Change state with FlexIO analog signal

Gregorio

Hi,

I want to use a Flex IO channel as analog input and change a state when a threshold is crossed. I managed to accomplish this change-state by setting the Flex channel as a digital input and adding a Flex1High change state event.

Because my signal is analog and does not always reach 5V, I tried to do the same thing but setting the Flex I/O channel to analog and the appropriate threshold value. To determine the threshold value I used the Flex I/O Analog Viewer.
BpodSystem.FlexIOConfig.channelTypes = [2 0 0 0]; BpodSystem.FlexIOConfig.threshold1 = ones(1,4)*2; % In range 0-5 BpodSystem.FlexIOConfig.polarity1 = zeros(1,4); % Polarity 0: Threshold activated when analog is > thresh

In the state matrix, I used Flex1Trig1 as a change-state event, but eventhough the signal crosses the threshold in the Felx I/O analog viewer, there is no actual state change.

I also tried adding in the OutputAction {'AnalogThreshEnable', 1} , but this didn't make any difference.

The only example protocol using flexIO that I found is FlexIOAnalogLight2AFC.m, but it does not use analog inputs to change states. What am I doing wrong? Is there any example protocol that I can use to see how this should be coded?

Cheers,

Josh

Hello Gregorio,

What you're doing looks correct.
Each Flex I/O channel has two thresholds.
When thresholds are crossed, they inactivate. Reactivating them can be done in two ways:

Manually
Using the second threshold.

Manual Reactivation
To reactivate manually, set {'AnalogThreshEnable', N} in output actions. Bits of N indicate the channels to activate, and both thresholds are reactivated on targeted channels.

Auto-Reactivation with second threshold
Initialize with:
BpodSystem.FlexIOConfig.thresholdMode(1) = 1;
In this mode, crossing threshold 1 re-enables threshold 2, and crossing threshold 2 re-enables threshold 1. Both thresholds are inactive by default, so you'll need {'AnalogThreshEnable', N} in the first state to get the initial event.

Please let me know if this was the issue. If not, please share the sections of your code where you set BpodSystem.FlexIOConfig and set up your states.

Thanks,
Josh

Gregorio

Hi Josh,

This is the code I am using:

% Configure Flex I/O Channels
BpodSystem.FlexIOConfig.nReadsPerSample = 1;
BpodSystem.FlexIOConfig.analogSamplingRate = 1000;
BpodSystem.FlexIOConfig.channelTypes = [4 4 4 4];

BpodSystem.FlexIOConfig.channelTypes(1) = 2; % 0 Digital in; 2 Analog In
BpodSystem.FlexIOConfig.thresholdMode(1) = 1;

BpodSystem.FlexIOConfig.threshold1(1) = 2.1;
BpodSystem.FlexIOConfig.polarity1(1) = 0;

BpodSystem.FlexIOConfig.threshold2(1) = 2;
BpodSystem.FlexIOConfig.polarity2(1) = 1;

%--- Initialize plots and start USB connections to any modules
BpodParameterGUI('init', S); % Initialize parameter GUI plugin

% Initialize analog viewer GUI (online monitor of FlexIO analog inputs, not necessary for data logging)
BpodSystem.startAnalogViewer;


% Main loop (runs once per trial)
for currentTrial = 1:maxTrials
    S = BpodParameterGUI('sync', S); 

    sma = NewStateMachine();

    sma = AddState(sma, 'Name', 'Start', ...
        'Timer', 1,...
        'StateChangeConditions', {'Tup', 'Start2'},...
        'OutputActions',  {'PWM3', 025, 'AnalogThreshEnable', 1});

    sma = AddState(sma, 'Name', 'Start2', ... 
        'Timer', 5,...
        'StateChangeConditions', {'Tup', 'exit','Port3In','stateTurnLedRedOn','Flex1Trig1','stateTurnLedRedOn'},... %Flex1Trig1  // Flex1High
        'OutputActions', {'PWM3', 0, 'PWM4', 0});

    sma = AddState(sma, 'Name', 'stateTurnLedRedOn', ... 
        'Timer', 1,...
        'StateChangeConditions', {'Tup', 'exit','Port3Out','Start2','Flex1Trig2','Start2'},... % Flex1Trig2 // Flex1Low
        'OutputActions', {'PWM4', 255});

I have tried using every Flex IO channel in my bpod machine and I also tried the bpod machine of a colleague of mine. I still don't get any change of state using the analog input mode. I tried different threshold values and threshold modes. As I mentioned earlier, if I set the Flex IO channel as digital input and the OutpuActions to Flex1High/Flex1Low the transitions work as expected.

Cheers,

Gregorio

Josh

Hello Gregorio,

Is your code located in /Bpod_Local/Protocols/My-Protocol-Name/ and are you launching it from the launch manager?

Flex I/O analog input is sampled and time-stamped on the session clock, which is reset and initialized by the protocol launch code.

Alternatively you may try adding the following line just before BpodSystem.startAnalogViewer; in your existing code:
BpodSystem.resetSessionClock();

Please let me know if this works.

Thanks,
Josh

Gregorio

Hello Josh,

I am using the launch manager and my protocol is located in \Bpod Local\Protocols\Protocol_Test_2\Protocol_Test_2.m

I added BpodSystem.resetSessionClock(); as you suggested but it still does not work.

Cheers

Josh

Hello Gregorio,

Can you please share your complete .m file or send it to support@sanworks.io?
I'll try to replicate the issue.

Thanks,
Josh

Gregorio

Dear Josh,

I sent the complete m file by email. Cheers

Josh

Hi Gregorio,

On line 51 you have:
'OutputActions', {'PWM3', 025, 'AnalogThreshEnable', 0});

Bits of AnalogThreshEnable are mapped to the four channels. Setting a channel's bit to 1 will enable both thresholds on the channel, while 0 has no effect. In your case, to enable thresholds of Ch1, you'd use:

{'PWM3', 025, 'AnalogThreshEnable', 1}

-Josh

Gregorio

Dear Josh,

I corrected the value of 'AnalogThreshEnable' to 1 and it still does not work for me.

Gregorio

Josh

Hello Gregorio,

While the task is running, does the signal display correctly in terms of volts per division on the Analog Viewer GUI?
The current V/Div setting is printed in yellow on the lower-left corner.

Thanks,
Josh

Gregorio

Hi Josh,

Yes, the signal looks fine, it ranges from 0 to 5 with a little offset.
imgur.com/a/n8XJEvD

Gregorio

Hi Josh,

I continued working on another protocol, and I realized that Flex1Trig1 is detected only if the state matrix has more than 5 states. I don't know if this makes any sense, but (in principle) this problem is solved for me.

Thanks for your prompt responses during this interaction period.

Cheers