New reference frame: y=0 is now at table height.

Dependencies:   HIDScope MODSERIAL QEI biquadFilter mbed

Fork of prog_forwardkin_feedback_copy by Elfi Hofmeijer

Revision:
44:43f200e04903
Parent:
43:2b2e0bff0b39
diff -r 2b2e0bff0b39 -r 43f200e04903 main.cpp
--- a/main.cpp	Sat Nov 05 13:54:09 2016 +0000
+++ b/main.cpp	Sat Nov 05 16:00:26 2016 +0000
@@ -7,178 +7,137 @@
 
 /*
 THINGS TO CONSIDER
-- Line 234, 239: motor action of motor 1 is inverted because it is mounted
+- Motor action of motor 1 is inverted because it is mounted
 opposite to motor 2 in the tower. Check if the clockwise directions of the 
 motors correspond to the positive q1, q2-directions (both counterclockwise)
  in the original IK-sketch.
-- Line 244,257: motor values have been scaled down for safety at first test, restore
-after testing to get proper action.
-- Set angle and length boundaries!!
-- Set robot constants (lengths etc.)
-- Set EMGgain and thresholds
-- Add tower height to ReferencePosition_y and Position_y AND inverse kinematics calculation!
-- Add (lower) boundaries to TotalErrors
-- MotorGain could change due to arm weight!!
-- Arms should be placed manually into reference position.
+- Arms should be placed manually into reference position before resetting board.
 */
 
 //set pins
-DigitalIn encoder1A (D13); //Channel A van Encoder 1
-DigitalIn encoder1B (D12); //Channel B van Encoder 1
-DigitalIn encoder2A (D11); //Channel A van Encoder 2, kan niet op D15
-DigitalIn encoder2B (D10); //Channel B van Encoder 2, kan niet op D14
-//DigitalOut led1 (D11); 
-//DigitalOut led2 (D10);
-//AnalogIn potMeter1(A2);
-//AnalogIn potMeter2(A1);
+DigitalIn encoder1A (D13);                                                  //Channel A from Encoder 1
+DigitalIn encoder1B (D12);                                                  //Channel B from Encoder 1
+DigitalIn encoder2A (D11);                                                  //Channel A from Encoder 2
+DigitalIn encoder2B (D10);                                                  //Channel B from Encoder 2
+AnalogIn emg0( A0 );
+AnalogIn emg1( A1 );
+DigitalIn button1(D3);
+DigitalIn button2(D9);
+
 DigitalOut motor1DirectionPin(D7);
 PwmOut motor1MagnitudePin(D6);
 DigitalOut motor2DirectionPin(D4);
 PwmOut motor2MagnitudePin(D5);
-DigitalIn button1(D3);
-DigitalIn button2(D9);
-AnalogIn    emg0( A0 );
-AnalogIn    emg1( A1 );
-
 DigitalOut ledGrn(LED_GREEN);
 DigitalOut ledRed(LED_RED);
 DigitalOut ledBlue(LED_BLUE);
 
 //library settings
 Serial pc(USBTX,USBRX);
-Ticker MeasureTicker, BiQuadTicker; //, TimeTracker; // sampleT;
 HIDScope    scope(6);
 
-//initial values
-float dx;
-float dy;
-double DerivativeCounts;
-//float referenceVelocity = 0;
-//float bqcDerivativeCounts = 0;
+//go-Ticker settings
+Ticker MeasureTicker;
+volatile bool MeasureTicker_go=false;
+void MeasureTicker_act(){MeasureTicker_go=true;};                           // Activates go-flag
+
+//constant values
 const float PI = 3.141592653589793;
-const int cw = 0;       //values for cw and ccw are inverted!! cw=0 and ccw=1
+const int cw = 0;                                                           //values for cw and ccw are inverted! cw=0 and ccw=1
 const int ccw = 1;
+double threshold_l=0.09;                                                    //left arm EMG threshold
+double threshold_r = 0.08;                                                  //right arm EMG threshold
+float EMGgain = 1.0;
 
-//set lengths (VALUES HAVE TO BE CHANGED)
-//float x0 = 1.0;
-float L0 = 0.232;
-float L1 = 0.45;
-float L2 = 0.35;
-float TowerHeight = 0.232;    //height of motor axes above table surface!
-float StampHeight = 0.056;    // height of end effector
-float y_stampup = 0.1;      //height stamp while not stamping: 10cm above table surface
-float y_stampdown = -0.04;    //height stamp while stamping: at table surface
+//set lengths
+//float L0 = 0.232;                                                           //height of motor axes above table surface
+float L1 = 0.45;                                                            //length of proximal arm
+float L2 = 0.35;                                                            //length of distal arm
+float TowerHeight = 0.232;                                                  //height of motor axes above table surface
+float StampHeight = 0.056;                                                  // height of end effector
+float y_stampup = 0.1;                                                      //height stamp while not stamping: 10cm above table surface
+float y_stampdown = -0.04;                                                  //height stamp while stamping: at table surface
 
-
-//set initial conditions
-float biceps_l = 0;
-float biceps_r = 0;
-float ReferencePosition_x = 0.35;        //L2;
-float ReferencePosition_y = L1 + TowerHeight - StampHeight;
-float ReferencePosition_xnew = 0.35;     //L2;
+//float dy_stampdown = 2.0; //0.05; //5 cm movement downward to stamp
+float MotorGain = 8.4;                                                      // rad/s for PWM, is max motor speed
+float MotorMaxSpeed = 0.1;                                                  //define a maximum PWM speed for the motor
+float t_sample = 0.002;                                                     //seconds
+const float maxStampDistance = 0.7;
+const float minStampDistance = 0.3;
+float Kp = 4.0;                                                             //proportional controller constant
+float Ki = 0.04;                                                            //integrative controller constant
+float Kd = 0.02;                                                            //derivative controller constant
+float N = 25;                                                               //PIDF filter constant
+//(Higher N is faster derivative action but more sensitive to noise)
+ 
+//set initial conditions for inputs and positions
+float biceps_l = 0, biceps_r = 0;
+double envelopeL = 0, envelopeR = 0;
+int T=0;                                                                    //EMG 'switch' variable
+float ReferencePosition_x = 0.35;                                           //starting position for x reference position        
+float ReferencePosition_y = L1 + TowerHeight - StampHeight;                 //starting position for y reference position
+float ReferencePosition_xnew = 0.35;     
 float ReferencePosition_ynew = L1 + TowerHeight - StampHeight;
 float Position_x = 0.0;
 float Position_y = 0.0;
-float q1 = 0;
-float q2 = PI/2;
-float q1_ref = 0;
-float q2_ref = 0;
-float q1start = 0;
+
+//set initial conditions for angles, errors and motor values
+float q1 = 0,q2 = PI/2;
+float q1_ref = 0, q2_ref = 0;
+float q1start = 0; 
 float q12start = PI/2;
-float q1Encoder = 0;
-float q12Encoder = 0;
+float q1Encoder = 0, q12Encoder = 0;
 float q12Out = 0;
 
-float q1_error_prev = 0;
-float q2_error_prev = 0;
-float DerTotalError1 = 0;
-float DerTotalError2 = 0;
-float q1IntError = 0;
-float q2IntError = 0;
-float TotalError1_prev = 0;
-float TotalError2_prev = 0;
-
-float motorValue1 = 0.0;
-float motorValue2 = 0.0;
-int counts1 = 0;
-int counts2 = 0;
-int counts1Prev = 0;
-int counts2Prev = 0;
-double envelopeL = 0;
-double envelopeR = 0;
+float q1_error_prev = 0, q2_error_prev = 0;
+float DerTotalError1 = 0, DerTotalError2 = 0;
+float q1IntError = 0, q2IntError = 0;
+float TotalError1_prev = 0, TotalError2_prev = 0;
+float TotalError1= 0, TotalError2= 0;
+//float TotalErrorMin= 0;
 
-//set constant or variable values (VALUES HAVE TO BE EDITED)
-int T=0;        //EMG 'switch' variable
-double threshold_l=0.09;   //left arm EMG threshold
-double threshold_r = 0.08; //right arm EMG threshold
-float EMGgain = 1.0;
-
-float dy_stampdown = 2.0; //0.05; //5 cm movement downward to stamp
-float MotorGain = 8.4; // rad/s for PWM, is max motor speed (motor value of 1)
-float Motor1ExtraGain = 1.0;
-float MotorMaxSpeed = 0.1;  //define a maximum PWM speed for the motor
-float t_sample = 0.01; //seconds
-const float maxStampDistance = 0.7;       //0.66;
-const float minStampDistance = 0.3;
-float Kp = 4.0;//potMeter2.read();
-float Ki = 0.04;  //0.01*Kp; //potMeter2.read();
-float Kd = 0.02;     //0.1;(unstable!) //0.05; //0.02;        //0.04*Kp; //potMeter2.read();
-float N = 25; //N=1/Tf, Higher N is faster derivative action but more sensitive to noise.
+float motorValue1 = 0.0, motorValue2 = 0.0;
+int counts1 = 0, counts2 = 0;
+int counts1Prev = 0, counts2Prev = 0;
 
-float q1_refOutNew = 0;
-float q1_refOutMin = 0;             //Physical min angle 0.00 radians + 0.1 rad
-float q1_refOutMax = 1.37;          //Physical max angle 1.47 radians - 0.1 rad
-float q2_refOutNew = 0;
-float q2_refOutMin = 0.91;     //Physical  min angle 0.81 radians + 0.1 rad
-float q2_refOutMax = 2.07;     //Physical max angle 2.17 radians - 0.1 rad
-float TotalError1= 0;
-float TotalError2= 0;
-float TotalErrorMin= 0;
- 
-//set BiQuad
-BiQuadChain bqc;
-BiQuad bq1(0.0186,    0.0743,    0.1114,    0.0743,    0.0186); //get numbers from butter filter MATLAB
-BiQuad bq2(1.0000,   -1.5704,    1.2756,   -0.4844,    0.0762);
+//set reference angle boundaries
+float q1_refOutNew = 0, q2_refOutNew = 0;
+float q1_refOutMin = 0;                                                     //Physical min angle 0.00 radians
+float q1_refOutMax = 1.37;                                                  //Physical max angle 1.47 radians - 0.1 rad
+float q2_refOutMin = 0.91;                                                  //Physical  min angle 0.81 radians + 0.1 rad
+float q2_refOutMax = 2.07;                                                  //Physical max angle 2.17 radians - 0.1 rad
 
-BiQuad pidf;
+//set BiQuad filters/filter chains
+
+BiQuad pidf;                                                                //PID Filter
 
-BiQuadChain bcq1R;
-BiQuadChain bcq2R;
-// Notch filter wo=50; bw=wo/35
-BiQuad bq1R(9.9110e-01,-1.6036e+00,9.9110e-01,-1.6036e+00,9.8221e-01);
-// High pass Butterworth filter 2nd order, Fc=10;
-BiQuad bq2R(9.1497e-01,-1.8299e+00,9.1497e-01,-1.8227e+00,8.3718e-01);
-// Low pass Butterworth filter 2nd order, Fc = 8;
-BiQuad bq3R(1.3487e-03,2.6974e-03,1.3487e-03,-1.8935e+00,8.9886e-01);
+BiQuadChain bcq1R;                                                          //Right EMG filter chain 1: notch filter+highpass
+BiQuadChain bcq2R;                                                          //Right EMG filter chain 2: lowpass
+BiQuad bq1R(9.9110e-01,-1.6036e+00,9.9110e-01,-1.6036e+00,9.8221e-01);      // Notch filter wo=50; bw=wo/35
+BiQuad bq2R(9.1497e-01,-1.8299e+00,9.1497e-01,-1.8227e+00,8.3718e-01);      // High pass Butterworth filter 2nd order, Fc=10;
+BiQuad bq3R(1.3487e-03,2.6974e-03,1.3487e-03,-1.8935e+00,8.9886e-01);       // Low pass Butterworth filter 2nd order, Fc = 8;
 
-BiQuadChain bcq1L;
-BiQuadChain bcq2L;
-// Notch filter wo=50; bw=wo/35
-BiQuad bq1L(9.9110e-01,-1.6036e+00,9.9110e-01,-1.6036e+00,9.8221e-01);
-// High pass Butterworth filter 2nd order, Fc=10;
-BiQuad bq2L(9.1497e-01,-1.8299e+00,9.1497e-01,-1.8227e+00,8.3718e-01);
-// Low pass Butterworth filter 2nd order, Fc = 8;
-BiQuad bq3L(1.3487e-03,2.6974e-03,1.3487e-03,-1.8935e+00,8.9886e-01);
-// In the following: R is used for right arm, L is used for left arm!
-
-//set go-Ticker settings
-volatile bool MeasureTicker_go=false, BiQuadTicker_go=false, FeedbackTicker_go=false, TimeTracker_go=false; // sampleT_go=false;
-void MeasureTicker_act(){MeasureTicker_go=true;}; // Activates go-flags
-void BiQuadTicker_act(){BiQuadTicker_go=true;};
-void FeedbackTicker_act(){FeedbackTicker_go=true;};
-void TimeTracker_act(){TimeTracker_go=true;};
-//void sampleT_act(){sampleT_go=true;};
+BiQuadChain bcq1L;                                                          //Left EMG filter chain 1: notch filter+highpass
+BiQuadChain bcq2L;                                                          //Left EMG filter chain 2: lowpass
+BiQuad bq1L(9.9110e-01,-1.6036e+00,9.9110e-01,-1.6036e+00,9.8221e-01);      // Notch filter wo=50; bw=wo/35
+BiQuad bq2L(9.1497e-01,-1.8299e+00,9.1497e-01,-1.8227e+00,8.3718e-01);      // High pass Butterworth filter 2nd order, Fc=10;
+BiQuad bq3L(1.3487e-03,2.6974e-03,1.3487e-03,-1.8935e+00,8.9886e-01);       // Low pass Butterworth filter 2nd order, Fc = 8;
+// In the following: R is used for right arm EMG, L is used for left arm EMG
 
 //define encoder counts and degrees
-QEI Encoder1(D12, D13, NC, 32); // turns on encoder
-QEI Encoder2(D10, D11, NC, 32); // turns on encoder
+QEI Encoder1(D12, D13, NC, 32);                                             // turns on encoder
+QEI Encoder2(D10, D11, NC, 32);                                             // turns on encoder
+const int counts_per_revolution = 4200;                                     //counts per motor axis revolution
+const int inverse_gear_ratio = 131;
+const float resolution = counts_per_revolution/(2*PI/inverse_gear_ratio);   //87567.0496892 counts per radian, encoder axis
 
-const int counts_per_revolution = 4200; //counts per motor axis revolution
-const int inverse_gear_ratio = 131;
-const float resolution = counts_per_revolution/(2*PI/inverse_gear_ratio);  //87567.0496892 counts per radian, encoder axis
+//--------------------------------------------------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------------------------------------------------
 
 void FilteredSample(int &Tout, double &envelopeLout, double &envelopeRout)
 {   
+//This function reads EMG, filters it and generates a T-switch value which specifies the movement of the robot
+
     double inLout = emg0.read();
     double inRout = emg1.read();
     
@@ -207,164 +166,119 @@
     else{
         //wait(0.2);
         Tout = 0;
-        }
-
-//    scope.set(0, inLout);
-//    scope.set(1, inRout);  
-    
+        }   
 }
 
-void GetReferenceKinematics1(float &q1Out, float &q2Out, float &q1_refOut, float &q2_refOut){
+//--------------------------------------------------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------------------------------------------------
+
+void GetReferenceKinematics1(float &q1Out, float &q2Out, float &q1_refOut, float &q2_refOut)
+{    
+//This function reads current position from encoder, calculates reference position from T-switch value,
+//converts reference position to reference angles and checks boundaries
     
     //get joint positions q feedback from encoder
-    float Encoder1Position = counts1/resolution;         //angular position in radians, encoder axis
-    float Encoder2Position = -1*counts2/resolution;     //NEGATIVE!
+    float Encoder1Position = counts1/resolution;                            //angular position of encoder in radians
+    float Encoder2Position = -1*counts2/resolution;                         //NEGATIVE due to opposite build up in tower
     
     q1Encoder = Encoder1Position*inverse_gear_ratio;
     q12Encoder = Encoder2Position*inverse_gear_ratio;
-    q1Out = q1start + q1Encoder;        //angular position in radians, motor axis
-    q12Out = q12start + q12Encoder;     //encoder 2 gives sum of both angles!
+    q1Out = q1start + q1Encoder;                                            //angular position of motor axis in radians
+    q12Out = q12start + q12Encoder;                                         //encoder 2 gives sum of q1 and q2!
     q2Out = q12Out - q1Out;             
-    float q1deg = q1Out*360/2/PI;
-    float q2deg = q2Out*360/2/PI;
+    //float q1deg = q1Out*360/2/PI;                                         //angle in degrees
+    //float q2deg = q2Out*360/2/PI;                                         //angle in degrees
     
-    /*
-    //get end effector position feedback with Brockett
-    float Position_x = ((L2 + x0)*(cos(q1)*cos(q2) - sin(q1)*sin(q2)) - L0*sin(q1) + (cos(q1)*sin(q2) + cos(q2)*sin(q1))*(L0 + L1) - cos(q1)*(L1*sin(q1) + L1*cos(q1)*sin(q2) - L1*cos(q2)*sin(q1)) - sin(q1)*(L1*cos(q1)*cos(q2) - L1*cos(q1) + L1*sin(q1)*sin(q2)));      //calculate end effector x-position from motor angles with Brockett, rx
-    float Position_y = (L0 - (L2 + x0)*(cos(q1)*sin(q2) + cos(q2)*sin(q1)) - L0*cos(q1) - cos(q1)*(L1*cos(q1)*cos(q2) - L1*cos(q1) + L1*sin(q1)*sin(q2)) + (cos(q1)*cos(q2) - sin(q1)*sin(q2))*(L0 + L1) + sin(q1)*(L1*sin(q1) + L1*cos(q1)*sin(q2) - L1*cos(q2)*sin(q1)));      //calculate end effector y-position from motor angles with Brockett, ry
-    */
-    //get end effector position feedback with trigonometry
+    //get end effector position with trigonometry
     Position_x = (L1*sin(q1) + L2*sin(q1+q2));
     Position_y = (L1*cos(q1) + L2*cos(q1+q2)) + TowerHeight - StampHeight;  
-    //float PositionVector = sqrt(pow(Position_x,2)+pow(Position_y,2));
     
-    /*
-    if (Position_y < (0.5*TowerHeight)){
-     wait(1.0); 
-     ReferencePosition_ynew = L1 + TowerHeight - StampHeight;      //Reset vertical position after stamping
-      }
-    else{      
-    */
-    //get velocity vector v = (Pe*- Pe) = [0; dx; dy] from EMG  
-    biceps_l = !button1.read() * EMGgain; //emg0.read();     //velocity or reference position change, EMG with a gain
-    biceps_r = !button2.read() * EMGgain; //emg1.read();
+    //get reference position from EMG based T-switch values  
     if (T == -2){
-        //both arms activated: stamp moves down
-        //led1 = 1;
-        //led2 = 1;
+        //both EMGs active: stamp moves down
         ReferencePosition_xnew = ReferencePosition_x;
-        ReferencePosition_ynew = ReferencePosition_y - 0.015; //ReferencePosition_y - dy_stampdown;   //into stamping vertical position ~the stamp down action
-        
+        ReferencePosition_ynew = ReferencePosition_y - 0.015;
         }
     else if (T==-1){
-        //arm 1 activated, move left
-        //led1 = 1;
-        //led2 = 0;
-        ReferencePosition_xnew = ReferencePosition_x - 0.0009; //biceps_l;
-        ReferencePosition_ynew = y_stampup; //ReferencePosition_y;
-        /*
-        PositionError_x = ReferencePosition_x - Position_x;        //Position error in dx,dy
-        PositionError_y = ReferencePosition_y - Position_y;        //Position error in dx,dy
-        
-        dx = PositionError_x;
-        dy = PositionError_y;
-        q1_dotOut = dy*(((x0 + L1*cos(q1))*(L0*L0 + L1*sin(q1)*L0 + x0*x0 + L1*cos(q1)*x0 + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1)) - (x0*(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + L0*L0 + x0*x0 + 2*L0*L1*sin(q1) + 2*L1*x0*cos(q1) + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1))) - dx*(((L0 + L1*sin(q1))*(L0*L0 + L1*sin(q1)*L0 + x0*x0 + L1*cos(q1)*x0 + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1)) - (L0*(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + L0*L0 + x0*x0 + 2*L0*L1*sin(q1) + 2*L1*x0*cos(q1) + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1)));
-        q2_dotOut = dy*((x0*(L0*L0 + L1*sin(q1)*L0 + x0*x0 + L1*cos(q1)*x0 + 1))/(L1*L1*pow(cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*pow(L1,2)*x0*cos(q1)*sin(q1)) - ((x0 + L1*cos(q1))*(pow(L0,2) + pow(x0,2) + 1))/(pow(L1*cos(q1),2)) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*pow(L1,2)*x0*cos(q1)*sin(q1)) - dx*((L0*(L0*L0+L1*sin(q1)*L0+x0*x0+L1*cos(q1)*x0+1))/(pow(L1*cos(q1),2)+pow(L1*sin(q1),2)+pow(L1*x0*sin(q1),2)+pow(L0*L1*cos(q1),2)-2*L0*L1*L1*x0*cos(q1)*sin(q1))-((L0 + L1*sin(q1))*(L0*L0 + x0*x0 + 1))/(pow(L1*cos(q1),2)+pow(L1*sin(q1),2)+pow(L1*x0*sin(q1),2)+pow(L0*L1*cos(q1),2)-2*L0*L1*L1*x0*cos(q1)*sin(q1)));
-        */
+        //left EMG active, move stamp left
+        ReferencePosition_xnew = ReferencePosition_x - 0.0009;
+        ReferencePosition_ynew = y_stampup;
         }
     else if (T==1){
-        //arm 1 activated, move right
-        //led1 = 0;
-        //led2 = 1;
-        ReferencePosition_xnew = ReferencePosition_x + 0.0009; //biceps_r;
-        ReferencePosition_ynew = y_stampup; //ReferencePosition_y;
-        /*PositionError_x = ReferencePosition_x - Position_x;        //Position error in dx,dy
-        PositionError_y = ReferencePosition_y - Position_y;        //Position error in dx,dy
-        
-        dx = PositionError_x;
-        dy = PositionError_y;
-        q1_dotOut = dy*(((x0 + L1*cos(q1))*(L0*L0 + L1*sin(q1)*L0 + x0*x0 + L1*cos(q1)*x0 + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1)) - (x0*(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + L0*L0 + x0*x0 + 2*L0*L1*sin(q1) + 2*L1*x0*cos(q1) + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1))) - dx*(((L0 + L1*sin(q1))*(L0*L0 + L1*sin(q1)*L0 + x0*x0 + L1*cos(q1)*x0 + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1)) - (L0*(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + L0*L0 + x0*x0 + 2*L0*L1*sin(q1) + 2*L1*x0*cos(q1) + 1))/(pow(L1*cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*L1*L1*x0*cos(q1)*sin(q1)));
-        q2_dotOut = dy*((x0*(L0*L0 + L1*sin(q1)*L0 + x0*x0 + L1*cos(q1)*x0 + 1))/(L1*L1*pow(cos(q1),2) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*pow(L1,2)*x0*cos(q1)*sin(q1)) - ((x0 + L1*cos(q1))*(pow(L0,2) + pow(x0,2) + 1))/(pow(L1*cos(q1),2)) + pow(L1*sin(q1),2) + pow(L1*x0*sin(q1),2) + pow(L0*L1*cos(q1),2) - 2*L0*pow(L1,2)*x0*cos(q1)*sin(q1)) - dx*((L0*(L0*L0+L1*sin(q1)*L0+x0*x0+L1*cos(q1)*x0+1))/(pow(L1*cos(q1),2)+pow(L1*sin(q1),2)+pow(L1*x0*sin(q1),2)+pow(L0*L1*cos(q1),2)-2*L0*L1*L1*x0*cos(q1)*sin(q1))-((L0 + L1*sin(q1))*(L0*L0 + x0*x0 + 1))/(pow(L1*cos(q1),2)+pow(L1*sin(q1),2)+pow(L1*x0*sin(q1),2)+pow(L0*L1*cos(q1),2)-2*L0*L1*L1*x0*cos(q1)*sin(q1)));
-*/
+        //right EMG active, move stamp right
+        ReferencePosition_xnew = ReferencePosition_x + 0.0009;
+        ReferencePosition_ynew = y_stampup;
+        }
+    else{                                                                   //T==0
+        //no EMG active, no x-movement, y-position restored to non-stamping position
+        ReferencePosition_ynew = y_stampup;
         }
-    else{       //T==0
-        //led1 = 0;
-        //led2 = 0;
-        //ReferencePosition_xnew = ReferencePosition_x;
-        ReferencePosition_ynew = y_stampup;     //ReferencePosition_y;   //
-        }
-      //  }
     
-    //check position boundaries
+    //check reference position boundaries
     if (ReferencePosition_xnew > maxStampDistance){
-        ReferencePosition_x = maxStampDistance; // - 0.1;
+        //target too far to be reached
+        ReferencePosition_x = maxStampDistance;
         ReferencePosition_y = y_stampup;
-        pc.printf("Target too far! \r\n");
+        //pc.printf("Target too far! \r\n");
         }
     else if (ReferencePosition_xnew < minStampDistance){
-        ReferencePosition_x = minStampDistance; // + 0.1;
+        //target too close
+        ReferencePosition_x = minStampDistance;
         ReferencePosition_y = y_stampup;
-        pc.printf("Target too close! \r\n");
+        //pc.printf("Target too close! \r\n");
         }
     else if (ReferencePosition_ynew < y_stampdown){
-        ReferencePosition_x = ReferencePosition_xnew; // + 0.1;
+        //target under table surface
+        ReferencePosition_x = ReferencePosition_xnew;
         ReferencePosition_y = y_stampdown;
-        pc.printf("Target too close! \r\n");
+        //pc.printf("Target too low! \r\n");
         }
     else {
+        //target within reach
         ReferencePosition_x = ReferencePosition_xnew;        
         ReferencePosition_y = ReferencePosition_ynew;
         }
     
+    //calculate reference joint angles for the new reference position
     float PointPositionArm2_x = ReferencePosition_x;
     float PointPositionArm2_y = ReferencePosition_y - TowerHeight + StampHeight;
     float PointVectorArm2 = sqrt(pow(PointPositionArm2_x,2)+pow(PointPositionArm2_y,2));
     
-    //calculate reference joint angles for the new reference position
     float alpha = atan(PointPositionArm2_y/PointPositionArm2_x);
     float beta = acos((L2*L2-L1*L1-pow(PointVectorArm2,2))/(-2*L1*PointVectorArm2));
     q1_refOutNew = PI/2 - (alpha+beta);
     q2_refOutNew = PI - asin(PointVectorArm2*sin(beta)/L2);
     
-    //check angle boundaries
+    //check reference angle boundaries
     if (q1_refOutNew < q1_refOutMin){
+        //new q1_ref too small
         q1_refOut = q1_refOutMin;
-        pc.printf("\r\n Under q1 angle boundaries\r\n");
+        //pc.printf("\r\n Under q1 angle boundaries\r\n");
         }
     else if (q1_refOutNew > q1_refOutMax){
+        //new q1_ref too large
         q1_refOut = q1_refOutMax;
-        pc.printf("\r\n Above q1 angle boundaries\r\n");
+        //pc.printf("\r\n Above q1 angle boundaries\r\n");
         }
     else {
+        //new q1_ref within reach
         q1_refOut = q1_refOutNew;
         }
         
     if (q2_refOutNew < q2_refOutMin){
+        //new q2_ref too small
         q2_refOut = q2_refOutMin;
         pc.printf("\r\n Under q2 angle boundaries");
         }
     else if (q2_refOutNew > q2_refOutMax){
+        //new q2_ref too large
         q2_refOut = q2_refOutMax;
         pc.printf("\r\n Above q2 angle boundaries");
         }
     else {
+        //new q2_ref within reach
         q2_refOut = q2_refOutNew;
         }        
-    //update joint angles
-    //q1Out = q1Out + q1_dotOut;  //in radians
-    //q2Out = q2Out + q2_dotOut;
-    
-    pc.baud(115200);
-    pc.printf("posX: %f ",Position_x);
-    pc.printf("posY: %f ",Position_y);
-    pc.printf("refX: %f ",ReferencePosition_xnew);
-    pc.printf("refY: %f ",ReferencePosition_ynew);
-    pc.printf("q1: %f   ", q1Out);
-    pc.printf("q1ref: %f    ", q1_refOut);
-    pc.printf("q2: %f   ", q2Out);
-    pc.printf("q2ref: %f    ", q2_refOut);
-    pc.printf("q1deg: %f   ", q1deg);
-    pc.printf("q2deg: %f   \r\n", q2deg);
     
     scope.set(0, ReferencePosition_xnew);
     scope.set(1, ReferencePosition_ynew);
@@ -372,137 +286,66 @@
     scope.set(3, envelopeR);
     scope.set(4, T);
     scope.send();
-    /*
-    pc.printf("dx:          %f \r\n", dx);
-    pc.printf("dy:          %f \r\n", dy);
-    pc.printf("q1:          %f \r\n", q1Out);
-    pc.printf("q1_dot:      %f \r\n", q1_dotOut);
-    pc.printf("q2:          %f \r\n", q2Out);
-    pc.printf("q2_dot:      %f \r\n", q2_dotOut);
+}    
+
+//--------------------------------------------------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------------------------------------------------
+
+void FeedbackControl1(float q1_ref, float q2_ref, float q1, float q2, float &motorValue1Out, float &motorValue2Out)
+{
+//This function calculates the error between angles and refernce angles, and provides motor values via a PIDF controller    
     
-    pc.printf("Counts1:     %f \r\n", counts1);
-    pc.printf("Encoder1:    %f \r\n", Encoder1Position);
-    pc.printf("Motor1:      %f \r\n", q1Out);
-    pc.printf("Counts2:    %f \r\n", counts2);
-    pc.printf("Encoder2:    %f \r\n", Encoder2Position);
-    pc.printf("Motor2:      %f \r\n", q2Out);
-    */
+    //calculate error values
+    float q1_error = q1_ref - q1;                                           // proportional angular error in radians
+    float q2_error = q2_ref - q2;                                           // proportional angular error in radians
     
-    }
-    
-
-void FeedbackControl1(float q1_ref, float q2_ref, float q1, float q2, float &motorValue1Out, float &motorValue2Out){
-    
-    // linear feedback control
-    float q1_error = q1_ref - q1; //referencePosition1 - Position1;             // proportional angular error in radians
-    float q2_error = q2_ref - q2; //referencePosition1 - Position1;             // proportional angular error in radians
-
+    //PIDF total error output
     float TotalError1 = pidf.step(q1_error);
     float TotalError2 = pidf.step(q2_error);
     
-    /*
-    float q1IntError = q1IntError + q1_error*t_sample;             // integrated error in radians
-    float q2IntError = q2IntError + q2_error*t_sample;             // integrated error in radians
-    //float maxKi = 0.2;
-    float Ki = 0.04*Kp;  //0.01*Kp; //potMeter2.read();
-    
-    float q1DerivativeError = (q1_error - q1_error_prev)/t_sample;  // derivative of error in radians
-    float q2DerivativeError = (q2_error_prev + q2_error)/t_sample;  // derivative of error in radians
-    //float maxKd = 0.2;
-    float Kd = 0.0;  //0.04*Kp; //potMeter2.read();
-    
-    //scope.set(0,referencePosition1);
-    //scope.set(1,Position1);
-    //scope.set(2,Ki);
-    //scope.send();
-    
-    TotalError1 = q1_error * Kp + q1IntError * Ki + q1DerivativeError * Kd;         //total controller output in radians = motor input
-    TotalError2 = q2_error * Kp + q2IntError * Ki + q2DerivativeError * Kd;         //total controller output in radians = motor input
-    */
-    /*
-    if (fabs(TotalError1) < TotalErrorMin) {
-        TotalError1=0;
-        }
-    else {
-        TotalError1=TotalError1;
-        }
-    if (fabs(TotalError2) < TotalErrorMin) {
-        TotalError2=0;
-        }
-    else {
-        TotalError2=TotalError2;
-        }
-    */
-    /*
-    DerTotalError1 = (TotalError1 - TotalError1_prev)/t_sample;
-    DerTotalError1 = (TotalError1 - TotalError1_prev)/t_sample;
-    motorValue1Out = DerTotalError1/MotorGain;       
-    motorValue2Out = DerTotalError2/MotorGain;       
-    */
-    
-    motorValue1Out = Motor1ExtraGain*(TotalError1/MotorGain);       
+    //calculate motor values from the total errors    
+    motorValue1Out = TotalError1/MotorGain;       
     motorValue2Out = TotalError2/MotorGain;       
     
-    /*
-    scope.set(0,q1_ref);
-    scope.set(1,q1);
-    scope.set(2,q2_ref);
-    scope.set(3,q2);
-    scope.set(4,motorValue1Out);
-    scope.set(5,motorValue2Out);
-    scope.send();
-    */
-    /*
-    pc.printf("E1: %f  ", q1_error);
-    pc.printf("IE1: %f  ", q1IntError);
-    pc.printf("DE1: %f  ", q2DerivativeError);
-    pc.printf("E2: %f  ", q2_error);
-    pc.printf("IE2: %f  ", q2IntError);
-    pc.printf("DE2: %f  ", q2DerivativeError);
-    */
-    //pc.printf("TE1: %f  ", TotalError1);
-    //pc.printf("TE2: %f  ", TotalError2);
-    pc.printf("M1: %f   \r\n", motorValue1Out);
-    pc.printf("M2: %f   \r\n", motorValue2Out);
-      
+    //prepare for next ticker cycle
     q1_error_prev = q1_error;
     q2_error_prev = q2_error;
     TotalError1_prev = TotalError1;
     TotalError2_prev = TotalError2;
 }
 
+//--------------------------------------------------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------------------------------------------------
+
 void SetMotor1(float motorValue1, float motorValue2)
 {
-    // Given -1<=motorValue<=1, this sets the PWM and direction
-    // bits for motor 1. Positive value makes motor rotating
-    // clockwise. motorValues outside range are truncated to
-    // within range
+//This function sets the PWM and direction bits for the motors. 
+//motorValues outside range are truncated to within range.
+
     //control motor 1
-    if (motorValue1 >=0) //clockwise rotation
-        {motor1DirectionPin=cw;        //inverted due to opposite (to other motor) build-up in tower
-        //led1=1;
-        //led2=0;
+    if (motorValue1 >=0){ 
+        //clockwise rotation
+        motor1DirectionPin=cw;
         }
-    else    //counterclockwise rotation 
-        {motor1DirectionPin=ccw;         //inverted due to opposite (to other motor) build-up in tower
-        //led1=0;
-        //led2=1;
+    else{
+        //counterclockwise rotation 
+        motor1DirectionPin=ccw;
         }
     if (fabs(motorValue1)>MotorMaxSpeed){
-        motor1MagnitudePin = MotorMaxSpeed;
+        motor1MagnitudePin = MotorMaxSpeed;                                 //motor values truncated
         }
     else{
-        motor1MagnitudePin = fabs(motorValue1);  //fabs(motorValue1);
+        motor1MagnitudePin = fabs(motorValue1);
         }
     
     //control motor 2
-    if (motorValue2 >=0)  //clockwise rotation
-        {motor2DirectionPin=cw; //action is ccw, due to faulty motor2DirectionPin (inverted)
-        //led1=1;
-        //led2=0;
+    if (motorValue2 >=0){  
+        //counterclockwise rotation due to inverse buildup in tower
+        motor2DirectionPin=cw;                                             //action is ccw, due to faulty motor2DirectionPin (inverted)
         }
-    else    //counterclockwise rotation 
-        {motor2DirectionPin=ccw;    //action is cw, due to faulty motor2DirectionPin (inverted)
+    else{    
+        //clockwise rotation due to inverse buildup in tower
+        motor2DirectionPin=ccw;                                            //action is cw, due to faulty motor2DirectionPin (inverted)
         //led1=0;
         //led2=1;
         }
@@ -512,83 +355,56 @@
     else{
         motor2MagnitudePin = fabs(motorValue2);
         }
-        float ReadDir1 = motor1DirectionPin.read();
-        float ReadDir2 = motor2DirectionPin.read();
-        pc.printf("M1 dir: %f \r\n", ReadDir1);
-        pc.printf("M2 dir: %f \r\n", ReadDir2);
 }
 
+//--------------------------------------------------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------------------------------------------------
+
 void MeasureAndControl()
 {
-    // This function measures the EMG of both arms, calculates via IK what
-    // the joint positions should be, and controls the motor with 
-    // a Feedback controller. This is called from a Ticker.
+// This function measures the EMG of both arms, calculates via inverse kinematics
+// what the joint reference positions should be, and controls the motor with 
+// a Feedback controller. This is called from a Ticker.
     FilteredSample(T, envelopeL, envelopeR);
     GetReferenceKinematics1(q1, q2, q1_ref, q2_ref);
     FeedbackControl1( q1_ref, q2_ref, q1, q2, motorValue1, motorValue2);
     SetMotor1(motorValue1, motorValue2);
 }
 
-void TimeTrackerF(){
-     //wait(1);   
-     //float Potmeter1 = potMeter1.read();
-     //float referencePosition1 = GetReferencePosition();
-     //pc.printf("TTReference Position: %d rad \r\n", referencePosition1);
-     //pc.printf("TTPotmeter1, for refpos: %f \r\n", Potmeter1);
-     //pc.printf("TTPotmeter2, Kp: %f \r\n", Potmeter2);
-     //pc.printf("TTCounts: %i \r\n", counts1);
-}
-
-/*
-void BiQuadFilter(){            //this function creates a BiQuad filter for the DerivativeCounts
-    //double in=DerivativeCounts();
-    bqcDerivativeCounts=bqc.step(DerivativeCounts);
-    //return(bqcDerivativeCounts);
-    }
-*/  
+//--------------------------------------------------------------------------------------------------------------------------
+//--------------------------------------------------------------------------------------------------------------------------
 
 int main()
 {
- //Initialize
- //int led1val = led1.read();
- //int led2val = led2.read();
- pc.baud(115200);
- pc.printf("Test putty IK");
-     ledRed=1;
-    ledBlue=1; 
-    ledRed=0; //red
+ //pc.baud(115200);
+ //pc.printf("Test putty IK");
+ ledRed=1;
+ ledBlue=1; 
+ ledRed=0;
 
-    bcq1R.add(&bq1R).add(&bq2R);        //set BiQuad chains
-    bcq2R.add(&bq3R);
-    
-    bcq1L.add(&bq1L).add(&bq2L);
-    bcq2L.add(&bq3L);
-
-            counts1 = Encoder1.getPulses();           // gives position of encoder 
-            counts2 = Encoder2.getPulses();           // gives position of encoder 
- wait(20.0);
- MeasureTicker.attach(&MeasureTicker_act, 0.002); //0.1f); 
- //bqc.add(&bq1).add(&bq2);                   //set BiQuad chain
- pidf.PIDF( Kp, Ki, Kd, N, t_sample );    //set PID filter
+ bcq1R.add(&bq1R).add(&bq2R);                                               //set BiQuad chains
+ bcq2R.add(&bq3R);
+ bcq1L.add(&bq1L).add(&bq2L);
+ bcq2L.add(&bq3L);
+ pidf.PIDF( Kp, Ki, Kd, N, t_sample );                                      //set PID filter
+ 
+ //start up encoders
+ counts1 = Encoder1.getPulses();                                            //gives position of encoder in counts 
+ counts2 = Encoder2.getPulses();                                            //gives position of encoder in counts
+ wait(20.0);                                                                //time to sart up HIDScope and EMG
+ MeasureTicker.attach(&MeasureTicker_act, 0.002);                           //initialize MeasureTicker, 500 Hz
+ 
  while(1)
     {
         if (MeasureTicker_go){
             MeasureTicker_go=false;
             ledGrn = 1;
             ledBlue = 0;
-            MeasureAndControl();
-            counts1 = Encoder1.getPulses();           // gives position of encoder 
-            counts2 = Encoder2.getPulses();           // gives position of encoder 
-            //pc.printf("counts1: %i  ", counts1);
-            //pc.printf("counts2: %i  \r\n", counts2);
+            MeasureAndControl();                                            //execute whole MeasureAndControl function
+            counts1 = Encoder1.getPulses();                                 //get encoder counts again
+            counts2 = Encoder2.getPulses();                                 //get encoder counts again
             ledBlue = 1;
             ledGrn = 0;
             }
-/*
-        if (BiQuadTicker_go){
-            BiQuadTicker_go=false;
-            BiQuadFilter();
-        }
-  */  
     }
 }
\ No newline at end of file