How to output Arduino digital HIGH when two boolean inputs are true in Bonsai?

[chengyuan717]

Hello everyone,

I’m currently working on a closed-loop optogenetics experiment controlled by Bonsai and Arduino. I want to use Arduino digital inputs to determine whether the behavior is in an inner trial or in the inter-trial interval. Specifically, I have two boolean logic values, and I want the Arduino digital output to send a HIGH signal only when both booleans are true (i.e., logical AND).

In Bonsai, I tried using CombineLatest to merge the two boolean streams, then used a PythonTransform node to perform an AND operation on them. However, during runtime, it seems the Arduino digital input cannot correctly detect the Arduino port state or output as expected.

I have attached my Bonsai program and screenshots for reference.

Has anyone encountered a similar issue or can provide advice on the best way to implement this logic for Arduino digital output control in Bonsai?

Thank you very much in advance for any help!

Best regards,
Yuan
close-loop_practice1.bonsai.zip

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[banchan86]

Hi Chengyuan so couple of things that you could do first:

1. You need to load the StandardFirmata sketch on the Arduino (Uno R3) or ConfigurableFirmata (UnoR4) for it to communicate with Bonsai.
2. You need to create a connection to the Arduino first with the CreateArduino operator, give it a Name, then set PortName in DigitalInput and DigitalOutput to the arduino.
3. I would then test it out first with a simpler example, can you send a DigitalOutput (Timer -> Bool -> DigitalOutput) and read it with a DigitalInput (by connecting those two pins together). If you can do that with the pins you want to use, then you can move on to adapting the close loop workflow
4. You don't need a python transform for the logical AND, the Bonsai Expressions library has a LogicalAnd operator, but you should check the output of the two branches that you want to LogicalAnd, you might need to do a conversion for one of the streams.

Hopefully these few steps can resolve the issues you have been facing, if you need more help after that, check back in here! There are also similar threads in the forums on how to set up the Arduino that you can search for.

[banchan86]

Hi @chengyuan717, the behaviour of CombineLatest is that it will retrieve the last emitted value from the other sequence whenever any of the sequences produces a value. In effect this means that even though your DigitalInput only issues a single value when it changes, it gets converted into a "continuous stream" when CombineLatest is triggered by the LessThan. So I think the issue lies somewhere else.

[chengyuan717]

Hi @banchan86, It seems the setup is getting a bit more complex. The digital input signal being high indicates that my behavioral control system is in the inner trial window, and low means it's in the inter-trial interval (ITI).
What I want to implement is: only track the distance between the two mice during the inner trial window, and trigger a digital output when they are close enough. During the ITI (when the input is low), I’d like to skip the distance tracking completely. How would you approach implementing this kind of logic？

[banchan86]

Hmm @chengyuan717 I might be a bit lost here. It seems that your workflow should do what you described, the only thing I might add is a DistinctUntilChanged after the LogicalAnd to only change the DigitalOutput when there is a change. Is there something that is not working? Or why do you want to skip the distance tracking?

[chengyuan717]

Hi @banchan86, Let me clarify a bit further. At the moment, my workflow isn't working as intended. The issue is that the digital input only detects the moment of a pin state change—so the signal is false most of the time, and only becomes true at the instant the pin switches state.

However, what I actually need is a level-based high signal to be interpreted as true, because that reflects the inner-trial time window during which behavior is active.

As a result, the digital output isn't behaving as I expect. Specifically, I want distance tracking to be active only during the inner-trial window (when digital input is high), and disabled during the ITI. Just to clarify, I’m not trying to skip distance tracking altogether—I simply want the digital output to reflect the distance tracking results only when digital input is true.

So the core issue isn't really with the logical AND logic, but with how the digital input is being sampled.

I could potentially solve this using Arduino’s analog input combined with a greater than condition, but I’d really like to know: is there a way to achieve continuous monitoring using digital input instead?

Also, you're absolutely right earlier—I don’t have to use Python for this, and using logicalAND should work fine for the logic layer.

Hope this explanation makes things clearer.

[banchan86]

Hey @chengyuan717 maybe you missed this, but as I explained before, you have a CombineLatest operator that will combine the latest value from DigitalInput when a distance tracking value is issued (and vice versa) thus it will effectively "sample" DigitalInput at the rate of the distance tracking measurement.

DigitalInput is the right way to report a state change from a digital pin, the workflow logic looks good to me, and should do what you explained you wanted it to do.

I suspect the issue lies somewhere else, I would first check the outputs from all the nodes to make sure they are reporting the right values. I noticed that the HsvThreshold values are too high, have you checked that you can segment the two objects correctly? And that the DigitalInput is indeed reading the right pin values?

If all else fails, I think you should give AnalogInput a try just to see if you run into the same issue.