Utilizing bonsai.scripting.python to reactively log messages using a python gui during onix data acquisition #2530

Aathok-Git · 2026-03-16T22:21:39Z

Aathok-Git
Mar 16, 2026

Hey all! I'm trying to use the python scripting module to be able to log events during onix experiments for a research lab I'm in. I'm having a little trouble with it, and a little trouble understanding how bonsai interacts with my python scripts.

The main goal I'm trying to achieve is as follows:

User presses a button on the onix board
Bonsai logs the time the button is pressed, and runs a command in the python namespace to open a gui
In the gui, the user can type in a message and press a submit button when they're done
Bonsai should read that the message is submitted, get the message, combine it with the sampled timestamp, and store it in a log.csv file
Bonsai then should run a command in the python namespace to hide the gui and reset the variables back to default, prepped for the next event to come in.

I'm not attached to my python file, so if it needs to be fully revamped to fit with the workflow, that's fine by me.
bonsai_logging.py

Here's what my workflow currently looks like. I've done a lot of experimenting and I'm still trying to figure out how exactly to get it to work the way I want. I have the take until also listening to the button as a temporary placeholder while I figure out the python aspect. I will change it to stop listening when i run the final eval on the strand with the button (or find a better way to check if the message is submitted)

And here's the XML:

<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.9.0"
                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                 xmlns:onix1="clr-namespace:OpenEphys.Onix1;assembly=OpenEphys.Onix1"
                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                 xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
                 xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
                 xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System"
                 xmlns="https://bonsai-rx.org/2018/workflow">
  <Workflow>
    <Nodes>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="onix1:CreateContext">
          <onix1:Driver>riffa</onix1:Driver>
          <onix1:Index>0</onix1:Index>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="onix1:ConfigureBreakoutBoard">
          <onix1:Name>BreakoutBoard</onix1:Name>
          <onix1:Heartbeat>
            <onix1:DeviceName>BreakoutBoard/PersistentHeartbeat</onix1:DeviceName>
            <onix1:DeviceAddress>0</onix1:DeviceAddress>
            <onix1:BeatsPerSecond>100000</onix1:BeatsPerSecond>
          </onix1:Heartbeat>
          <onix1:AnalogIO>
            <onix1:DeviceName>BreakoutBoard/AnalogIO</onix1:DeviceName>
            <onix1:DeviceAddress>6</onix1:DeviceAddress>
            <onix1:Enable>true</onix1:Enable>
            <onix1:InputRange0>TenVolts</onix1:InputRange0>
            <onix1:InputRange1>TenVolts</onix1:InputRange1>
            <onix1:InputRange2>TenVolts</onix1:InputRange2>
            <onix1:InputRange3>TenVolts</onix1:InputRange3>
            <onix1:InputRange4>TenVolts</onix1:InputRange4>
            <onix1:InputRange5>TenVolts</onix1:InputRange5>
            <onix1:InputRange6>TenVolts</onix1:InputRange6>
            <onix1:InputRange7>TenVolts</onix1:InputRange7>
            <onix1:InputRange8>TenVolts</onix1:InputRange8>
            <onix1:InputRange9>TenVolts</onix1:InputRange9>
            <onix1:InputRange10>TenVolts</onix1:InputRange10>
            <onix1:InputRange11>TenVolts</onix1:InputRange11>
            <onix1:Direction0>Input</onix1:Direction0>
            <onix1:Direction1>Input</onix1:Direction1>
            <onix1:Direction2>Input</onix1:Direction2>
            <onix1:Direction3>Input</onix1:Direction3>
            <onix1:Direction4>Input</onix1:Direction4>
            <onix1:Direction5>Input</onix1:Direction5>
            <onix1:Direction6>Input</onix1:Direction6>
            <onix1:Direction7>Input</onix1:Direction7>
            <onix1:Direction8>Input</onix1:Direction8>
            <onix1:Direction9>Input</onix1:Direction9>
            <onix1:Direction10>Input</onix1:Direction10>
            <onix1:Direction11>Input</onix1:Direction11>
          </onix1:AnalogIO>
          <onix1:DigitalIO>
            <onix1:DeviceName>BreakoutBoard/DigitalIO</onix1:DeviceName>
            <onix1:DeviceAddress>7</onix1:DeviceAddress>
            <onix1:Enable>true</onix1:Enable>
            <onix1:DeadTime>0</onix1:DeadTime>
            <onix1:SampleRate xsi:nil="true" />
          </onix1:DigitalIO>
          <onix1:ClockOutput>
            <onix1:DeviceName>BreakoutBoard/OutputClock</onix1:DeviceName>
            <onix1:DeviceAddress>5</onix1:DeviceAddress>
            <onix1:ClockGate>false</onix1:ClockGate>
            <onix1:Frequency>1000000</onix1:Frequency>
            <onix1:DutyCycle>50</onix1:DutyCycle>
            <onix1:Delay>0</onix1:Delay>
          </onix1:ClockOutput>
          <onix1:HarpInput>
            <onix1:DeviceName>BreakoutBoard/HarpSyncInput</onix1:DeviceName>
            <onix1:DeviceAddress>12</onix1:DeviceAddress>
            <onix1:Enable>true</onix1:Enable>
            <onix1:Source>Breakout</onix1:Source>
          </onix1:HarpInput>
          <onix1:MemoryMonitor>
            <onix1:DeviceName>BreakoutBoard/MemoryMonitor</onix1:DeviceName>
            <onix1:DeviceAddress>10</onix1:DeviceAddress>
            <onix1:Enable>false</onix1:Enable>
            <onix1:SamplesPerSecond>10</onix1:SamplesPerSecond>
          </onix1:MemoryMonitor>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="onix1:StartAcquisition">
          <onix1:ReadSize>2048</onix1:ReadSize>
          <onix1:WriteSize>2048</onix1:WriteSize>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:Timer">
          <rx:DueTime>PT0S</rx:DueTime>
        </Combinator>
      </Expression>
      <Expression xsi:type="SubscribeSubject">
        <Name>Button Clicked</Name>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:SubscribeWhen" />
      </Expression>
      <Expression xsi:type="SubscribeSubject">
        <Name>Button Clicked</Name>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:TakeUntil" />
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:ObserveOnGIL" />
      </Expression>
      <Expression xsi:type="SubscribeSubject">
        <Name>Logger</Name>
      </Expression>
      <Expression xsi:type="PropertyMapping">
        <PropertyMappings>
          <Property Name="Module" />
        </PropertyMappings>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:Get">
          <py:VariableName>submitted</py:VariableName>
        </Combinator>
      </Expression>
      <Expression xsi:type="rx:Condition">
        <Name>Check if Submitted</Name>
        <Description>Check if "submitted" is true</Description>
        <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="Equal">
              <Operand xsi:type="BooleanProperty">
                <Value>true</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" />
          </Edges>
        </Workflow>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:Get">
          <py:VariableName>message</py:VariableName>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:Eval">
          <py:Expression>logger.stop()</py:Expression>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="onix1:DigitalInput">
          <onix1:DeviceName>BreakoutBoard/DigitalIO</onix1:DeviceName>
        </Combinator>
      </Expression>
      <Expression xsi:type="MemberSelector">
        <Selector>Buttons</Selector>
      </Expression>
      <Expression xsi:type="rx:Condition">
        <Name>Verify Button</Name>
        <Workflow>
          <Nodes>
            <Expression xsi:type="WorkflowInput">
              <Name>Source1</Name>
            </Expression>
            <Expression xsi:type="HasFlag">
              <Operand xsi:type="WorkflowProperty" TypeArguments="onix1:BreakoutButtonState">
                <Value>Check</Value>
              </Operand>
            </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="rx:PublishSubject">
        <Name>Button Clicked</Name>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:ObserveOnGIL" />
      </Expression>
      <Expression xsi:type="SubscribeSubject">
        <Name>Logger</Name>
      </Expression>
      <Expression xsi:type="PropertyMapping">
        <PropertyMappings>
          <Property Name="Module" />
        </PropertyMappings>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:Eval">
          <py:Expression>logger.start()</py:Expression>
        </Combinator>
      </Expression>
      <Expression xsi:type="MemberSelector">
        <Selector>Clock</Selector>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="dsp:MatrixWriter">
          <dsp:Path>digital-clock_.raw</dsp:Path>
          <dsp:Suffix>FileCount</dsp:Suffix>
          <dsp:Overwrite>false</dsp:Overwrite>
          <dsp:Layout>ColumnMajor</dsp:Layout>
        </Combinator>
      </Expression>
      <Expression xsi:type="SubscribeSubject">
        <Name>Button Clicked</Name>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:Sample" />
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:ObserveOnGIL" />
      </Expression>
      <Expression xsi:type="PropertyMapping">
        <PropertyMappings>
          <Property Name="Value" />
        </PropertyMappings>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="StringProperty" />
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:CombineLatest" />
      </Expression>
      <Expression xsi:type="io:CsvWriter">
        <io:FileName>log_.csv</io:FileName>
        <io:Append>false</io:Append>
        <io:Overwrite>false</io:Overwrite>
        <io:Suffix>Timestamp</io:Suffix>
        <io:IncludeHeader>false</io:IncludeHeader>
        <io:Selector>Timestamp,Value.Item1.Clock,Value.Item1.HubClock,Value.Item2</io:Selector>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:CreateRuntime">
          <py:PythonHome>C:\Users\melonakos_lab\miniconda3\envs\data_acquisition</py:PythonHome>
        </Combinator>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:CreateModule">
          <py:Name>Logger</py:Name>
          <py:ScriptPath>C:\Users\melonakos_lab\Documents\data_acquisition\bonsai_logging.py</py:ScriptPath>
        </Combinator>
      </Expression>
      <Expression xsi:type="rx:ResourceSubject">
        <Name>Logger</Name>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="py:Exec" />
      </Expression>
    </Nodes>
    <Edges>
      <Edge From="0" To="1" Label="Source1" />
      <Edge From="1" To="2" Label="Source1" />
      <Edge From="3" To="5" Label="Source1" />
      <Edge From="4" To="5" Label="Source2" />
      <Edge From="5" To="7" Label="Source1" />
      <Edge From="6" To="7" Label="Source2" />
      <Edge From="7" To="8" Label="Source1" />
      <Edge From="8" To="11" Label="Source1" />
      <Edge From="9" To="10" Label="Source1" />
      <Edge From="10" To="11" Label="Source2" />
      <Edge From="10" To="13" Label="Source2" />
      <Edge From="10" To="14" Label="Source2" />
      <Edge From="11" To="12" Label="Source1" />
      <Edge From="12" To="13" Label="Source1" />
      <Edge From="13" To="14" Label="Source1" />
      <Edge From="13" To="28" Label="Source1" />
      <Edge From="15" To="16" Label="Source1" />
      <Edge From="15" To="23" Label="Source1" />
      <Edge From="16" To="17" Label="Source1" />
      <Edge From="17" To="18" Label="Source1" />
      <Edge From="18" To="19" Label="Source1" />
      <Edge From="19" To="22" Label="Source1" />
      <Edge From="20" To="21" Label="Source1" />
      <Edge From="21" To="22" Label="Source2" />
      <Edge From="23" To="24" Label="Source1" />
      <Edge From="24" To="26" Label="Source1" />
      <Edge From="25" To="26" Label="Source2" />
      <Edge From="26" To="27" Label="Source1" />
      <Edge From="27" To="30" Label="Source1" />
      <Edge From="28" To="29" Label="Source1" />
      <Edge From="29" To="30" Label="Source2" />
      <Edge From="30" To="31" Label="Source1" />
      <Edge From="33" To="34" Label="Source1" />
      <Edge From="34" To="35" Label="Source1" />
    </Edges>
  </Workflow>
</WorkflowBuilder>

Answered by bruno-f-cruz

Mar 17, 2026

I encourage you to give the native GUI package a try. I would avoid using the python scripting package, especially in workflows that rely high frequency data acquisition as it is the case with yours. Managing the GIL is notoriously annoying, and it will easily add bottlenecks to your workflow.

<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.9.0"
                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                 xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui"
                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                 xmlns="https://bonsai-rx.org/2018/workflow">
  <Workflow>
    <Nodes>
      <Expression xsi

View full answer

bruno-f-cruz · 2026-03-17T13:38:15Z

bruno-f-cruz
Mar 17, 2026
Collaborator

I encourage you to give the native GUI package a try. I would avoid using the python scripting package, especially in workflows that rely high frequency data acquisition as it is the case with yours. Managing the GIL is notoriously annoying, and it will easily add bottlenecks to your workflow.

<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.9.0"
                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                 xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui"
                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                 xmlns="https://bonsai-rx.org/2018/workflow">
  <Workflow>
    <Nodes>
      <Expression xsi:type="gui:ButtonBuilder">
        <gui:Enabled>true</gui:Enabled>
        <gui:Visible>true</gui:Visible>
        <gui:Text>Send</gui:Text>
      </Expression>
      <Expression xsi:type="gui:TextBoxBuilder">
        <gui:Enabled>true</gui:Enabled>
        <gui:Visible>true</gui:Visible>
        <gui:Text>Hello</gui:Text>
        <gui:Multiline>true</gui:Multiline>
      </Expression>
      <Expression xsi:type="Combinator">
        <Combinator xsi:type="rx:WithLatestFrom" />
      </Expression>
    </Nodes>
    <Edges>
      <Edge From="0" To="2" Label="Source1" />
      <Edge From="1" To="2" Label="Source2" />
    </Edges>
  </Workflow>
</WorkflowBuilder>

0 replies

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Bonsai

Utilizing bonsai.scripting.python to reactively log messages using a python gui during onix data acquisition #2530

Uh oh!

{{title}}

Uh oh!

Replies: 1 comment

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{editor}}'s edit

{{editor}}'s edit

Uh oh!

Select a reply

Uh oh!

Bonsai

Utilizing bonsai.scripting.python to reactively log messages using a python gui during onix data acquisition #2530

Uh oh!

Aathok-Git Mar 16, 2026

Replies: 1 comment

Uh oh!

Uh oh!

bruno-f-cruz Mar 17, 2026 Collaborator

Aathok-Git
Mar 16, 2026

bruno-f-cruz
Mar 17, 2026
Collaborator