File content as of revision 2:27081b83a58e:

#include "mbed.h"
#include "BiQuad.h"
#define SERIAL_BAUD 115200

AnalogIn    emg0( A0 );
AnalogIn    emg1( A1 );
Serial pc(USBTX,USBRX);

Ticker      sample_timer, average_timer, filter_timer, t;
//HIDScope    scope( 6 );
DigitalOut  led1(LED_RED);
DigitalOut  led2(LED_BLUE);

volatile int time_passed = 0;
volatile bool filter_timer_go=false;

double EMGright, EMGleft, inR;
double averageEMGr =0;
double averageEMGl =0;
//average_timer_go=false,
 // Activates go-flags
//void average_timer_act(){average_timer_go=true;};
void filter_timer_act(){filter_timer_go=true;};



BiQuadChain bcq;
// Notch filter wo=50; bw=wo/35
BiQuad bq1(9.7805e-01,-1.1978e-16,9.7805e-01,1.0000e+00,-1.1978e-16,9.5610e-01);
// High pass Butterworth filter 2nd order, Fc=10;
BiQuad bq2(9.8239e-01,-1.9648e+00,9.8239e-01,1.0000e+00,-1.9645e+00,9.6508e-01);
// Low pass Butterworth filter 2nd order, Fc = 8;
BiQuad bq3(5.6248e-05,1.1250e-04,5.6248e-05,1.0000e+00,-1.9787e+00,9.7890e-01);
// Low pass Butterworth filter 4th order, Fc = 450; plited up in 2x2nd order
BiQuad bq4(1.0000e+00,2.0000e+00,1.0000e+00,1.0000e+00,-4.6382e-01,8.9354e-02);
BiQuad bq5(1.0000e+00,2.0000e+00,1.0000e+00,1.0000e+00,-6.3254e-01,4.8559e-01);

void KeepTrackOfTime()
{
    time_passed++;
}

// In the following: R is used for right arm, L is used for left arm!
void FilteredSample(double averageEMGr, double averageEMGl)
{   
    double inR = emg0.read()-averageEMGr;
    double inL = emg1.read()-averageEMGl;
    //double inLcal = inL-averageL(sumL,size);
    double outRnotch = bq1.step(inR);
    double outRhigh = bq2.step(outRnotch);
    double outRrect = fabs(outRhigh);
    double outRlow = bcq.step(outRrect);
    double outLnotch = bq1.step(inL);
    double outLhigh = bq2.step(outLnotch);
    double outLrect = fabs(outLhigh);
    double outLlow = bcq.step(outLrect);
    
    pc.printf("Detrend EMG = %f\n\r",inR);
    pc.printf("EMG signal= %f\n\r",emg0.read());
    pc.printf("average EMG right = %f\n\r",averageEMGr);
    
    led2 = !led2;
    
    /*scope.set(0, inR);
    scope.set(1, inL);
    scope.set(2, outRlow);
    scope.set(3, outLlow);
    
    
    scope.send();
    // To indicate that the function is working, the LED is toggled*/
}

int main()
{   
    pc.baud(115200);
    led1=1;
    led2=1;
    t.attach(&KeepTrackOfTime,1.0); //taking the time in seconds

    for (;;) {
        if (time_passed<=5) 
        {
        
        led1 =!led1;
        //sample_timer.attach(&sample, 0.002); //500Hz
        pc.printf("\rStart IF-loop\r\n");
        
        int size = 12500;
        int i; 
        double EMGsumR;
        double EMGsumL; 
            
            while(i<size)
            {
                EMGsumR = emg0.read()+EMGsumR;
                EMGsumL = emg1.read()+EMGsumL;
                i++;
                wait(0.0004);
            }
            
        averageEMGr = (double) EMGsumR/size;
        averageEMGl = (double) EMGsumL/size;
        double InRcal = emg0.read()-averageEMGr;
        double InLcal = emg1.read()-averageEMGl;
        
        scope.set(0, emg0.read() );
        scope.set(1, 1 );
        scope.set(2, averageEMGr);
        scope.set(3, averageL(sumL,size));
        scope.set(5, InRcal );
        scope.set(6, InLcal );
        
        scope.send();*/
        //pc.printf("EMG-signal = %f\n\r",emg0.read());
        
        /*pc.printf("\r\nIF-loop end:");
        pc.printf("time is %i sec\n",time_passed);
        pc.printf("averageR = %f\n\r", averageEMGr);*/
        }
        else
        {        
        led1 = 1; 
        led2=!led2;
        
        bcq.add(&bq3).add(&bq4).add(&bq5);
      
        filter_timer.attach(&filter_timer_act, 0.0004); //2500Hz (same as with filter coefficients on matlab!!! Thus adjust!)
        pc.printf("\rMain-loop\n\r");
        //pc.printf("Detrend EMG = %f\n\r",inR);
        
           while(1)
            {
            if (filter_timer_go){
                filter_timer_go=false;
                FilteredSample(averageEMGr, averageEMGl);}
            }
        
        }
}
}