Chanel Richardson / Mbed OS vitalsplus-max86150_chanel

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Dependencies:   max32630fthr USBDevice

main.cpp@15:b15b4b6c6da8, 2020-03-10 (annotated)

Committer:
saleiferis
Date:
Tue Mar 10 20:33:49 2020 +0000
Revision:
15:b15b4b6c6da8
Parent:
14:ee2175578993
Child:
16:f6bfa6b66e96
preprocessing, BLE, and serial, before pan-tompkins

Who changed what in which revision?

UserRevisionLine numberNew contents of line
saleiferis 0:89ec48e52250 1 #include "mbed.h"
saleiferis 0:89ec48e52250 2 #include "math.h"
saleiferis 0:89ec48e52250 3 #include "max32630fthr.h"
saleiferis 0:89ec48e52250 4 #include "max86150.h"
saleiferis 0:89ec48e52250 5 #include "I2C.h"
saleiferis 0:89ec48e52250 6 #include "ble/BLE.h"
saleiferis 0:89ec48e52250 7 #include "ble/Gap.h"
saleiferis 7:4debec043316 8 //#include "ble/services/HeartRateService.h"
saleiferis 7:4debec043316 9 #include "ECGService.h"
saleiferis 1:6e6f7e3cc1e1 10 #include <events/mbed_events.h>
saleiferis 1:6e6f7e3cc1e1 11 #include "bt32630.h"
saleiferis 14:ee2175578993 12 //#include "filters.h"
saleiferis 0:89ec48e52250 13
saleiferis 0:89ec48e52250 14 //Register definitions
saleiferis 0:89ec48e52250 15 #define MAX86150_Addr 0xBC //updated per I2Cscanner, 8 bit version of 7 bit code 0x5E
saleiferis 0:89ec48e52250 16 #define maxi2cFreq 1000000
saleiferis 0:89ec48e52250 17 #define recommendedi2cFreq 400000
saleiferis 10:28b8729cf5dc 18
saleiferis 10:28b8729cf5dc 19 #define BaudRate 115200
saleiferis 0:89ec48e52250 20
saleiferis 13:a555fd1253e7 21 #define WINDOW_SIZE 25 // number of samples for moving winfow integration for HR algo preprocessing. Effective window_size is half of this value
saleiferis 14:ee2175578993 22 #define BUFF_SIZE 136 // TODO: decouple BUFF_SIZE and FIR_SIZE. now program crashes if != 136
saleiferis 14:ee2175578993 23 #define FIR_SIZE 136
saleiferis 0:89ec48e52250 24
saleiferis 10:28b8729cf5dc 25 Serial pc(USBTX,USBRX,NULL,BaudRate);
saleiferis 10:28b8729cf5dc 26 InterruptIn intPin(P5_5); // interrupts currently not used
saleiferis 0:89ec48e52250 27 I2C i2c(I2C2_SDA, I2C2_SCL);
saleiferis 8:2005014df05c 28 MAX86150 max86150Sensor;
saleiferis 0:89ec48e52250 29
saleiferis 10:28b8729cf5dc 30 ECGService *hrServicePtr;
saleiferis 14:ee2175578993 31 int k; // loop iteration
saleiferis 14:ee2175578993 32 float signal[BUFF_SIZE]={0}; //store signal segment to be filtered
saleiferis 14:ee2175578993 33 float bp_signal[BUFF_SIZE]={0};
saleiferis 14:ee2175578993 34 float derivative[BUFF_SIZE]={0};
saleiferis 14:ee2175578993 35 float squared[BUFF_SIZE]={0};
saleiferis 14:ee2175578993 36 float integral[BUFF_SIZE] = {0};
saleiferis 14:ee2175578993 37
saleiferis 14:ee2175578993 38 // Variables for preprocessing
saleiferis 14:ee2175578993 39 float y = 0.0; //filtered sample to be displayed
saleiferis 14:ee2175578993 40 float prev_y = 0.0; // keep track of previous output to calculate derivative
saleiferis 14:ee2175578993 41 float sq_y = 0.0;
saleiferis 14:ee2175578993 42 float movmean = 0.0; // result of moving window integration
saleiferis 14:ee2175578993 43
saleiferis 14:ee2175578993 44
saleiferis 14:ee2175578993 45 // Variables for peak-finding
saleiferis 14:ee2175578993 46 int rr1[8], rr2[8], rravg1, rravg2, rrlow = 0, rrhigh = 0, rrmiss = 0;
saleiferis 14:ee2175578993 47 long unsigned int i, j, sample_idx = 0, curr = 0, lastQRS = 0, lastSlope = 0, currentSlope = 0;
saleiferis 14:ee2175578993 48 float peak_i = 0, peak_f = 0, threshold_i1 = 0, threshold_i2 = 0, threshold_f1 = 0, threshold_f2 = 0, spk_i = 0, spk_f = 0, npk_i = 0, npk_f = 0;
saleiferis 14:ee2175578993 49 bool qrs, regular = true, prevRegular;
saleiferis 14:ee2175578993 50
saleiferis 9:171171516ebd 51
saleiferis 12:ad628acddbf7 52 //Timer timer;
saleiferis 9:171171516ebd 53
saleiferis 1:6e6f7e3cc1e1 54 static events::EventQueue event_queue(/* event count */ 16 * EVENTS_EVENT_SIZE);
saleiferis 1:6e6f7e3cc1e1 55
saleiferis 15:b15b4b6c6da8 56
saleiferis 9:171171516ebd 57
saleiferis 15:b15b4b6c6da8 58
saleiferis 10:28b8729cf5dc 59
saleiferis 0:89ec48e52250 60 //////////
saleiferis 10:28b8729cf5dc 61 int main(){
saleiferis 14:ee2175578993 62 /*
saleiferis 0:89ec48e52250 63 max86150Sensor.begin(i2c, recommendedi2cFreq, MAX86150_Addr);
saleiferis 0:89ec48e52250 64 wait_ms(300);
saleiferis 4:4233f5538abf 65
saleiferis 0:89ec48e52250 66 //unsigned char partID = max86150Sensor.readPartID();
saleiferis 0:89ec48e52250 67 unsigned char partID = max86150Sensor.readRegister8(MAX86150_Addr,0xFF);
saleiferis 0:89ec48e52250 68 pc.printf("Part ID is: %X\n",partID);
saleiferis 14:ee2175578993 69 while (partID != 0x1E) { } // Connection to sensor is not established
saleiferis 2:a96a53e6c6a3 70
saleiferis 2:a96a53e6c6a3 71
saleiferis 14:ee2175578993 72 // SETUP SENSOR
saleiferis 10:28b8729cf5dc 73 max86150Sensor.setup(); //Configure sensor
saleiferis 10:28b8729cf5dc 74 wait_ms(300);
saleiferis 10:28b8729cf5dc 75 pc.printf("SYSCONTOL REG: %x\n", max86150Sensor.readRegister8(MAX86150_Addr,0x0D));
saleiferis 10:28b8729cf5dc 76 pc.printf("FIFO CONFIG: %X\n",max86150Sensor.readRegister8(MAX86150_Addr,0x08));
saleiferis 10:28b8729cf5dc 77 pc.printf("INT_EN1: %X\n", max86150Sensor.readRegister8(MAX86150_Addr,0x02));
saleiferis 10:28b8729cf5dc 78 pc.printf("INT_EN2: %X\n", max86150Sensor.readRegister8(MAX86150_Addr,0x03));
saleiferis 10:28b8729cf5dc 79 pc.printf("INT STATUS1: %X\n",max86150Sensor.readRegister8(MAX86150_Addr,0x00));
saleiferis 10:28b8729cf5dc 80 pc.printf("INT STATUS2: %X\n",max86150Sensor.readRegister8(MAX86150_Addr,0x01));
saleiferis 10:28b8729cf5dc 81
saleiferis 14:ee2175578993 82 ////
saleiferis 10:28b8729cf5dc 83
saleiferis 10:28b8729cf5dc 84 max86150Sensor.clearFIFO();
saleiferis 10:28b8729cf5dc 85 max86150Sensor.writeRegister8(MAX86150_Addr,0x0D,0x04); //start FIFO
saleiferis 14:ee2175578993 86 */
saleiferis 10:28b8729cf5dc 87 //******* SETUP BLUETOOTH *********
saleiferis 10:28b8729cf5dc 88 eventQueue.call_every(1, periodicCallback); // poll sensor every 1ms. New samples come every 5ms, so polling freq can potentially be decreased
saleiferis 1:6e6f7e3cc1e1 89 BLE &ble = BLE::Instance();
saleiferis 10:28b8729cf5dc 90 ble.onEventsToProcess(scheduleBleEventsProcessing);
saleiferis 14:ee2175578993 91 ble.init(bleInitComplete);
saleiferis 14:ee2175578993 92 eventQueue.dispatch_forever();
saleiferis 14:ee2175578993 93
saleiferis 13:a555fd1253e7 94
saleiferis 14:ee2175578993 95 /*
saleiferis 14:ee2175578993 96 int16_t ecgsigned16;
saleiferis 13:a555fd1253e7 97 while(1){
saleiferis 13:a555fd1253e7 98 if(max86150Sensor.check()>0){
saleiferis 13:a555fd1253e7 99
saleiferis 13:a555fd1253e7 100 ecgsigned16 = (int16_t) (max86150Sensor.getFIFOECG()>>2);
saleiferis 13:a555fd1253e7 101 max86150Sensor.nextSample();
saleiferis 13:a555fd1253e7 102 ble.updateHeartRate(ecgsigned16);
saleiferis 14:ee2175578993 103 pc.printf("%f\n",(float)ecgsigned16);
saleiferis 14:ee2175578993 104 */
saleiferis 13:a555fd1253e7 105
saleiferis 4:4233f5538abf 106
saleiferis 10:28b8729cf5dc 107 // Below code is for testing interrupts and sensor polling without involving bluetooth API
saleiferis 14:ee2175578993 108 /* UNCOMMENT HERE
saleiferis 10:28b8729cf5dc 109 // max86150Sensor.clearFIFO();
saleiferis 10:28b8729cf5dc 110 //intPin.fall(&ISR_DATA_READY);
saleiferis 10:28b8729cf5dc 111 // max86150Sensor.writeRegister8(MAX86150_Addr,0x0D,0x04);
saleiferis 10:28b8729cf5dc 112 int16_t ecgsigned16;
saleiferis 13:a555fd1253e7 113 int k; // loop iteration
saleiferis 12:ad628acddbf7 114 float signal[BUFF_SIZE]={0}; //store signal segment to be filtered
saleiferis 12:ad628acddbf7 115 float bp_signal[BUFF_SIZE]={0};
saleiferis 12:ad628acddbf7 116 float derivative[BUFF_SIZE]={0};
saleiferis 12:ad628acddbf7 117 float squared[BUFF_SIZE]={0};
saleiferis 12:ad628acddbf7 118 float integral[BUFF_SIZE] = {0};
saleiferis 12:ad628acddbf7 119
saleiferis 12:ad628acddbf7 120 // Variables for preprocessing
saleiferis 11:cbd9182d14d2 121 float y = 0.0; //filtered sample to be displayed
saleiferis 12:ad628acddbf7 122 float prev_y = 0.0; // keep track of previous output to calculate derivative
saleiferis 12:ad628acddbf7 123 float sq_y = 0.0;
saleiferis 12:ad628acddbf7 124 float movmean = 0.0; // result of moving window integration
saleiferis 12:ad628acddbf7 125
saleiferis 12:ad628acddbf7 126 // Variables for peak-finding
saleiferis 12:ad628acddbf7 127 int rr1[8], rr2[8], rravg1, rravg2, rrlow = 0, rrhigh = 0, rrmiss = 0;
saleiferis 14:ee2175578993 128 long unsigned int i, j, sample_idx = 0, curr = 0, lastQRS = 0, lastSlope = 0, currentSlope = 0;
saleiferis 12:ad628acddbf7 129 float peak_i = 0, peak_f = 0, threshold_i1 = 0, threshold_i2 = 0, threshold_f1 = 0, threshold_f2 = 0, spk_i = 0, spk_f = 0, npk_i = 0, npk_f = 0;
saleiferis 12:ad628acddbf7 130 bool qrs, regular = true, prevRegular;
saleiferis 12:ad628acddbf7 131 // Initializing the RR averages
saleiferis 12:ad628acddbf7 132 for (i = 0; i < 8; i++)
saleiferis 12:ad628acddbf7 133 {
saleiferis 12:ad628acddbf7 134 rr1[i] = 0;
saleiferis 12:ad628acddbf7 135 rr2[i] = 0;
saleiferis 12:ad628acddbf7 136 }
saleiferis 12:ad628acddbf7 137
saleiferis 9:171171516ebd 138
saleiferis 8:2005014df05c 139 while(1){
saleiferis 10:28b8729cf5dc 140 if(max86150Sensor.check()>0){
saleiferis 10:28b8729cf5dc 141
saleiferis 11:cbd9182d14d2 142 //ecgsigned16 = (int16_t) (max86150Sensor.getFIFOECG()>>2);
saleiferis 11:cbd9182d14d2 143 //max86150Sensor.nextSample();
saleiferis 11:cbd9182d14d2 144 //pc.printf("%f\n",(float)ecgsigned16);
saleiferis 11:cbd9182d14d2 145
saleiferis 12:ad628acddbf7 146 // if buffer is full
saleiferis 11:cbd9182d14d2 147 if (sample_idx >= BUFF_SIZE){
saleiferis 13:a555fd1253e7 148 for (k=0; k<BUFF_SIZE-1; k++){ //discard oldest sample, shift samples in buffer
saleiferis 13:a555fd1253e7 149 signal[k] = signal[k+1];
saleiferis 13:a555fd1253e7 150 bp_signal[k] = bp_signal[k+1];
saleiferis 13:a555fd1253e7 151 derivative[k] = derivative[k+1];
saleiferis 13:a555fd1253e7 152 integral[k] = integral[k+1];
saleiferis 13:a555fd1253e7 153 squared[k] = squared[k+1];
saleiferis 12:ad628acddbf7 154
saleiferis 11:cbd9182d14d2 155 }
saleiferis 11:cbd9182d14d2 156 curr = BUFF_SIZE-1; // indicates that buffer is full
saleiferis 12:ad628acddbf7 157 prev_y = y;
saleiferis 11:cbd9182d14d2 158 y = 0.0; // reset filter output for current sample
saleiferis 11:cbd9182d14d2 159 }else{ //Buffer is not full yet
saleiferis 14:ee2175578993 160 curr = sample_idx; //position at buffer is same as sample number
saleiferis 11:cbd9182d14d2 161 }
saleiferis 11:cbd9182d14d2 162 ecgsigned16 = (int16_t) (max86150Sensor.getFIFOECG()>>2); //read a sample
saleiferis 11:cbd9182d14d2 163 max86150Sensor.nextSample(); // advance tail to get sample in next iteration
saleiferis 12:ad628acddbf7 164 signal[curr] = (float)ecgsigned16; //add sample to buffer
saleiferis 11:cbd9182d14d2 165 sample_idx++;
saleiferis 11:cbd9182d14d2 166
saleiferis 14:ee2175578993 167 if (curr< FIR_SIZE-1){
saleiferis 11:cbd9182d14d2 168 // buffer is not full yet
saleiferis 11:cbd9182d14d2 169 }else{ //buffer is full, filter current sample
saleiferis 14:ee2175578993 170 for(k = 0; k < FIR_SIZE; k++){ //FIR bandpass filter
saleiferis 14:ee2175578993 171 y = y + FIR_BP[k] * signal[curr-k];
saleiferis 11:cbd9182d14d2 172 }
saleiferis 12:ad628acddbf7 173 bp_signal[curr] = y;
saleiferis 12:ad628acddbf7 174 }
saleiferis 12:ad628acddbf7 175 sq_y = pow(y-prev_y,2);
saleiferis 12:ad628acddbf7 176 squared[curr] = sq_y;
saleiferis 12:ad628acddbf7 177 //moving window integration
saleiferis 12:ad628acddbf7 178 movmean = 0.0; // reset for current sample
saleiferis 13:a555fd1253e7 179 for(k=0; k<(int)WINDOW_SIZE/2; k++){
saleiferis 12:ad628acddbf7 180 //pc.printf("%d\n",(int)curr - (int)(WINDOW_SIZE));
saleiferis 13:a555fd1253e7 181 if ((int)curr - (int)(WINDOW_SIZE) > k){ //there are enough samples in squared[]
saleiferis 13:a555fd1253e7 182 // movmean = movmean + squared[(curr-k-(int)WINDOW_SIZE/2)] + squared[curr+k-(int)WINDOW_SIZE/2];
saleiferis 13:a555fd1253e7 183 movmean = movmean + squared[curr-k];
saleiferis 12:ad628acddbf7 184
saleiferis 12:ad628acddbf7 185 }else{
saleiferis 12:ad628acddbf7 186 break;
saleiferis 12:ad628acddbf7 187 }
saleiferis 11:cbd9182d14d2 188 }
saleiferis 13:a555fd1253e7 189 movmean = movmean/(float)(k+1);
saleiferis 12:ad628acddbf7 190 integral[curr] = movmean;
saleiferis 12:ad628acddbf7 191
saleiferis 12:ad628acddbf7 192 pc.printf("%f %f\n",movmean/1000, y/50);
saleiferis 12:ad628acddbf7 193
saleiferis 12:ad628acddbf7 194 // Preprocessing done
saleiferis 14:ee2175578993 195
saleiferis 12:ad628acddbf7 196 // Start peak-finding
saleiferis 13:a555fd1253e7 197 qrs = false;
saleiferis 13:a555fd1253e7 198 if (integral[curr] >= threshold_i1 || highpass[current] >= threshold_f1){
saleiferis 13:a555fd1253e7 199 peak_i = integral[curr];
saleiferis 13:a555fd1253e7 200 peak_f = bp_signal[curr];
saleiferis 14:ee2175578993 201 }
saleiferis 12:ad628acddbf7 202
saleiferis 12:ad628acddbf7 203
saleiferis 12:ad628acddbf7 204
saleiferis 12:ad628acddbf7 205
saleiferis 10:28b8729cf5dc 206 }
saleiferis 14:ee2175578993 207 } end while(1)*/
saleiferis 10:28b8729cf5dc 208
saleiferis 0:89ec48e52250 209 }