File content as of revision 3:48438eea184e:

#include "mbed.h"
#include "QEI.h"
#include "HIDScope.h"
#include "Biquad.h"
#include "controlandadjust.h"

//info out
HIDScope scope(4);
Ticker scope_ticker;
const double scope_frequency=500;
Serial pc(USBTX,USBRX);

////////////////ENCODERS
QEI encoder1(D12,D13,NC,32);
QEI encoder2(D10,D11,NC,32);

//////////////////////////////////CONTROLLER
controlandadjust mycontroller; // make a controller
//controller constants
float Kp=0.5;
float Ki=0.01;
float Kd=0.001;
Ticker control_ticker;
const double control_frequency=25;

double error1_int=0;// storage variables for the errors
double error2_int=0;
double error1_prev=0;
double error2_prev=0;

InterruptIn valuechangebutton(PTC6);//button to change controller constants

//safetyandthreshold
AnalogIn safety_pot(A3);//pot 2, used for the safety cutoff value for the pwm
AnalogIn threshold_pot(A2);//pot1, used to adjust threshold if signal differs per person

Ticker safetyandthreshold_ticker; // ticker to read potmeters
const double safetyandthreshold_frequency=1; // frequency for the ticker

float threshold_value=1;

////////////////////////////////FILTER
#include "filtervalues.h"
Ticker filter_ticker;
const double filter_frequency=500;
Biquad myfilter1;
Biquad myfilter2;

AnalogIn emg1_input(A0);
AnalogIn emg2_input(A1);

double filteredsignal1=0;
double filteredsignal2=0;
double filter_extragain=1;

/////////////////READSIGNAL
Ticker readsignal_ticker;
const double readsignal_frequency=25;

DigitalOut led(D4);

//////////////////////GO FLAGS AND ACTIVATION FUNCTIONS
volatile bool scopedata_go=false,
              control_go=false,
              filter_go=false,
              safetyandthreshold_go=false,
              readsignal_go=false;

void scopedata_activate()
{
    scopedata_go=true;
}
void control_activate()
{
    control_go=true;
}
void filter_activate()
{
    filter_go=true;
}
void safetyandthreshold_activate()
{
    safetyandthreshold_go=true;
}
void readsignal_activate()
{
    readsignal_go=true;
}


////////////////////////FUNCTIONS
//gather data and send to scope
void scopedata()
{
    scope.set(0,emg1_input.read());
    scope.set(1,filteredsignal1);
    scope.send();
    }
//read potmeters and adjust the safetyfactor and threshold
void safetyandthreshold()
{
    mycontroller.cutoff((ceil (10*safety_pot.read()) )/10); // adjust the safetyfactor value between 0 and 1 rounded to 1 decimal
    threshold_value=((ceil (10*threshold_pot.read()) )/10); // adjust the threshold value between 0 and 1 rounded to 1 decimal
}
/////filter
void filtereverything()
{
    //filter_timer.reset();
    // filter_timer.start();
    //pass1 so f1
    double pass1_emg1 = myfilter1.filter(emg1_input.read(), v1_f1_emg1 , v2_f1_emg1 , a1_f1 , a2_f1 , b0_f1 , b1_f1 , b2_f1);
    double pass1_emg2 = myfilter2.filter(emg2_input.read(), v1_f1_emg2 , v2_f1_emg2 , a1_f1 , a2_f1 , b0_f1 , b1_f1 , b2_f1);

    //pass2 so f2
    double pass2_emg1 = myfilter1.filter(pass1_emg1, v1_f2_emg1 , v2_f2_emg1 , a1_f2 , a2_f2 , b0_f2 , b1_f2 , b2_f2);
    double pass2_emg2 = myfilter2.filter(pass1_emg2, v1_f2_emg2 , v2_f2_emg2 , a1_f2 , a2_f2 , b0_f2 , b1_f2 , b2_f2);

    //pass3 so f3
    double pass3_emg1 = myfilter1.filter(pass2_emg1, v1_f3_emg1 , v2_f3_emg1 , a1_f3 , a2_f3 , b0_f3 , b1_f3 , b2_f3);
    double pass3_emg2 = myfilter2.filter(pass2_emg2, v1_f3_emg2 , v2_f3_emg2 , a1_f3 , a2_f3 , b0_f3 , b1_f3 , b2_f3);

    //pass4 so f4
    double pass4_emg1 = myfilter1.filter(pass3_emg1, v1_f4_emg1 , v2_f4_emg1 , a1_f4 , a2_f4 , b0_f4 , b1_f4 , b2_f4);
    double pass4_emg2 = myfilter2.filter(pass3_emg2, v1_f4_emg2 , v2_f4_emg2 , a1_f4 , a2_f4 , b0_f4 , b1_f4 , b2_f4);

    //pass5 so f5
    double pass5_emg1 = myfilter1.filter(pass4_emg1, v1_f5_emg1 , v2_f5_emg1 , a1_f5 , a2_f5 , b0_f5 , b1_f5 , b2_f5);
    double pass5_emg2 = myfilter2.filter(pass4_emg2, v1_f5_emg2 , v2_f5_emg2 , a1_f5 , a2_f5 , b0_f5 , b1_f5 , b2_f5);

    ///// take absolute value
    double pass5_emg1_abs=(fabs(pass5_emg1));
    double pass5_emg2_abs=(fabs(pass5_emg2));

    //pass6 so f6
    double pass6_emg1 = myfilter1.filter(pass5_emg1_abs, v1_f6_emg1 , v2_f6_emg1 , a1_f6 , a2_f6 , b0_f6 , b1_f6 , b2_f6);
    double pass6_emg2 = myfilter2.filter(pass5_emg2_abs, v1_f6_emg2 , v2_f6_emg2 , a1_f6 , a2_f6 , b0_f6 , b1_f6 , b2_f6);


    //pass7 so f7
    double pass7_emg1 = myfilter1.filter(pass6_emg1, v1_f7_emg1 , v2_f7_emg1 , a1_f7 , a2_f7 , b0_f7 , b1_f7 , b2_f7);
    double pass7_emg2 = myfilter2.filter(pass6_emg2, v1_f7_emg2 , v2_f7_emg2 , a1_f7 , a2_f7 , b0_f7 , b1_f7 , b2_f7);

    filteredsignal1=(pass7_emg1*9e11*filter_extragain);
    filteredsignal2=(pass7_emg2*9e11*filter_extragain);

    //filter_timer.stop();
}

void control()
{
    ///call desired controller here
}

//adjust controller values when sw2 is pressed
void valuechange()
{
    mycontroller.STOP();
    /*pc.printf("KP is now %f, enter new value\n",Kp);
    pc.scanf("%f", &Kp);

    pc.printf("KI is now %f, enter new value\n",Ki);
    pc.scanf("%f", &Ki);

    pc.printf("KD is now %f, enter new value\n",Kd);
    pc.scanf("%f", &Kd);*/

    pc.printf("Extra gain is now %f, enter new value\n",filter_extragain);
    pc.scanf("%f",&filter_extragain);
}
void readsignal()
{
    if (filteredsignal1>=threshold_value) {
        led=1;
    } else {
        led=0;
    }
}


int main()
{
    //tickers
    safetyandthreshold_ticker.attach(&safetyandthreshold_activate,1.0/safetyandthreshold_frequency);
    filter_ticker.attach(&filter_activate,1.0/filter_frequency);
    control_ticker.attach(&control_activate,1.0/control_frequency);
    scope_ticker.attach(&scopedata_activate,1.0/scope_frequency);
    readsignal_ticker.attach(&readsignal_activate, 1.0/readsignal_frequency);

    while(1) {
        if (scopedata_go==true) {
            scopedata();
            scopedata_go=false;
        }
        if (filter_go==true) {
            filtereverything();
            filter_go=false;
        }
        if (safetyandthreshold_go==true) {
            safetyandthreshold();
            safetyandthreshold_go=false;
        }
        if (control_go==true) {
            control();
            control_go=false;
        }
        if (readsignal_go==true) {
            readsignal();
            readsignal_go=false;
        }
        valuechangebutton.fall(&valuechange);
    }
}