Virtual reality and Bpod timing

sebromano

Hello Josh,

I am planning some experiments of head-fixed mice running on a wheel connected to a rotary encoder and a virtual reality engine. Do you think that running the VR engine and the Bpod on the same CPU could affect Bpod timing? I'll keep the VR simple, a linear corridor, but mice will receive rewards when reaching specific spots on the corridor, so the Bpod should read a threshold position to deliver the rewards.
I am using a v0.7 Bpod, with Gen2 repository and the StateMachine_v16_Bpod0_789 firmware, on a Intel i5 CPU with 4 processors and 8Gb RAM, and a Gefroce GT 730 graphics card.
In principle, I was checking out the ViRMEn VR engine from the Tank lab, which runs on Matlab. I already noticed that I should probably run a second Matlab instance to run the VR, since ViRMEn overrides the Bpod when both are run in the same Matlab instance (I still haven't checked if running Bpod with TrialManagerObject instead of RunStateMachine helps on this).
Anyway, just wanted to know if you had any experience on VR+Bpod and machine usage.
Thank you very much!
Sebastian.

Josh

Hi Sebastian

I haven't tried a VR application and Bpod on the same computer. Since you have multiple cores, the OS will most likely run most processes in each matlab instance on a separate processor. In Windows 7 (and possibly others), you can set the core affinity of each MATLAB instance manually if necessary.

The two MATLAB instances can exchange data (i.e. the next trial's visual parameters, the previous trial's position data) using TCP/IP on a local port. If you have Instrument Control Toolbox, your starting point is here. Otherwise, it's possible with PsychToolbox's fork of PNET.

If you're using the rotary encoder module, the VR MATLAB instance can retrieve the current position via USB to render the environment using the currentPosition() method. A direct CAT5e line from the encoder module to the state machine, can transfer position threshold crossing events at lower latency than via the computer.

I hope this helps!
-Josh

sebromano

Josh wrote[quote='Josh' pid='399' dateline='1514525705']
Hi Sebastian

I haven't tried a VR application and Bpod on the same computer. Since you have multiple cores, the OS will most likely run most processes in each matlab instance on a separate processor. In Windows 7 (and possibly others), you can set the core affinity of each MATLAB instance manually if necessary.

The two MATLAB instances can exchange data (i.e. the next trial's visual parameters, the previous trial's position data) using TCP/IP on a local port. If you have Instrument Control Toolbox, your starting point is here. Otherwise, it's possible with PsychToolbox's fork of PNET.

If you're using the rotary encoder module, the VR MATLAB instance can retrieve the current position via USB to render the environment using the currentPosition() method. A direct CAT5e line from the encoder module to the state machine, can transfer position threshold crossing events at lower latency than via the computer.

I hope this helps!
-Josh

Thanks for your reply Josh!

Let me ask you something else. I already have a rotary encoder from US Digital that I plan to use, and I have an Arduino code to read the signal in an Arduino Uno that is working fine. The next task is to send this data to Matlab. For that, I thought I could use your ArCOM interface. But I am having an issue when trying to run the example code that you provide in the ArCOM site. It seems that the ArCOM setup instructions are not up to date with the current ArCOM github folder organization. Thus, I copied to the Arduino Libraries folder the files ArCOM.h and ArCOM.cpp from the ArCOM/Arduino/src/ folder found in the github repository.

I then tried to run in my Arduino Uno the following example code found in your site:

Arduino code:
#include "ArCOM.h" // Import the ArCOM library
ArCOM myUSB(SerialUSB); // Create an ArCOM wrapper for the SerialUSB interface
unsigned short myDataArray[10] = {0}; // Create a 1x10 uint16 array
 void setup() {
         SerialUSB.begin(115200); // Initialize the USB serial port
    myUSB.writeUint16Array(myDataArray,10); // Send the array to MATLAB's buffer
}
void loop() {}

But I get the following error:

Arduino:1.8.2 (Windows 7), Tarjeta:"Arduino/Genuino Uno"

test:2: error: 'SerialUSB' was not declared in this scope

 ArCOM myUSB(SerialUSB); // Create an ArCOM wrapper for the SerialUSB interface

             ^

C:\Users\Usuario\Documents\Arduino\test\test.ino: In function 'void setup()':

test:5: error: 'SerialUSB' was not declared in this scope

          SerialUSB.begin(115200); // Initialize the USB serial port

          ^

exit status 1
'SerialUSB' was not declared in this scope

Do you know what is the problem?
I am aware that this is not related to the Bpod, so I am sorry for taking your time, but maybe you can guide me on this.
Thanks again.
Sebastian.

Josh

Hi Sebastian

The example code was meant to run on Arduino Leonardo, or Arduino Due. On both of these boards, SerialUSB is defined (in code automatically included by the Arduino IDE when you select the board from the "boards" menu). The syntax 'SerialUSB' is used to identify the board's native USB connection, as a separate interface from the UART connection on pins 0 and 1 (Serial, or Serial1 depending on the board).

On Arduino Uno, there is only one USB connection, which is via UART on pins 0 and 1. It is called 'Serial'.

Thus, to run the code on Arduino Uno, replace "SerialUSB" with "Serial":

ArCOM myUSB(Serial);

then, in the setup() function,

Serial.begin(115200);

-Josh