M9 Biorobotics Group 8 / Mbed 2 deprecated EMGfiltering_EMG

Dit is alleen het EMG gedeelte

Dependencies:   mbed HIDScope biquadFilter MODSERIAL FXOS8700Q

main.cpp@12:70f0710400c2, 2019-10-21 (annotated)

Committer:
Jellehierck
Date:
Mon Oct 21 14:36:24 2019 +0000
Revision:
12:70f0710400c2
Parent:
11:042170a9b93a
Child:
13:2724d2e747f1
Child:
15:421d3d9c563b
EMG Calibration (almost) finished, working on making scale factors

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 2:d3e9788ab1b3 13 // PC serial connection
Jellehierck 11:042170a9b93a 14 HIDScope scope( 3 );
Jellehierck 8:ea3de43c9e8b 15 MODSERIAL pc(USBTX, USBRX);
IsaRobin 0:6972d0e91af1 16
IsaRobin 0:6972d0e91af1 17 //EMG inputs definieren
IsaRobin 0:6972d0e91af1 18 AnalogIn emg1_in (A1); //emg van rechterbicep, voor de x-richting
IsaRobin 0:6972d0e91af1 19 AnalogIn emg2_in (A2); //emg van linkerbicep, voor de y-richting
IsaRobin 0:6972d0e91af1 20 AnalogIn emg3_in (A3); //emg van een derde (nog te bepalen) spier, voor het vernaderen van de richting
IsaRobin 0:6972d0e91af1 21
Jellehierck 4:09a01d2db8f7 22 // LED
Jellehierck 6:5437cc97e1e6 23 DigitalOut led_g(LED_GREEN);
Jellehierck 6:5437cc97e1e6 24 DigitalOut led_r(LED_RED);
Jellehierck 8:ea3de43c9e8b 25 DigitalOut led_b(LED_BLUE);
Jellehierck 8:ea3de43c9e8b 26
Jellehierck 8:ea3de43c9e8b 27 // Buttons
Jellehierck 8:ea3de43c9e8b 28 InterruptIn button1(D11);
Jellehierck 8:ea3de43c9e8b 29 InterruptIn button2(D10);
Jellehierck 12:70f0710400c2 30 InterruptIn button3(SW3);
Jellehierck 4:09a01d2db8f7 31
IsaRobin 0:6972d0e91af1 32 //variablen voor EMG
IsaRobin 0:6972d0e91af1 33 double emg1;
IsaRobin 0:6972d0e91af1 34 double emg2;
IsaRobin 0:6972d0e91af1 35 double emg3;
Jellehierck 12:70f0710400c2 36 double emg1_MVC;
Jellehierck 12:70f0710400c2 37 double emg1_MVC_stdev;
Jellehierck 12:70f0710400c2 38 double emg1_rest;
Jellehierck 12:70f0710400c2 39 double emg1_rest_stdev;
Jellehierck 7:7a088536f1c9 40
Jellehierck 7:7a088536f1c9 41 vector<double> emg1_cal;
Jellehierck 7:7a088536f1c9 42
IsaRobin 0:6972d0e91af1 43
Jellehierck 4:09a01d2db8f7 44 // Initialize tickers
Jellehierck 4:09a01d2db8f7 45 Ticker tickSample;
Jellehierck 7:7a088536f1c9 46 Timeout timeoutCalibrationMVC;
Jellehierck 12:70f0710400c2 47 Timeout timeoutCalibrationRest;
Jellehierck 7:7a088536f1c9 48 Ticker tickSampleCalibration;
Jellehierck 4:09a01d2db8f7 49
Jellehierck 4:09a01d2db8f7 50 // Sample rate
Jellehierck 11:042170a9b93a 51 const double Fs = 500; // Sampling frequency (s)
Jellehierck 11:042170a9b93a 52 const double Ts = 1/Fs; // Sampling time (s)
Jellehierck 11:042170a9b93a 53
Jellehierck 11:042170a9b93a 54 const double Tcal = 10.0f; // Calibration duration (s)
Jellehierck 11:042170a9b93a 55
Jellehierck 11:042170a9b93a 56 int trim_cal = 1; // Trim the beginning of the calibration vector to reduce transient behaviour by X seconds
Jellehierck 11:042170a9b93a 57 int trim_cal_i = trim_cal * Fs - 1;
Jellehierck 4:09a01d2db8f7 58
Jellehierck 3:c0ece64850db 59 // Notch filter coefficients (iirnotch Q factor 35 @50Hz) from MATLAB in the following form:
Jellehierck 3:c0ece64850db 60 // b01 b11 b21 a01 a11 a21
Jellehierck 11:042170a9b93a 61 BiQuad bq_notch( 0.995636295063941, -1.89829218816065, 0.995636295063941, 1, -1.89829218816065, 0.991272590127882);
Jellehierck 11:042170a9b93a 62 BiQuadChain bqc_notch;
Jellehierck 1:059cca298369 63
Jellehierck 3:c0ece64850db 64 // Highpass filter coefficients (butter 4th order @10Hz cutoff) from MATLAB in the following form:
Jellehierck 3:c0ece64850db 65 // b01 b11 b21 a01 a11 a21
Jellehierck 3:c0ece64850db 66 // b02 b12 b22 a02 a12 a22
Jellehierck 3:c0ece64850db 67 BiQuad bq_H1(0.922946103200875, -1.84589220640175, 0.922946103200875, 1, -1.88920703055163, 0.892769008131025);
Jellehierck 3:c0ece64850db 68 BiQuad bq_H2(1, -2, 1, 1, -1.95046575793011, 0.954143234875078);
Jellehierck 11:042170a9b93a 69 BiQuadChain bqc_high; // Used to chain two 2nd other filters into a 4th order filter
IsaRobin 0:6972d0e91af1 70
Jellehierck 3:c0ece64850db 71 // Lowpass filter coefficients (butter 4th order @5Hz cutoff) from MATLAB in the following form:
Jellehierck 3:c0ece64850db 72 // b01 b11 b21 a01 a11 a21
Jellehierck 3:c0ece64850db 73 // b02 b12 b22 a02 a12 a22
Jellehierck 3:c0ece64850db 74 BiQuad bq_L1(5.32116245737504e-08, 1.06423249147501e-07, 5.32116245737504e-08, 1, -1.94396715039462, 0.944882378004138);
Jellehierck 3:c0ece64850db 75 BiQuad bq_L2(1, 2, 1, 1, -1.97586467534468, 0.976794920438162);
Jellehierck 3:c0ece64850db 76 BiQuadChain bqc_low; // Used to chain two 2nd other filters into a 4th order filter
Jellehierck 2:d3e9788ab1b3 77
Jellehierck 8:ea3de43c9e8b 78 double getMean(const vector<double> &vect)
Jellehierck 7:7a088536f1c9 79 {
Jellehierck 8:ea3de43c9e8b 80 double sum = 0.0;
Jellehierck 8:ea3de43c9e8b 81 int vect_n = vect.size();
Jellehierck 8:ea3de43c9e8b 82
Jellehierck 8:ea3de43c9e8b 83 for ( int i = 0; i < vect_n; i++ ) {
Jellehierck 8:ea3de43c9e8b 84 sum += vect[i];
Jellehierck 8:ea3de43c9e8b 85 }
Jellehierck 8:ea3de43c9e8b 86 return sum/vect_n;
Jellehierck 8:ea3de43c9e8b 87 }
Jellehierck 8:ea3de43c9e8b 88
Jellehierck 8:ea3de43c9e8b 89 double getStdev(const vector<double> &vect, const double vect_mean)
Jellehierck 8:ea3de43c9e8b 90 {
Jellehierck 8:ea3de43c9e8b 91 double sum2 = 0.0;
Jellehierck 8:ea3de43c9e8b 92 int vect_n = vect.size();
Jellehierck 8:ea3de43c9e8b 93
Jellehierck 8:ea3de43c9e8b 94 for ( int i = 0; i < vect_n; i++ ) {
Jellehierck 8:ea3de43c9e8b 95 sum2 += pow( vect[i] - vect_mean, 2 );
Jellehierck 8:ea3de43c9e8b 96 }
Jellehierck 8:ea3de43c9e8b 97 double output = sqrt( sum2 / vect_n );
Jellehierck 8:ea3de43c9e8b 98 return output;
Jellehierck 7:7a088536f1c9 99 }
Jellehierck 7:7a088536f1c9 100
Jellehierck 6:5437cc97e1e6 101 // Check if filters are stable
Jellehierck 6:5437cc97e1e6 102 bool checkBQChainStable()
Jellehierck 6:5437cc97e1e6 103 {
Jellehierck 11:042170a9b93a 104 bool n_stable = bqc_notch.stable();
Jellehierck 11:042170a9b93a 105 bool hp_stable = bqc_high.stable();
Jellehierck 6:5437cc97e1e6 106 bool l_stable = bqc_low.stable();
Jellehierck 6:5437cc97e1e6 107
Jellehierck 11:042170a9b93a 108 if (n_stable && hp_stable && l_stable) {
Jellehierck 6:5437cc97e1e6 109 return true;
Jellehierck 6:5437cc97e1e6 110 } else {
Jellehierck 6:5437cc97e1e6 111 return false;
Jellehierck 6:5437cc97e1e6 112 }
Jellehierck 6:5437cc97e1e6 113 }
Jellehierck 6:5437cc97e1e6 114
Jellehierck 6:5437cc97e1e6 115
Jellehierck 11:042170a9b93a 116 /*
Jellehierck 6:5437cc97e1e6 117 // Read samples, filter samples and output to HIDScope
Jellehierck 2:d3e9788ab1b3 118 void sample()
Jellehierck 2:d3e9788ab1b3 119 {
Jellehierck 4:09a01d2db8f7 120 // Read EMG inputs
Jellehierck 2:d3e9788ab1b3 121 emg1 = emg1_in.read();
Jellehierck 2:d3e9788ab1b3 122 emg2 = emg2_in.read();
Jellehierck 2:d3e9788ab1b3 123 emg3 = emg3_in.read();
Jellehierck 4:09a01d2db8f7 124
Jellehierck 4:09a01d2db8f7 125 // Output raw EMG input
Jellehierck 4:09a01d2db8f7 126 scope.set(0, emg1 );
Jellehierck 6:5437cc97e1e6 127
Jellehierck 5:3d65f89e3755 128 // Filter notch and highpass
Jellehierck 5:3d65f89e3755 129 double emg1_n_hp = bqc_notch_high.step( emg1 );
Jellehierck 6:5437cc97e1e6 130
Jellehierck 5:3d65f89e3755 131 // Rectify
Jellehierck 5:3d65f89e3755 132 double emg1_rectify = fabs( emg1_n_hp );
Jellehierck 6:5437cc97e1e6 133
Jellehierck 5:3d65f89e3755 134 // Filter lowpass (completes envelope)
Jellehierck 5:3d65f89e3755 135 double emg1_env = bqc_low.step( emg1_rectify );
Jellehierck 4:09a01d2db8f7 136
Jellehierck 4:09a01d2db8f7 137 // Output EMG after filters
Jellehierck 5:3d65f89e3755 138 scope.set(1, emg1_env );
Jellehierck 4:09a01d2db8f7 139 scope.send();
Jellehierck 2:d3e9788ab1b3 140 }
Jellehierck 11:042170a9b93a 141 */
IsaRobin 0:6972d0e91af1 142
Jellehierck 7:7a088536f1c9 143 void sampleCalibration()
Jellehierck 7:7a088536f1c9 144 {
Jellehierck 7:7a088536f1c9 145 // Read EMG inputs
Jellehierck 7:7a088536f1c9 146 emg1 = emg1_in.read();
Jellehierck 7:7a088536f1c9 147 emg2 = emg2_in.read();
Jellehierck 7:7a088536f1c9 148 emg3 = emg3_in.read();
Jellehierck 7:7a088536f1c9 149
Jellehierck 7:7a088536f1c9 150 // Output raw EMG input
Jellehierck 7:7a088536f1c9 151 scope.set(0, emg1 );
Jellehierck 10:97a79aa10a56 152
Jellehierck 10:97a79aa10a56 153 double emg1_n = bqc_notch.step( emg1 ); // Filter notch
Jellehierck 11:042170a9b93a 154 scope.set(1, emg1_n);
Jellehierck 10:97a79aa10a56 155 double emg1_hp = bqc_high.step( emg1_n ); // Filter highpass
Jellehierck 11:042170a9b93a 156 double emg1_rectify = fabs( emg1_hp ); // Rectify
Jellehierck 7:7a088536f1c9 157 double emg1_env = bqc_low.step( emg1_rectify ); // Filter lowpass (completes envelope)
Jellehierck 7:7a088536f1c9 158
Jellehierck 7:7a088536f1c9 159 // Output EMG after filters
Jellehierck 11:042170a9b93a 160 scope.set(2, emg1_env );
Jellehierck 7:7a088536f1c9 161 scope.send();
Jellehierck 7:7a088536f1c9 162
Jellehierck 7:7a088536f1c9 163 emg1_cal.push_back(emg1_env);
Jellehierck 7:7a088536f1c9 164 }
Jellehierck 7:7a088536f1c9 165
Jellehierck 7:7a088536f1c9 166 void calibrationMVCFinished()
Jellehierck 7:7a088536f1c9 167 {
Jellehierck 7:7a088536f1c9 168 tickSampleCalibration.detach();
Jellehierck 11:042170a9b93a 169
Jellehierck 12:70f0710400c2 170 emg1_MVC = getMean(emg1_cal);
Jellehierck 12:70f0710400c2 171 emg1_MVC_stdev = getStdev(emg1_cal, emg1_MVC);
Jellehierck 10:97a79aa10a56 172
Jellehierck 10:97a79aa10a56 173 emg1_cal.clear();
Jellehierck 8:ea3de43c9e8b 174
Jellehierck 8:ea3de43c9e8b 175 led_b = 1;
Jellehierck 7:7a088536f1c9 176 }
Jellehierck 7:7a088536f1c9 177
Jellehierck 7:7a088536f1c9 178 void calibrationMVC()
Jellehierck 7:7a088536f1c9 179 {
Jellehierck 11:042170a9b93a 180 timeoutCalibrationMVC.attach( &calibrationMVCFinished, Tcal);
Jellehierck 7:7a088536f1c9 181 tickSampleCalibration.attach( &sampleCalibration, Ts );
Jellehierck 8:ea3de43c9e8b 182 led_b = 0;
Jellehierck 7:7a088536f1c9 183 }
Jellehierck 7:7a088536f1c9 184
Jellehierck 12:70f0710400c2 185 void calibrationRestFinished()
Jellehierck 12:70f0710400c2 186 {
Jellehierck 12:70f0710400c2 187 tickSampleCalibration.detach();
Jellehierck 12:70f0710400c2 188
Jellehierck 12:70f0710400c2 189 emg1_rest = getMean(emg1_cal);
Jellehierck 12:70f0710400c2 190 emg1_rest_stdev = getStdev(emg1_cal, emg1_rest);
Jellehierck 12:70f0710400c2 191
Jellehierck 12:70f0710400c2 192 emg1_cal.clear();
Jellehierck 7:7a088536f1c9 193
Jellehierck 12:70f0710400c2 194 led_b = 1;
Jellehierck 12:70f0710400c2 195 }
Jellehierck 12:70f0710400c2 196
Jellehierck 12:70f0710400c2 197 void calibrationRest()
Jellehierck 12:70f0710400c2 198 {
Jellehierck 12:70f0710400c2 199 timeoutCalibrationRest.attach( &calibrationRestFinished, Tcal);
Jellehierck 12:70f0710400c2 200 tickSampleCalibration.attach( &sampleCalibration, Ts );
Jellehierck 12:70f0710400c2 201 led_b = 0;
Jellehierck 12:70f0710400c2 202 }
Jellehierck 12:70f0710400c2 203
Jellehierck 12:70f0710400c2 204 void makeScale()
Jellehierck 12:70f0710400c2 205 {
Jellehierck 12:70f0710400c2 206 double margin_percentage = 10;
Jellehierck 12:70f0710400c2 207 double factor1 = 1 / emg1_MVC;
Jellehierck 12:70f0710400c2 208 double emg1_th = emg1_rest * factor1 + margin_percentage/100;
Jellehierck 12:70f0710400c2 209
Jellehierck 12:70f0710400c2 210 pc.printf("Factor: %f TH: %f\r\n", factor1, emg1_th);
Jellehierck 12:70f0710400c2 211 }
Jellehierck 7:7a088536f1c9 212
Jellehierck 5:3d65f89e3755 213 void main()
Jellehierck 4:09a01d2db8f7 214 {
Jellehierck 8:ea3de43c9e8b 215 pc.baud(115200);
Jellehierck 8:ea3de43c9e8b 216 pc.printf("Starting\r\n");
Jellehierck 6:5437cc97e1e6 217 // Initialize sample ticker
Jellehierck 8:ea3de43c9e8b 218 // tickSample.attach(&sample, Ts);
Jellehierck 6:5437cc97e1e6 219
Jellehierck 6:5437cc97e1e6 220 // Create BQ chains to reduce computations
Jellehierck 10:97a79aa10a56 221 bqc_notch.add( &bq_notch );
Jellehierck 10:97a79aa10a56 222 bqc_high.add( &bq_H1 ).add( &bq_H2 );
Jellehierck 5:3d65f89e3755 223 bqc_low.add( &bq_L1 ).add( &bq_L2 );
Jellehierck 4:09a01d2db8f7 224
Jellehierck 8:ea3de43c9e8b 225 led_b = 1; // Turn led off at startup
Jellehierck 8:ea3de43c9e8b 226 led_g = 1;
Jellehierck 8:ea3de43c9e8b 227
Jellehierck 6:5437cc97e1e6 228 // If any filter chain is unstable, red led will light up
Jellehierck 6:5437cc97e1e6 229 if (checkBQChainStable) {
Jellehierck 6:5437cc97e1e6 230 led_r = 1; // LED off
Jellehierck 6:5437cc97e1e6 231 } else {
Jellehierck 6:5437cc97e1e6 232 led_r = 0; // LED on
Jellehierck 6:5437cc97e1e6 233 }
Jellehierck 6:5437cc97e1e6 234
Jellehierck 8:ea3de43c9e8b 235 button1.fall( &calibrationMVC );
Jellehierck 12:70f0710400c2 236 button2.fall( &calibrationRest );
Jellehierck 12:70f0710400c2 237 button3.fall( &makeScale );
Jellehierck 8:ea3de43c9e8b 238
Jellehierck 4:09a01d2db8f7 239 while(true) {
Jellehierck 7:7a088536f1c9 240
Jellehierck 6:5437cc97e1e6 241 // Show that system is running
Jellehierck 8:ea3de43c9e8b 242 // led_g = !led_g;
Jellehierck 12:70f0710400c2 243 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 244 wait(0.5);
Jellehierck 4:09a01d2db8f7 245 }
Jellehierck 4:09a01d2db8f7 246 }