Harp behavior states (using bonsai)

[mmoaoj]

Hello

I'm trying to create a bonsai workflow(attached) for control of a conditional task in mice. The simplest part of the task is as follows, where a nose poke is required within a given time, after a cue is presented:

I have followed this tutorial with arduino, but when I try to replicate with Harp I hit some walls.. For instance, certain Multicast nodes display an error (No coercion operator is defined between types 'System.Boolean' and 'Bonsai.Harp.HarpMessage'). If I work around this by using a different node (i.e SubscribeSubject) eventually I can get the light to turn on, but I notice this way the infrared beam break is always being detected and the timers happen simultaneously (sometimes even before the light cue is presented).

I understand that currently there is no harp-bonsai documentation but I'd really appreciate it if someone could point me in a direction, literally any help is welcomed!

Thanks in advance,
Joao

harpstateattempt.zip

[artursilva0]

Hi,

The documentation for the Harp Bonsai is still under development, but to start I would suggest taking a look here, where the new Bonsai.Harp library operators are described.

Taking your workflow as an example, you can see below an equivalent implementation with the Harp Operators (thanks @bruno-f-cruz). This workflow uses the Harp Behavior board connected to a poke with an LED and valve at Port 0. The reward consists of activating the valve for a short period of time.

Workflow (copy-paste)

<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.0"
                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                 xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior"
                 xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                 xmlns:sys="clr-namespace:System;assembly=mscorlib"
                 xmlns="https://bonsai-rx.org/2018/workflow">
  <Workflow>
    <Nodes>
      <Expression xsi:type="GroupWorkflow">
        <Name>Harp Init</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="beh:CreateMessage">
              <harp:MessageType>Write</harp:MessageType>
              <harp:Payload xsi:type="beh:CreatePulseSupplyPort0Payload">
                <beh:PulseSupplyPort0>10</beh:PulseSupplyPort0>
              </harp:Payload>
            </Expression>
            <Expression xsi:type="MulticastSubject">
              <Name>DeviceCommands</Name>
            </Expression>
            <Expression xsi:type="beh:CreateMessage">
              <harp:MessageType>Write</harp:MessageType>
              <harp:Payload xsi:type="beh:CreateOutputPulseEnablePayload">
                <beh:OutputPulseEnable>SupplyPort0</beh:OutputPulseEnable>
              </harp:Payload>
            </Expression>
            <Expression xsi:type="MulticastSubject">
              <Name>DeviceCommands</Name>
            </Expression>
            <Expression xsi:type="rx:BehaviorSubject" TypeArguments="harp:HarpMessage">
              <rx:Name>DeviceCommands</rx:Name>
            </Expression>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="harp:Device">
                <harp:OperationMode>Active</harp:OperationMode>
                <harp:OperationLed>On</harp:OperationLed>
                <harp:DumpRegisters>true</harp:DumpRegisters>
                <harp:VisualIndicators>On</harp:VisualIndicators>
                <harp:Heartbeat>Disabled</harp:Heartbeat>
                <harp:IgnoreErrors>false</harp:IgnoreErrors>
                <harp:PortName>COM15</harp:PortName>
              </Combinator>
            </Expression>
            <Expression xsi:type="rx:PublishSubject">
              <Name>DeviceEvents</Name>
            </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="4" To="5" Label="Source1" />
            <Edge From="5" To="6" Label="Source1" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:Timer">
          <rx:DueTime>PT3S</rx:DueTime>
          <rx:Period>PT0S</rx:Period>
        </Combinator>
      </Expression>
      <Expression xsi:type="rx:Sink">
        <Name>StimOn</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="WorkflowInput">
              <Name>Source1</Name>
            </Expression>
            <Expression xsi:type="beh:CreateMessage">
              <harp:MessageType>Write</harp:MessageType>
              <harp:Payload xsi:type="beh:CreateOutputSetPayload">
                <beh:OutputSet>DOPort0</beh:OutputSet>
              </harp:Payload>
            </Expression>
            <Expression xsi:type="MulticastSubject">
              <Name>DeviceCommands</Name>
            </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" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="rx:SelectMany">
        <Name>Response</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="rx:Timer">
                <rx:DueTime>PT10S</rx:DueTime>
                <rx:Period>PT0S</rx:Period>
              </Combinator>
            </Expression>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="BooleanProperty">
                <Value>false</Value>
              </Combinator>
            </Expression>
            <Expression xsi:type="SubscribeSubject">
              <Name>DeviceEvents</Name>
            </Expression>
            <Expression xsi:type="beh:Parse">
              <harp:Register xsi:type="beh:DigitalInputState" />
            </Expression>
            <Expression xsi:type="BitwiseAnd">
              <Operand xsi:type="WorkflowProperty" TypeArguments="beh:DigitalInputs">
                <Value>DIPort0</Value>
              </Operand>
            </Expression>
            <Expression xsi:type="GreaterThan">
              <Operand xsi:type="WorkflowProperty" TypeArguments="sys:Byte">
                <Value>0</Value>
              </Operand>
            </Expression>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="rx:DistinctUntilChanged" />
            </Expression>
            <Expression xsi:type="rx:Condition">
              <Name>High</Name>
              <Workflow>
                <Nodes>
                  <Expression xsi:type="WorkflowInput">
                    <Name>Source1</Name>
                  </Expression>
                  <Expression xsi:type="Combinator">
                    <Combinator xsi:type="BooleanProperty">
                      <Value>true</Value>
                    </Combinator>
                  </Expression>
                  <Expression xsi:type="WorkflowOutput" />
                </Nodes>
                <Edges>
                  <Edge From="0" To="1" Label="Source1" />
                  <Edge From="1" To="2" Label="Source1" />
                </Edges>
              </Workflow>
            </Expression>
            <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="rx:Take">
                <rx:Count>1</rx:Count>
              </Combinator>
            </Expression>
            <Expression xsi:type="WorkflowOutput" />
          </Nodes>
          <Edges>
            <Edge From="0" To="1" Label="Source1" />
            <Edge From="1" To="9" 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="5" To="6" Label="Source1" />
            <Edge From="6" To="7" Label="Source1" />
            <Edge From="7" To="8" Label="Source1" />
            <Edge From="8" To="9" Label="Source2" />
            <Edge From="9" To="10" Label="Source1" />
            <Edge From="10" To="11" Label="Source1" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="rx:Sink">
        <Name>StimOff</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="WorkflowInput">
              <Name>Source1</Name>
            </Expression>
            <Expression xsi:type="beh:CreateMessage">
              <harp:MessageType>Write</harp:MessageType>
              <harp:Payload xsi:type="beh:CreateOutputClearPayload">
                <beh:OutputClear>DOPort0</beh:OutputClear>
              </harp:Payload>
            </Expression>
            <Expression xsi:type="MulticastSubject">
              <Name>DeviceCommands</Name>
            </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" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="rx:Condition">
        <Name>Success</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="WorkflowInput">
              <Name>Source1</Name>
            </Expression>
            <Expression xsi:type="WorkflowOutput" />
          </Nodes>
          <Edges>
            <Edge From="0" To="1" Label="Source1" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="rx:SelectMany">
        <Name>Reward</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="beh:CreateMessage">
              <harp:MessageType>Write</harp:MessageType>
              <harp:Payload xsi:type="beh:CreateOutputSetPayload">
                <beh:OutputSet>SupplyPort0</beh:OutputSet>
              </harp:Payload>
            </Expression>
            <Expression xsi:type="MulticastSubject">
              <Name>DeviceCommands</Name>
            </Expression>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="rx:Take">
                <rx:Count>6</rx:Count>
              </Combinator>
            </Expression>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="BooleanProperty">
                <Value>true</Value>
              </Combinator>
            </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" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="rx:Condition">
        <Name>Miss</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="WorkflowInput">
              <Name>Source1</Name>
            </Expression>
            <Expression xsi:type="BitwiseNot" />
            <Expression xsi:type="WorkflowOutput" />
          </Nodes>
          <Edges>
            <Edge From="0" To="1" Label="Source1" />
            <Edge From="1" To="2" Label="Source1" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="rx:SelectMany">
        <Name>Fail</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="BooleanProperty">
                <Value>false</Value>
              </Combinator>
            </Expression>
            <Expression xsi:type="Combinator">
              <Combinator xsi:type="rx:Take">
                <rx:Count>1</rx:Count>
              </Combinator>
            </Expression>
            <Expression xsi:type="WorkflowOutput" />
          </Nodes>
          <Edges>
            <Edge From="0" To="1" Label="Source1" />
            <Edge From="1" To="2" Label="Source1" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:Merge" />
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:Take">
          <rx:Count>1</rx:Count>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:Repeat" />
      </Expression>
    </Nodes>
    <Edges>
      <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="7" Label="Source1" />
      <Edge From="5" To="6" Label="Source1" />
      <Edge From="6" To="9" Label="Source1" />
      <Edge From="7" To="8" Label="Source1" />
      <Edge From="8" To="9" Label="Source2" />
      <Edge From="9" To="10" Label="Source1" />
      <Edge From="10" To="11" Label="Source1" />
    </Edges>
  </Workflow>
</WorkflowBuilder>

Hope it helps,
Artur