File content as of revision 12:70f0710400c2:

//c++ script for filtering of measured EMG signals
#include "mbed.h" //Base library
#include "HIDScope.h" // to see if program is working and EMG is filtered properly
// #include "QEI.h"// is needed for the encoder
#include "MODSERIAL.h"// in order for connection with the pc
#include "BiQuad.h"
// #include "FastPWM.h"
// #include "Arduino.h" //misschien handig omdat we het EMG arduino board gebruiken (?)
// #include "EMGFilters.h"
#include <vector> // For easy array management
#include <numeric> // For manipulating array data

// PC serial connection
HIDScope        scope( 3 );
MODSERIAL pc(USBTX, USBRX);

//EMG inputs definieren
AnalogIn emg1_in (A1); //emg van rechterbicep, voor de x-richting
AnalogIn emg2_in (A2); //emg van linkerbicep, voor de y-richting
AnalogIn emg3_in (A3); //emg van een derde (nog te bepalen) spier, voor het vernaderen van de richting

// LED
DigitalOut      led_g(LED_GREEN);
DigitalOut      led_r(LED_RED);
DigitalOut      led_b(LED_BLUE);

// Buttons
InterruptIn button1(D11);
InterruptIn button2(D10);
InterruptIn button3(SW3);

//variablen voor EMG
double emg1;
double emg2;
double emg3;
double emg1_MVC;
double emg1_MVC_stdev;
double emg1_rest;
double emg1_rest_stdev;

vector<double> emg1_cal;


// Initialize tickers
Ticker tickSample;
Timeout timeoutCalibrationMVC;
Timeout timeoutCalibrationRest;
Ticker tickSampleCalibration;

// Sample rate
const double Fs = 500; // Sampling frequency (s)
const double Ts = 1/Fs; // Sampling time (s)

const double Tcal = 10.0f; // Calibration duration (s)

int trim_cal = 1; // Trim the beginning of the calibration vector to reduce transient behaviour by X seconds
int trim_cal_i = trim_cal * Fs - 1;

// Notch filter coefficients (iirnotch Q factor 35 @50Hz) from MATLAB in the following form:
// b01 b11 b21 a01 a11 a21
BiQuad bq_notch( 0.995636295063941,  -1.89829218816065,   0.995636295063941,  1, -1.89829218816065,   0.991272590127882);
BiQuadChain bqc_notch;

// Highpass filter coefficients (butter 4th order @10Hz cutoff) from MATLAB in the following form:
// b01 b11 b21 a01 a11 a21
// b02 b12 b22 a02 a12 a22
BiQuad bq_H1(0.922946103200875, -1.84589220640175,  0.922946103200875,  1,  -1.88920703055163,  0.892769008131025);
BiQuad bq_H2(1,                 -2,                 1,                  1,  -1.95046575793011,  0.954143234875078);
BiQuadChain bqc_high; // Used to chain two 2nd other filters into a 4th order filter

// Lowpass filter coefficients (butter 4th order @5Hz cutoff) from MATLAB in the following form:
// b01 b11 b21 a01 a11 a21
// b02 b12 b22 a02 a12 a22
BiQuad bq_L1(5.32116245737504e-08,  1.06423249147501e-07,   5.32116245737504e-08,   1,  -1.94396715039462,  0.944882378004138);
BiQuad bq_L2(1,                     2,                      1,                      1,  -1.97586467534468,  0.976794920438162);
BiQuadChain bqc_low; // Used to chain two 2nd other filters into a 4th order filter

double getMean(const vector<double> &vect)
{
    double sum = 0.0;
    int vect_n = vect.size();

    for ( int i = 0; i < vect_n; i++ ) {
        sum += vect[i];
    }
    return sum/vect_n;
}

double getStdev(const vector<double> &vect, const double vect_mean)
{
    double sum2 = 0.0;
    int vect_n = vect.size();

    for ( int i = 0; i < vect_n; i++ ) {
        sum2 += pow( vect[i] - vect_mean, 2 );
    }
    double output = sqrt( sum2 / vect_n );
    return output;
}

// Check if filters are stable
bool checkBQChainStable()
{
    bool n_stable = bqc_notch.stable();
    bool hp_stable =  bqc_high.stable();
    bool l_stable = bqc_low.stable();

    if (n_stable && hp_stable && l_stable) {
        return true;
    } else {
        return false;
    }
}


/*
// Read samples, filter samples and output to HIDScope
void sample()
{
    // Read EMG inputs
    emg1 = emg1_in.read();
    emg2 = emg2_in.read();
    emg3 = emg3_in.read();

    // Output raw EMG input
    scope.set(0, emg1 );

    // Filter notch and highpass
    double emg1_n_hp = bqc_notch_high.step( emg1 );

    // Rectify
    double emg1_rectify = fabs( emg1_n_hp );

    // Filter lowpass (completes envelope)
    double emg1_env = bqc_low.step( emg1_rectify );

    // Output EMG after filters
    scope.set(1, emg1_env );
    scope.send();
}
*/

void sampleCalibration()
{
    // Read EMG inputs
    emg1 = emg1_in.read();
    emg2 = emg2_in.read();
    emg3 = emg3_in.read();

    // Output raw EMG input
    scope.set(0, emg1 );
    
    double emg1_n = bqc_notch.step( emg1 ); // Filter notch
    scope.set(1, emg1_n);
    double emg1_hp = bqc_high.step( emg1_n ); // Filter highpass
    double emg1_rectify = fabs( emg1_hp ); // Rectify
    double emg1_env = bqc_low.step( emg1_rectify ); // Filter lowpass (completes envelope)

    // Output EMG after filters
    scope.set(2, emg1_env );
    scope.send();

    emg1_cal.push_back(emg1_env);
}

void calibrationMVCFinished()
{
    tickSampleCalibration.detach();
    
    emg1_MVC = getMean(emg1_cal);
    emg1_MVC_stdev = getStdev(emg1_cal, emg1_MVC);
    
    emg1_cal.clear();

    led_b = 1;
}

void calibrationMVC()
{
    timeoutCalibrationMVC.attach( &calibrationMVCFinished, Tcal);
    tickSampleCalibration.attach( &sampleCalibration, Ts );
    led_b = 0;
}

void calibrationRestFinished()
{
    tickSampleCalibration.detach();
    
    emg1_rest = getMean(emg1_cal);
    emg1_rest_stdev = getStdev(emg1_cal, emg1_rest);
    
    emg1_cal.clear();

    led_b = 1;
}

void calibrationRest()
{
    timeoutCalibrationRest.attach( &calibrationRestFinished, Tcal);
    tickSampleCalibration.attach( &sampleCalibration, Ts );
    led_b = 0;
}

void makeScale()
{
    double margin_percentage = 10;
    double factor1 = 1 / emg1_MVC;
    double emg1_th = emg1_rest * factor1 + margin_percentage/100;
    
    pc.printf("Factor: %f   TH: %f\r\n", factor1, emg1_th); 
}

void main()
{
    pc.baud(115200);  
    pc.printf("Starting\r\n");
    // Initialize sample ticker
    // tickSample.attach(&sample, Ts);

    // Create BQ chains to reduce computations
    bqc_notch.add( &bq_notch );
    bqc_high.add( &bq_H1 ).add( &bq_H2 );
    bqc_low.add( &bq_L1 ).add( &bq_L2 );

    led_b = 1; // Turn led off at startup
    led_g = 1;

    // If any filter chain is unstable, red led will light up
    if (checkBQChainStable) {
        led_r = 1; // LED off
    } else {
        led_r = 0; // LED on
    }

    button1.fall( &calibrationMVC );
    button2.fall( &calibrationRest );
    button3.fall( &makeScale );

    while(true) {

        // Show that system is running
        // led_g = !led_g;
        pc.printf("EMG MVC:  %f   stdev: %f\r\nEMG Rest: %f   stdev: %f\r\n", emg1_MVC, emg1_MVC_stdev, emg1_rest, emg1_rest_stdev);
        wait(0.5);
    }
}