Chanel Richardson / Mbed OS vitalsplus-max86150_chanel

Chanel's edits

Dependencies:   max32630fthr USBDevice

main.cpp@14:ee2175578993, 2020-03-10 (annotated)

Committer:
saleiferis
Date:
Tue Mar 10 08:22:53 2020 +0000
Revision:
14:ee2175578993
Parent:
13:a555fd1253e7
Child:
15:b15b4b6c6da8
complete preprocessing + BLE streaming

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 10:28b8729cf5dc 31
saleiferis 14:ee2175578993 32 // Variables for ECG pre-processing
saleiferis 14:ee2175578993 33 int k; // loop iteration
saleiferis 14:ee2175578993 34 float signal[BUFF_SIZE]={0}; //store signal segment to be filtered
saleiferis 14:ee2175578993 35 float bp_signal[BUFF_SIZE]={0};
saleiferis 14:ee2175578993 36 float derivative[BUFF_SIZE]={0};
saleiferis 14:ee2175578993 37 float squared[BUFF_SIZE]={0};
saleiferis 14:ee2175578993 38 float integral[BUFF_SIZE] = {0};
saleiferis 14:ee2175578993 39
saleiferis 14:ee2175578993 40 // Variables for preprocessing
saleiferis 14:ee2175578993 41 float y = 0.0; //filtered sample to be displayed
saleiferis 14:ee2175578993 42 float prev_y = 0.0; // keep track of previous output to calculate derivative
saleiferis 14:ee2175578993 43 float sq_y = 0.0;
saleiferis 14:ee2175578993 44 float movmean = 0.0; // result of moving window integration
saleiferis 14:ee2175578993 45
saleiferis 14:ee2175578993 46
saleiferis 14:ee2175578993 47 // Variables for peak-finding
saleiferis 14:ee2175578993 48 int rr1[8], rr2[8], rravg1, rravg2, rrlow = 0, rrhigh = 0, rrmiss = 0;
saleiferis 14:ee2175578993 49 long unsigned int i, j, sample_idx = 0, curr = 0, lastQRS = 0, lastSlope = 0, currentSlope = 0;
saleiferis 14:ee2175578993 50 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 51 bool qrs, regular = true, prevRegular;
saleiferis 14:ee2175578993 52
saleiferis 10:28b8729cf5dc 53 //Variables modified in inerrupt routine
saleiferis 12:ad628acddbf7 54 /*
saleiferis 10:28b8729cf5dc 55 volatile uint32_t intCount = 0;
saleiferis 8:2005014df05c 56 volatile bool intFlag = false;
saleiferis 9:171171516ebd 57 volatile uint8_t writePointer;
saleiferis 9:171171516ebd 58 volatile uint8_t readPointer;
saleiferis 9:171171516ebd 59 volatile uint32_t curr_time;
saleiferis 9:171171516ebd 60 volatile uint32_t prev_time;
saleiferis 9:171171516ebd 61 volatile int16_t samplesToRead;
saleiferis 12:ad628acddbf7 62 */
saleiferis 9:171171516ebd 63
saleiferis 12:ad628acddbf7 64 //Timer timer;
saleiferis 9:171171516ebd 65
saleiferis 1:6e6f7e3cc1e1 66 static events::EventQueue event_queue(/* event count */ 16 * EVENTS_EVENT_SIZE);
saleiferis 1:6e6f7e3cc1e1 67
saleiferis 10:28b8729cf5dc 68 /*
saleiferis 8:2005014df05c 69 void ISR_AFULL()
saleiferis 8:2005014df05c 70 {
saleiferis 9:171171516ebd 71 intPin.disable_irq();
saleiferis 8:2005014df05c 72 intFlag = true;
saleiferis 9:171171516ebd 73 readPointer = max86150Sensor.getReadPointer();
saleiferis 9:171171516ebd 74 writePointer = max86150Sensor.getWritePointer();
saleiferis 10:28b8729cf5dc 75 samplesToRead = (int8_t)writePointer - (int8_t)readPointer;
saleiferis 10:28b8729cf5dc 76 //if (samplesToRead < 0) samplesToRead+=32;
saleiferis 10:28b8729cf5dc 77 intCount++;
saleiferis 10:28b8729cf5dc 78 //intPin.enable_irq();
saleiferis 10:28b8729cf5dc 79
saleiferis 10:28b8729cf5dc 80 }*/
saleiferis 9:171171516ebd 81
saleiferis 10:28b8729cf5dc 82 /*
saleiferis 10:28b8729cf5dc 83 void ISR_DATA_READY()
saleiferis 10:28b8729cf5dc 84 {
saleiferis 10:28b8729cf5dc 85 intPin.disable_irq();
saleiferis 10:28b8729cf5dc 86 readPointer = max86150Sensor.getReadPointer();
saleiferis 10:28b8729cf5dc 87 writePointer = max86150Sensor.getWritePointer();
saleiferis 10:28b8729cf5dc 88 samplesToRead = (int8_t)writePointer - (int8_t)readPointer;
saleiferis 10:28b8729cf5dc 89 //if (samplesToRead < 0) samplesToRead+=32;
saleiferis 10:28b8729cf5dc 90 intCount++;
saleiferis 10:28b8729cf5dc 91 char data[3];
saleiferis 10:28b8729cf5dc 92 //char *p = data;
saleiferis 10:28b8729cf5dc 93 max86150Sensor.writeRegister8(MAX86150_Addr,0x07,0x01);
saleiferis 10:28b8729cf5dc 94 i2c.write(MAX86150_Addr,command, 1);
saleiferis 10:28b8729cf5dc 95 i2c.read(MAX86150_Addr, data, 3, false);
saleiferis 10:28b8729cf5dc 96 uint8_t temp[sizeof(int32_t)]; //Array of 4 bytes that we will convert into long
saleiferis 10:28b8729cf5dc 97 int32_t tempLong;
saleiferis 10:28b8729cf5dc 98 temp[1] = data[0];
saleiferis 10:28b8729cf5dc 99 temp[2] = data[1];
saleiferis 10:28b8729cf5dc 100 temp[3] = data[2];
saleiferis 10:28b8729cf5dc 101 temp[0] = 0;
saleiferis 10:28b8729cf5dc 102 //Convert array to long
saleiferis 10:28b8729cf5dc 103 memcpy(&tempLong, temp, sizeof(tempLong));
saleiferis 10:28b8729cf5dc 104 pc.printf("%d\n",tempLong);
saleiferis 10:28b8729cf5dc 105 intPin.enable_irq();
saleiferis 10:28b8729cf5dc 106 }*/
saleiferis 10:28b8729cf5dc 107
saleiferis 0:89ec48e52250 108 //////////
saleiferis 10:28b8729cf5dc 109 int main(){
saleiferis 14:ee2175578993 110 /*
saleiferis 0:89ec48e52250 111 max86150Sensor.begin(i2c, recommendedi2cFreq, MAX86150_Addr);
saleiferis 0:89ec48e52250 112 wait_ms(300);
saleiferis 4:4233f5538abf 113
saleiferis 0:89ec48e52250 114 //unsigned char partID = max86150Sensor.readPartID();
saleiferis 0:89ec48e52250 115 unsigned char partID = max86150Sensor.readRegister8(MAX86150_Addr,0xFF);
saleiferis 0:89ec48e52250 116 pc.printf("Part ID is: %X\n",partID);
saleiferis 14:ee2175578993 117 while (partID != 0x1E) { } // Connection to sensor is not established
saleiferis 2:a96a53e6c6a3 118
saleiferis 2:a96a53e6c6a3 119
saleiferis 14:ee2175578993 120 // SETUP SENSOR
saleiferis 10:28b8729cf5dc 121 max86150Sensor.setup(); //Configure sensor
saleiferis 10:28b8729cf5dc 122 wait_ms(300);
saleiferis 10:28b8729cf5dc 123 pc.printf("SYSCONTOL REG: %x\n", max86150Sensor.readRegister8(MAX86150_Addr,0x0D));
saleiferis 10:28b8729cf5dc 124 pc.printf("FIFO CONFIG: %X\n",max86150Sensor.readRegister8(MAX86150_Addr,0x08));
saleiferis 10:28b8729cf5dc 125 pc.printf("INT_EN1: %X\n", max86150Sensor.readRegister8(MAX86150_Addr,0x02));
saleiferis 10:28b8729cf5dc 126 pc.printf("INT_EN2: %X\n", max86150Sensor.readRegister8(MAX86150_Addr,0x03));
saleiferis 10:28b8729cf5dc 127 pc.printf("INT STATUS1: %X\n",max86150Sensor.readRegister8(MAX86150_Addr,0x00));
saleiferis 10:28b8729cf5dc 128 pc.printf("INT STATUS2: %X\n",max86150Sensor.readRegister8(MAX86150_Addr,0x01));
saleiferis 10:28b8729cf5dc 129
saleiferis 14:ee2175578993 130 ////
saleiferis 10:28b8729cf5dc 131
saleiferis 10:28b8729cf5dc 132 max86150Sensor.clearFIFO();
saleiferis 10:28b8729cf5dc 133 max86150Sensor.writeRegister8(MAX86150_Addr,0x0D,0x04); //start FIFO
saleiferis 14:ee2175578993 134 */
saleiferis 10:28b8729cf5dc 135 //******* SETUP BLUETOOTH *********
saleiferis 10:28b8729cf5dc 136 eventQueue.call_every(1, periodicCallback); // poll sensor every 1ms. New samples come every 5ms, so polling freq can potentially be decreased
saleiferis 1:6e6f7e3cc1e1 137 BLE &ble = BLE::Instance();
saleiferis 10:28b8729cf5dc 138 ble.onEventsToProcess(scheduleBleEventsProcessing);
saleiferis 14:ee2175578993 139 ble.init(bleInitComplete);
saleiferis 14:ee2175578993 140 eventQueue.dispatch_forever();
saleiferis 14:ee2175578993 141
saleiferis 13:a555fd1253e7 142
saleiferis 14:ee2175578993 143 /*
saleiferis 14:ee2175578993 144 int16_t ecgsigned16;
saleiferis 13:a555fd1253e7 145 while(1){
saleiferis 13:a555fd1253e7 146 if(max86150Sensor.check()>0){
saleiferis 13:a555fd1253e7 147
saleiferis 13:a555fd1253e7 148 ecgsigned16 = (int16_t) (max86150Sensor.getFIFOECG()>>2);
saleiferis 13:a555fd1253e7 149 max86150Sensor.nextSample();
saleiferis 13:a555fd1253e7 150 ble.updateHeartRate(ecgsigned16);
saleiferis 14:ee2175578993 151 pc.printf("%f\n",(float)ecgsigned16);
saleiferis 14:ee2175578993 152 */
saleiferis 13:a555fd1253e7 153
saleiferis 4:4233f5538abf 154
saleiferis 10:28b8729cf5dc 155 // Below code is for testing interrupts and sensor polling without involving bluetooth API
saleiferis 14:ee2175578993 156 /* UNCOMMENT HERE
saleiferis 10:28b8729cf5dc 157 // max86150Sensor.clearFIFO();
saleiferis 10:28b8729cf5dc 158 //intPin.fall(&ISR_DATA_READY);
saleiferis 10:28b8729cf5dc 159 // max86150Sensor.writeRegister8(MAX86150_Addr,0x0D,0x04);
saleiferis 10:28b8729cf5dc 160 int16_t ecgsigned16;
saleiferis 13:a555fd1253e7 161 int k; // loop iteration
saleiferis 12:ad628acddbf7 162 float signal[BUFF_SIZE]={0}; //store signal segment to be filtered
saleiferis 12:ad628acddbf7 163 float bp_signal[BUFF_SIZE]={0};
saleiferis 12:ad628acddbf7 164 float derivative[BUFF_SIZE]={0};
saleiferis 12:ad628acddbf7 165 float squared[BUFF_SIZE]={0};
saleiferis 12:ad628acddbf7 166 float integral[BUFF_SIZE] = {0};
saleiferis 12:ad628acddbf7 167
saleiferis 12:ad628acddbf7 168 // Variables for preprocessing
saleiferis 11:cbd9182d14d2 169 float y = 0.0; //filtered sample to be displayed
saleiferis 12:ad628acddbf7 170 float prev_y = 0.0; // keep track of previous output to calculate derivative
saleiferis 12:ad628acddbf7 171 float sq_y = 0.0;
saleiferis 12:ad628acddbf7 172 float movmean = 0.0; // result of moving window integration
saleiferis 12:ad628acddbf7 173
saleiferis 12:ad628acddbf7 174 // Variables for peak-finding
saleiferis 12:ad628acddbf7 175 int rr1[8], rr2[8], rravg1, rravg2, rrlow = 0, rrhigh = 0, rrmiss = 0;
saleiferis 14:ee2175578993 176 long unsigned int i, j, sample_idx = 0, curr = 0, lastQRS = 0, lastSlope = 0, currentSlope = 0;
saleiferis 12:ad628acddbf7 177 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 178 bool qrs, regular = true, prevRegular;
saleiferis 12:ad628acddbf7 179 // Initializing the RR averages
saleiferis 12:ad628acddbf7 180 for (i = 0; i < 8; i++)
saleiferis 12:ad628acddbf7 181 {
saleiferis 12:ad628acddbf7 182 rr1[i] = 0;
saleiferis 12:ad628acddbf7 183 rr2[i] = 0;
saleiferis 12:ad628acddbf7 184 }
saleiferis 12:ad628acddbf7 185
saleiferis 9:171171516ebd 186
saleiferis 8:2005014df05c 187 while(1){
saleiferis 10:28b8729cf5dc 188 if(max86150Sensor.check()>0){
saleiferis 10:28b8729cf5dc 189
saleiferis 11:cbd9182d14d2 190 //ecgsigned16 = (int16_t) (max86150Sensor.getFIFOECG()>>2);
saleiferis 11:cbd9182d14d2 191 //max86150Sensor.nextSample();
saleiferis 11:cbd9182d14d2 192 //pc.printf("%f\n",(float)ecgsigned16);
saleiferis 11:cbd9182d14d2 193
saleiferis 12:ad628acddbf7 194 // if buffer is full
saleiferis 11:cbd9182d14d2 195 if (sample_idx >= BUFF_SIZE){
saleiferis 13:a555fd1253e7 196 for (k=0; k<BUFF_SIZE-1; k++){ //discard oldest sample, shift samples in buffer
saleiferis 13:a555fd1253e7 197 signal[k] = signal[k+1];
saleiferis 13:a555fd1253e7 198 bp_signal[k] = bp_signal[k+1];
saleiferis 13:a555fd1253e7 199 derivative[k] = derivative[k+1];
saleiferis 13:a555fd1253e7 200 integral[k] = integral[k+1];
saleiferis 13:a555fd1253e7 201 squared[k] = squared[k+1];
saleiferis 12:ad628acddbf7 202
saleiferis 11:cbd9182d14d2 203 }
saleiferis 11:cbd9182d14d2 204 curr = BUFF_SIZE-1; // indicates that buffer is full
saleiferis 12:ad628acddbf7 205 prev_y = y;
saleiferis 11:cbd9182d14d2 206 y = 0.0; // reset filter output for current sample
saleiferis 11:cbd9182d14d2 207 }else{ //Buffer is not full yet
saleiferis 14:ee2175578993 208 curr = sample_idx; //position at buffer is same as sample number
saleiferis 11:cbd9182d14d2 209 }
saleiferis 11:cbd9182d14d2 210 ecgsigned16 = (int16_t) (max86150Sensor.getFIFOECG()>>2); //read a sample
saleiferis 11:cbd9182d14d2 211 max86150Sensor.nextSample(); // advance tail to get sample in next iteration
saleiferis 12:ad628acddbf7 212 signal[curr] = (float)ecgsigned16; //add sample to buffer
saleiferis 11:cbd9182d14d2 213 sample_idx++;
saleiferis 11:cbd9182d14d2 214
saleiferis 14:ee2175578993 215 if (curr< FIR_SIZE-1){
saleiferis 11:cbd9182d14d2 216 // buffer is not full yet
saleiferis 11:cbd9182d14d2 217 }else{ //buffer is full, filter current sample
saleiferis 14:ee2175578993 218 for(k = 0; k < FIR_SIZE; k++){ //FIR bandpass filter
saleiferis 14:ee2175578993 219 y = y + FIR_BP[k] * signal[curr-k];
saleiferis 11:cbd9182d14d2 220 }
saleiferis 12:ad628acddbf7 221 bp_signal[curr] = y;
saleiferis 12:ad628acddbf7 222 }
saleiferis 12:ad628acddbf7 223 sq_y = pow(y-prev_y,2);
saleiferis 12:ad628acddbf7 224 squared[curr] = sq_y;
saleiferis 12:ad628acddbf7 225 //moving window integration
saleiferis 12:ad628acddbf7 226 movmean = 0.0; // reset for current sample
saleiferis 13:a555fd1253e7 227 for(k=0; k<(int)WINDOW_SIZE/2; k++){
saleiferis 12:ad628acddbf7 228 //pc.printf("%d\n",(int)curr - (int)(WINDOW_SIZE));
saleiferis 13:a555fd1253e7 229 if ((int)curr - (int)(WINDOW_SIZE) > k){ //there are enough samples in squared[]
saleiferis 13:a555fd1253e7 230 // movmean = movmean + squared[(curr-k-(int)WINDOW_SIZE/2)] + squared[curr+k-(int)WINDOW_SIZE/2];
saleiferis 13:a555fd1253e7 231 movmean = movmean + squared[curr-k];
saleiferis 12:ad628acddbf7 232
saleiferis 12:ad628acddbf7 233 }else{
saleiferis 12:ad628acddbf7 234 break;
saleiferis 12:ad628acddbf7 235 }
saleiferis 11:cbd9182d14d2 236 }
saleiferis 13:a555fd1253e7 237 movmean = movmean/(float)(k+1);
saleiferis 12:ad628acddbf7 238 integral[curr] = movmean;
saleiferis 12:ad628acddbf7 239
saleiferis 12:ad628acddbf7 240 pc.printf("%f %f\n",movmean/1000, y/50);
saleiferis 12:ad628acddbf7 241
saleiferis 12:ad628acddbf7 242 // Preprocessing done
saleiferis 14:ee2175578993 243
saleiferis 12:ad628acddbf7 244 // Start peak-finding
saleiferis 13:a555fd1253e7 245 qrs = false;
saleiferis 13:a555fd1253e7 246 if (integral[curr] >= threshold_i1 || highpass[current] >= threshold_f1){
saleiferis 13:a555fd1253e7 247 peak_i = integral[curr];
saleiferis 13:a555fd1253e7 248 peak_f = bp_signal[curr];
saleiferis 14:ee2175578993 249 }
saleiferis 12:ad628acddbf7 250
saleiferis 12:ad628acddbf7 251
saleiferis 12:ad628acddbf7 252
saleiferis 12:ad628acddbf7 253
saleiferis 10:28b8729cf5dc 254 }
saleiferis 14:ee2175578993 255 } end while(1)*/
saleiferis 10:28b8729cf5dc 256
saleiferis 0:89ec48e52250 257 }