Setting new RE position in the state machine

Giul

Hi Josh,
I am trying to "teleport" the position of a wheel at the beginning of a new state by setting a new position using the output action {'RotaryEncoder1' ['P' 2-bytearray]} with no luck. Here is my code.

%% startingPositionsWheelInDegree = [-90 90]; startingPositionsWheelInTics = round(startingPositionsWheelInDegree*1024/360); startingPositionsWheelInTics_TwoBytesArray = []; for idxPos = 1:length(startingPositionsWheelInTics) int16Number = int16(startingPositionsWheelInTics(idxPos)); byteArray = typecast(int16Number, 'uint8'); byteArray = fliplr(byteArray); startingPositionsWheelInTics_TwoBytesArray = [startingPositionsWheelInTics_TwoBytesArray; byteArray]; end newPosition1 = {'RotaryEncoder1', ['P' char(startingPositionsWheelInTics_TwoBytesArray( 1, : ))]}; newPosition2 = {'RotaryEncoder1', ['P' char(startingPositionsWheelInTics_TwoBytesArray( 2, : ))]}; BpodSystem.Data.StartingPositionsWheelInDegree = []; R = RotaryEncoderModule('/dev/cu.usbmodem35800201'); R.wrapPoint = 360 * 32; R.startUSBStream; for currentTrial = 1:2 S = BpodParameterGUI('sync', S); sma = NewStateMachine(); sma = AddState(sma, 'Name', 'State1', ... 'Timer', 2,... 'StateChangeConditions', {'Tup', 'State2'},... 'OutputActions', newPosition1); sma = AddState(sma, 'Name', 'State2', ... 'Timer', 2,... 'StateChangeConditions', {'Tup', 'State3'},... 'OutputActions', newPosition2); sma = AddState(sma, 'Name', 'State3', ... 'Timer', 2,... 'StateChangeConditions', {'Tup', '>exit'},... 'OutputActions', {'RotaryEncoder1' 'Z'}); SendStateMachine(sma); RawEvents = RunStateMachine; if ~isempty(fieldnames(RawEvents)) BpodSystem.Data = AddTrialEvents(BpodSystem.Data,RawEvents); BpodSystem.Data.TrialSettings(currentTrial) = S; BpodSystem.Data.EncoderData{currentTrial} = R.readUSBStream(); BpodSystem.Data.StartingPositionsWheelInDegree(currentTrial) = startingPositionsWheelInDegree(currentTrial); SaveBpodSessionData; end HandlePauseCondition; if BpodSystem.Status.BeingUsed == 0 R.stopUSBStream; return end end R.stopUSBStream; %%

I also tried 'OutputActions,' {'RotaryEncoder1', ['P' 'x' '1']} at the end of State1 and State2; however, plotting the recorded Encoder.Data revealed that the position had not been changed at the beginning of the two states. Can you please help me?

Josh

Hello Giul,

Looking at the Rotary Encoder Module's serial interface, operations are divided into two types:

State Machine Command Interface
SerialUSB Command Interface

All state machine commands can also be sent by USB, but the USB commands are USB-only.
Unfortunately the 'P' operation is a USB command, and will be ignored if sent from the state machine.

There is no good reason why the state machine shouldn't be able to do this, so I've added it to our stack for a future firmware release.

-Josh

Giul

Josh I see. I was misled by this example in the wiki at the bottom of the page (https://sanworks.github.io/Bpod_Wiki/module-documentation/rotary-encoder-module/). Indeed, it would be useful to set the RE position from the state machine. I will look more carefully into the firmware and see if I can add this. In the meantime, I tried to get around it with some tricks, but none worked.

What I want to do.
The mouse turns a wheel like in the IBL task but without visual stimuli. I want the mouse to start from a random position xº on the arcs [-50º -10º] U [10º 50º] and turn the wheel to reach the target region [-5º 5º]. The mouse gets rewarded if it stays in the target region for 2 seconds. The mouse hopefully knows its current position because the REM controls two mass flow controllers that mix two odorants, creating a 1D odor path that gives sensory feedback to the animal. I am using a rotary encoder Version 1 modified to output two analog signals from two pins to the MFCs.

What I already tried and didn't work.
The first workaround I tried was setting the starting position through R.setPosition(xº) at the beginning of each trial before sending the state machine while streaming the data from the REM. This workaround failed because the REM often doesn't send the confirmation bit in response to R.setPosition() if R.startUSBStream is already on. Also, in this case, R.readUSBStream() failed.
The second workaround I tried was starting the USB streaming with R.startUSBStream() at the beginning of each trial after R.setPosition(xº) and stopping it at the end of the trial. This didn't work because opening a new USB serial communication ('S') resets the position of the RE to 0, nullifying my R.setPosition(xº).
The third workaround I tried was doing without R.startUSBStream and, instead, using R.startLogging() at the beginning of each trial after R.setPosition(xº). This didn't work either because, apparently, the REM doesn't output any current position if the wheel is not moving (no data are recorded on the microSD). The bpod seems to interpret this lack of data as if the wheel is at position 0 instead of the last position. Therefore, for example, if the wheel moves from -50º to -40º and stops, the state machine seems to act like the wheel suddenly jumped into the target region, even if it never got there.

I really need to collect some data with this protocol for a grant, so I will try and see if I can modify the firmware somehow to get the protocol to work. At any rate, if you have any suggestions for other workarounds, I would really appreciate it. Thanks.

-Giul

Josh

Hello Giul,

Thanks for pointing out the issue with the docs. I've marked it for revision.

I modded the firmware to fix the issue on the develop branch, here. I'm traveling so I haven't been able to test it yet. Please let me know if this works for you.

The bytes that follow 'P' should encode a 16-bit signed integer indicating the new position. The docs do this incorrectly. In MATLAB you'd use: typecast(int16(myNewPosition), 'uint8')

Thanks,
Josh

Giul

Dope! It works like a charm. I further modified the REM firmware to allow the thresholds to be crossed in both directions for our specific task. Now, we can run our experiments!

Thanks a lot, Josh!
G-

Josh

Glad it worked! Please follow up if you run into any issues.

-Josh