File content as of revision 29:948b0b14f6be:

#include "mbed.h"
#include "HIDScope.h"
#include "MODSERIAL.h"
#include "biquadFilter.h"
#include "QEI.h"
#include "math.h"
#include <string> 

/*--------------------------------------------------------------------------------------------------------------------
-------------------------------- BIOROBOTICS GROUP 14 ----------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

//Define important constants in memory
#define     PI              3.14159265
#define     SAMPLE_RATE     0.002   //500 Hz EMG sample rate
#define     CONTROL_RATE    0.01    //100 Hz Control rate
#define     ENCODER1_CPR    4200    //encoders have 64 (X4), 32 (X2) counts per revolution of motor shaft
#define     ENCODER2_CPR    4200    //gearbox 1:131.25 ->  4200 counts per revolution of the output shaft (X2), 
#define     PWM_PERIOD      0.0001  //10k Hz pwm motor frequency. Higher -> too hot, lower -> motor doesnt respond correctly
/*--------------------------------------------------------------------------------------------------------------------
---- OBJECTS ---------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

MODSERIAL pc(USBTX,USBRX);      //serial communication

//Debug legs
DigitalOut red(LED_RED);
DigitalOut green(LED_GREEN);
DigitalOut blue(LED_BLUE);

//EMG shields
AnalogIn    emg1(A0);           //Analog input - Biceps EMG
AnalogIn    emg2(A1);           //Analog input - Triceps EMG
AnalogIn    emg3(A2);           //Analog input - Flexor EMG
AnalogIn    emg4(A3);           //Analog input - Extensor EMG

Ticker      sample_timer;       //Ticker for EMG sampling
Ticker      control_timer;      //Ticker for control loop
HIDScope    scope(4);           //Scope 4 channels

// AnalogIn potmeter(A4);       //potmeters
// AnalogIn potmeter2(A5);      //

//Encoders 
QEI Encoder1(D13,D12,NC,32);    //channel A and B from encoder, counts = Encoder.getPulses();
QEI Encoder2(D10,D9,NC,32);     //channel A and B from encoder, 

//Speed and Direction of motors - D4 (dir) and D5(speed) = motor 2, D7(dir) and D6(speed) = motor 1
PwmOut pwm_motor1(D6);          //PWM motor 1
PwmOut pwm_motor2(D5);          //PWM motor 2

DigitalOut dir_motor1(D7);      //Direction motor 1
DigitalOut dir_motor2(D4);      //Direction motor 2

//Limit Switches
InterruptIn shoulder_limit(D2);  //using FRDM buttons 
InterruptIn elbow_limit(D3);     //using FRDM buttons

//Other buttons
DigitalIn button1(PTA4);        //using FRDM buttons 
DigitalIn button2(PTC6);        //using FRDM buttons

/*Text colors ASCII code: Set Attribute Mode    <ESC>[{attr1};...;{attrn}m

\ 0 3 3  - ESC 
[ 3 0 m  - black
[ 3 1 m  - red
[ 3 2 m  - green
[ 3 3 m  - yellow
[ 3 4 m  - blue
[ 3 5 m  - magenta
[ 3 6 m  - cyan
[ 3 7 m  - white 
[ 0 m    - reset attributes

Put the text you want to color between GREEN_ and _GREEN
*/
string GREEN_ = "\033[32m";    //esc - green
string _GREEN = "\033[0m";     //esc - reset 


/*--------------------------------------------------------------------------------------------------------------------
---- DECLARE VARIABLES -----------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

//EMG variables: raw EMG - filtered EMG - maximum voluntary contraction
double emg_biceps; double biceps_power; double bicepsMVC = 0;
double emg_triceps; double triceps_power; double tricepsMVC = 0;
double emg_flexor; double flexor_power; double flexorMVC = 0;
double emg_extens; double extens_power; double extensMVC = 0;

int muscle;             //Muscle selector for MVC measurement
double calibrate_time;  //Elapsed time for each MVC measurement

//PID variables
double u1; double u2;                                               //Output of PID controller (PWM value for motor 1 and 2)
double m1_error=0; double m1_e_int=0; double m1_e_prev=0;           //Error, integrated error, previous error
const double m1_kp=0.001; const double m1_ki=0.0125; const double m1_kd=0.1;   //Proportional, integral and derivative gains.

double m2_error=0; double m2_e_int=0; double m2_e_prev=0;           //Error, integrated error, previous error
const double m2_kp=0.001; const double m2_ki=0.0125; const double m2_kd=0.1;   //Proportional, integral and derivative gains.

//highpass filter 20 Hz
const double high_b0 = 0.956543225556877;
const double high_b1 = -1.91308645113754;
const double high_b2 = 0.956543225556877;
const double high_a1 = -1.91197067426073;
const double high_a2 = 0.9149758348014341;
 
//notchfilter 50Hz
/*  ** Primary Filter (H1)**
Filter Arithmetic = Floating Point (Double Precision)
Architecture = IIR
Response = Bandstop
Method = Butterworth
Biquad = Yes
Stable = Yes
Sampling Frequency = 500Hz
Filter Order = 2

Band  Frequencies (Hz)    Att/Ripple (dB)       Biquad #1                                               Biquad #2

1     0, 48               0.001                 Gain = 1.000000                                         Gain = 0.973674
2     49, 51              -60.000               B = [ 1.00000000000, -1.61816176147,  1.00000000000]    B = [ 1.00000000000, -1.61816176147,  1.00000000000]
3     52, 250             0.001                 A = [ 1.00000000000, -1.58071559235,  0.97319685401]    A = [ 1.00000000000, -1.61244708381,  0.97415116257]
*/

//biquad 1
const double notch1gain = 1.000000;
const double notch1_b0 = 1;
const double notch1_b1 = -1.61816176147 * notch1gain;
const double notch1_b2 = 1.00000000000 * notch1gain;
const double notch1_a1 = -1.58071559235 * notch1gain;
const double notch1_a2 = 0.97319685401 * notch1gain;
 
//biquad 2
const double notch2gain = 0.973674;
const double notch2_b0 = 1 * notch2gain;
const double notch2_b1 = -1.61816176147 * notch2gain;
const double notch2_b2 = 1.00000000000 * notch2gain;
const double notch2_a1 = -1.61244708381 * notch2gain;
const double notch2_a2 = 0.97415116257 * notch2gain;
 
//lowpass filter 7 Hz  - envelope
const double low_b0 = 0.000119046743110057;
const double low_b1 = 0.000238093486220118;
const double low_b2 = 0.000119046743110057;
const double low_a1 = -1.968902268531908;
const double low_a2 = 0.9693784555043481;

//Forward and Inverse Kinematics
const double l1 = 0.25; const double l2 = 0.25;
double current_x; double current_y;
double theta1; double theta2;
double dtheta1; double dtheta2;
double rpc;
double x; double y;
double x_error; double y_error;
double costheta1; double sintheta1;
double costheta2; double sintheta2;

/*--------------------------------------------------------------------------------------------------------------------
---- Filters ---------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

//Using biquadFilter library
//Syntax: biquadFilter     filter(a1, a2, b0, b1, b2); coefficients. Call with: filter.step(u), with u signal to be filtered.
//Biceps
biquadFilter     highpass( high_a1 , high_a2 , high_b0 , high_b1 , high_b2 );               // removes DC and movement artefacts
biquadFilter     notch1( notch1_a1 , notch1_a2 , notch1_b0 , notch1_b1 , notch1_b2 );       // removes 49-51 Hz power interference
biquadFilter     notch2( notch2_a1 , notch2_a2 , notch2_b0 , notch2_b1 , notch2_b2 );       //
biquadFilter     lowpass( low_a1 , low_a2 , low_b0 , low_b1 , low_b2 );                     // EMG envelope    

//Triceps
biquadFilter     highpass2( high_a1 , high_a2 , high_b0 , high_b1 , high_b2 );               // removes DC and movement artefacts
biquadFilter     notch1_2( notch1_a1 , notch1_a2 , notch1_b0 , notch1_b1 , notch1_b2 );      // removes 49-51 Hz power interference
biquadFilter     notch2_2( notch2_a1 , notch2_a2 , notch2_b0 , notch2_b1 , notch2_b2 );      //
biquadFilter     lowpass2( low_a1 , low_a2 , low_b0 , low_b1 , low_b2 );                     // EMG envelope    

//Flexor
biquadFilter     highpass3( high_a1 , high_a2 , high_b0 , high_b1 , high_b2 );               // removes DC and movement artefacts
biquadFilter     notch1_3( notch1_a1 , notch1_a2 , notch1_b0 , notch1_b1 , notch1_b2 );      // removes 49-51 Hz power interference
biquadFilter     notch2_3( notch2_a1 , notch2_a2 , notch2_b0 , notch2_b1 , notch2_b2 );      //
biquadFilter     lowpass3( low_a1 , low_a2 , low_b0 , low_b1 , low_b2 );                     // EMG envelope    

//Extensor
biquadFilter     highpass4( high_a1 , high_a2 , high_b0 , high_b1 , high_b2 );               // removes DC and movement artefacts
biquadFilter     notch1_4( notch1_a1 , notch1_a2 , notch1_b0 , notch1_b1 , notch1_b2 );      // removes 49-51 Hz power interference
biquadFilter     notch2_4( notch2_a1 , notch2_a2 , notch2_b0 , notch2_b1 , notch2_b2 );      //
biquadFilter     lowpass4( low_a1 , low_a2 , low_b0 , low_b1 , low_b2 );                     // EMG envelope    

//PID filter (lowpass ??? Hz)
biquadFilter     derfilter( low_a1 , low_a2 , low_b0 , low_b1 , low_b2 );   // derivative filter

/*--------------------------------------------------------------------------------------------------------------------
---- DECLARE FUNCTION NAMES ------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

void sample_filter(void);   //Sampling and filtering
void control();             //Control - reference -> error -> pid -> motor output
void calibrate_emg();       //Instructions + measurement of MVC of each muscle 
void emg_mvc();             //Helper funcion for storing MVC value
void calibrate_arm(void);   //Calibration of the arm with limit switches
void start_sampling(void);  //Attaches the sample_filter function to a 500Hz ticker
void stop_sampling(void);   //Stops sample_filter
void start_control(void);   //Attaches the control function to a 100Hz ticker
void stop_control(void);    //Stops control function

//Keeps the input between min and max value
void keep_in_range(double * in, double min, double max);

//Reusable PID controller, previous and integral error need to be passed by reference
double pid(double error, double kp, double ki, double kd,double &e_int, double &e_prev);

//Menu functions
void mainMenu();
void caliMenu();
void controlMenu();
void controlButtons();
void clearTerminal();
void emgInstructions();
void titleBox();


/*--------------------------------------------------------------------------------------------------------------------
---- MAIN LOOP -------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

int main()
{
    pc.baud(115200);            //serial baudrate
    red=1; green=1; blue=1;     //Make sure debug LEDS are off  
    
    //Set PwmOut frequency to 10k Hz
    //pwm_motor1.period(PWM_PERIOD);    
    //pwm_motor2.period(PWM_PERIOD);
    
    clearTerminal();            //Clear the putty window
    
    // make a menu, user has to initiate next step
    titleBox();
    mainMenu();
    //caliMenu();            // Menu function
    //calibrate_arm();        //Start Calibration
    
    //calibrate_emg();        
    
    
    x=0.5; y=0;
    //start_control();        //100 Hz control
    
    //maybe some stop commands when a button is pressed: detach from timers.
    //stop_control();
    start_sampling();
    wait(60);
    //char c;
    
    
    
    char command;
    
    while(command != 'Q' && command != 'q')
    {
        if(pc.readable()){
            command = pc.getc();
            
            switch(command){
            
            case 'c':
            case 'C':
                pc.printf("\n\r => You chose calibration.\r\n\n");
                caliMenu();
                
                char command2=0;
                
                while(command2 != 'B' && command2 != 'b'){
                    command2 = pc.getc();
                switch(command2){
                 case 'a':
                 case 'A':
                  pc.printf("\n\r => Arm Calibration Starting... please wait \n\r");
                  calibrate_arm();
                  wait(1);
                  caliMenu();
                 break;
                 
                 case 'e':  
                 case 'E':   
                   pc.printf("\n\r => EMG Calibration Starting... please wait \n\r"); 
                   wait(1);
                   emgInstructions();
                   calibrate_emg(); 
                   pc.printf("\n\r ------------------------ \n\r"); 
                   pc.printf("\n\r EMG Calibration complete \n\r"); 
                   pc.printf("\n\r ------------------------ \n\r"); 
                   caliMenu(); 
                  break;
                  
                 case 'b':
                 case 'B':
                    pc.printf("\n\r => Going back to main menu.. \n\r"); 
                    mainMenu();
                    break;
                }//end switch
                
                }//end while
                break;
            case 's':
            case 'S':
                pc.printf("=> You chose control \r\n\n");
                wait(1);
                start_sampling();
                wait(1);
                start_control();
                wait(1);   
                controlButtons();
                break;
            case 'R':
                red=!red;
                pc.printf("=> Red LED triggered \n\r");
                break;
            case 'G':
                green=!green;
                pc.printf("=> Green LED triggered \n\r");
                break;
            case 'B':
                blue=!blue;
                pc.printf("=> Blue LED triggered \n\r");
                break;
            case 'q':
            case 'Q':
              
                break;
            default:
                pc.printf("=> Invalid Input \n\r");
                break;
            } //end switch
        } // end if pc readable
    
    } // end while loop
    

    
    //When end of while loop reached (user chose quit program) - detach all timers and stop motors.

    pc.printf("\r\n------------------------------ \n\r");
    pc.printf("Program Offline \n\r");
    pc.printf("Reset to start\r\n");
    pc.printf("------------------------------ \n\r");
}
//end of main

/*--------------------------------------------------------------------------------------------------------------------
---- FUNCTIONS -------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

void controlButtons()
{
    controlMenu();
    char c=0;
    while(c != 'Q' && c != 'q') {
    
    if( pc.readable() ){
        c = pc.getc();
        switch (c) 
            {
            case '1' :  
                     x = x + 0.01; 
                     //controlMenu();
                     //running=false;
                     break;
          
            case '2' :
                     x-=0.01;
                     //controlMenu();
                     //running=false;
                     break;
                    
            case '3' :
                     y+=0.01;
                     //controlMenu();
                     //running=false;
                     break;
                     
          
            case '4' :
                     y-=0.01;
                     //controlMenu();                    
                     //running=false;
                     break;
                     
            case 'q' :
            case 'Q' :
                      pc.printf("=> Quitting control... \r\n"); wait(1);
                      stop_sampling();
                      stop_control();
                      pwm_motor1=0; pwm_motor2=0;
                      pc.printf("Sampling and Control detached \n\r"); wait(1);
                      pc.printf("Returning to Main Menu \r\n\n"); wait(1);
                      mainMenu();
                      
                      //running = false;                    
                      break;
    }//end switch
    if(c!='q' && c!='Q'){
    pc.printf("Reference position: %f and %f \r\n",x,y);
    pc.printf("Current position: %f and %f \r\n",current_x,current_y);
    pc.printf("Current angles: %f and %f \r\n",theta1,theta2);
    pc.printf("Error in angles: %f and %f \r\n",dtheta1,dtheta2);
    pc.printf("PID output: %f and %f \r\n",u1,u2);
    pc.printf("----------------------------------------\r\n\n");
    }
    }
    //end if
    }
    //end of while loop
    }

//Sample and Filter  
void sample_filter(void)
{
    double emg_biceps = emg1.read();    //Biceps
    double emg_triceps = emg2.read();    //Triceps
    double emg_flexor = emg3.read();    //Flexor
    double emg_extens = emg4.read();    //Extensor
    
    //Filter: high-pass -> notch -> rectify -> lowpass or moving average
    // Can we use same biquadFilter (eg. highpass) for other muscles or does each muscle need its own biquad?
    biceps_power = highpass.step(emg_biceps); triceps_power = highpass2.step(emg_triceps); flexor_power = highpass3.step(emg_flexor); extens_power = highpass4.step(emg_extens);
    biceps_power = notch1.step(biceps_power); triceps_power = notch1_2.step(triceps_power); flexor_power = notch1_3.step(flexor_power); extens_power = notch1_4.step(extens_power);
    biceps_power = notch2.step(biceps_power); triceps_power = notch2_2.step(triceps_power); flexor_power = notch2_3.step(flexor_power); extens_power = notch2_4.step(extens_power);
    biceps_power = abs(biceps_power); triceps_power = abs(triceps_power); flexor_power = abs(flexor_power); extens_power = abs(extens_power);
    biceps_power = lowpass.step(biceps_power); triceps_power = lowpass2.step(triceps_power); flexor_power = lowpass3.step(flexor_power); extens_power = lowpass4.step(extens_power);
    
    scope.set(0,emg_biceps);
    scope.set(1,biceps_power);
    scope.set(2,biceps_power);
    scope.set(3,biceps_power);
    scope.send();
    /* alternative for lowpass filter: moving average
    window=30;                      //30 samples
    int i=0;                        //buffer index
    bicepsbuffer[i]=biceps_power    //fill array
    
    i++;                             
    if(i==window){
        i=0;
    }
    
    for(int x = 0; x < window; x++){
        avg1 += bicepsbuffer[x];
        }
    avg1 = avg1/window;    
    */
    
}

void controlMenu()
{
         //Title Box
   pc.putc(201); 
   for(int j=0;j<33;j++){
   pc.putc(205);
   }
   pc.putc(187); 
   pc.printf("\n\r");
   pc.putc(186); pc.printf("          Control Menu           "); pc.putc(186);
   pc.printf("\n\r");
   pc.putc(200);
   for(int k=0;k<33;k++){
   pc.putc(205);
   }
   pc.putc(188); 
   
   pc.printf("\n\r");
   //endbox
     pc.printf("1) Move Arm Left\r\n");
     pc.printf("2) Move Arm Right\r\n");
     pc.printf("3) Move Arm Up\r\n");
     pc.printf("4) Move Arm Down\r\n");
     pc.printf("q) Exit \r\n");
     pc.printf("Please make a choice => \r\n");
}

//Send arm to mechanical limits, and set encoder to 0. Then send arm to starting position.
void calibrate_arm(void)
{
    pc.printf("Calibrate_arm() entered\r\n");
    bool calibrating = true;
    bool done1 = false;
    bool done2 = false;
    pc.printf("To start arm calibration, press any key =>");
    pc.getc();
    pc.printf("\r\n Calibrating... \r\n");
    dir_motor1=1;   //cw
    dir_motor2=0;   //cw
    pwm_motor1.write(0.2);     //move upper arm slowly cw
       
    
    while(calibrating){
        red=0; blue=0;              //Debug light is purple during arm calibration
        
        if(done1==true){
            pwm_motor2.write(0.2);     //move forearm slowly cw
        }
        
        //when limit switches are hit, stop motor and reset encoder
        if(shoulder_limit.read() < 0.5){   //polling 
            pwm_motor1.write(0);
            Encoder1.reset();
            done1 = true;
            pc.printf("Shoulder Limit hit - shutting down motor 1\r\n");
        }
        if(elbow_limit.read() < 0.5){     //polling
            pwm_motor2.write(0);
            Encoder2.reset();
            done2 = true;
            pc.printf("Elbow Limit hit - shutting down motor 2. \r\n");
        }    
        if(done1 && done2){
            calibrating=false;      //Leave while loop when both limits are reached
            red=1; blue=1;          //Turn debug light off when calibration complete
        }
   
    }//end while
    
    //TO DO:
    //mechanical angle limits -> pulses. If 40 degrees -> counts = floor( 40 / (2*pi/4200) )
    //Encoder1.setPulses(100);       //edited QEI library: added setPulses()
    //Encoder2.setPulses(100);       //edited QEI library: added setPulses()
    //pc.printf("Elbow Limit hit - shutting down motor 2. Current pulsecount: %i \r\n",Encoder1.getPulses());
    wait(1);
    pc.printf("\n\r ------------------------ \n\r"); 
    pc.printf("Arm Calibration Complete\r\n");
    pc.printf(" ------------------------ \n\r"); 

}

//EMG Maximum Voluntary Contraction measurement
void emg_mvc()
{  
    //double sampletime=0;
    //sampletime=+SAMPLE_RATE;
    //
    // if(sampletime<5)
    //int muscle=1;
    //for(int index=0; index<2500;index++){   //measure 5 seconds@500hz = 2500 samples
     
        if(muscle==1){
            
            if(biceps_power>bicepsMVC){
            //printf("+ ");
            printf("%s+ %s",GREEN_,_GREEN);
            bicepsMVC=biceps_power;
            }    
            else
            printf("- ");
        }  
        
        if(muscle==2){
            
            if(triceps_power>tricepsMVC){
            printf("%s+ %s",GREEN_,_GREEN);
            tricepsMVC=triceps_power;
            }    
            else
            printf("- ");
        }
        
        if(muscle==3){
            
            if(flexor_power>flexorMVC){
            printf("%s+ %s",GREEN_,_GREEN);    
            flexorMVC=flexor_power;
            }    
            else
            printf("- ");
        }
        
        if(muscle==4){
            
            if(extens_power>extensMVC){
            printf("%s+ %s",GREEN_,_GREEN);    
            extensMVC=extens_power;
            }    
            else
            printf("- ");
        }
        
    //}
    calibrate_time = calibrate_time + 0.002;
    
    
   
}

//EMG calibration
void calibrate_emg()
{
   Ticker timer;
   
   pc.printf("Testcode calibration \r\n");
   wait(1);
   pc.printf("+ means current sample is higher than stored MVC\r\n");
   pc.printf("- means current sample is lower than stored MVC\r\n");
   wait(2);
   pc.printf("\r\n----------------\r\n "); 
   pc.printf(" Biceps is first.\r\n "); 
   pc.printf("----------------\r\n "); 
   wait(1);
   pc.printf(" Press any key to begin... "); wait(1);
   char input;
   input=pc.getc();
   pc.putc(input);
   pc.printf(" \r\n  Starting in 3... \r\n"); wait(1);
   pc.printf(" \r\n  Starting in 2... \r\n"); wait(1);
   pc.printf(" \r\n  Starting in 1... \r\n"); wait(1);
   
   start_sampling();
   muscle=1;
   timer.attach(&emg_mvc,SAMPLE_RATE);
   wait(5);
   timer.detach();
  
   pc.printf("\r\n Measurement complete."); wait(1);
   pc.printf("\r\n Biceps MVC = %f \r\n",bicepsMVC); wait(1);
      pc.printf("Calibrate_emg() exited \r\n"); wait(1);
   pc.printf("Measured time: %f seconds \r\n\n",calibrate_time);
   calibrate_time=0;
   
   // Triceps:
   muscle=2;
   pc.printf("\r\n----------------\r\n "); 
   pc.printf(" Triceps is next.\r\n "); 
   pc.printf("----------------\r\n "); 
   wait(1);

   pc.printf(" Press any key to begin... "); wait(1);
   input=pc.getc();
   pc.putc(input);
   pc.printf(" \r\n  Starting in 3... \r\n"); wait(1);
   pc.printf(" \r\n  Starting in 2... \r\n"); wait(1);
   pc.printf(" \r\n  Starting in 1... \r\n"); wait(1);
   start_sampling();
   muscle=1;
   timer.attach(&emg_mvc,0.002);
   wait(5);
   timer.detach();
   pc.printf("\r\n Triceps MVC = %f \r\n",tricepsMVC);
   
   pc.printf("Calibrate_emg() exited \r\n");
   pc.printf("Measured time: %f seconds \r\n",calibrate_time);
   calibrate_time=0;
   
   //Flexor:
   muscle=3;
   //Extensor:
   muscle=4;
   
   //Stop sampling, detach ticker
   stop_sampling();
   
}


//Input error and Kp, Kd, Ki, output control signal
double pid(double error, double kp, double ki, double kd,double &e_int, double &e_prev)
{
    // Derivative
    double e_der = (error-e_prev)/ CONTROL_RATE;
    e_der = derfilter.step(e_der);
    e_prev = error;
    // Integral
    e_int = e_int + CONTROL_RATE * error;
    // PID
    return kp*error + ki*e_int + kd * e_der;
 
}

//Analyze filtered EMG, calculate reference position from EMG, compare reference position with current position,convert to angles, send error through pid(), send PWM and DIR to motors 
void control()
{
    //analyze emg (= velocity, averages?)
    
    //calculate reference position based on the average emg (integrate)
    
    //Current position - Encoder counts -> current angle -> Forward Kinematics 
    rpc=(2*PI)/ENCODER1_CPR;               //radians per count (resolution) - 2pi divided by 4200
    theta1 = Encoder1.getPulses() * rpc;   //multiply resolution with number of counts
    theta2 = Encoder2.getPulses() * rpc;
    current_x = l1 * cos(theta1) + l2 * cos(theta1 + theta2);
    current_y = l1 * sin(theta1) + l2 * sin(theta1 + theta2);
    
    //pc.printf("Calculated current position: x = %f and y = %f \r\n",current_x,current_y);
    
    
    //pc.printf("X is %f and Y is %f \r\n",x,y);
        
    //calculate error (refpos-currentpos) currentpos = forward kinematics
    x_error = x - current_x;
    y_error = y - current_y;
    
    //pc.printf("X error is %f and Y error is %f \r\n",x_error,y_error);
    
    //inverse kinematics (refpos to refangle)
    
    costheta2 = (pow(x,2) + pow(y,2) - pow(l1,2) - pow(l2,2)) / (2*l1*l2) ;
    sintheta2 = sqrt( 1 - pow(costheta2,2) );
     
    //pc.printf("costheta2 = %f and sostheta2 = %f \r\n",costheta2,sostheta2);
    
    dtheta2 = atan2(sintheta2,costheta2);
    
    costheta1 = ( x * (l1 + l2 * costheta2) + y * l2 * sintheta2 ) / ( pow(x,2) + pow(y,2) );
    sintheta1 = sqrt( 1 - pow(costheta1,2) );
    
    //pc.printf("costheta1 = %f and sostheta1 = %f \r\n",costheta1,sostheta1);
    
    dtheta1 = atan2(sintheta1,costheta1);
    
    
    //Angle error
    
    m1_error = dtheta1-theta1;
    m2_error = dtheta2-theta2;
    
    //pc.printf("m1 error is %f and m2 error is %f \r\n",m1_error,m2_error);
    
    //PID controller
    
    u1=pid(m1_error,m1_kp,m1_ki,m1_kd,m1_e_int,m1_e_prev);    //motor 1
    u2=pid(m2_error,m2_kp,m2_ki,m2_kd,m2_e_int,m2_e_prev);    //motor 2
    
    keep_in_range(&u1,-0.6,0.6);    //keep u between -1 and 1, sign = direction, PWM = 0-1
    keep_in_range(&u2,-0.6,0.6);
    
    //send PWM and DIR to motor 1
    dir_motor1 = u1>0 ? 1 : 0;          //conditional statement dir_motor1 = [condition] ? [if met 1] : [else 0]], same as if else below. 
    pwm_motor1.write(abs(u1));
    
    //send PWM and DIR to motor 2
    dir_motor2 = u2>0 ? 0 : 1;          //conditional statement, same as if else below
    pwm_motor2.write(abs(u2));
    
    /*if(u1 > 0)
    {
        dir_motor1 = 0;
    else{
        dir_motor1 = 1;
        }
    }    
    pwm_motor1.write(abs(u1));
    
  
    if(u2 > 0)
    {
        dir_motor1 = 1;
    else{
        dir_motor1 = 0;
        }
    }    
    pwm_motor1.write(abs(u2));*/
    
}

void mainMenu()
{
       //Title Box
   pc.putc(201); 
   for(int j=0;j<33;j++){
   pc.putc(205);
   }
   pc.putc(187); 
   pc.printf("\n\r");
   pc.putc(186); pc.printf("            Main Menu            "); pc.putc(186);
   pc.printf("\n\r");
   pc.putc(200);
   for(int k=0;k<33;k++){
   pc.putc(205);
   }
   pc.putc(188); 
   
   pc.printf("\n\r");
   //endbox
   wait(1);
   pc.printf("[C]alibration\r\n"); wait(0.2);
   pc.printf("[S]tart Control with buttons\r\n"); wait(0.2);
   pc.printf("[Q]uit Robot Program\r\n"); wait(0.2);
   pc.printf("[R]ed LED\r\n"); wait(0.2); 
   pc.printf("[G]reen LED\r\n"); wait(0.2);
   pc.printf("[B]lue LED\r\n"); wait(0.2);
   pc.printf("Please make a choice => \r\n");
}

//Start sampling
void start_sampling(void)
{
    sample_timer.attach(&sample_filter,SAMPLE_RATE);   //500 Hz EMG 
    
    //Debug LED will be green when sampling is active
    green=0;    
    pc.printf("||- started sampling -|| \r\n");
}

//stop sampling
void stop_sampling(void)
{
    sample_timer.detach();
    
    //Debug LED will be turned off when sampling stops
    green=1;
    pc.printf("||- stopped sampling -|| \r\n");
}

//Start control
void start_control(void)
{
    control_timer.attach(&control,CONTROL_RATE);     //100 Hz control
    
    //Debug LED will be blue when control is on. If sampling and control are on -> blue + green = cyan.
    blue=0;
    pc.printf("||- started control -|| \r\n");
}

//stop control
void stop_control(void)
{
    control_timer.detach();
    
    //Debug LED will be off when control is off
    blue=1;
    pc.printf("||- stopped control -|| \r\n");
}


void calibrate()
{

}

//Clears the putty (or other terminal) window
void clearTerminal()
{
   pc.putc(27); 
   pc.printf("[2J"); // clear screen 
   pc.putc(27); // ESC 
   pc.printf("[H"); // cursor to home 
}

void caliMenu(){
     
        //Title Box
   pc.putc(201); 
   for(int j=0;j<33;j++){
   pc.putc(205);
   }
   pc.putc(187); 
   pc.printf("\n\r");
   pc.putc(186); pc.printf("         Calibration Menu        "); pc.putc(186);
   pc.printf("\n\r");
   pc.putc(200);
   for(int k=0;k<33;k++){
   pc.putc(205);
   }
   pc.putc(188); 
   
   pc.printf("\n\r");
   //endbox
     
     pc.printf("[A]rm Calibration\r\n");
     pc.printf("[E]MG Calibration\r\n");
     pc.printf("[B]ack to main menu\r\n");
     pc.printf("Please make a choice => \r\n");
    
}

void titleBox(){
     
  //Title Box
   pc.putc(201); 
   for(int j=0;j<33;j++){
   pc.putc(205);
   }
   pc.putc(187); 
   pc.printf("\n\r");
   pc.putc(186); pc.printf("    BioRobotics M9 - Group 14    "); pc.putc(186);
   pc.printf("\n\r");
   pc.putc(186); pc.printf("         Robot powered ON        "); pc.putc(186);
   pc.printf("\n\r");
   pc.putc(200);
   for(int k=0;k<33;k++){
   pc.putc(205);
   }
   pc.putc(188); 
   
   pc.printf("\n\r");
   //endbox
}

void emgInstructions(){
    pc.printf("\r\nPrepare the skin before applying electrodes: \n\r"); wait(1);
    pc.printf("-> Shave electrode locations if needed and clean with alcohol \n\r"); wait(1);
    pc.printf("\n\r Relax for a few minutes after electrodes are placed and check if EMG signal looks normal \n\r "); wait(1);
    pc.printf("\n\r To calibrate the EMG signals we will measure the Maximum Voluntary Contraction of each muscle \n\r"); wait(1);
    pc.printf("You will need to flex the mentioned muscle as much as possible for 5 seconds \n\r"); wait(1);
    pc.printf("The measurement will begin once you confirm you're ready [Hit any key] \n\r \n\r"); wait(1);
}

//keeps input limited between min max
void keep_in_range(double * in, double min, double max)
{
    *in > min ? *in < max? : *in = max: *in = min;
}