Feat/merge rig version

.gitattributes

@@ -1,4 +1,21 @@
-* text=auto
-*.cmd text eol=crlf
-*.bat text eol=crlf
-*.bonsai text
+# Default: text files normalized to LF in repo, converted on checkout as needed
+*               text=auto eol=lf
+
+# Code & docs: LF
+*.py            text eol=lf
+*.toml          text eol=lf
+*.yml           text eol=lf
+*.yaml          text eol=lf
+*.md            text eol=lf
+*.rst           text eol=lf
+*.svg           text eol=lf
+*.json          text eol=lf
+
+# Windows scripts / MSBuild / DOTNET: CRLF
+*.ps1           text eol=crlf
+*.bat           text eol=crlf
+*.cmd           text eol=crlf
+*.sln           text eol=crlf
+*.csproj        text eol=crlf
+*.props         text eol=crlf
+*.targets       text eol=crlf

.gitignore

@@ -83,3 +83,23 @@ ipython_config.py
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
 # .python-version
+# Python
+venv/
+__pycache__/
+*.py[cod]
+*.pyo
+.pytest_cache/
+
+# Editors/OS
+.vscode/
+.idea/
+.DS_Store
+
+# Packaging/build
+dist/
+build/
+*.egg-info/
+
+# Bonsai/.NET build artifacts (keep the source Extensions but ignore build dirs)
+**/bin/
+**/obj/

MPE_workflows/Allen.DrawPhotodiode.bonsai

@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.6.2"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders"
+                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="gl:RenderFrame" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="rx:ElementIndex" />
+      </Expression>
+      <Expression xsi:type="MemberSelector">
+        <Selector>Index</Selector>
+      </Expression>
+      <Expression xsi:type="Mod">
+        <Operand xsi:type="IntProperty">
+          <Value>60</Value>
+        </Operand>
+      </Expression>
+      <Expression xsi:type="Divide">
+        <Operand xsi:type="IntProperty">
+          <Value>30</Value>
+        </Operand>
+      </Expression>
+      <Expression xsi:type="PropertyMapping">
+        <PropertyMappings>
+          <Property Name="ColorR" />
+          <Property Name="ColorG" />
+          <Property Name="ColorB" />
+        </PropertyMappings>
+      </Expression>
+      <Expression xsi:type="WorkflowInput">
+        <Name>Source1</Name>
+      </Expression>
+      <Expression xsi:type="IncludeWorkflow" Path="BonVision:Primitives.DrawQuad.bonsai">
+        <ExtentX>10</ExtentX>
+        <ExtentY>10</ExtentY>
+        <LocationX>45</LocationX>
+        <LocationY>27</LocationY>
+        <Layer>0</Layer>
+        <Angle>0</Angle>
+        <ColorR>1</ColorR>
+        <ColorG>1</ColorG>
+        <ColorB>1</ColorB>
+        <ColorA>1</ColorA>
+      </Expression>
+      <Expression xsi:type="GreaterThan">
+        <Operand xsi:type="IntProperty">
+          <Value>0</Value>
+        </Operand>
+      </Expression>
+      <Expression xsi:type="WorkflowOutput" />
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+      <Edge From="2" To="3" Label="Source1" />
+      <Edge From="3" To="4" Label="Source1" />
+      <Edge From="4" To="5" Label="Source1" />
+      <Edge From="4" To="8" Label="Source1" />
+      <Edge From="5" To="7" Label="Source1" />
+      <Edge From="6" To="7" Label="Source2" />
+      <Edge From="8" To="9" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>

MPE_workflows/Allen.End.bonsai

@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.6.2"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:p1="clr-namespace:MPE;assembly=MPEBonsai"
+                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
+                 xmlns:mx="clr-namespace:Bonsai.DAQmx;assembly=Bonsai.DAQmx"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="WorkflowInput">
+        <Name>Source1</Name>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="BooleanProperty">
+          <Value>false</Value>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:NotifyEndStimulus">
+          <p1:publish_port>5556</p1:publish_port>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="WorkflowOutput" />
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="BooleanProperty">
+          <Value>true</Value>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="rx:Merge" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="mx:DigitalOutput">
+          <mx:Channels>
+            <mx:DigitalOutputChannelConfiguration>
+              <mx:ChannelName />
+              <mx:Grouping>OneChannelForEachLine</mx:Grouping>
+              <mx:Lines>Dev1/port1/line7</mx:Lines>
+            </mx:DigitalOutputChannelConfiguration>
+          </mx:Channels>
+        </Combinator>
+      </Expression>
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+      <Edge From="2" To="3" Label="Source1" />
+      <Edge From="2" To="5" Label="Source2" />
+      <Edge From="4" To="5" Label="Source1" />
+      <Edge From="5" To="6" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>

MPE_workflows/Allen.InitLick.bonsai

@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.6.3"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:wie="clr-namespace:Bonsai.Windows.Input;assembly=Bonsai.Windows.Input"
+                 xmlns:p1="clr-namespace:MPE;assembly=MPEBonsai"
+                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="wie:KeyDown">
+          <wie:Filter>L</wie:Filter>
+          <wie:SuppressRepetitions>false</wie:SuppressRepetitions>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:LickSensor">
+          <p1:Device>Dev1</p1:Device>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="IntProperty">
+          <Value>1</Value>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="wie:KeyDown">
+          <wie:Filter>T</wie:Filter>
+          <wie:SuppressRepetitions>false</wie:SuppressRepetitions>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="rx:SubscribeWhen" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="IntProperty">
+          <Value>1</Value>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="rx:Merge" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="BooleanProperty">
+          <Value>true</Value>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="WorkflowOutput" />
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="4" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+      <Edge From="2" To="6" Label="Source2" />
+      <Edge From="3" To="4" Label="Source2" />
+      <Edge From="4" To="5" Label="Source1" />
+      <Edge From="5" To="6" Label="Source1" />
+      <Edge From="6" To="7" Label="Source1" />
+      <Edge From="7" To="8" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>

MPE_workflows/Allen.InitView.bonsai

@@ -0,0 +1,100 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.6.2"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders"
+                 xmlns:res="clr-namespace:Bonsai.Resources;assembly=Bonsai.System"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="gl:CreateWindow">
+          <gl:Width>640</gl:Width>
+          <gl:Height>480</gl:Height>
+          <gl:VSync>On</gl:VSync>
+          <gl:SwapSync>false</gl:SwapSync>
+          <gl:ClearColor>Black</gl:ClearColor>
+          <gl:ClearMask>DepthBufferBit ColorBufferBit</gl:ClearMask>
+          <gl:CursorVisible>true</gl:CursorVisible>
+          <gl:Location xsi:nil="true" />
+          <gl:WindowBorder>Resizable</gl:WindowBorder>
+          <gl:WindowState>Fullscreen</gl:WindowState>
+          <gl:DisplayDevice>Primary</gl:DisplayDevice>
+          <gl:TargetRenderFrequency>30</gl:TargetRenderFrequency>
+          <gl:TargetUpdateFrequency>480</gl:TargetUpdateFrequency>
+          <gl:RenderState />
+          <gl:GraphicsMode>
+            <gl:ColorFormat>
+              <gl:Red>8</gl:Red>
+              <gl:Green>8</gl:Green>
+              <gl:Blue>8</gl:Blue>
+              <gl:Alpha>8</gl:Alpha>
+            </gl:ColorFormat>
+            <gl:Depth>16</gl:Depth>
+            <gl:Stencil>0</gl:Stencil>
+            <gl:Samples>0</gl:Samples>
+            <gl:AccumulatorFormat>
+              <gl:Red>0</gl:Red>
+              <gl:Green>0</gl:Green>
+              <gl:Blue>0</gl:Blue>
+              <gl:Alpha>0</gl:Alpha>
+            </gl:AccumulatorFormat>
+            <gl:Buffers>2</gl:Buffers>
+            <gl:Stereo>false</gl:Stereo>
+          </gl:GraphicsMode>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="IncludeWorkflow" Path="BonVision:Primitives.BonVisionResources.bonsai" />
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="res:LoadResources" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="gl:RenderFrame" />
+      </Expression>
+      <Expression xsi:type="IncludeWorkflow" Path="BonVision:Environment.OrthographicView.bonsai">
+        <Left>-180</Left>
+        <Right>180</Right>
+        <Bottom>-90</Bottom>
+        <Top>90</Top>
+      </Expression>
+      <Expression xsi:type="IncludeWorkflow" Path="BonVision:Environment.SphereMapping.bonsai">
+        <FaceSize xsi:nil="true" />
+        <ClearColor>Gray</ClearColor>
+        <Width xsi:nil="true" />
+        <Height xsi:nil="true" />
+        <RotationZ>0</RotationZ>
+        <RotationY>0</RotationY>
+        <RotationX>0</RotationX>
+      </Expression>
+      <Expression xsi:type="IncludeWorkflow" Path="BonVision:Environment.ViewWindow.bonsai">
+        <Width>20</Width>
+        <Height>15</Height>
+        <Rotation>
+          <X>0</X>
+          <Y>0</Y>
+          <Z>0</Z>
+        </Rotation>
+        <Translation>
+          <X>0</X>
+          <Y>0</Y>
+          <Z>-10</Z>
+        </Translation>
+      </Expression>
+      <Expression xsi:type="Disable">
+        <Builder xsi:type="IncludeWorkflow" Path="BonVision:Environment.GammaCorrection.bonsai">
+          <ClearColor>Gray</ClearColor>
+          <GammaLut xsi:nil="true" />
+        </Builder>
+      </Expression>
+      <Expression xsi:type="WorkflowOutput" />
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+      <Edge From="3" To="4" Label="Source1" />
+      <Edge From="4" To="5" Label="Source1" />
+      <Edge From="4" To="8" Label="Source1" />
+      <Edge From="5" To="6" Label="Source1" />
+      <Edge From="6" To="7" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>

MPE_workflows/Allen.Logger.bonsai

@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.6.3"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:p1="clr-namespace:MPE;assembly=MPEBonsai"
+                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
+                 xmlns:mx="clr-namespace:Bonsai.DAQmx;assembly=Bonsai.DAQmx"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="WorkflowInput">
+        <Name>Source1</Name>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="p1:Configuration" />
+      </Expression>
+      <Expression xsi:type="MemberSelector">
+        <Selector>Reward.reward_volume</Selector>
+      </Expression>
+      <Expression xsi:type="PropertyMapping">
+        <PropertyMappings>
+          <Property Name="DueTime" />
+        </PropertyMappings>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="rx:Timer">
+          <rx:DueTime>PT0S</rx:DueTime>
+          <rx:Period>PT0S</rx:Period>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="rx:Merge" />
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="mx:DigitalOutput">
+          <mx:Channels />
+        </Combinator>
+      </Expression>
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="5" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+      <Edge From="2" To="3" Label="Source1" />
+      <Edge From="3" To="4" Label="Source1" />
+      <Edge From="4" To="5" Label="Source2" />
+      <Edge From="5" To="6" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>