File content as of revision 4:fd29407c3115:

#include "mbed.h"
#include "HIDScope.h"
#include "biquadFilter.h"        // Require the HIDScope library
#include "MODSERIAL.h"
//Define objects
AnalogIn    emg(A0); //Analog of EMG input
Ticker      sample_timer;
HIDScope    scope(2);        // Instantize a 2-channel HIDScope object
DigitalIn button1(PTA4);//test button for starting motor 1
DigitalOut led1(LED_RED);
DigitalOut led2(LED_BLUE);
MODSERIAL pc(USBTX,USBRX);
/*The biquad filters required to transform the EMG signal into an usable signal*/
biquadFilter filterhigh1(-1.1430, 0.4128, 0.6389, -1.2779, 0.6389);
biquadFilter filterlow1(1.9556, 0.9565, 0.9780, 1.9561, 0.9780);
biquadFilter notch(-1.1978e-16, 0.9561, 0.9780, -1.1978e-16, 0.9780);
biquadFilter filterlow2(-1.9645, 0.9651, 1.5515e-4, 3.1030e-4, 1.5515e-4);
double emg_value;
double signalpart1;
double signalpart2;
double signalpart3;
double signalpart4;
double signalfinal;
double onoffsignal;
double maxcal=0;        
/* 
 */
void filter(){
        emg_value = emg.read();//read the emg value from the elektrodes
        signalpart1 = notch.step(emg_value);//Highpass filter for removing offset and artifacts
        signalpart2 = filterhigh1.step(signalpart1);//rectify the filtered signal
        signalpart3 = abs(signalpart2);//low pass filter to envelope the emg
        signalpart4 = filterlow1.step(signalpart3);//notch filter to remove 50Hz signal
        signalfinal = filterlow2.step(signalpart4);//2nd low pass filter to envelope the emg
        onoffsignal=signalfinal/maxcal;//divide the emg signal by the max EMG to calibrate the signal per person
        scope.set(0,emg_value);//set emg signal to scope in channel 1
        scope.set(1,onoffsignal);//set filtered signal to scope in channel 2
    scope.send();//send the signals to the scope
}
double normalcal(){
    double signalmeasure =emg.read();
    if (signalmeasure > maxcal){
        signalmeasure = maxcal;
        }
    return maxcal;
}

int main()
{
    pc.baud(115200);
    led1.write(1);
    led2.write(1);
    bool calyes=0;

    if(calyes==1){
        sample_timer.attach(&filter, 0.002);//continously execute the EMG reader and filter
        }
        while(1){
                 if(button1.read()==false){
                     for(int n =0; n<5000;n++){
                             double signalmeasure =emg.read();
                             pc.printf("%d", signalmeasure);
                             if (signalmeasure > maxcal){
                                 signalmeasure = maxcal;
                                 }
                                 calyes=1;
                      }
                  }  
                   
              //     pc.printf("%f \n", onoffsignal);
            if(onoffsignal<=0.02){
             led1.write(0);
             led2.write(1);
             }
             else if(onoffsignal >= 0.05){
                 led1.write(1);
                 led2.write(0);
             }
        }     
}