File content as of revision 64:21fbff25d80b:

#include "mbed.h"
#include "HIDScope.h"
#include "MODSERIAL.h"
#include "biquadFilter.h"
#include "Servo.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     SERVO_RATE      0.05    //50 Hz Servo Control rate
#define     ENCODER_CPR     4200    //both motor encoders have 64 (X4), 32 (X2) counts per revolution of motor shaft
                                    //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 LEDs
DigitalOut red(LED_RED);
DigitalOut green(LED_GREEN);
DigitalOut blue(LED_BLUE);

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

Ticker      sample_timer;       //Ticker for EMG sampling
Ticker      control_timer;      //Ticker for control loop
Ticker      servo_timer;        //Ticker for servo control
Ticker      debug_timer;        //Ticker for debug printf

//Turn hidscope off if not needed anymore
//HIDScope    scope(2);         //Scope 4 channels

//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
Servo servoPwm(D11);            //PWM servomotor     

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

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

//Other buttons
InterruptIn debugbtn(PTA4);     //using FRDM buttons - debug on or off 
DigitalIn button2(PTC6);        //using FRDM buttons - not used

/*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 -----------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/
//Debugging on or off
volatile bool debug = true; //default is on

//EMG variables: raw EMG - filtered EMG - maximum voluntary contraction - max amplitude during relaxation. 
double emg_biceps; double biceps_power; double bicepsMVC = 0; double bicepsmin=0;  
double emg_triceps; double triceps_power; double tricepsMVC = 0; double tricepsmin=0;
double emg_flexor; double flexor_power; double flexorMVC = 0; double flexormin=0;
double emg_extens; double extens_power; double extensMVC = 0; double extensmin=0;

//Normalize and compare variables
double biceps, triceps, flexor, extens;         //Storage for normalized emg
double xdir, ydir;                              //EMG reference position directions
double xpower, ypower;                          //EMG reference magnitude
double dx, dy;                                  //Integral
double emg_control_time;                        //Elapsed time in EMG control

//Threshold moving average window
const int window=30;                            //30 samples
int i=0;                                        //movavg array index 
double movavg1[window];                         //moving average arrays with size of window
double movavg2[window];
double movavg3[window];
double movavg4[window];
double biceps_avg, triceps_avg,flexor_avg, extens_avg;  //sum divided by window size

int muscle;             //Muscle selector for MVC measurement, 1 = first emg etc.
double calibrate_time;  //Elapsed time for each 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 motor 1
const double m1_kp=1; const double m1_ki=0.01; const double m1_kd=0.05;       //Proportional, integral and derivative gains.

double m2_error=0; double m2_e_int=0; double m2_e_prev=0;                     //Error, integrated error, previous error motor 2
const double m2_kp=1; const double m2_ki=0.01; const double m2_kd=0.05;       //Proportional, integral and derivative gains.

//Calibration bools, checks if elbow/shoulder limits are hit and if calibration is complete
volatile bool done1 = false;
volatile bool done2 = false;
volatile bool calibrating = false;

//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
/* 
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;

//Derivative lowpass filter 60 Hz  - remove derivative error noise
const double derlow_b0 = 0.027859766117136;
const double derlow_b1 = 0.0557195322342721;
const double derlow_b2 = 0.027859766117136;
const double derlow_a1 = -1.47548044359265;
const double derlow_a2 = 0.58691950806119;

//Forward Kinematics
const double l1 = 0.25; const double l2 = 0.25;     //Arm lengths
double current_x; double current_y;                 //Current position
double theta1; double theta2; double theta3;        //Current angles
double deltatheta1; double deltatheta2;             //Change in angles compared to mechanical lower limit - for servo
double servopos;                                    //servo position in usec
double rpc;                                         //Encoder resolution: radians per count

//Reference position
double x; double y;

//Select whether to use Trig (1) or DLS method (2), emg control true or false
int control_method;
bool emg_control;

//Inverse Kinematics - Trig / Gonio method. 
//First convert reference position to angle needed, then compare that angle to current angle.
double reftheta1; double reftheta2;                 //reference angles
double costheta1; double sintheta1;                 //helper variables
double costheta2; double sintheta2;                 //    

//Inverse Kinematics - Damped least squares method. 
//Angle error is directly calculated from position error: dq = [DLS matrix] * position_error
                                                    //             |DLS1 DLS2|
double dls1, dls2, dls3, dls4;                      //DLS matrix:  |DLS3 DLS4|
double q1_error, q2_error;                          //Angle errors
double x_error, y_error;                            //Position errors
double lambda=0.1;                                  //Damping constant
double powlambda2, powlambda4;                      //helper variables to reduce calculation time
double powl1, powl2;                                //
double sintheta1theta2, costheta1theta2;            //

//Mechanical Limits (pulse counts and radians)
int theta1_cal, theta2_cal;                         //Pulse counts at mechanical limits.  
double theta1_lower=0.698132, theta1_upper=2.35619; //motor1: lower limit 40 degrees, upper limit 135
double theta2_lower=0.750492, theta2_upper=2.40855; //motor2: lower limit 43 degrees, upper limit 138 degrees.

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

//Using biquadFilter library
//Syntax: biquadFilter     filter(a1, a2, b0, b1, b2); coefficients. Call with: filter.step(u), with u signal to be filtered.
//Each biquadFilter object can only be used by one signal - memory variables are unique for each emg. 
//This means 4 biquads for each muscle.
//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 60 Hz, 6*crossoverfreq)
biquadFilter     derfilter1( derlow_a1 , derlow_a2 , derlow_b0 , derlow_b1 , derlow_b2 );   // derivative filter
biquadFilter     derfilter2( derlow_a1 , derlow_a2 , derlow_b0 , derlow_b1 , derlow_b2 );   // derivative filter

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

void sample_filter(void);   //Sampling and filtering
void control();             //Control loop - reference -> error -> pid -> motor output
void servo_control();       //Mouse alignment feed forward for servo
void calibrate_emg();       //Instructions + measurement of Min and MVC of each muscle 
void emg_mvc();             //Helper funcion for storing MVC value
void emg_min();             //Helper function for storing Min 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 and the servo_control to a 50Hz ticker
void stop_control(void);    //Stops control and servo control 

//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. 
//Need two because of different derivative filter biquads.
double pid(double error, double kp, double ki, double kd,double &e_int, double &e_prev);
double pid2(double error, double kp, double ki, double kd,double &e_int, double &e_prev);

//Menu functions
void debugging();           //Prints useful debug parameters if debugging is turned on.
void debug_trigger();       //Triggers debug on or off - attach to 1 hz ticker
void mainMenu();            //Prints the main menu
void caliMenu();            //Prints the calibration menu
void controlMenu();         //Prints the control menu with WASD button control
void controlButtons();      //
void clearTerminal();       //Clears the putty window
void emgInstructions();     //Optional - prints instructions for preparing the skin for EMG
void titleBox();            //Prints a fancy box. To view correctly putty translation-character set needs to be set to CP437.

//Limit switches - power off motors if switches hit (rising edge interrupt)
void calibrate(void);       //Rotates arm clockwise slowly untill switches are hit
void shoulder();            //Functions attached to buttons - when hit: encoder pulses are set to mechanical limit angles and motor turned off.
void elbow();               //

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

int main()
{
    pc.baud(115200);            //serial baudrate
    red=1; green=1; blue=1;     //Make sure debug LEDs are off  
    
    servoPwm.Enable(602,20000); //Start position servo, PWM period in usecs
    
    //Set PwmOut frequency to 50 Hz
    pwm_motor1.period(0.02);    
    pwm_motor2.period(0.02);
    
    debugbtn.fall(&debug_trigger);  //turn debug printf's on or off
    
    clearTerminal();            //Clear the putty window
    
    // make a menu, user has to initiate next step
    titleBox();
    mainMenu();
       
    char command=0;
    //Main menu:
    while(command != 'Q' && command != 'q')
    {
        if(pc.readable()){
            command = pc.getc();
            
            switch(command){
            
            //User chooses 'c'
            case 'c':
            case 'C': {
                pc.printf("\n\r => You chose calibration.\r\n\n");
                caliMenu();
                
                char command2=0;
             //Calibration menu:   
             while(command2 != 'B' && command2 != 'b'){
                command2 = pc.getc();
                switch(command2){
                 //user chooses 'a'
                 case 'a':
                 case 'A':
                  pc.printf("\n\r => Arm Calibration Starting... please wait \n\r");
                  calibrate_arm(); wait(1);
                  caliMenu();
                 break;
                 //user chooses 'e'
                 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;
                 //user chooses 'b' 
                 case 'b':
                 case 'B':
                    pc.printf("\n\r => Going back to main menu.. \n\r"); 
                    mainMenu();
                    break;
                }//end switch
                
             }//end while
             break;
            }//end case c C
            
            //user chooses 't'
            case 't':
            case 'T':
                pc.printf("=> You chose TRIG button control \r\n\n"); wait(1);
                emg_control=false;
                control_method=1;
                start_control(); wait(1);
                if(debug)
                {
                    debug_timer.attach(&debugging,1);
                }   
                controlButtons();
                break;
            //user chooses 'd'
            case 'd':
            case 'D':
                pc.printf("=> You chose DLS button control \r\n\n"); wait(1);
                emg_control=false;
                control_method=2;
                start_control(); wait(1);
                if(debug)
                {
                    debug_timer.attach(&debugging,1);
                }    
                controlButtons();
                break;    
            //user chooses 'e'
            case 'e':
            case 'E':
                pc.printf("=> You chose EMG DLS control \r\n\n"); wait(1);
                start_sampling(); wait(1);
                emg_control_time = 0;
                emg_control=true;
                control_method=2;
                start_control(); wait(1);   
             
                controlButtons();
                
                break;        
            //user chooses 'q'
            case 'q':
            case 'Q':
              
                break;
            //other inputs 
            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).

    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 -------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------*/

//Debug function: prints important variables to check if things are calculating correctly - find errors
void debug_trigger(){
    debug=!debug;
    printf("Debug triggered: %s \r\n", debug ? "ON" : "OFF");
}

void debugging()
{
    if(debug==true){
    //Choose which debugging values to show:
    pc.printf("\r\nRef pos: %f and %f \r\n",x,y);
    pc.printf("Cur pos: %f and %f \r\n",current_x,current_y);
    //pc.printf("Pos Error: %f and %f \r\n",x_error,y_error);
    //pc.printf("Cur angles: %f and %f \r\n",theta1,theta2);
    //pc.printf("DLS1: %f and DLS2 %f and DLS3 %f and DLS4: %f \r\n",dls1,dls2,dls3,dls4);
    //pc.printf("Error angles: %f and %f \r\n",m1_error,m2_error);
    pc.printf("PID output: %f and %f \r\n",u1,u2);
    pc.printf("----------------------------------------\r\n");
    pc.printf("Buffer1: %f \r\n",biceps_avg);                
    pc.printf("Buffer2: %f \r\n",triceps_avg);
    pc.printf("Buffer3: %f \r\n",flexor_avg);
    pc.printf("Buffer4: %f \r\n",extens_avg);
    //pc.printf("----------------------------------------\r\n");
    //pc.printf("Theta3: %f \r\n",theta3);
    //pc.printf("Servopos us: %f \r\n",servopos);
    pc.printf("----------------------------------------\r\n");
    
    }
}

//Calculates how much servo needs to move to keep mouse aligned
void servo_control(){
    //Servo alignment
    //When shoulder or elbow angle increases from starting position --> servo needs to turn counterclockwise to keep mouse aligned.
    deltatheta1 = theta1 - theta1_lower;
    deltatheta2 = theta2 - theta2_lower;
    theta3 = deltatheta1 + deltatheta2;
    servopos = (2100/PI)*theta3 + 600;
    servoPwm.SetPosition(servopos);
    
}   

//Use WASD keys to change reference position, x is a and d, y is w and s.
void controlButtons()
{
    controlMenu();
    debug_timer.attach(&debugging,1);       //debug printing at 1 hz
    char c=0;
    //control menu
    while(c != 'Q' && c != 'q') {

    
    if( pc.readable() ){
        c = pc.getc();
        switch (c) 
            {
            //user chooses 'd'
            case 'd' :  
                     x = x + 0.01; 
                    
                     break;
          
            //user chooses 'a'
            case 'a' :
                     x-=0.01;

                     break;
            
            //user chooses 'w'        
            case 'w' :
                     y+=0.01;

                     break;
                     
          
            //user chooses 's'
            case 's' :
                     y-=0.01;

                     break;
                     
            case 'g' :
                    debug=true;
                    break;
            //user chooses 'q'
            case 'q' :
            case 'Q' :
                      pc.printf("=> Quitting control... \r\n"); wait(1);
                      stop_sampling();
                      stop_control();
                      debug_timer.detach();
                      pc.printf("Sampling and Control detached \n\r"); wait(1);
                      pc.printf("Returning to Main Menu \r\n\n"); wait(1);
                      mainMenu();
                                        
                      break;
    }//end switch
 
    }
    //end if pc readable
    
    
    }
    //end of while loop
}

//Sample and Filter  
void sample_filter(void)
{
    emg_biceps = emg1.read();    //Biceps
    emg_triceps = emg2.read();    //Triceps
    emg_flexor = emg3.read();    //Flexor
    emg_extens = emg4.read();    //Extensor
    
    //Filter: high-pass -> notch -> rectify -> lowpass
    //each muscle need its own biquad per filter
    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);
   
    //send filtered emg to scope 
    /*scope.set(0,biceps_power);
    scope.set(1,triceps_power);
    scope.set(2,flexor_power);
    scope.set(3,extens_power);
    scope.send();
    */
    //send normalized emg to scope 
    //scope.set(0,biceps);
    //scope.set(1,triceps);
    //scope.set(2,flexor);
    //scope.set(3,extens);
    //scope.send();
       
}
    
//Send arm to mechanical limits, and set encoder to these angles. 
void calibrate_arm(void)
{
    pc.printf("Calibrate_arm() entered\r\n");

    calibrating = true;
    done1 = false;
    done2 = false;
    
    pc.printf("To start arm calibration, press any key =>");
    pc.getc(); 
    pc.printf("\r\n Calibrating... \r\n");
    red=0; blue=0;              //Debug light is purple during arm calibration
    
    dir_motor1=0;   //cw
    dir_motor2=1;   //cw
    
    control_timer.attach(&calibrate,CONTROL_RATE);
    
    while(calibrating){
       shoulder_limit.fall(&shoulder);
       elbow_limit.fall(&elbow);
       if(done1 && done2){ 
        pwm_motor2=0; 
        control_timer.detach();      //Leave while loop when both limits are reached
        red=1; blue=1;          //Turn debug light off when calibration complete
        //set reference position to mechanical limits
        calibrating=false;
        
        x = l1 * cos(theta1_lower) + l2 * cos(theta1_lower + theta2_lower);
        y = l1 * sin(theta1_lower) + l2 * sin(theta1_lower + theta2_lower);
        //x = 0.2220;   position at limits
        //y = 0.4088;
       }
    }
        pc.printf("Current pulsecount motor 1: %i, motor 2: %i \r\n",Encoder1.getPulses(),Encoder2.getPulses());
        pc.printf("Current reference. X: %f, Y: %f \r\n",x,y);
        wait(1);
        pc.printf("\n\r-------------------------- \n\r"); 
        pc.printf(" Arm Calibration Complete\r\n");
        pc.printf("-------------------------- \n\r"); 
  
}

//Limit switch - if hit: set pulsecount of encoder to angle of lower mechanical limit
void shoulder()
{
    pwm_motor1=0;
    done1 = true;
    pc.printf("Shoulder Limit hit - shutting down motor 1\r\n");
    //mechanical angle limits -> pulses. If 40 degrees -> counts = floor( 40 * (4200/360) )
    theta1_cal = floor(theta1_lower * (4200/(2*PI)));
    Encoder1.setPulses(theta1_cal);       //edited QEI library: added setPulses(int p)  
}

void elbow(){
    pwm_motor2=0;
    done2 = true;
    pc.printf("Elbow Limit hit - shutting down motor 2\r\n");
    
    //Mechanical limit 43 degrees -> 43*(4200/360) = 350
    theta2_cal = floor(theta2_lower * (4200/(2*PI)));
    Encoder2.setPulses(theta2_cal);       //edited QEI library: added setPulses(int p)    
}

//Run motors slowly clockwise to mechanical limit. Attached to 100Hz ticker
void calibrate(void){
    if(done1==false){                   //if motor 1 limit has not been hit yet
            pwm_motor1=0.1;             //move upper arm slowly cw
          //  pc.printf("Motor 1 running %f \r\n");
        }
    if(done1==true && done2==false){    //if limit motor 1 has been hit
            pwm_motor1=0;               //stop motor1
            pwm_motor2=0.1;             //start moving forearm slowly cw
          //  pc.printf("Motor 2 running %f \r\n");    
        }   
}

//EMG calibration
void calibrate_emg()
{
   Ticker timer;
   
   start_sampling();
   wait(0.5);
   
   /******************* All muscles: minimum measurement *************************/
   pc.printf("Start of minimum measurement, relax all muscles.\r\n");
   wait(0.5);
   pc.printf(" Press any key to begin... "); wait(1);
   char input;
   input=pc.getc();
   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);
   pc.printf(" \r\n  Measuring... \r\n"); 
   
   timer.attach(&emg_min,SAMPLE_RATE);
   wait(3);
   timer.detach();
   pc.printf("\r\n Measurement complete."); wait(1);
   pc.printf("\r\n Right Flexor min = %f \r\n",bicepsmin); 
   pc.printf("\r\n Right Extensor min = %f \r\n",tricepsmin); 
   pc.printf("\r\n Left Flexor min = %f \r\n",flexormin); 
   pc.printf("\r\n Left Extensor min = %f \r\n",extensmin); wait(1);
   /******************************** Done ****************************************/
   
   pc.printf("\r\n Now we will measure maximum amplitudes \r\n"); wait(0.5); 
   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(1);
   calibrate_time=0;
   
   /********************* 1st channel: MVC measurement ***************************/
   pc.printf("\r\n---------------------\r\n "); 
   pc.printf("Right Flexor is first.\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);
   
   muscle=1;
   timer.attach(&emg_mvc,SAMPLE_RATE);
   wait(3);
   timer.detach();
  
   pc.printf("\r\n Measurement complete."); wait(1);
   pc.printf("\r\n Right Flexor MVC = %f \r\n",bicepsMVC); wait(1);
   pc.printf("Measured time: %f seconds \r\n\n",calibrate_time);
   calibrate_time=0;
   /******************************** Done ****************************************/
   
   /********************* 2nd channel: MVC measurement ***************************/
   muscle=2;
   pc.printf("\r\n-------------------\r\n "); 
   pc.printf("Right Extensor 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);

   timer.attach(&emg_mvc,0.002);
   wait(3);
   timer.detach();
   pc.printf("\r\n Right Extensor MVC = %f \r\n",tricepsMVC);
   
   pc.printf("Measured time: %f seconds \r\n",calibrate_time);
   calibrate_time=0;
   /******************************** Done ****************************************/
      
   /********************* 3rd channel: MVC measurement ***************************/
   muscle=3;
   pc.printf("\r\n--------------------\r\n "); 
   pc.printf("Left Flexor 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);

   timer.attach(&emg_mvc,0.002);
   wait(3);
   timer.detach();
   pc.printf("\r\n Left Flexor MVC = %f \r\n",flexorMVC);
   
   pc.printf("Measured time: %f seconds \r\n",calibrate_time);
   calibrate_time=0;
   /******************************** Done ****************************************/
   
   /********************* 4th channel: MVC measurement ***************************/
   muscle=4;
   pc.printf("\r\n--------------------\r\n "); 
   pc.printf("Left Extensor 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);

   timer.attach(&emg_mvc,0.002);
   wait(3);
   timer.detach();
   pc.printf("\r\n Left Extensor MVC = %f \r\n",extensMVC);
   
   pc.printf("Measured time: %f seconds \r\n",calibrate_time);
   calibrate_time=0;
   /******************************** Done ****************************************/
   
   //Stop sampling: detach ticker
   stop_sampling();
   
}


//EMG Maximum Voluntary Contraction measurement
void emg_mvc()
{  
        if(muscle==1){
            
            if(biceps_power>bicepsMVC){
            pc.printf("%s+ %s",GREEN_,_GREEN);
            bicepsMVC=biceps_power;
            }    
            else
            pc.printf("- ");
        }  
        
        if(muscle==2){
            
            if(triceps_power>tricepsMVC){
            pc.printf("%s+ %s",GREEN_,_GREEN);
            tricepsMVC=triceps_power;
            }    
            else
            pc.printf("- ");
        }
        
        if(muscle==3){
            
            if(flexor_power>flexorMVC){
            pc.printf("%s+ %s",GREEN_,_GREEN);    
            flexorMVC=flexor_power;
            }    
            else
            pc.printf("- ");
        }
        
        if(muscle==4){
            
            if(extens_power>extensMVC){
            pc.printf("%s+ %s",GREEN_,_GREEN);    
            extensMVC=extens_power;
            }    
            else
            pc.printf("- ");
        }
        
    //}
    calibrate_time = calibrate_time + 0.002;

}

//Minimum measurement during relaxation
void emg_min()
{          
            if(biceps_power>bicepsmin){
            bicepsmin=biceps_power;
            }    
            
            if(triceps_power>tricepsmin){
            tricepsmin=triceps_power;
            }            

            if(flexor_power>flexormin){
            flexormin=flexor_power;
            }            
 
            if(extens_power > extensmin){   
            extensmin = extens_power;
            }    
        
    calibrate_time = calibrate_time + 0.002;
    
}


//PID motor 1 - 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 = derfilter1.step(e_der);                 //derfilter1 - seperate 60hz low-pass biquad for this PID 
    e_prev = error;
    // Integral
    e_int = e_int + CONTROL_RATE * error;
    // PID
    return kp*error + ki*e_int + kd * e_der;
 
}

//PID for motor 2 - needed because of biquadfilter memory variables
double pid2(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 = derfilter2.step(e_der);                 //derfilter2 - seperate 60hz low-pass biquad for this PID 
    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()
{     
      
   /********************* START OF EMG REFERENCE CALCULATION ***************************/
    if(emg_control==true){
    //TODO some idle time with static reference before EMG kicks in. or go to reference in the first 5 seconds.

    //normalize emg to value between 0-1
    biceps = (biceps_power - bicepsmin) / (bicepsMVC - bicepsmin);
    triceps = (triceps_power - tricepsmin) / (tricepsMVC - tricepsmin);
    flexor = (flexor_power - flexormin) / (flexorMVC - flexormin);
    extens = (extens_power - extensmin) / (extensMVC - extensmin);
    //make sure values stay between 0-1 over time
    keep_in_range(&biceps,0,1);
    keep_in_range(&triceps,0,1);
    keep_in_range(&flexor,0,1);
    keep_in_range(&extens,0,1);
    
    
    //threshold detection! buffer or two thresholds? If average of 100 samples > threshold, then muscle considered on.    
    movavg1[i]=biceps;   //fill array with 100 normalized samples
    movavg2[i]=triceps;
    movavg3[i]=flexor;
    movavg4[i]=extens;
    i++;                             
    if(i==window){       //if array full,set i to 0
        i=0;
    }
    
    
    //Sum all values in the array. The sum needs to be overwritten or it will continue to sum the next 100 samples on top it 
    //and will grow out of control.
    //So the variable name for the sum in the for loop is not really correct since the average is calculated after the loop.
    for(int j = 0; j < window; j++){        
        biceps_avg += movavg1[j];
        triceps_avg += movavg2[j];
        flexor_avg += movavg3[j];
        extens_avg += movavg4[j];
        }
    biceps_avg = biceps_avg/window;                       //divide sum by number of samples -> average
    triceps_avg = triceps_avg/window;
    flexor_avg = flexor_avg/window;
    extens_avg = extens_avg/window;
    
    emg_control_time += CONTROL_RATE; 
    
    //Move mouse to starting position - bottom right corner of used workspace - when EMG control starts. After 5 seconds reference can be changed with EMG.
    if(emg_control_time < 5){
        
        x=0; y=0.3;             
    }
    else{
        
        
    //Compare muscle amplitudes and determine their influence on x and y reference position.
    if (biceps_avg>triceps_avg && biceps_avg > 0.2){
        xdir = 0;                            
        xpower = biceps_avg;}
    else if (triceps_avg>biceps_avg && triceps_avg>0.2){
        xdir = 1;
        xpower = triceps_avg;}
    else 
        xpower=0;
        
    if (flexor_avg>extens_avg && flexor_avg > 0.2){
        ydir = 0;
        ypower = flexor_avg;
        }
    else if (extens_avg>flexor_avg && extens_avg > 0.2){
        ydir = 1;
        ypower = extens_avg;
        }
    else
        ypower = 0;
            
    //power: the longer a signal is active, the further the reference goes. So integrate to determine reference position
    dx = xpower * CONTROL_RATE * 0.15;           //last value is a factor to control how fast the reference (so also end effector) changes 
    dy = ypower * CONTROL_RATE * 0.15; 
    
    //Direction! Sum dx and dy but make sure xdir and ydir are considered.
    if (xdir>0)     //if x direction of sample is positive, add it to reference position
        x += dx;    
    else            //if x direction of sample is negative, substract it from reference position
        x += -dx;
        
    if (ydir>0)     //if y direction of sample is positive, add it to reference position
        y += dy;
    else
        y += -dy;   //if y direction of sample is negative, substract it from reference position
   }//end else control time>5
        
    //now we have x and y -> reference position. Keep in desired range.
    keep_in_range(&x,-0.5,0);   
    keep_in_range(&y,0.2,0.55);
    
    }//end emg_control if
    /******************************** END OF EMG REFERENCE CALCULATION ****************************************/
    
        
    //Current position - Encoder counts -> current angle -> Forward Kinematics 
    rpc=(2*PI)/ENCODER_CPR;                //radians per count (resolution) - 2pi divided by 4200
    theta1 = Encoder1.getPulses() * rpc;   //multiply resolution with number of counts to get current angles
    theta2 = Encoder2.getPulses() * rpc;
    current_x = l1 * cos(theta1) + l2 * cos(theta1 + theta2);   //Forward kinematics for current position
    current_y = l1 * sin(theta1) + l2 * sin(theta1 + theta2);
    
        
    //calculate error (refpos-currentpos) 
    x_error = x - current_x;
    y_error = y - current_y;
    
    /******************************** START OF TRIG INVERSE KINEMATICS ****************************************/    
    if (control_method==1){
    //inverse kinematics (refpos to refangle)
    
    costheta2 = (pow(x,2) + pow(y,2) - pow(l1,2) - pow(l2,2)) / (2*l1*l2) ;
    //absolute in sqrt to avoid imaginary numbers -> bigger steady state error when reference out of workspace
    sintheta2 = sqrt( abs( 1 - pow(costheta2,2) ) );                
    
    //Reference angle 2 
    reftheta2 = atan2(sintheta2,costheta2);
    
    double k1 = l1 + l2*costheta2;
    double k2 = l2*sintheta2;
    
    //Reference angle 1
    reftheta1 = atan2(y, x) - atan2(k2, k1);
    
    /* alternative, but extra square root
    costheta1 = ( x * (l1 + l2 * costheta2) + y * l2 * sintheta2 ) / ( pow(x,2) + pow(y,2) );
    sintheta1 = sqrt( abs( 1 - pow(costheta1,2) ) );
    
    reftheta1 = atan2(sintheta1,costheta1);
    */
    
    //Angle error
    m1_error = reftheta1-theta1;
    m2_error = reftheta2-theta2;
    }// end control method 1
    /******************************** END OF TRIG INVERSE KINEMATICS ****************************************/
    
    
    /******************************** START OF DLS INVERSE KINEMATICS ****************************************/
    if(control_method==2){
    //inverse kinematics (error in position to error in angles)
    powlambda2 = pow(lambda,2);             //help functions to reduce amount of calculations
    powlambda4 = pow(lambda,4);             //
    powl2 = pow(l2,2);                      //
    powl1 = pow(l1,2);                      //
    sintheta1theta2 = sin(theta1 + theta2); //
    costheta1theta2 = cos(theta1 + theta2); //
    
    //calculate DLS matrix
    dls1= -(l2*powlambda2*sintheta1theta2 + l1*powlambda2*sin(theta1) + l1*powl2*pow(costheta1theta2,2)*sin(theta1) - l1*powl2*costheta1theta2*sintheta1theta2*cos(theta1))/(powlambda4 + 2*powl2*powlambda2*pow(costheta1theta2,2) + 2*powl2*powlambda2*pow(sintheta1theta2,2) + powl1*powlambda2*pow(cos(theta1),2) + powl1*powlambda2*pow(sin(theta1),2) + powl1*powl2*pow(costheta1theta2,2)*pow(sin(theta1),2) + powl1*powl2*pow(sintheta1theta2,2)*pow(cos(theta1),2) + 2*l1*l2*powlambda2*costheta1theta2*cos(theta1) + 2*l1*l2*powlambda2*sintheta1theta2*sin(theta1) - 2*powl1*powl2*costheta1theta2*sintheta1theta2*cos(theta1)*sin(theta1));
    dls2= (l2*powlambda2*costheta1theta2 + l1*powlambda2*cos(theta1) + l1*powl2*pow(sintheta1theta2,2)*cos(theta1) - l1*powl2*costheta1theta2*sintheta1theta2*sin(theta1))/(powlambda4 + 2*powl2*powlambda2*pow(costheta1theta2,2) + 2*powl2*powlambda2*pow(sintheta1theta2,2) + powl1*powlambda2*pow(cos(theta1),2) + powl1*powlambda2*pow(sin(theta1),2) + powl1*powl2*pow(costheta1theta2,2)*pow(sin(theta1),2) + powl1*powl2*pow(sintheta1theta2,2)*pow(cos(theta1),2) + 2*l1*l2*powlambda2*costheta1theta2*cos(theta1) + 2*l1*l2*powlambda2*sintheta1theta2*sin(theta1) - 2*powl1*powl2*costheta1theta2*sintheta1theta2*cos(theta1)*sin(theta1));
    dls3= -(l2*powlambda2*sintheta1theta2 - l1*powl2*pow(costheta1theta2,2)*sin(theta1) + powl1*l2*sintheta1theta2*pow(cos(theta1),2) - powl1*l2*costheta1theta2*cos(theta1)*sin(theta1) + l1*powl2*costheta1theta2*sintheta1theta2*cos(theta1))/(powlambda4 + 2*powl2*powlambda2*pow(costheta1theta2,2) + 2*powl2*powlambda2*pow(sintheta1theta2,2) + powl1*powlambda2*pow(cos(theta1),2) + powl1*powlambda2*pow(sin(theta1),2) + powl1*powl2*pow(costheta1theta2,2)*pow(sin(theta1),2) + powl1*powl2*pow(sintheta1theta2,2)*pow(cos(theta1),2) + 2*l1*l2*powlambda2*costheta1theta2*cos(theta1) + 2*l1*l2*powlambda2*sintheta1theta2*sin(theta1) - 2*powl1*powl2*costheta1theta2*sintheta1theta2*cos(theta1)*sin(theta1));
    dls4= (l2*powlambda2*costheta1theta2 - l1*powl2*pow(sintheta1theta2,2)*cos(theta1) + powl1*l2*costheta1theta2*pow(sin(theta1),2) - powl1*l2*sintheta1theta2*cos(theta1)*sin(theta1) + l1*powl2*costheta1theta2*sintheta1theta2*sin(theta1))/(powlambda4 + 2*powl2*powlambda2*pow(costheta1theta2,2) + 2*powl2*powlambda2*pow(sintheta1theta2,2) + powl1*powlambda2*pow(cos(theta1),2) + powl1*powlambda2*pow(sin(theta1),2) + powl1*powl2*pow(costheta1theta2,2)*pow(sin(theta1),2) + powl1*powl2*pow(sintheta1theta2,2)*pow(cos(theta1),2) + 2*l1*l2*powlambda2*costheta1theta2*cos(theta1) + 2*l1*l2*powlambda2*sintheta1theta2*sin(theta1) - 2*powl1*powl2*costheta1theta2*sintheta1theta2*cos(theta1)*sin(theta1));
    
    //calculate angle errors from position error
    q1_error = dls1 * x_error + dls2 * y_error;
    q2_error = dls3 * x_error + dls4 * y_error;
    
    //Angle error
    m1_error = q1_error;
    m2_error = q2_error;
    }//end control method 2
    /******************************** END OF DLS INVERSE KINEMATICS ****************************************/
    
    
    /* Set limits to the error! 
    motor1: lower limit 40 degrees, upper limit 135
    motor2: lower 43 degrees, upper limit 138 degrees. */
   
   //lower limits:   Negative error not allowed to go further. 
   if (theta1 < theta1_lower){
        if (m1_error > 0)
            m1_error = m1_error;
        else 
            m1_error = 0; }
   if (theta2 < theta2_lower){
        if (m2_error > 0)
            m2_error = m2_error;
        else 
            m2_error = 0;
   }
   //upper limit: Positive error not allowed to go further
   if (theta1 > theta1_upper){
        if (m1_error < 0 )
            m1_error = m1_error;
        else
            m1_error = 0;
   }
   if (theta2 > theta2_upper){
        if (m2_error < 0 )
            m2_error = m2_error;
        else
            m2_error = 0;
   }
             
    //PID controller
    u1=pid(m1_error,m1_kp,m1_ki,m1_kd,m1_e_int,m1_e_prev);    //motor 1
    u2=pid2(m2_error,m2_kp,m2_ki,m2_kd,m2_e_int,m2_e_prev);    //motor 2
    
    //keep PWM between limits, sign = direction
    keep_in_range(&u1,-0.3,0.3);    
    keep_in_range(&u2,-0.3,0.3);
    
    //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));*/
    
}

//Prints the main menu
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(0.2);
   pc.printf("[C]alibration\r\n"); wait(0.2);
   pc.printf("[T]RIG Control with WASD\r\n"); wait(0.2);
   pc.printf("[D]LS Control with WASD\r\n"); wait(0.2);
   pc.printf("[E]MG Control - DLS \r\n"); wait(0.2);
   pc.printf("[Q]uit Robot Program\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
    servo_timer.attach(&servo_control, SERVO_RATE);  //50 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();
    servo_timer.detach();
    pwm_motor1=0; pwm_motor2=0;
    //Debug LED will be off when control is off
    blue=1;
    pc.printf("||- stopped control -|| \r\n");
}


//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 
}

//Prints control menu
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("A) Move Arm Left\r\n");
     pc.printf("D) Move Arm Right\r\n");
     pc.printf("W) Move Arm Up\r\n");
     pc.printf("S) Move Arm Down\r\n");
     pc.printf("g) Turn debugging on / off \r\n");
     pc.printf("q) Exit \r\n");
     pc.printf("Please make a choice => \r\n");
}

//prints calibration menu
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");
    
}
//prints square title box
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
}

//prints emg instructions
void emgInstructions(){
    pc.printf("\r\nPrepare the skin before applying electrodes: \n\r"); 
    pc.printf("-> Shave electrode locations if needed and clean with alcohol \n\r"); wait(1);
    //pc.printf(" Check whether EMG signal looks normal. \n\r "); wait(1);
    pc.printf("\r\n To calibrate the EMG signals we will measure: \n\r ");
    pc.printf("- Minimum amplitude, while relaxing all muscles. \n\r ");
    pc.printf("- Maximum Voluntary Contraction of each muscle. \n\r"); wait(1);
    pc.printf("\r\nFor the MVC you need to flex the mentioned muscle for 3 seconds \n\r"); wait(0.5);
    pc.printf("The measurements will begin once you confirm you're ready [Hit any key] \n\r \n\r"); wait(0.5);
}

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