M9 Biorobotics Group 8 / Mbed 2 deprecated EMGfiltering_EMG

Dit is alleen het EMG gedeelte

Dependencies:   mbed HIDScope biquadFilter MODSERIAL FXOS8700Q

main.cpp@16:7acbcc4aa35c, 2019-10-22 (annotated)

Committer:
Jellehierck
Date:
Tue Oct 22 10:25:22 2019 +0000
Revision:
16:7acbcc4aa35c
Parent:
15:421d3d9c563b
Child:
17:e4e7b1fbb263
Started work in EMG substate machine. We first need to draw the substate machine on paper

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 16:7acbcc4aa35c 31 // EMG Substates
Jellehierck 16:7acbcc4aa35c 32 enum EMG_States = { emg_wait, emg_cal_MVC, emg_cal_rest, emg_scale, emg_operation }; // Define EMG substates
Jellehierck 16:7acbcc4aa35c 33 EMG_States emg_curr_state; // Initialize EMG substate variable
Jellehierck 16:7acbcc4aa35c 34
Jellehierck 15:421d3d9c563b 35 // Global variables for EMG reading
Jellehierck 15:421d3d9c563b 36 AnalogIn emg1_in (A1); // Right biceps, x axis
Jellehierck 15:421d3d9c563b 37 AnalogIn emg2_in (A2); // Left biceps, y axis
Jellehierck 15:421d3d9c563b 38 AnalogIn emg3_in (A3); // Third muscle, TBD
Jellehierck 15:421d3d9c563b 39
IsaRobin 0:6972d0e91af1 40 double emg1;
Jellehierck 12:70f0710400c2 41 double emg1_MVC;
Jellehierck 12:70f0710400c2 42 double emg1_MVC_stdev;
Jellehierck 12:70f0710400c2 43 double emg1_rest;
Jellehierck 12:70f0710400c2 44 double emg1_rest_stdev;
Jellehierck 7:7a088536f1c9 45 vector<double> emg1_cal;
Jellehierck 7:7a088536f1c9 46
Jellehierck 15:421d3d9c563b 47 double emg2;
Jellehierck 15:421d3d9c563b 48 double emg2_MVC;
Jellehierck 15:421d3d9c563b 49 double emg2_MVC_stdev;
Jellehierck 15:421d3d9c563b 50 double emg2_rest;
Jellehierck 15:421d3d9c563b 51 double emg2_rest_stdev;
Jellehierck 15:421d3d9c563b 52 vector<double> emg2_cal;
IsaRobin 0:6972d0e91af1 53
Jellehierck 15:421d3d9c563b 54 double emg3;
Jellehierck 15:421d3d9c563b 55 double emg3_MVC;
Jellehierck 15:421d3d9c563b 56 double emg3_MVC_stdev;
Jellehierck 15:421d3d9c563b 57 double emg3_rest;
Jellehierck 15:421d3d9c563b 58 double emg3_rest_stdev;
Jellehierck 15:421d3d9c563b 59 vector<double> emg3_cal;
Jellehierck 15:421d3d9c563b 60
Jellehierck 15:421d3d9c563b 61 // Initialize tickers and timeouts
Jellehierck 4:09a01d2db8f7 62 Ticker tickSample;
Jellehierck 15:421d3d9c563b 63 Ticker tickSampleCalibration;
Jellehierck 7:7a088536f1c9 64 Timeout timeoutCalibrationMVC;
Jellehierck 12:70f0710400c2 65 Timeout timeoutCalibrationRest;
Jellehierck 4:09a01d2db8f7 66
Jellehierck 15:421d3d9c563b 67 /*
Jellehierck 15:421d3d9c563b 68 ------ GLOBAL VARIABLES ------
Jellehierck 15:421d3d9c563b 69 */
Jellehierck 11:042170a9b93a 70 const double Fs = 500; // Sampling frequency (s)
Jellehierck 11:042170a9b93a 71 const double Tcal = 10.0f; // Calibration duration (s)
Jellehierck 15:421d3d9c563b 72 int trim_cal = 1; // Trim transient behaviour of calibration (s)
Jellehierck 4:09a01d2db8f7 73
Jellehierck 15:421d3d9c563b 74 // Calculate global variables
Jellehierck 15:421d3d9c563b 75 const double Ts = 1/Fs; // Sampling time (s)
Jellehierck 15:421d3d9c563b 76 int trim_cal_i = trim_cal * Fs - 1; // Determine iterator of transient behaviour trim
Jellehierck 15:421d3d9c563b 77
Jellehierck 15:421d3d9c563b 78 // Notch biquad filter coefficients (iirnotch Q factor 35 @50Hz) from MATLAB:
Jellehierck 15:421d3d9c563b 79 BiQuad bq_notch( 0.995636295063941, -1.89829218816065, 0.995636295063941, 1, -1.89829218816065, 0.991272590127882); // b01 b11 b21 a01 a11 a21
Jellehierck 11:042170a9b93a 80 BiQuadChain bqc_notch;
Jellehierck 1:059cca298369 81
Jellehierck 15:421d3d9c563b 82 // Highpass biquad filter coefficients (butter 4th order @10Hz cutoff) from MATLAB
Jellehierck 15:421d3d9c563b 83 BiQuad bq_H1(0.922946103200875, -1.84589220640175, 0.922946103200875, 1, -1.88920703055163, 0.892769008131025); // b01 b11 b21 a01 a11 a21
Jellehierck 15:421d3d9c563b 84 BiQuad bq_H2(1, -2, 1, 1, -1.95046575793011, 0.954143234875078); // b02 b12 b22 a02 a12 a22
Jellehierck 15:421d3d9c563b 85 BiQuadChain bqc_high;
IsaRobin 0:6972d0e91af1 86
Jellehierck 15:421d3d9c563b 87 // Lowpass biquad filter coefficients (butter 4th order @5Hz cutoff) from MATLAB:
Jellehierck 15:421d3d9c563b 88 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 89 BiQuad bq_L2(1, 2, 1, 1, -1.97586467534468, 0.976794920438162); // b02 b12 b22 a02 a12 a22
Jellehierck 15:421d3d9c563b 90 BiQuadChain bqc_low;
Jellehierck 2:d3e9788ab1b3 91
Jellehierck 15:421d3d9c563b 92 /*
Jellehierck 15:421d3d9c563b 93 ------ HELPER FUNCTIONS ------
Jellehierck 15:421d3d9c563b 94 */
Jellehierck 15:421d3d9c563b 95
Jellehierck 15:421d3d9c563b 96 // Return mean of vector
Jellehierck 8:ea3de43c9e8b 97 double getMean(const vector<double> &vect)
Jellehierck 7:7a088536f1c9 98 {
Jellehierck 8:ea3de43c9e8b 99 double sum = 0.0;
Jellehierck 8:ea3de43c9e8b 100 int vect_n = vect.size();
Jellehierck 8:ea3de43c9e8b 101
Jellehierck 8:ea3de43c9e8b 102 for ( int i = 0; i < vect_n; i++ ) {
Jellehierck 8:ea3de43c9e8b 103 sum += vect[i];
Jellehierck 8:ea3de43c9e8b 104 }
Jellehierck 8:ea3de43c9e8b 105 return sum/vect_n;
Jellehierck 8:ea3de43c9e8b 106 }
Jellehierck 8:ea3de43c9e8b 107
Jellehierck 15:421d3d9c563b 108 // Return standard deviation of vector
Jellehierck 8:ea3de43c9e8b 109 double getStdev(const vector<double> &vect, const double vect_mean)
Jellehierck 8:ea3de43c9e8b 110 {
Jellehierck 8:ea3de43c9e8b 111 double sum2 = 0.0;
Jellehierck 8:ea3de43c9e8b 112 int vect_n = vect.size();
Jellehierck 8:ea3de43c9e8b 113
Jellehierck 8:ea3de43c9e8b 114 for ( int i = 0; i < vect_n; i++ ) {
Jellehierck 8:ea3de43c9e8b 115 sum2 += pow( vect[i] - vect_mean, 2 );
Jellehierck 8:ea3de43c9e8b 116 }
Jellehierck 8:ea3de43c9e8b 117 double output = sqrt( sum2 / vect_n );
Jellehierck 8:ea3de43c9e8b 118 return output;
Jellehierck 7:7a088536f1c9 119 }
Jellehierck 7:7a088536f1c9 120
Jellehierck 15:421d3d9c563b 121 // Check filter stability
Jellehierck 6:5437cc97e1e6 122 bool checkBQChainStable()
Jellehierck 6:5437cc97e1e6 123 {
Jellehierck 11:042170a9b93a 124 bool n_stable = bqc_notch.stable();
Jellehierck 11:042170a9b93a 125 bool hp_stable = bqc_high.stable();
Jellehierck 6:5437cc97e1e6 126 bool l_stable = bqc_low.stable();
Jellehierck 6:5437cc97e1e6 127
Jellehierck 11:042170a9b93a 128 if (n_stable && hp_stable && l_stable) {
Jellehierck 6:5437cc97e1e6 129 return true;
Jellehierck 6:5437cc97e1e6 130 } else {
Jellehierck 6:5437cc97e1e6 131 return false;
Jellehierck 6:5437cc97e1e6 132 }
Jellehierck 6:5437cc97e1e6 133 }
Jellehierck 6:5437cc97e1e6 134
Jellehierck 15:421d3d9c563b 135 /*
Jellehierck 15:421d3d9c563b 136 ------ TICKER FUNCTIONS ------
Jellehierck 15:421d3d9c563b 137 */
Jellehierck 11:042170a9b93a 138 /*
Jellehierck 6:5437cc97e1e6 139 // Read samples, filter samples and output to HIDScope
Jellehierck 2:d3e9788ab1b3 140 void sample()
Jellehierck 2:d3e9788ab1b3 141 {
Jellehierck 4:09a01d2db8f7 142 // Read EMG inputs
Jellehierck 2:d3e9788ab1b3 143 emg1 = emg1_in.read();
Jellehierck 2:d3e9788ab1b3 144 emg2 = emg2_in.read();
Jellehierck 2:d3e9788ab1b3 145 emg3 = emg3_in.read();
Jellehierck 4:09a01d2db8f7 146
Jellehierck 4:09a01d2db8f7 147 // Output raw EMG input
Jellehierck 4:09a01d2db8f7 148 scope.set(0, emg1 );
Jellehierck 6:5437cc97e1e6 149
Jellehierck 5:3d65f89e3755 150 // Filter notch and highpass
Jellehierck 5:3d65f89e3755 151 double emg1_n_hp = bqc_notch_high.step( emg1 );
Jellehierck 6:5437cc97e1e6 152
Jellehierck 5:3d65f89e3755 153 // Rectify
Jellehierck 5:3d65f89e3755 154 double emg1_rectify = fabs( emg1_n_hp );
Jellehierck 6:5437cc97e1e6 155
Jellehierck 5:3d65f89e3755 156 // Filter lowpass (completes envelope)
Jellehierck 5:3d65f89e3755 157 double emg1_env = bqc_low.step( emg1_rectify );
Jellehierck 4:09a01d2db8f7 158
Jellehierck 4:09a01d2db8f7 159 // Output EMG after filters
Jellehierck 5:3d65f89e3755 160 scope.set(1, emg1_env );
Jellehierck 4:09a01d2db8f7 161 scope.send();
Jellehierck 2:d3e9788ab1b3 162 }
Jellehierck 11:042170a9b93a 163 */
IsaRobin 0:6972d0e91af1 164
Jellehierck 7:7a088536f1c9 165 void sampleCalibration()
Jellehierck 7:7a088536f1c9 166 {
Jellehierck 7:7a088536f1c9 167 // Read EMG inputs
Jellehierck 7:7a088536f1c9 168 emg1 = emg1_in.read();
Jellehierck 7:7a088536f1c9 169 emg2 = emg2_in.read();
Jellehierck 7:7a088536f1c9 170 emg3 = emg3_in.read();
Jellehierck 7:7a088536f1c9 171
Jellehierck 7:7a088536f1c9 172 // Output raw EMG input
Jellehierck 7:7a088536f1c9 173 scope.set(0, emg1 );
Jellehierck 10:97a79aa10a56 174
Jellehierck 10:97a79aa10a56 175 double emg1_n = bqc_notch.step( emg1 ); // Filter notch
Jellehierck 11:042170a9b93a 176 scope.set(1, emg1_n);
Jellehierck 10:97a79aa10a56 177 double emg1_hp = bqc_high.step( emg1_n ); // Filter highpass
Jellehierck 15:421d3d9c563b 178 scope.set(2, emg1_hp);
Jellehierck 11:042170a9b93a 179 double emg1_rectify = fabs( emg1_hp ); // Rectify
Jellehierck 15:421d3d9c563b 180 scope.set(3, emg1_rectify);
Jellehierck 7:7a088536f1c9 181 double emg1_env = bqc_low.step( emg1_rectify ); // Filter lowpass (completes envelope)
Jellehierck 7:7a088536f1c9 182
Jellehierck 7:7a088536f1c9 183 // Output EMG after filters
Jellehierck 15:421d3d9c563b 184 scope.set(4, emg1_env );
Jellehierck 7:7a088536f1c9 185 scope.send();
Jellehierck 7:7a088536f1c9 186
Jellehierck 7:7a088536f1c9 187 emg1_cal.push_back(emg1_env);
Jellehierck 7:7a088536f1c9 188 }
Jellehierck 7:7a088536f1c9 189
Jellehierck 15:421d3d9c563b 190 /*
Jellehierck 15:421d3d9c563b 191 ------ EMG CALIBRATION FUNCTIONS ------
Jellehierck 15:421d3d9c563b 192 */
Jellehierck 15:421d3d9c563b 193
Jellehierck 15:421d3d9c563b 194 // Finish up calibration of MVC
Jellehierck 7:7a088536f1c9 195 void calibrationMVCFinished()
Jellehierck 7:7a088536f1c9 196 {
Jellehierck 15:421d3d9c563b 197 tickSampleCalibration.detach(); // Stop calibration ticker to remove interrupt
Jellehierck 15:421d3d9c563b 198 emg1_MVC = getMean(emg1_cal); // Store MVC globally
Jellehierck 15:421d3d9c563b 199 emg1_MVC_stdev = getStdev(emg1_cal, emg1_MVC); // Store MVC stde globally
Jellehierck 15:421d3d9c563b 200 emg1_cal.clear(); // Empty vector to prevent memory overflow
Jellehierck 15:421d3d9c563b 201 led_b = 1; // Turn off calibration led
Jellehierck 7:7a088536f1c9 202 }
Jellehierck 7:7a088536f1c9 203
Jellehierck 15:421d3d9c563b 204 // Run calibration of MVC
Jellehierck 7:7a088536f1c9 205 void calibrationMVC()
Jellehierck 7:7a088536f1c9 206 {
Jellehierck 15:421d3d9c563b 207 timeoutCalibrationMVC.attach( &calibrationMVCFinished, Tcal); // Stop MVC calibration after interval
Jellehierck 15:421d3d9c563b 208 tickSampleCalibration.attach( &sampleCalibration, Ts ); // Start sample ticker
Jellehierck 15:421d3d9c563b 209 led_b = 0; // Turn on calibration led
Jellehierck 7:7a088536f1c9 210 }
Jellehierck 7:7a088536f1c9 211
Jellehierck 15:421d3d9c563b 212 // Finish up calibration in rest
Jellehierck 12:70f0710400c2 213 void calibrationRestFinished()
Jellehierck 12:70f0710400c2 214 {
Jellehierck 15:421d3d9c563b 215 tickSampleCalibration.detach(); // Stop calibration ticker to remove interrupt
Jellehierck 15:421d3d9c563b 216 emg1_rest = getMean(emg1_cal); // Store rest globally
Jellehierck 15:421d3d9c563b 217 emg1_rest_stdev = getStdev(emg1_cal, emg1_rest);// Store rest stdev globally
Jellehierck 15:421d3d9c563b 218 emg1_cal.clear(); // Empty vector to prevent memory overflow
Jellehierck 15:421d3d9c563b 219 led_b = 1; // Turn off calibration led
Jellehierck 12:70f0710400c2 220 }
Jellehierck 12:70f0710400c2 221
Jellehierck 16:7acbcc4aa35c 222 // Run calibration in rest
Jellehierck 12:70f0710400c2 223 void calibrationRest()
Jellehierck 12:70f0710400c2 224 {
Jellehierck 15:421d3d9c563b 225 timeoutCalibrationRest.attach( &calibrationRestFinished, Tcal); // Stop rest calibration after interval
Jellehierck 15:421d3d9c563b 226 tickSampleCalibration.attach( &sampleCalibration, Ts ); // Start sample ticker
Jellehierck 15:421d3d9c563b 227 led_b = 0; // Turn on calibration led
Jellehierck 12:70f0710400c2 228 }
Jellehierck 12:70f0710400c2 229
Jellehierck 15:421d3d9c563b 230 // Determine scale factors for operation mode
Jellehierck 12:70f0710400c2 231 void makeScale()
Jellehierck 12:70f0710400c2 232 {
Jellehierck 15:421d3d9c563b 233 double margin_percentage = 10; // Set up % margin for rest
Jellehierck 15:421d3d9c563b 234 double factor1 = 1 / emg1_MVC; // Factor to normalize MVC
Jellehierck 15:421d3d9c563b 235 double emg1_th = emg1_rest * factor1 + margin_percentage/100; // Set normalized rest threshold
Jellehierck 12:70f0710400c2 236
Jellehierck 12:70f0710400c2 237 pc.printf("Factor: %f TH: %f\r\n", factor1, emg1_th);
Jellehierck 12:70f0710400c2 238 }
Jellehierck 7:7a088536f1c9 239
Jellehierck 16:7acbcc4aa35c 240 /*
Jellehierck 16:7acbcc4aa35c 241 ------ EMG SUBSTATE MACHINE ------
Jellehierck 16:7acbcc4aa35c 242 */
Jellehierck 16:7acbcc4aa35c 243
Jellehierck 16:7acbcc4aa35c 244
Jellehierck 16:7acbcc4aa35c 245
Jellehierck 5:3d65f89e3755 246 void main()
Jellehierck 4:09a01d2db8f7 247 {
Jellehierck 15:421d3d9c563b 248 pc.baud(115200); // MODSERIAL rate
Jellehierck 8:ea3de43c9e8b 249 pc.printf("Starting\r\n");
Jellehierck 15:421d3d9c563b 250
Jellehierck 15:421d3d9c563b 251 // tickSample.attach(&sample, Ts); // Initialize sample ticker
Jellehierck 6:5437cc97e1e6 252
Jellehierck 6:5437cc97e1e6 253 // Create BQ chains to reduce computations
Jellehierck 10:97a79aa10a56 254 bqc_notch.add( &bq_notch );
Jellehierck 10:97a79aa10a56 255 bqc_high.add( &bq_H1 ).add( &bq_H2 );
Jellehierck 5:3d65f89e3755 256 bqc_low.add( &bq_L1 ).add( &bq_L2 );
Jellehierck 4:09a01d2db8f7 257
Jellehierck 15:421d3d9c563b 258 led_b = 1; // Turn blue led off at startup
Jellehierck 15:421d3d9c563b 259 led_g = 1; // Turn green led off at startup
Jellehierck 15:421d3d9c563b 260 led_r = 1; // Turn red led off at startup
Jellehierck 8:ea3de43c9e8b 261
Jellehierck 6:5437cc97e1e6 262 // If any filter chain is unstable, red led will light up
Jellehierck 6:5437cc97e1e6 263 if (checkBQChainStable) {
Jellehierck 6:5437cc97e1e6 264 led_r = 1; // LED off
Jellehierck 6:5437cc97e1e6 265 } else {
Jellehierck 6:5437cc97e1e6 266 led_r = 0; // LED on
Jellehierck 6:5437cc97e1e6 267 }
Jellehierck 6:5437cc97e1e6 268
Jellehierck 15:421d3d9c563b 269 button1.fall( &calibrationMVC ); // Run MVC calibration on button press
Jellehierck 15:421d3d9c563b 270 button2.fall( &calibrationRest ); // Run rest calibration on button press
Jellehierck 15:421d3d9c563b 271 button3.fall( &makeScale ); // Create scale factors and close calibration at button press
Jellehierck 8:ea3de43c9e8b 272
Jellehierck 4:09a01d2db8f7 273 while(true) {
Jellehierck 7:7a088536f1c9 274
Jellehierck 6:5437cc97e1e6 275 // Show that system is running
Jellehierck 8:ea3de43c9e8b 276 // led_g = !led_g;
Jellehierck 12:70f0710400c2 277 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 278 wait(0.5);
Jellehierck 4:09a01d2db8f7 279 }
Jellehierck 4:09a01d2db8f7 280 }