Update workflows

- Electrical/Optical Stimulator - Add ScalarBuffer to BreakoutAnalogOutput - Display workflows in templates
open-ephys · Jul 31, 2024 · a46f0c0 · a46f0c0
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Showing 9 changed files with 176 additions and 30 deletions.
diff --git a/articles/devices/electricalstimulator.md b/articles/devices/electricalstimulator.md
@@ -13,4 +13,4 @@ workflow_file: ~/workflows/devices/ElectricalStimulator.bonsai
 
 ## Send Trigger
 
-In the workflow, pressing the middle button on the mouse will send a trigger, delivering the stimulation waveform that is configured. The `MouseButtonDown` node can be found in the `Bonsai.Windows.Input` package.
+While the workflow is running, pressing the middle button on the mouse will send a trigger delivering the stimulation waveform that is configured. The `MouseButtonDown` node can be found in the `Bonsai.Windows.Input` package.
diff --git a/articles/devices/opticalstimulator.md b/articles/devices/opticalstimulator.md
@@ -0,0 +1,16 @@
+---
+uid: device-opticalstimulator
+title: Headstage64OpticalStimulator
+isGuide: true
+isDevice: true
+device: OpticalStimulator
+headstage: Headstage64
+workflow: true
+workflow_file: ~/workflows/devices/OpticalStimulator.bonsai
+---
+
+<br>
+
+## Send Trigger
+
+While the workflow is running, pressing the middle button on the mouse will send a trigger delivering the stimulation waveform that is configured. The `MouseButtonDown` node can be found in the `Bonsai.Windows.Input` package.
diff --git a/articles/toc.yml b/articles/toc.yml
@@ -28,6 +28,7 @@
   - href: devices/breakoutanalogio.md
   - href: devices/breakoutdigitalio.md
   - href: devices/electricalstimulator.md
+  - href: devices/opticalstimulator.md
   - href: devices/heartbeat.md
   - href: devices/memorymonitor.md
   - href: devices/neuropixelsv1e.md

diff --git a/template/ManagedReference.extension.js b/template/ManagedReference.extension.js
@@ -154,18 +154,23 @@ function defineOperatorType(model){
       for (let i = 0; i < inheritanceLength; i++){
         if (model.inheritance[i].uid.includes('Bonsai.Source')){
           operatorType.source = true;
+          operatorType.showWorkflow = true;
         }
         else if (model.inheritance[i].uid.includes('Bonsai.Sink')){
           operatorType.sink = true;
+          operatorType.showWorkflow = true;
         }
         else if (model.inheritance[i].uid.includes('Bonsai.Combinator')){
           operatorType.combinator = true;
+          operatorType.showWorkflow = true;
         }
         else if (model.inheritance[i].uid.includes('HubDeviceFactory')){
           operatorType.hub = true;
+          operatorType.showWorkflow = true;
         }
         else if (model.inheritance[i].uid.includes('DeviceFactory')){
           operatorType.device = true;
+          operatorType.showWorkflow = true;
         }
       }
     }
@@ -359,6 +364,10 @@ exports.preTransform = function (model) {
     model.oe.operatorType = 'combinator';
   }
 
+  if (operatorType.hasOwnProperty('showWorkflow')) {
+    model.showWorkflow = operatorType.showWorkflow;
+  }
+
   properties = defineProperties(model);
   if (properties.length > 0){
     model.oe.hasProperties = true;

diff --git a/workflows/devices/ElectricalStimulator.bonsai b/workflows/devices/ElectricalStimulator.bonsai
@@ -1,9 +1,8 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.8.1"
+<WorkflowBuilder Version="2.8.5"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:onix="clr-namespace:OpenEphys.Onix;assembly=OpenEphys.Onix"
                  xmlns:wie="clr-namespace:Bonsai.Windows.Input;assembly=Bonsai.Windows.Input"
-                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
@@ -20,7 +19,6 @@
             <onix:DeviceName>Headstage64/Rhd2164</onix:DeviceName>
             <onix:DeviceAddress>256</onix:DeviceAddress>
             <onix:Enable>true</onix:Enable>
-            <onix:AmplifierDataFormat>Unsigned</onix:AmplifierDataFormat>
             <onix:DspCutoff>Dsp146mHz</onix:DspCutoff>
             <onix:AnalogLowCutoff>Low100mHz</onix:AnalogLowCutoff>
             <onix:AnalogHighCutoff>High10000Hz</onix:AnalogHighCutoff>
@@ -39,6 +37,10 @@
             <onix:DeviceName>Headstage64/Headstage64ElectricalStimulator</onix:DeviceName>
             <onix:DeviceAddress>259</onix:DeviceAddress>
           </onix:ElectricalStimulator>
+          <onix:OpticalStimulator>
+            <onix:DeviceName>Headstage64/Headstage64OpticalStimulator</onix:DeviceName>
+            <onix:DeviceAddress>260</onix:DeviceAddress>
+          </onix:OpticalStimulator>
           <onix:Port>PortA</onix:Port>
           <onix:PortVoltage xsi:nil="true" />
         </Combinator>
@@ -59,46 +61,30 @@
           <Value>true</Value>
         </Combinator>
       </Expression>
-      <Expression xsi:type="Combinator">
-        <Combinator xsi:type="BooleanProperty">
-          <Value>false</Value>
-        </Combinator>
-      </Expression>
-      <Expression xsi:type="Combinator">
-        <Combinator xsi:type="rx:Delay">
-          <rx:DueTime>PT0.5S</rx:DueTime>
-        </Combinator>
-      </Expression>
-      <Expression xsi:type="Combinator">
-        <Combinator xsi:type="rx:Merge" />
-      </Expression>
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="onix:Headstage64ElectricalStimulatorTrigger">
+          <onix:DeviceName>Headstage64/Headstage64ElectricalStimulator</onix:DeviceName>
           <onix:Enable>true</onix:Enable>
+          <onix:PowerEnable>false</onix:PowerEnable>
+          <onix:TriggerDelay>0</onix:TriggerDelay>
           <onix:PhaseOneCurrent>0</onix:PhaseOneCurrent>
           <onix:InterPhaseCurrent>0</onix:InterPhaseCurrent>
           <onix:PhaseTwoCurrent>0</onix:PhaseTwoCurrent>
-          <onix:TrainDelay>0</onix:TrainDelay>
           <onix:PhaseOneDuration>0</onix:PhaseOneDuration>
           <onix:InterPhaseInterval>0</onix:InterPhaseInterval>
           <onix:PhaseTwoDuration>0</onix:PhaseTwoDuration>
           <onix:InterPulseInterval>0</onix:InterPulseInterval>
           <onix:InterBurstInterval>0</onix:InterBurstInterval>
           <onix:BurstPulseCount>0</onix:BurstPulseCount>
           <onix:TrainBurstCount>0</onix:TrainBurstCount>
-          <onix:PowerEnable>false</onix:PowerEnable>
         </Combinator>
       </Expression>
     </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="3" To="5" Label="Source1" />
-      <Edge From="4" To="7" Label="Source1" />
-      <Edge From="5" To="6" Label="Source1" />
-      <Edge From="6" To="7" Label="Source2" />
-      <Edge From="7" To="8" Label="Source1" />
+      <Edge From="4" To="5" Label="Source1" />
     </Edges>
   </Workflow>
 </WorkflowBuilder>
diff --git a/workflows/devices/OpticalStimulator.bonsai b/workflows/devices/OpticalStimulator.bonsai
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.8.5"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:onix="clr-namespace:OpenEphys.Onix;assembly=OpenEphys.Onix"
+                 xmlns:wie="clr-namespace:Bonsai.Windows.Input;assembly=Bonsai.Windows.Input"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="onix:CreateContext">
+          <onix:Driver>riffa</onix:Driver>
+          <onix:Index>0</onix:Index>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="onix:ConfigureHeadstage64">
+          <onix:Name>Headstage64</onix:Name>
+          <onix:Rhd2164>
+            <onix:DeviceName>Headstage64/Rhd2164</onix:DeviceName>
+            <onix:DeviceAddress>256</onix:DeviceAddress>
+            <onix:Enable>true</onix:Enable>
+            <onix:DspCutoff>Dsp146mHz</onix:DspCutoff>
+            <onix:AnalogLowCutoff>Low100mHz</onix:AnalogLowCutoff>
+            <onix:AnalogHighCutoff>High10000Hz</onix:AnalogHighCutoff>
+          </onix:Rhd2164>
+          <onix:Bno055>
+            <onix:DeviceName>Headstage64/Bno055</onix:DeviceName>
+            <onix:DeviceAddress>257</onix:DeviceAddress>
+            <onix:Enable>true</onix:Enable>
+          </onix:Bno055>
+          <onix:TS4231>
+            <onix:DeviceName>Headstage64/TS4231</onix:DeviceName>
+            <onix:DeviceAddress>258</onix:DeviceAddress>
+            <onix:Enable>false</onix:Enable>
+          </onix:TS4231>
+          <onix:ElectricalStimulator>
+            <onix:DeviceName>Headstage64/Headstage64ElectricalStimulator</onix:DeviceName>
+            <onix:DeviceAddress>259</onix:DeviceAddress>
+          </onix:ElectricalStimulator>
+          <onix:OpticalStimulator>
+            <onix:DeviceName>Headstage64/Headstage64OpticalStimulator</onix:DeviceName>
+            <onix:DeviceAddress>260</onix:DeviceAddress>
+          </onix:OpticalStimulator>
+          <onix:Port>PortA</onix:Port>
+          <onix:PortVoltage xsi:nil="true" />
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="onix:StartAcquisition">
+          <onix:ReadSize>2048</onix:ReadSize>
+          <onix:WriteSize>2048</onix:WriteSize>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="wie:MouseButtonDown">
+          <wie:Filter>Middle</wie:Filter>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="BooleanProperty">
+          <Value>true</Value>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="onix:Headstage64OpticalStimulatorTrigger">
+          <onix:DeviceName>Headstage64/Headstage64OpticalStimulator</onix:DeviceName>
+          <onix:Enable>true</onix:Enable>
+          <onix:Delay>0</onix:Delay>
+          <onix:MaxCurrent>100</onix:MaxCurrent>
+          <onix:ChannelOneCurrent>100</onix:ChannelOneCurrent>
+          <onix:ChannelTwoCurrent>0</onix:ChannelTwoCurrent>
+          <onix:PulseDuration>5</onix:PulseDuration>
+          <onix:PulsesPerSecond>50</onix:PulsesPerSecond>
+          <onix:PulsesPerBurst>20</onix:PulsesPerBurst>
+          <onix:InterBurstInterval>0</onix:InterBurstInterval>
+          <onix:BurstsPerTrain>1</onix:BurstsPerTrain>
+        </Combinator>
+      </Expression>
+    </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" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>
diff --git a/workflows/operators/BreakoutAnalogOutput.bonsai b/workflows/operators/BreakoutAnalogOutput.bonsai
@@ -1,16 +1,35 @@
 <?xml version="1.0" encoding="utf-8"?>
 <WorkflowBuilder Version="2.8.5"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
                  xmlns:onix="clr-namespace:OpenEphys.Onix;assembly=OpenEphys.Onix"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="dsp:ScalarBuffer">
+          <dsp:Size>
+            <dsp:Width>12</dsp:Width>
+            <dsp:Height>1</dsp:Height>
+          </dsp:Size>
+          <dsp:Depth>F32</dsp:Depth>
+          <dsp:Channels>1</dsp:Channels>
+          <dsp:Value>
+            <dsp:Val0>1</dsp:Val0>
+            <dsp:Val1>0</dsp:Val1>
+            <dsp:Val2>0</dsp:Val2>
+            <dsp:Val3>0</dsp:Val3>
+          </dsp:Value>
+        </Combinator>
+      </Expression>
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="onix:BreakoutAnalogOutput">
-          <onix:DataType>S16</onix:DataType>
+          <onix:DataType>Volts</onix:DataType>
         </Combinator>
       </Expression>
     </Nodes>
-    <Edges />
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+    </Edges>
   </Workflow>
 </WorkflowBuilder>
diff --git a/workflows/operators/Headstage64ElectricalStimulatorTrigger.bonsai b/workflows/operators/Headstage64ElectricalStimulatorTrigger.bonsai
@@ -1,10 +1,21 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.8.1"
+<WorkflowBuilder Version="2.8.5"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:wie="clr-namespace:Bonsai.Windows.Input;assembly=Bonsai.Windows.Input"
                  xmlns:onix="clr-namespace:OpenEphys.Onix;assembly=OpenEphys.Onix"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="wie:MouseButtonDown">
+          <wie:Filter>Middle</wie:Filter>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="BooleanProperty">
+          <Value>true</Value>
+        </Combinator>
+      </Expression>
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="onix:Headstage64ElectricalStimulatorTrigger">
           <onix:DeviceName>Headstage64/Headstage64ElectricalStimulator</onix:DeviceName>
@@ -24,6 +35,9 @@
         </Combinator>
       </Expression>
     </Nodes>
-    <Edges />
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+    </Edges>
   </Workflow>
 </WorkflowBuilder>
diff --git a/workflows/operators/Headstage64OpticalStimulatorTrigger.bonsai b/workflows/operators/Headstage64OpticalStimulatorTrigger.bonsai
@@ -1,10 +1,21 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.8.1"
+<WorkflowBuilder Version="2.8.5"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:wie="clr-namespace:Bonsai.Windows.Input;assembly=Bonsai.Windows.Input"
                  xmlns:onix="clr-namespace:OpenEphys.Onix;assembly=OpenEphys.Onix"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="wie:MouseButtonDown">
+          <wie:Filter>Middle</wie:Filter>
+        </Combinator>
+      </Expression>
+      <Expression xsi:type="Combinator">
+        <Combinator xsi:type="BooleanProperty">
+          <Value>true</Value>
+        </Combinator>
+      </Expression>
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="onix:Headstage64OpticalStimulatorTrigger">
           <onix:DeviceName>Headstage64/Headstage64OpticalStimulator</onix:DeviceName>
@@ -21,6 +32,9 @@
         </Combinator>
       </Expression>
     </Nodes>
-    <Edges />
+    <Edges>
+      <Edge From="0" To="1" Label="Source1" />
+      <Edge From="1" To="2" Label="Source1" />
+    </Edges>
   </Workflow>
 </WorkflowBuilder>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -13,4 +13,4 @@ workflow_file: ~/workflows/devices/ElectricalStimulator.bonsai

		## Send Trigger

		In the workflow, pressing the middle button on the mouse will send a trigger, delivering the stimulation waveform that is configured. The `MouseButtonDown` node can be found in the `Bonsai.Windows.Input` package.
		While the workflow is running, pressing the middle button on the mouse will send a trigger delivering the stimulation waveform that is configured. The `MouseButtonDown` node can be found in the `Bonsai.Windows.Input` package.