M9 Biorobotics Group 8 / Mbed 2 deprecated EMGfiltering_EMG

Dit is alleen het EMG gedeelte

Dependencies:   mbed HIDScope biquadFilter MODSERIAL FXOS8700Q

main.cpp@15:421d3d9c563b, 2019-10-22 (annotated)

Committer:
Jellehierck
Date:
Tue Oct 22 09:07:29 2019 +0000
Revision:
15:421d3d9c563b
Parent:
12:70f0710400c2
Child:
16:7acbcc4aa35c
Fixed bug which caused memory overflow, fixed wrong HIDScope outputs

Who changed what in which revision?

UserRevisionLine numberNew contents of line
IsaRobin 0:6972d0e91af1 1 //c++ script for filtering of measured EMG signals
IsaRobin 0:6972d0e91af1 2 #include "mbed.h" //Base library
IsaRobin 0:6972d0e91af1 3 #include "HIDScope.h" // to see if program is working and EMG is filtered properly
Jellehierck 2:d3e9788ab1b3 4 // #include "QEI.h"// is needed for the encoder
Jellehierck 8:ea3de43c9e8b 5 #include "MODSERIAL.h"// in order for connection with the pc
Jellehierck 2:d3e9788ab1b3 6 #include "BiQuad.h"
Jellehierck 2:d3e9788ab1b3 7 // #include "FastPWM.h"
Jellehierck 2:d3e9788ab1b3 8 // #include "Arduino.h" //misschien handig omdat we het EMG arduino board gebruiken (?)
Jellehierck 2:d3e9788ab1b3 9 // #include "EMGFilters.h"
IsaRobin 0:6972d0e91af1 10 #include <vector> // For easy array management
Jellehierck 7:7a088536f1c9 11 #include <numeric> // For manipulating array data
IsaRobin 0:6972d0e91af1 12
Jellehierck 15:421d3d9c563b 13 /*
Jellehierck 15:421d3d9c563b 14 ------ DEFINE MBED CONNECTIONS ------
Jellehierck 15:421d3d9c563b 15 */
IsaRobin 0:6972d0e91af1 16
Jellehierck 15:421d3d9c563b 17 // PC serial connection
Jellehierck 15:421d3d9c563b 18 HIDScope scope( 5 );
Jellehierck 15:421d3d9c563b 19 MODSERIAL pc(USBTX, USBRX);
IsaRobin 0:6972d0e91af1 20
Jellehierck 4:09a01d2db8f7 21 // LED
Jellehierck 6:5437cc97e1e6 22 DigitalOut led_g(LED_GREEN);
Jellehierck 6:5437cc97e1e6 23 DigitalOut led_r(LED_RED);
Jellehierck 8:ea3de43c9e8b 24 DigitalOut led_b(LED_BLUE);
Jellehierck 8:ea3de43c9e8b 25
Jellehierck 8:ea3de43c9e8b 26 // Buttons
Jellehierck 8:ea3de43c9e8b 27 InterruptIn button1(D11);
Jellehierck 8:ea3de43c9e8b 28 InterruptIn button2(D10);
Jellehierck 12:70f0710400c2 29 InterruptIn button3(SW3);
Jellehierck 4:09a01d2db8f7 30
Jellehierck 15:421d3d9c563b 31 // Global variables for EMG reading
Jellehierck 15:421d3d9c563b 32 AnalogIn emg1_in (A1); // Right biceps, x axis
Jellehierck 15:421d3d9c563b 33 AnalogIn emg2_in (A2); // Left biceps, y axis
Jellehierck 15:421d3d9c563b 34 AnalogIn emg3_in (A3); // Third muscle, TBD
Jellehierck 15:421d3d9c563b 35
IsaRobin 0:6972d0e91af1 36 double emg1;
Jellehierck 12:70f0710400c2 37 double emg1_MVC;
Jellehierck 12:70f0710400c2 38 double emg1_MVC_stdev;
Jellehierck 12:70f0710400c2 39 double emg1_rest;
Jellehierck 12:70f0710400c2 40 double emg1_rest_stdev;
Jellehierck 7:7a088536f1c9 41 vector<double> emg1_cal;
Jellehierck 7:7a088536f1c9 42
Jellehierck 15:421d3d9c563b 43 double emg2;
Jellehierck 15:421d3d9c563b 44 double emg2_MVC;
Jellehierck 15:421d3d9c563b 45 double emg2_MVC_stdev;
Jellehierck 15:421d3d9c563b 46 double emg2_rest;
Jellehierck 15:421d3d9c563b 47 double emg2_rest_stdev;
Jellehierck 15:421d3d9c563b 48 vector<double> emg2_cal;
IsaRobin 0:6972d0e91af1 49
Jellehierck 15:421d3d9c563b 50 double emg3;
Jellehierck 15:421d3d9c563b 51 double emg3_MVC;
Jellehierck 15:421d3d9c563b 52 double emg3_MVC_stdev;
Jellehierck 15:421d3d9c563b 53 double emg3_rest;
Jellehierck 15:421d3d9c563b 54 double emg3_rest_stdev;
Jellehierck 15:421d3d9c563b 55 vector<double> emg3_cal;
Jellehierck 15:421d3d9c563b 56
Jellehierck 15:421d3d9c563b 57 // Initialize tickers and timeouts
Jellehierck 4:09a01d2db8f7 58 Ticker tickSample;
Jellehierck 15:421d3d9c563b 59 Ticker tickSampleCalibration;
Jellehierck 7:7a088536f1c9 60 Timeout timeoutCalibrationMVC;
Jellehierck 12:70f0710400c2 61 Timeout timeoutCalibrationRest;
Jellehierck 4:09a01d2db8f7 62
Jellehierck 15:421d3d9c563b 63 /*
Jellehierck 15:421d3d9c563b 64 ------ GLOBAL VARIABLES ------
Jellehierck 15:421d3d9c563b 65 */
Jellehierck 11:042170a9b93a 66 const double Fs = 500; // Sampling frequency (s)
Jellehierck 11:042170a9b93a 67 const double Tcal = 10.0f; // Calibration duration (s)
Jellehierck 15:421d3d9c563b 68 int trim_cal = 1; // Trim transient behaviour of calibration (s)
Jellehierck 4:09a01d2db8f7 69
Jellehierck 15:421d3d9c563b 70 // Calculate global variables
Jellehierck 15:421d3d9c563b 71 const double Ts = 1/Fs; // Sampling time (s)
Jellehierck 15:421d3d9c563b 72 int trim_cal_i = trim_cal * Fs - 1; // Determine iterator of transient behaviour trim
Jellehierck 15:421d3d9c563b 73
Jellehierck 15:421d3d9c563b 74 // Notch biquad filter coefficients (iirnotch Q factor 35 @50Hz) from MATLAB:
Jellehierck 15:421d3d9c563b 75 BiQuad bq_notch( 0.995636295063941, -1.89829218816065, 0.995636295063941, 1, -1.89829218816065, 0.991272590127882); // b01 b11 b21 a01 a11 a21
Jellehierck 11:042170a9b93a 76 BiQuadChain bqc_notch;
Jellehierck 1:059cca298369 77
Jellehierck 15:421d3d9c563b 78 // Highpass biquad filter coefficients (butter 4th order @10Hz cutoff) from MATLAB
Jellehierck 15:421d3d9c563b 79 BiQuad bq_H1(0.922946103200875, -1.84589220640175, 0.922946103200875, 1, -1.88920703055163, 0.892769008131025); // b01 b11 b21 a01 a11 a21
Jellehierck 15:421d3d9c563b 80 BiQuad bq_H2(1, -2, 1, 1, -1.95046575793011, 0.954143234875078); // b02 b12 b22 a02 a12 a22
Jellehierck 15:421d3d9c563b 81 BiQuadChain bqc_high;
IsaRobin 0:6972d0e91af1 82
Jellehierck 15:421d3d9c563b 83 // Lowpass biquad filter coefficients (butter 4th order @5Hz cutoff) from MATLAB:
Jellehierck 15:421d3d9c563b 84 BiQuad bq_L1(5.32116245737504e-08, 1.06423249147501e-07, 5.32116245737504e-08, 1, -1.94396715039462, 0.944882378004138); // b01 b11 b21 a01 a11 a21
Jellehierck 15:421d3d9c563b 85 BiQuad bq_L2(1, 2, 1, 1, -1.97586467534468, 0.976794920438162); // b02 b12 b22 a02 a12 a22
Jellehierck 15:421d3d9c563b 86 BiQuadChain bqc_low;
Jellehierck 2:d3e9788ab1b3 87
Jellehierck 15:421d3d9c563b 88 /*
Jellehierck 15:421d3d9c563b 89 ------ HELPER FUNCTIONS ------
Jellehierck 15:421d3d9c563b 90 */
Jellehierck 15:421d3d9c563b 91
Jellehierck 15:421d3d9c563b 92 // Return mean of vector
Jellehierck 8:ea3de43c9e8b 93 double getMean(const vector<double> &vect)
Jellehierck 7:7a088536f1c9 94 {
Jellehierck 8:ea3de43c9e8b 95 double sum = 0.0;
Jellehierck 8:ea3de43c9e8b 96 int vect_n = vect.size();
Jellehierck 8:ea3de43c9e8b 97
Jellehierck 8:ea3de43c9e8b 98 for ( int i = 0; i < vect_n; i++ ) {
Jellehierck 8:ea3de43c9e8b 99 sum += vect[i];
Jellehierck 8:ea3de43c9e8b 100 }
Jellehierck 8:ea3de43c9e8b 101 return sum/vect_n;
Jellehierck 8:ea3de43c9e8b 102 }
Jellehierck 8:ea3de43c9e8b 103
Jellehierck 15:421d3d9c563b 104 // Return standard deviation of vector
Jellehierck 8:ea3de43c9e8b 105 double getStdev(const vector<double> &vect, const double vect_mean)
Jellehierck 8:ea3de43c9e8b 106 {
Jellehierck 8:ea3de43c9e8b 107 double sum2 = 0.0;
Jellehierck 8:ea3de43c9e8b 108 int vect_n = vect.size();
Jellehierck 8:ea3de43c9e8b 109
Jellehierck 8:ea3de43c9e8b 110 for ( int i = 0; i < vect_n; i++ ) {
Jellehierck 8:ea3de43c9e8b 111 sum2 += pow( vect[i] - vect_mean, 2 );
Jellehierck 8:ea3de43c9e8b 112 }
Jellehierck 8:ea3de43c9e8b 113 double output = sqrt( sum2 / vect_n );
Jellehierck 8:ea3de43c9e8b 114 return output;
Jellehierck 7:7a088536f1c9 115 }
Jellehierck 7:7a088536f1c9 116
Jellehierck 15:421d3d9c563b 117 // Check filter stability
Jellehierck 6:5437cc97e1e6 118 bool checkBQChainStable()
Jellehierck 6:5437cc97e1e6 119 {
Jellehierck 11:042170a9b93a 120 bool n_stable = bqc_notch.stable();
Jellehierck 11:042170a9b93a 121 bool hp_stable = bqc_high.stable();
Jellehierck 6:5437cc97e1e6 122 bool l_stable = bqc_low.stable();
Jellehierck 6:5437cc97e1e6 123
Jellehierck 11:042170a9b93a 124 if (n_stable && hp_stable && l_stable) {
Jellehierck 6:5437cc97e1e6 125 return true;
Jellehierck 6:5437cc97e1e6 126 } else {
Jellehierck 6:5437cc97e1e6 127 return false;
Jellehierck 6:5437cc97e1e6 128 }
Jellehierck 6:5437cc97e1e6 129 }
Jellehierck 6:5437cc97e1e6 130
Jellehierck 15:421d3d9c563b 131 /*
Jellehierck 15:421d3d9c563b 132 ------ TICKER FUNCTIONS ------
Jellehierck 15:421d3d9c563b 133 */
Jellehierck 11:042170a9b93a 134 /*
Jellehierck 6:5437cc97e1e6 135 // Read samples, filter samples and output to HIDScope
Jellehierck 2:d3e9788ab1b3 136 void sample()
Jellehierck 2:d3e9788ab1b3 137 {
Jellehierck 4:09a01d2db8f7 138 // Read EMG inputs
Jellehierck 2:d3e9788ab1b3 139 emg1 = emg1_in.read();
Jellehierck 2:d3e9788ab1b3 140 emg2 = emg2_in.read();
Jellehierck 2:d3e9788ab1b3 141 emg3 = emg3_in.read();
Jellehierck 4:09a01d2db8f7 142
Jellehierck 4:09a01d2db8f7 143 // Output raw EMG input
Jellehierck 4:09a01d2db8f7 144 scope.set(0, emg1 );
Jellehierck 6:5437cc97e1e6 145
Jellehierck 5:3d65f89e3755 146 // Filter notch and highpass
Jellehierck 5:3d65f89e3755 147 double emg1_n_hp = bqc_notch_high.step( emg1 );
Jellehierck 6:5437cc97e1e6 148
Jellehierck 5:3d65f89e3755 149 // Rectify
Jellehierck 5:3d65f89e3755 150 double emg1_rectify = fabs( emg1_n_hp );
Jellehierck 6:5437cc97e1e6 151
Jellehierck 5:3d65f89e3755 152 // Filter lowpass (completes envelope)
Jellehierck 5:3d65f89e3755 153 double emg1_env = bqc_low.step( emg1_rectify );
Jellehierck 4:09a01d2db8f7 154
Jellehierck 4:09a01d2db8f7 155 // Output EMG after filters
Jellehierck 5:3d65f89e3755 156 scope.set(1, emg1_env );
Jellehierck 4:09a01d2db8f7 157 scope.send();
Jellehierck 2:d3e9788ab1b3 158 }
Jellehierck 11:042170a9b93a 159 */
IsaRobin 0:6972d0e91af1 160
Jellehierck 7:7a088536f1c9 161 void sampleCalibration()
Jellehierck 7:7a088536f1c9 162 {
Jellehierck 7:7a088536f1c9 163 // Read EMG inputs
Jellehierck 7:7a088536f1c9 164 emg1 = emg1_in.read();
Jellehierck 7:7a088536f1c9 165 emg2 = emg2_in.read();
Jellehierck 7:7a088536f1c9 166 emg3 = emg3_in.read();
Jellehierck 7:7a088536f1c9 167
Jellehierck 7:7a088536f1c9 168 // Output raw EMG input
Jellehierck 7:7a088536f1c9 169 scope.set(0, emg1 );
Jellehierck 10:97a79aa10a56 170
Jellehierck 10:97a79aa10a56 171 double emg1_n = bqc_notch.step( emg1 ); // Filter notch
Jellehierck 11:042170a9b93a 172 scope.set(1, emg1_n);
Jellehierck 10:97a79aa10a56 173 double emg1_hp = bqc_high.step( emg1_n ); // Filter highpass
Jellehierck 15:421d3d9c563b 174 scope.set(2, emg1_hp);
Jellehierck 11:042170a9b93a 175 double emg1_rectify = fabs( emg1_hp ); // Rectify
Jellehierck 15:421d3d9c563b 176 scope.set(3, emg1_rectify);
Jellehierck 7:7a088536f1c9 177 double emg1_env = bqc_low.step( emg1_rectify ); // Filter lowpass (completes envelope)
Jellehierck 7:7a088536f1c9 178
Jellehierck 7:7a088536f1c9 179 // Output EMG after filters
Jellehierck 15:421d3d9c563b 180 scope.set(4, emg1_env );
Jellehierck 7:7a088536f1c9 181 scope.send();
Jellehierck 7:7a088536f1c9 182
Jellehierck 7:7a088536f1c9 183 emg1_cal.push_back(emg1_env);
Jellehierck 7:7a088536f1c9 184 }
Jellehierck 7:7a088536f1c9 185
Jellehierck 15:421d3d9c563b 186 /*
Jellehierck 15:421d3d9c563b 187 ------ EMG CALIBRATION FUNCTIONS ------
Jellehierck 15:421d3d9c563b 188 */
Jellehierck 15:421d3d9c563b 189
Jellehierck 15:421d3d9c563b 190 // Finish up calibration of MVC
Jellehierck 7:7a088536f1c9 191 void calibrationMVCFinished()
Jellehierck 7:7a088536f1c9 192 {
Jellehierck 15:421d3d9c563b 193 tickSampleCalibration.detach(); // Stop calibration ticker to remove interrupt
Jellehierck 15:421d3d9c563b 194 emg1_MVC = getMean(emg1_cal); // Store MVC globally
Jellehierck 15:421d3d9c563b 195 emg1_MVC_stdev = getStdev(emg1_cal, emg1_MVC); // Store MVC stde globally
Jellehierck 15:421d3d9c563b 196 emg1_cal.clear(); // Empty vector to prevent memory overflow
Jellehierck 15:421d3d9c563b 197 led_b = 1; // Turn off calibration led
Jellehierck 7:7a088536f1c9 198 }
Jellehierck 7:7a088536f1c9 199
Jellehierck 15:421d3d9c563b 200 // Run calibration of MVC
Jellehierck 7:7a088536f1c9 201 void calibrationMVC()
Jellehierck 7:7a088536f1c9 202 {
Jellehierck 15:421d3d9c563b 203 timeoutCalibrationMVC.attach( &calibrationMVCFinished, Tcal); // Stop MVC calibration after interval
Jellehierck 15:421d3d9c563b 204 tickSampleCalibration.attach( &sampleCalibration, Ts ); // Start sample ticker
Jellehierck 15:421d3d9c563b 205 led_b = 0; // Turn on calibration led
Jellehierck 7:7a088536f1c9 206 }
Jellehierck 7:7a088536f1c9 207
Jellehierck 15:421d3d9c563b 208 // Finish up calibration in rest
Jellehierck 12:70f0710400c2 209 void calibrationRestFinished()
Jellehierck 12:70f0710400c2 210 {
Jellehierck 15:421d3d9c563b 211 tickSampleCalibration.detach(); // Stop calibration ticker to remove interrupt
Jellehierck 15:421d3d9c563b 212 emg1_rest = getMean(emg1_cal); // Store rest globally
Jellehierck 15:421d3d9c563b 213 emg1_rest_stdev = getStdev(emg1_cal, emg1_rest);// Store rest stdev globally
Jellehierck 15:421d3d9c563b 214 emg1_cal.clear(); // Empty vector to prevent memory overflow
Jellehierck 15:421d3d9c563b 215 led_b = 1; // Turn off calibration led
Jellehierck 12:70f0710400c2 216 }
Jellehierck 12:70f0710400c2 217
Jellehierck 12:70f0710400c2 218 void calibrationRest()
Jellehierck 12:70f0710400c2 219 {
Jellehierck 15:421d3d9c563b 220 timeoutCalibrationRest.attach( &calibrationRestFinished, Tcal); // Stop rest calibration after interval
Jellehierck 15:421d3d9c563b 221 tickSampleCalibration.attach( &sampleCalibration, Ts ); // Start sample ticker
Jellehierck 15:421d3d9c563b 222 led_b = 0; // Turn on calibration led
Jellehierck 12:70f0710400c2 223 }
Jellehierck 12:70f0710400c2 224
Jellehierck 15:421d3d9c563b 225 // Determine scale factors for operation mode
Jellehierck 12:70f0710400c2 226 void makeScale()
Jellehierck 12:70f0710400c2 227 {
Jellehierck 15:421d3d9c563b 228 double margin_percentage = 10; // Set up % margin for rest
Jellehierck 15:421d3d9c563b 229 double factor1 = 1 / emg1_MVC; // Factor to normalize MVC
Jellehierck 15:421d3d9c563b 230 double emg1_th = emg1_rest * factor1 + margin_percentage/100; // Set normalized rest threshold
Jellehierck 12:70f0710400c2 231
Jellehierck 12:70f0710400c2 232 pc.printf("Factor: %f TH: %f\r\n", factor1, emg1_th);
Jellehierck 12:70f0710400c2 233 }
Jellehierck 7:7a088536f1c9 234
Jellehierck 5:3d65f89e3755 235 void main()
Jellehierck 4:09a01d2db8f7 236 {
Jellehierck 15:421d3d9c563b 237 pc.baud(115200); // MODSERIAL rate
Jellehierck 8:ea3de43c9e8b 238 pc.printf("Starting\r\n");
Jellehierck 15:421d3d9c563b 239
Jellehierck 15:421d3d9c563b 240 // tickSample.attach(&sample, Ts); // Initialize sample ticker
Jellehierck 6:5437cc97e1e6 241
Jellehierck 6:5437cc97e1e6 242 // Create BQ chains to reduce computations
Jellehierck 10:97a79aa10a56 243 bqc_notch.add( &bq_notch );
Jellehierck 10:97a79aa10a56 244 bqc_high.add( &bq_H1 ).add( &bq_H2 );
Jellehierck 5:3d65f89e3755 245 bqc_low.add( &bq_L1 ).add( &bq_L2 );
Jellehierck 4:09a01d2db8f7 246
Jellehierck 15:421d3d9c563b 247 led_b = 1; // Turn blue led off at startup
Jellehierck 15:421d3d9c563b 248 led_g = 1; // Turn green led off at startup
Jellehierck 15:421d3d9c563b 249 led_r = 1; // Turn red led off at startup
Jellehierck 8:ea3de43c9e8b 250
Jellehierck 6:5437cc97e1e6 251 // If any filter chain is unstable, red led will light up
Jellehierck 6:5437cc97e1e6 252 if (checkBQChainStable) {
Jellehierck 6:5437cc97e1e6 253 led_r = 1; // LED off
Jellehierck 6:5437cc97e1e6 254 } else {
Jellehierck 6:5437cc97e1e6 255 led_r = 0; // LED on
Jellehierck 6:5437cc97e1e6 256 }
Jellehierck 6:5437cc97e1e6 257
Jellehierck 15:421d3d9c563b 258 button1.fall( &calibrationMVC ); // Run MVC calibration on button press
Jellehierck 15:421d3d9c563b 259 button2.fall( &calibrationRest ); // Run rest calibration on button press
Jellehierck 15:421d3d9c563b 260 button3.fall( &makeScale ); // Create scale factors and close calibration at button press
Jellehierck 8:ea3de43c9e8b 261
Jellehierck 4:09a01d2db8f7 262 while(true) {
Jellehierck 7:7a088536f1c9 263
Jellehierck 6:5437cc97e1e6 264 // Show that system is running
Jellehierck 8:ea3de43c9e8b 265 // led_g = !led_g;
Jellehierck 12:70f0710400c2 266 pc.printf("EMG MVC: %f stdev: %f\r\nEMG Rest: %f stdev: %f\r\n", emg1_MVC, emg1_MVC_stdev, emg1_rest, emg1_rest_stdev);
Jellehierck 4:09a01d2db8f7 267 wait(0.5);
Jellehierck 4:09a01d2db8f7 268 }
Jellehierck 4:09a01d2db8f7 269 }