + [Newtonsoft.Json.JsonPropertyAttribute("receivedBytesThreshold")] + [System.ComponentModel.DescriptionAttribute("Minimum number of bytes in the buffer that triggers a read event.")] + public int ReceivedBytesThreshold + { + get + { + return _receivedBytesThreshold; + } + set + { + _receivedBytesThreshold = value; + } + } + + /// + /// Name of the subject to which parsed serial messages are published. + /// + [Newtonsoft.Json.JsonPropertyAttribute("serialMessageSubjectName")] + [System.ComponentModel.DescriptionAttribute("Name of the subject to which parsed serial messages are published.")] + public string SerialMessageSubjectName + { + get + { + return _serialMessageSubjectName; + } + set + { + _serialMessageSubjectName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new MatrixArduinoPhotodiode(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new MatrixArduinoPhotodiode(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("PortName = " + _portName + ", "); + stringBuilder.Append("BaudRate = " + _baudRate + ", "); + stringBuilder.Append("Encoding = " + _encoding + ", "); + stringBuilder.Append("NewLine = " + _newLine + ", "); + stringBuilder.Append("Parity = " + _parity + ", "); + stringBuilder.Append("ParityReplace = " + _parityReplace + ", "); + stringBuilder.Append("DataBits = " + _dataBits + ", "); + stringBuilder.Append("StopBits = " + _stopBits + ", "); + stringBuilder.Append("Handshake = " + _handshake + ", "); + stringBuilder.Append("DiscardNull = " + _discardNull + ", "); + stringBuilder.Append("DtrEnable = " + _dtrEnable + ", "); + stringBuilder.Append("RtsEnable = " + _rtsEnable + ", "); + stringBuilder.Append("ReadBufferSize = " + _readBufferSize + ", "); + stringBuilder.Append("WriteBufferSize = " + _writeBufferSize + ", "); + stringBuilder.Append("ReceivedBytesThreshold = " + _receivedBytesThreshold + ", "); + stringBuilder.Append("SerialMessageSubjectName = " + _serialMessageSubjectName); + 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class MatrixArduinoPhotodiodeData + { + + private int _photodiodeVal; + + private int _syncVal; + + public MatrixArduinoPhotodiodeData() + { + } + + protected MatrixArduinoPhotodiodeData(MatrixArduinoPhotodiodeData other) + { + _photodiodeVal = other._photodiodeVal; + _syncVal = other._syncVal; + } + + [Newtonsoft.Json.JsonPropertyAttribute("photodiodeVal", Required=Newtonsoft.Json.Required.Always)] + public int PhotodiodeVal + { + get + { + return _photodiodeVal; + } + set + { + _photodiodeVal = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("syncVal", Required=Newtonsoft.Json.Required.Always)] + public int SyncVal + { + get + { + return _syncVal; + } + set + { + _syncVal = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new MatrixArduinoPhotodiodeData(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new MatrixArduinoPhotodiodeData(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("PhotodiodeVal = " + _photodiodeVal + ", "); + stringBuilder.Append("SyncVal = " + _syncVal); + 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -1099,181 +1589,6 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class SpinnakerCamera - { - - private string _cameraType; - - private double _triggerFrequency; - - private double _exposureTime; - - private string _serialNumber; - - private double _gain; - - private int _binning; - - public SpinnakerCamera() - { - _cameraType = "Spinnaker"; - _triggerFrequency = 50D; - _exposureTime = 15000D; - _gain = 1D; - _binning = 1; - } - - protected SpinnakerCamera(SpinnakerCamera other) - { - _cameraType = other._cameraType; - _triggerFrequency = other._triggerFrequency; - _exposureTime = other._exposureTime; - _serialNumber = other._serialNumber; - _gain = other._gain; - _binning = other._binning; - } - - /// - /// Camera type discriminator for Spinnaker devices. - /// - [Newtonsoft.Json.JsonPropertyAttribute("cameraType")] - [System.ComponentModel.DescriptionAttribute("Camera type discriminator for Spinnaker devices.")] - public string CameraType - { - get - { - return _cameraType; - } - set - { - _cameraType = value; - } - } - - /// - /// The frequency at which the camera is triggered (in Hz). - /// - [Newtonsoft.Json.JsonPropertyAttribute("triggerFrequency")] - [System.ComponentModel.DescriptionAttribute("The frequency at which the camera is triggered (in Hz).")] - public double TriggerFrequency - { - get - { - return _triggerFrequency; - } - set - { - _triggerFrequency = value; - } - } - - /// - /// The exposure time for the camera (in microseconds). - /// - [Newtonsoft.Json.JsonPropertyAttribute("exposureTime")] - [System.ComponentModel.DescriptionAttribute("The exposure time for the camera (in microseconds).")] - public double ExposureTime - { - get - { - return _exposureTime; - } - set - { - _exposureTime = value; - } - } - - /// - /// The serial number of the camera. - /// - [Newtonsoft.Json.JsonPropertyAttribute("serialNumber")] - [System.ComponentModel.DescriptionAttribute("The serial number of the camera.")] - public string SerialNumber - { - get - { - return _serialNumber; - } - set - { - _serialNumber = value; - } - } - - /// - /// The camera gain. - /// - [Newtonsoft.Json.JsonPropertyAttribute("gain")] - [System.ComponentModel.DescriptionAttribute("The camera gain.")] - public double Gain - { - get - { - return _gain; - } - set - { - _gain = value; - } - } - - /// - /// The binning setting for the camera. - /// - [Newtonsoft.Json.JsonPropertyAttribute("binning")] - [System.ComponentModel.DescriptionAttribute("The binning setting for the camera.")] - public int Binning - { - get - { - return _binning; - } - set - { - _binning = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SpinnakerCamera(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new SpinnakerCamera(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("CameraType = " + _cameraType + ", "); - stringBuilder.Append("TriggerFrequency = " + _triggerFrequency + ", "); - stringBuilder.Append("ExposureTime = " + _exposureTime + ", "); - stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); - stringBuilder.Append("Gain = " + _gain + ", "); - stringBuilder.Append("Binning = " + _binning); - 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -1400,7 +1715,7 @@ public partial class UclOpenHfVisualRig private MatrixArduino _arduino; - private SpinnakerCamera _eyeCamera; + private MatrixArduinoPhotodiode _arduinoPhotodiode; public UclOpenHfVisualRig() { @@ -1408,7 +1723,7 @@ public UclOpenHfVisualRig() _screen = new Screen(); _syncQuad = new SyncQuad(); _arduino = new MatrixArduino(); - _eyeCamera = new SpinnakerCamera(); + _arduinoPhotodiode = new MatrixArduinoPhotodiode(); } protected UclOpenHfVisualRig(UclOpenHfVisualRig other) @@ -1417,7 +1732,7 @@ protected UclOpenHfVisualRig(UclOpenHfVisualRig other) _screen = other._screen; _syncQuad = other._syncQuad; _arduino = other._arduino; - _eyeCamera = other._eyeCamera; + _arduinoPhotodiode = other._arduinoPhotodiode; } [Newtonsoft.Json.JsonPropertyAttribute("version")] @@ -1476,16 +1791,16 @@ public MatrixArduino Arduino } [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("eyeCamera", Required=Newtonsoft.Json.Required.Always)] - public SpinnakerCamera EyeCamera + [Newtonsoft.Json.JsonPropertyAttribute("arduinoPhotodiode", Required=Newtonsoft.Json.Required.Always)] + public MatrixArduinoPhotodiode ArduinoPhotodiode { get { - return _eyeCamera; + return _arduinoPhotodiode; } set { - _eyeCamera = value; + _arduinoPhotodiode = value; } } @@ -1505,7 +1820,7 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("Screen = " + _screen + ", "); stringBuilder.Append("SyncQuad = " + _syncQuad + ", "); stringBuilder.Append("Arduino = " + _arduino + ", "); - stringBuilder.Append("EyeCamera = " + _eyeCamera); + stringBuilder.Append("ArduinoPhotodiode = " + _arduinoPhotodiode); return true; } @@ -2075,14 +2390,19 @@ public System.IObservable Process(System.IObservable return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -2129,8 +2449,9 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] diff --git a/src/main.bonsai b/src/main.bonsai index cdfd568..8af293c 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -190,8 +190,7 @@ COM10 1000000 - - + None 63 8 @@ -204,10 +203,51 @@ 2048 1 Arduino - SerialMessages + SerialMessagesMatrix - SerialMessages + RigSchema + + + ArduinoPhotodiode + + + + + + + + + + COM10 + 1000000 + + + None + 63 + 8 + One + None + false + false + false + 4096 + 2048 + 1 + Arduino + SerialMessagesPhotodiode + + + SerialMessagesPhotodiode + + + + + + MatrixPhotodiode + + + SerialMessagesMatrix @@ -571,6 +611,11 @@ + + + + + @@ -1279,6 +1324,125 @@ + + MatrixPhotodiode + + + MatrixArduino + + + Seconds + + + + + + + + + LogData + + + + Source1 + + + + + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + ArduinoPhotodiode + + + + + 1 + + + + + + + + + + + csv + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\Arduino\Arduino.csv + false + false + None + true + it + + + + + + + + + + + + + CurrentTexture @@ -1753,16 +1917,21 @@ - + - + + - + - - - + + + + + + + diff --git a/src/ucl_open_hf_visual/data_types.py b/src/ucl_open_hf_visual/data_types.py index 06933f7..0e0e3f0 100644 --- a/src/ucl_open_hf_visual/data_types.py +++ b/src/ucl_open_hf_visual/data_types.py @@ -6,4 +6,8 @@ class MatrixArduinoData(BaseSchema): lick_count_right: int last_sync_pulse_time: int photodiode_val: int - current_ms: int \ No newline at end of file + current_ms: int + +class MatrixArduinoPhotodiodeData(BaseSchema): + photodiode_val: int + sync_val: int \ No newline at end of file diff --git a/src/ucl_open_hf_visual/regenerate.py b/src/ucl_open_hf_visual/regenerate.py index a5853a1..ada4d08 100644 --- a/src/ucl_open_hf_visual/regenerate.py +++ b/src/ucl_open_hf_visual/regenerate.py @@ -20,7 +20,8 @@ def main(): ucl_open_hf_visual.task.UclOpenHfVisualTaskLogic, ucl_open_hf_visual.rig.UclOpenHfVisualRig, ucl_open_hf_visual.session.UclOpenSession, - ucl_open_hf_visual.data_types.MatrixArduinoData + ucl_open_hf_visual.data_types.MatrixArduinoData, + ucl_open_hf_visual.data_types.MatrixArduinoPhotodiodeData ] model = pydantic.RootModel[Union[tuple(models)]] diff --git a/src/ucl_open_hf_visual/rig.py b/src/ucl_open_hf_visual/rig.py index 23ce0d2..4e0270e 100644 --- a/src/ucl_open_hf_visual/rig.py +++ b/src/ucl_open_hf_visual/rig.py @@ -5,7 +5,7 @@ from ucl_open.rigs.base import BaseSchema from ucl_open.rigs.device import Screen # TODO - change to ucl rigs from ucl_open.rigs.device import SerialDeviceModule -from ucl_open.rigs.video import SpinnakerCamera +# from ucl_open.rigs.video import ArducamOV9180 from ucl_open_hf_visual import __semver__ @@ -19,11 +19,14 @@ class SyncQuad(BaseSchema): class MatrixArduino(SerialDeviceModule): device_type: Literal["MatrixArduino"] = "MatrixArduino" + +class MatrixArduinoPhotodiode(SerialDeviceModule): + device_type: Literal["MatrixArduinoPhotodiode"] = "MatrixArduinoPhotodiode" class UclOpenHfVisualRig(BaseSchema): version: Literal[__semver__] = __semver__ # type: ignore screen: Screen sync_quad: SyncQuad arduino: MatrixArduino - eye_camera: SpinnakerCamera + arduino_photodiode: MatrixArduinoPhotodiode ... \ No newline at end of file From 0ca4dd9e4c1237c226f48e94b5ae1f36005ba9d2 Mon Sep 17 00:00:00 2001 From: RoboDoig Date: Thu, 11 Dec 2025 16:50:07 +0000 Subject: [PATCH 13/17] quick testing --- .bonsai/Settings/src/main.editor | 2 +- examples/rig.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index f4e3c7d..227521a 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/examples/rig.py b/examples/rig.py index 54afa08..933efb4 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -41,7 +41,7 @@ new_line="\n" ), arduino_photodiode=MatrixArduinoPhotodiode( - port_name="COM11", + port_name="COM10", baud_rate=250000, new_line="\n" ) From 9b39f7ff6ebc38a1dac0795494ff2177ae090b8a Mon Sep 17 00:00:00 2001 From: eabhorrocks <36156626+eabhorrocks@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:14:28 +0000 Subject: [PATCH 14/17] Setting up for test run --- .bonsai/Settings/src/main.editor | 2 +- examples/rig.py | 4 ++-- examples/session.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 227521a..4d66df5 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/examples/rig.py b/examples/rig.py index 933efb4..b623194 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -36,12 +36,12 @@ location_y=1 ), arduino=MatrixArduino( - port_name="COM10", + port_name="COM4", baud_rate=1000000, new_line="\n" ), arduino_photodiode=MatrixArduinoPhotodiode( - port_name="COM10", + port_name="COM5", baud_rate=250000, new_line="\n" ) diff --git a/examples/session.py b/examples/session.py index b9b7aad..9cdff97 100644 --- a/examples/session.py +++ b/examples/session.py @@ -9,7 +9,7 @@ workflow="main.bonsai", commit="", repository_url="https://github.com/ucl-open/hf-visual", - logging_root_path="C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data", + logging_root_path="C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data", animal_id="Plimbo", session_id="001" ) From 207f3a2a9171b2c245f30cf09f1e9285fda2c4f9 Mon Sep 17 00:00:00 2001 From: eabhorrocks <36156626+eabhorrocks@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:38:23 +0000 Subject: [PATCH 15/17] Getting things to work on rig --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 57 +++++++++++++++++++++++--- examples/rig.py | 8 ++-- src/main.bonsai | 70 ++++++++++++++++---------------- 4 files changed, 91 insertions(+), 46 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 4d66df5..227521a 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index f476e24..679d45b 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -2,6 +2,21 @@ + + false + + 130 + 130 + + + 336 + 82 + + Bonsai.Design.ObjectTextVisualizer + + + + @@ -70,12 +85,42 @@ + + false + + 468 + 132 + + + 336 + 75 + + Bonsai.Design.ObjectTextVisualizer + + + + + + false + + 182 + 182 + + + 336 + 137 + + Bonsai.Design.ObjectTextVisualizer + + + + - 120 - 130 + 119 + 205 418 @@ -150,8 +195,8 @@ 0 - 0.95 - 1.05 + 0 + 1.1 true @@ -181,8 +226,8 @@ 640 - 934 - 948 + 0 + 160 true diff --git a/examples/rig.py b/examples/rig.py index b623194..53ffcfc 100644 --- a/examples/rig.py +++ b/examples/rig.py @@ -32,18 +32,18 @@ sync_quad=SyncQuad( extent_x=0.1, extent_y=0.1, - location_x=1, - location_y=1 + location_x=-1, + location_y=-1 ), arduino=MatrixArduino( port_name="COM4", baud_rate=1000000, - new_line="\n" + new_line=r"\n" ), arduino_photodiode=MatrixArduinoPhotodiode( port_name="COM5", baud_rate=250000, - new_line="\n" + new_line=r"\n" ) ) diff --git a/src/main.bonsai b/src/main.bonsai index 8af293c..91e7048 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -37,7 +37,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\local\UclOpenSession.json + C:\Users\saleem_lab\Documents\GitHub\hf-visual\local\UclOpenSession.json @@ -48,7 +48,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\local\UclOpenHfVisualRig.json + C:\Users\saleem_lab\Documents\GitHub\hf-visual\local\UclOpenHfVisualRig.json @@ -59,7 +59,7 @@ - C:\Users\neurogears\source\repos\ucl-open\hf-visual\local\UclOpenHfVisualTaskLogic.json + C:\Users\saleem_lab\Documents\GitHub\hf-visual\local\UclOpenHfVisualTaskLogic.json @@ -187,17 +187,17 @@ - COM10 + COM4 1000000 - - + us-ascii + \n None 63 8 One None false - false + true false 4096 2048 @@ -219,41 +219,41 @@ - COM10 - 1000000 - - + COM5 + 250000 + us-ascii + \n None 63 8 One None false - false + true false 4096 2048 1 - Arduino + ArduinoPhotodiode SerialMessagesPhotodiode - SerialMessagesPhotodiode + SerialMessagesMatrix - + - MatrixPhotodiode + MatrixArduino - SerialMessagesMatrix + SerialMessagesPhotodiode - + - MatrixArduino + MatrixPhotodiode Display @@ -321,7 +321,7 @@ true Resizable - Normal + Fullscreen Second 60 120 @@ -548,13 +548,13 @@ 0.1 0.1 - 1 - 1 + -1 + -1 0 0 - 0 - 0 - 0 + 1 + 1 + 1 1 @@ -783,7 +783,7 @@ - SN_1_1 + SynthIm_1_1 @@ -1102,10 +1102,10 @@ - MatrixArduino + MatrixPhotodiode - Value.PhotodiodeVal + PhotodiodeVal @@ -1211,7 +1211,7 @@ Plimbo 001 - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data MatrixArduino @@ -1305,7 +1305,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\Arduino\Arduino.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\Arduino\Arduino.csv false false None @@ -1424,7 +1424,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\Arduino\Arduino.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-27-51\ArduinoPhotodiode\ArduinoPhotodiode.csv false false None @@ -1543,7 +1543,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\Texture\Texture.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\Texture\Texture.csv false false None @@ -1657,7 +1657,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\RigSchema\RigSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\RigSchema\RigSchema.json None false @@ -1768,7 +1768,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\TaskLogicSchema\TaskLogicSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\TaskLogicSchema\TaskLogicSchema.json None false @@ -1883,7 +1883,7 @@ - C:/Users/neurogears/source/repos/ucl-open/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T16-11-23\SessionSchema\SessionSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\SessionSchema\SessionSchema.json None false From c87bd976f4ff51eb3bdfd2c8de465c4b7fc15d70 Mon Sep 17 00:00:00 2001 From: eabhorrocks <36156626+eabhorrocks@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:49:07 +0000 Subject: [PATCH 16/17] Add basic camera logging --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 22 ++- src/main.bonsai | 277 ++++++++++++++++++++++++++++--- 3 files changed, 272 insertions(+), 29 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index 227521a..f4e3c7d 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index 679d45b..c61a78f 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -119,12 +119,12 @@ - 119 - 205 + 451 + 134 418 - 377 + 606 Bonsai.Gui.TableLayoutPanelVisualizer @@ -177,8 +177,8 @@ 0 - -1 - 1 + -10000 + 100000 true @@ -226,8 +226,8 @@ 640 - 0 - 160 + 120 + 150 true @@ -235,12 +235,18 @@ + + Bonsai.Vision.Design.IplImageVisualizer + + + + - + false 144 diff --git a/src/main.bonsai b/src/main.bonsai index 91e7048..5d7b113 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -10,6 +10,7 @@ xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders" xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" + xmlns:cv="clr-namespace:Bonsai.Vision;assembly=Bonsai.Vision" xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics" xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" xmlns:zg="clr-namespace:Bonsai.Gui.ZedGraph;assembly=Bonsai.Gui.ZedGraph" @@ -604,6 +605,21 @@ + + + 0 + + + + + MatrixArduino + + + + + + CameraStream + @@ -616,6 +632,9 @@ + + + @@ -1115,15 +1134,27 @@ Photodiode + + CameraStream + + ExperimentPanel true true 2 - 3 + 4 - + + + + + + + + + @@ -1137,17 +1168,17 @@ - + - + - + @@ -1157,17 +1188,19 @@ - + - + - + + + @@ -1305,7 +1338,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\Arduino\Arduino.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\Arduino\Arduino.csv false false None @@ -1424,7 +1457,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-27-51\ArduinoPhotodiode\ArduinoPhotodiode.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\ArduinoPhotodiode\ArduinoPhotodiode.csv false false None @@ -1543,7 +1576,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\Texture\Texture.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\Texture\Texture.csv false false None @@ -1562,6 +1595,205 @@ + + CameraStream + + + MatrixArduino + + + Seconds + + + + + + + + + LogVideo + + + + Source1 + + + + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + VideoData + + + + + + + + + + + csv + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + false + false + None + true + Seconds,Value.Size + + + Value + + + FormatFileName + Generates a log filename based on the input timestamp. + + + + PathPrefix + + + Source1 + + + + + + + VideoData + + + + + + + + + + + avi + + + + + 1 + + + + + + + {0}\{1}\{2}.{3} + Item1,Item2,Item3,Item4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + None + true + false + FMP4 + 50 + + 0 + 0 + + NearestNeighbor + + + + + + + + + + + + + + + + + + + RigSchema @@ -1657,7 +1889,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\RigSchema\RigSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\RigSchema\RigSchema.json None false @@ -1768,7 +2000,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\TaskLogicSchema\TaskLogicSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\TaskLogicSchema\TaskLogicSchema.json None false @@ -1883,7 +2115,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-34-28\SessionSchema\SessionSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\SessionSchema\SessionSchema.json None false @@ -1922,16 +2154,21 @@ - + - + + - + - - - + + + + + + + From f797f4603c528419efa62695e09bc855ec3ab03b Mon Sep 17 00:00:00 2001 From: eabhorrocks <36156626+eabhorrocks@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:56:30 +0000 Subject: [PATCH 17/17] specific settings for test run --- .bonsai/Settings/src/main.editor | 2 +- .bonsai/Settings/src/main.layout | 8 ++++---- examples/session.py | 2 +- examples/task.py | 6 +++--- src/main.bonsai | 24 ++++++++++++------------ 5 files changed, 21 insertions(+), 21 deletions(-) diff --git a/.bonsai/Settings/src/main.editor b/.bonsai/Settings/src/main.editor index f4e3c7d..227521a 100644 --- a/.bonsai/Settings/src/main.editor +++ b/.bonsai/Settings/src/main.editor @@ -4,7 +4,7 @@ - + diff --git a/.bonsai/Settings/src/main.layout b/.bonsai/Settings/src/main.layout index c61a78f..16a2d20 100644 --- a/.bonsai/Settings/src/main.layout +++ b/.bonsai/Settings/src/main.layout @@ -177,8 +177,8 @@ 0 - -10000 - 100000 + -1 + 1 true @@ -226,8 +226,8 @@ 640 - 120 - 150 + 10 + 30 true diff --git a/examples/session.py b/examples/session.py index 9cdff97..100f045 100644 --- a/examples/session.py +++ b/examples/session.py @@ -10,7 +10,7 @@ commit="", repository_url="https://github.com/ucl-open/hf-visual", logging_root_path="C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data", - animal_id="Plimbo", + animal_id="mouse-001", session_id="001" ) diff --git a/examples/task.py b/examples/task.py index cb12854..8617adf 100644 --- a/examples/task.py +++ b/examples/task.py @@ -7,10 +7,10 @@ task_logic = UclOpenHfVisualTaskLogic( task_parameters=UclOpenHfVisualTaskParameters( - available_textures=["SN_1_1", "SynthIm_1_1"], + available_textures=["SN_1_1", "SynthIm_1_1", "SynthIm_1_5"], inter_presentation_texture="blankStim_1", - presentation_time=1, - inter_presentation_time=0.5 + presentation_time=0.25, + inter_presentation_time=0.75 ), ) diff --git a/src/main.bonsai b/src/main.bonsai index 5d7b113..70224c3 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -553,9 +553,9 @@ -1 0 0 - 1 - 1 - 1 + 0 + 0 + 0 1 @@ -802,7 +802,7 @@ - SynthIm_1_1 + SN_1_1 @@ -1338,7 +1338,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\Arduino\Arduino.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\Arduino\Arduino.csv false false None @@ -1457,7 +1457,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\ArduinoPhotodiode\ArduinoPhotodiode.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\ArduinoPhotodiode\ArduinoPhotodiode.csv false false None @@ -1576,7 +1576,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\Texture\Texture.csv + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\Texture\Texture.csv false false None @@ -1685,7 +1685,7 @@ - + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\VideoData\VideoData.csv false false None @@ -1764,7 +1764,7 @@ - + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\VideoData\VideoData.avi None true false @@ -1889,7 +1889,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\RigSchema\RigSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\RigSchema\RigSchema.json None false @@ -2000,7 +2000,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\TaskLogicSchema\TaskLogicSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\TaskLogicSchema\TaskLogicSchema.json None false @@ -2115,7 +2115,7 @@ - C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-40-28\SessionSchema\SessionSchema.json + C:/Users/saleem_lab/Documents/GitHub/hf-visual/temp_data\sub-Plimbo\ses-001_date-2025-12-11T17-45-39\SessionSchema\SessionSchema.json None false