nikita teggi / Mbed 2 deprecated merged_code2_3rd_nov_2017

Changes done in ECG and BT

Dependencies:   SDFileSystem ds3231 eeprom_Nikita mbed testUniGraphic_150217

Fork of merged_code2_20sept_2017_4th_oct_2017 by nikita teggi

ecgg.cpp@19:1650bbc923cc, 2017-06-09 (annotated)

Committer:
nikitateggi
Date:
Fri Jun 09 17:12:21 2017 +0000
Revision:
19:1650bbc923cc
Parent:
17:22a87e12fb3a
Child:
20:7c64e6ecad76
integrated code with bluetooth

Who changed what in which revision?

UserRevisionLine numberNew contents of line
nikitateggi 1:8316c23ec6b9 1 /** ECG ADS1291 Test program.
nikitateggi 1:8316c23ec6b9 2 ADS1291 is a single channel ECG chip
nikitateggi 1:8316c23ec6b9 3 with a 24 bit Sigma-Delta ADC
nikitateggi 1:8316c23ec6b9 4 */
nikitateggi 1:8316c23ec6b9 5
nikitateggi 1:8316c23ec6b9 6 #include "mbed.h"
nikitateggi 1:8316c23ec6b9 7 #include <string.h>
nikitateggi 1:8316c23ec6b9 8 #include <stdio.h>
nikitateggi 1:8316c23ec6b9 9 #include "ds3231.h"
nikitateggi 1:8316c23ec6b9 10 #include "SDFileSystem.h"
nikitateggi 1:8316c23ec6b9 11 #include "ecg_dec.h"
nikitateggi 1:8316c23ec6b9 12 #include "rtc.h"
nikitateggi 1:8316c23ec6b9 13 #include "sdcard.h"
nikitateggi 3:9a06c2bed650 14 #include "ec_bp.h"
nidhinvarghese 14:f5c62d30c6fc 15
nidhinvarghese 14:f5c62d30c6fc 16 #include "struct.h" // Added on 31/5/17_Nidhin
nikitateggi 19:1650bbc923cc 17 //#include "test_type.h" //Added on 31/5/17_Nidhin
nikitateggi 3:9a06c2bed650 18 Serial pc(USBTX,USBRX);
nikitateggi 1:8316c23ec6b9 19
nikitateggi 1:8316c23ec6b9 20
nikitateggi 1:8316c23ec6b9 21
suhasini 13:5d3b478ea9c7 22 float ecg(int pid)
nikitateggi 3:9a06c2bed650 23 {
nidhinvarghese 14:f5c62d30c6fc 24 //----------------------- Structure for Bluetooth Added Nidhin 1/6/2017-------------------//
nidhinvarghese 14:f5c62d30c6fc 25
nidhinvarghese 14:f5c62d30c6fc 26 //BLUETOOTH STRUCTURE
nidhinvarghese 14:f5c62d30c6fc 27
nidhinvarghese 14:f5c62d30c6fc 28 BLEMsg_info *ptr_BLEMsg_info_ecg, BLEMsg_info_ecg; // A copy of master strcuture [ "BLEMsg_info" ] by name "BLEMsg_info_ecg" is created
nidhinvarghese 14:f5c62d30c6fc 29 ptr_BLEMsg_info_ecg = &BLEMsg_info_ecg; // *ptr_BLEMsg_info_bp is the pointer to local copy;
nidhinvarghese 14:f5c62d30c6fc 30
nidhinvarghese 14:f5c62d30c6fc 31 // Declaration of Date Structure
nidhinvarghese 14:f5c62d30c6fc 32 DateTime_info *ptr_DateTime_info_ecg, DateTime_info_ecg; // A copy of Master Structure "DateTime_info" created,
nidhinvarghese 14:f5c62d30c6fc 33 ptr_DateTime_info_ecg = &DateTime_info_ecg; // Structure pointer points to that copy.
nidhinvarghese 14:f5c62d30c6fc 34
nidhinvarghese 14:f5c62d30c6fc 35
nidhinvarghese 14:f5c62d30c6fc 36 // RTC operations
nidhinvarghese 14:f5c62d30c6fc 37 time_t epoch_time_ecg; //A copy of time_t by name epoch_time_bp is created
nidhinvarghese 14:f5c62d30c6fc 38 epoch_time_ecg = rtc_read(); // time is got from get epoch function.
nidhinvarghese 14:f5c62d30c6fc 39
nidhinvarghese 14:f5c62d30c6fc 40 struct tm * ptr_time_info_ecg, time_info_ecg; // Sturucture copy of tm is created
nidhinvarghese 14:f5c62d30c6fc 41 ptr_time_info_ecg = localtime(&epoch_time_ecg); // Structure accepts the time in local format from "time_t" type.
nidhinvarghese 14:f5c62d30c6fc 42
nidhinvarghese 14:f5c62d30c6fc 43 //BELOW LINE IS TO CHECK Date and TIME
nidhinvarghese 15:208b146151ba 44 //pc.printf("Time is %d: %d: %d\n", (*ptr_time_info_ecg).tm_hour, (*ptr_time_info_ecg).tm_min, (*ptr_time_info_ecg).tm_sec);
nidhinvarghese 15:208b146151ba 45 //pc.printf("Date is %d:%d:%d\n", (*ptr_time_info_ecg).tm_mday, (*ptr_time_info_ecg).tm_mon+1, (*ptr_time_info_ecg).tm_year-100);
nidhinvarghese 14:f5c62d30c6fc 46
nidhinvarghese 14:f5c62d30c6fc 47 //Copying from one structure to the other using variables
nidhinvarghese 14:f5c62d30c6fc 48 DateTime_info_ecg.hour = (uint8_t)(*ptr_time_info_ecg).tm_hour;
nidhinvarghese 14:f5c62d30c6fc 49 DateTime_info_ecg.mins = (uint8_t)(*ptr_time_info_ecg).tm_min;
nidhinvarghese 14:f5c62d30c6fc 50 DateTime_info_ecg.sec = (uint8_t)(*ptr_time_info_ecg).tm_sec;
nidhinvarghese 14:f5c62d30c6fc 51
nidhinvarghese 14:f5c62d30c6fc 52 DateTime_info_ecg.date = (uint8_t) (*ptr_time_info_ecg).tm_mday;
nidhinvarghese 14:f5c62d30c6fc 53 DateTime_info_ecg.month =(uint8_t)(*ptr_time_info_ecg).tm_mon+1;
nidhinvarghese 14:f5c62d30c6fc 54 DateTime_info_ecg.year = (uint8_t)(*ptr_time_info_ecg).tm_year-100;
nidhinvarghese 14:f5c62d30c6fc 55
nidhinvarghese 14:f5c62d30c6fc 56 // Copying Time to Main structure
nidhinvarghese 14:f5c62d30c6fc 57 BLEMsg_info_ecg.date_time.hour = DateTime_info_ecg.hour;
nidhinvarghese 14:f5c62d30c6fc 58 BLEMsg_info_ecg.date_time.mins = DateTime_info_ecg.mins;
nidhinvarghese 14:f5c62d30c6fc 59 BLEMsg_info_ecg.date_time.sec = DateTime_info_ecg.sec;
nidhinvarghese 14:f5c62d30c6fc 60
nidhinvarghese 14:f5c62d30c6fc 61 BLEMsg_info_ecg.date_time.date = DateTime_info_ecg.date ;
nidhinvarghese 14:f5c62d30c6fc 62 BLEMsg_info_ecg.date_time.month = DateTime_info_ecg.month ;
nidhinvarghese 14:f5c62d30c6fc 63 BLEMsg_info_ecg.date_time.year = DateTime_info_ecg.year ;
nidhinvarghese 14:f5c62d30c6fc 64
nidhinvarghese 14:f5c62d30c6fc 65
nidhinvarghese 14:f5c62d30c6fc 66 //Checking if the structure has these values
nidhinvarghese 15:208b146151ba 67 //pc.printf("Time 2 is %d:%d:%d\n", DateTime_info_ecg.hour, DateTime_info_ecg.mins, DateTime_info_ecg.sec);
nidhinvarghese 15:208b146151ba 68 //pc.printf("\t Date is %d:%d:%d\n",DateTime_info_ecg.date, DateTime_info_ecg.month, DateTime_info_ecg.year);
nidhinvarghese 14:f5c62d30c6fc 69
nidhinvarghese 14:f5c62d30c6fc 70
nidhinvarghese 14:f5c62d30c6fc 71 //Loading values to of Test type
nidhinvarghese 14:f5c62d30c6fc 72 test_type_info test_type_info_ecg; // copy of " test_type_info" created
nidhinvarghese 14:f5c62d30c6fc 73 test_type_info_ecg = ECG_Test; // Loaded value 00 to the test type
nidhinvarghese 14:f5c62d30c6fc 74
nidhinvarghese 14:f5c62d30c6fc 75 BLEMsg_info_ecg.test_type = test_type_info_ecg;
nidhinvarghese 14:f5c62d30c6fc 76 //Check if 00 is getting printed
nidhinvarghese 15:208b146151ba 77 //pc.printf("Test Type is : %d\n", test_type_info_ecg);
nidhinvarghese 14:f5c62d30c6fc 78
nidhinvarghese 14:f5c62d30c6fc 79
nidhinvarghese 14:f5c62d30c6fc 80 // Loading values of Length , PID, DID, sampling frequency, number of samples, calculated data.
nidhinvarghese 14:f5c62d30c6fc 81 BLEMsg_info_ecg.device_id = 01; // Device ID fixed
nidhinvarghese 14:f5c62d30c6fc 82 BLEMsg_info_ecg.patient_id = (uint32_t)pid; // Patient ID
nidhinvarghese 14:f5c62d30c6fc 83 BLEMsg_info_ecg.sampling_freq = 500; // sampling frrquency
nidhinvarghese 14:f5c62d30c6fc 84 BLEMsg_info_ecg.length = 4026; //Total length of data in bytes 22 B+10752 B
nidhinvarghese 14:f5c62d30c6fc 85
nidhinvarghese 14:f5c62d30c6fc 86 /*
nidhinvarghese 14:f5c62d30c6fc 87 //Loading number of samples
nidhinvarghese 14:f5c62d30c6fc 88 NumSamples_info NumSamples_info_bp; //Copy of structure NumSamples_info
nidhinvarghese 14:f5c62d30c6fc 89 NumSamples_info_bp.num_ppg_sample = 1664; // PPG & ECG Sample number loaded in structure copy
nidhinvarghese 14:f5c62d30c6fc 90 NumSamples_info_bp.num_ecg_sample = 1024;
nidhinvarghese 14:f5c62d30c6fc 91 */
nidhinvarghese 14:f5c62d30c6fc 92
nidhinvarghese 14:f5c62d30c6fc 93 BLEMsg_info_ecg.num_samples.num_sample_ppg_dummy = 0 ;// PPG number of samples copied to master struct
nidhinvarghese 14:f5c62d30c6fc 94 BLEMsg_info_ecg.num_samples.num_sample_ecg_OTtyp = 1000 ; // ECG number of samples copied to master struct
nidhinvarghese 14:f5c62d30c6fc 95
nidhinvarghese 14:f5c62d30c6fc 96 //----------------------------------------END Structure for Bluetooth - Added Nidhin 1/6/2017-------
nidhinvarghese 14:f5c62d30c6fc 97
nidhinvarghese 14:f5c62d30c6fc 98
nikitateggi 1:8316c23ec6b9 99
nidhinvarghese 15:208b146151ba 100 int32_t concatenate_value2 = 0; // ORG. "int concatenate_value2 = 0;" Nidhin 1/6/17
nidhinvarghese 15:208b146151ba 101 int32_t *ecg_ptr; // Added 1/6/2017 Nidhin
nidhinvarghese 14:f5c62d30c6fc 102 ecg_ptr = &concatenate_value2; // Pointer to pass for ECG write into SD card Nidhin 1/6/2017
nidhinvarghese 14:f5c62d30c6fc 103
suhasini 13:5d3b478ea9c7 104 // int32_t sample_sum; // static int32_t avg[1500];
suhasini 13:5d3b478ea9c7 105 int32_t count = 0; int32_t fs = 500;
nidhinvarghese 17:22a87e12fb3a 106 uint32_t ecg_buf[N_ECG]; // Moved out of func() Nidhin 9/6/17
nikitateggi 3:9a06c2bed650 107 Timer t;
suhasini 13:5d3b478ea9c7 108
suhasini 13:5d3b478ea9c7 109 //------------------ Declaration for Peak value detection ------------------------------------
suhasini 13:5d3b478ea9c7 110
suhasini 13:5d3b478ea9c7 111 uint32_t hi_val;uint32_t pk_val[20];unsigned int pk_pos[20]={0};unsigned int a; //uint32_t pk=0;
suhasini 13:5d3b478ea9c7 112 int hi_dif = 0;int j=0; // int count1 = N_ECG/fs, a_dif=0, fs1 = fs ,h=0;
suhasini 13:5d3b478ea9c7 113 // ------------------------- Declaration for Heart Rate calculation --------------------------
suhasini 13:5d3b478ea9c7 114 int n=0; //int n=10;
suhasini 13:5d3b478ea9c7 115 float pos_dif, HR[2], HR1,t_pos_dif;int t_sec = 60; float HR_sum = 0,HR_avg;
suhasini 13:5d3b478ea9c7 116 // -------------------------------------------------------------------------------------------
suhasini 13:5d3b478ea9c7 117
suhasini 13:5d3b478ea9c7 118 // unsigned char chk = 1;
nikitateggi 3:9a06c2bed650 119 pc.baud(baud_rate);
nikitateggi 4:6bd81bb1790d 120 freqset(); // setting the frequency
nikitateggi 4:6bd81bb1790d 121 setupfunc();
nikitateggi 3:9a06c2bed650 122 ecgsetupfunc();
suhasini 13:5d3b478ea9c7 123 // chk = 1;
nidhinvarghese 14:f5c62d30c6fc 124
nidhinvarghese 14:f5c62d30c6fc 125 //ORIGINAL sd_open_ECGfile(pid); // opening the ecg file COMMENTED Nidhin 1/6/2017
nidhinvarghese 14:f5c62d30c6fc 126 sd_open_ECGfilee(pid); // REPLACED Nidhin 1/6/2017 Nidhin
nidhinvarghese 14:f5c62d30c6fc 127
suhasini 13:5d3b478ea9c7 128 pc.printf( "Raw data is = \n");
nikitateggi 3:9a06c2bed650 129 for(int i=0; i<N_ECG; i++)
nikitateggi 3:9a06c2bed650 130 {
nikitateggi 3:9a06c2bed650 131 concatenate_value2= readvalue();
nidhinvarghese 14:f5c62d30c6fc 132
nidhinvarghese 14:f5c62d30c6fc 133 //ORIGINAL sd_write(concatenate_value2); // writing into the sd card COMMENTED Nidhin 1/6/2017
nidhinvarghese 14:f5c62d30c6fc 134 sd_ecgwrite(ecg_ptr); // REPLACED Nidhin 1/6/2017
nidhinvarghese 14:f5c62d30c6fc 135
suhasini 13:5d3b478ea9c7 136 ecg_buf[i] = concatenate_value2;
nidhinvarghese 15:208b146151ba 137 pc.printf( "%d\n", concatenate_value2); //COMMENTED Nidhin 1/6/2017
nikitateggi 3:9a06c2bed650 138 }
nidhinvarghese 14:f5c62d30c6fc 139
nidhinvarghese 14:f5c62d30c6fc 140 //sd_close(); // closing the file COMMENTED Nidhin 1/6/2017
nidhinvarghese 14:f5c62d30c6fc 141 sd_close_ecg(); // closing the ECG file REPLACED Nidhin 1/6/2017 Nidhin
suhasini 13:5d3b478ea9c7 142 /*
suhasini 13:5d3b478ea9c7 143 // ---------- reading back SD data for processing --------------------
suhasini 13:5d3b478ea9c7 144 sd_read_file(15);
suhasini 13:5d3b478ea9c7 145 printf("Reading back SD data\n");
suhasini 13:5d3b478ea9c7 146 for(int i=10;i<N_ECG;i++)
suhasini 13:5d3b478ea9c7 147 {
suhasini 13:5d3b478ea9c7 148 ecg_buf= sd_read();
suhasini 13:5d3b478ea9c7 149 //printf("%d\n",ecg_buf[i]);
suhasini 13:5d3b478ea9c7 150 }
suhasini 13:5d3b478ea9c7 151
suhasini 13:5d3b478ea9c7 152 sd_close(); */
suhasini 13:5d3b478ea9c7 153
suhasini 13:5d3b478ea9c7 154 //----------------------------- PEAK DETECTION AND HEART RATE CALCULATION ---------------------------------------------------
suhasini 13:5d3b478ea9c7 155 // -------------------------------------- PEAK DETECTION -------------------------------------------------------------
suhasini 13:5d3b478ea9c7 156
suhasini 13:5d3b478ea9c7 157 // ------------------ Main loop ---------------------------------
nikitateggi 3:9a06c2bed650 158
suhasini 13:5d3b478ea9c7 159 for(int i=0;i<N_ECG-10;i++){
suhasini 13:5d3b478ea9c7 160 if(ecg_buf[i]>ecg_buf[i+1])
suhasini 13:5d3b478ea9c7 161 {
suhasini 13:5d3b478ea9c7 162 hi_val = ecg_buf[i]; //To find the high value
suhasini 13:5d3b478ea9c7 163 //printf("high value= %d\n",hi_val);
suhasini 13:5d3b478ea9c7 164 a = i;
suhasini 13:5d3b478ea9c7 165 //printf("a= %d\n",a);
suhasini 13:5d3b478ea9c7 166 hi_dif = hi_val-ecg_buf[a+10];
suhasini 13:5d3b478ea9c7 167
suhasini 13:5d3b478ea9c7 168 //a_dif = ecg_buf[a+2] - ecg_buf[a+1];
suhasini 13:5d3b478ea9c7 169 //printf("The difference between high and low value is = %d\n",hi_dif);
suhasini 13:5d3b478ea9c7 170
suhasini 13:5d3b478ea9c7 171 // ---------------------------- If hi_val is greater than next ten input values, then compare the hi_val with the tenth input value.
suhasini 13:5d3b478ea9c7 172 // If the diff is greater than 10000, then it is a valid peak (pls chk the below condition)--------------------------------------------------
suhasini 13:5d3b478ea9c7 173 // if((hi_dif > 10000) && ((a+10) < N_ECG))
suhasini 13:5d3b478ea9c7 174 if(hi_dif > 10000)
suhasini 13:5d3b478ea9c7 175 {
suhasini 13:5d3b478ea9c7 176 // if(a_dif <= 0) ------------------------ add this condition if needed ----------------------
suhasini 13:5d3b478ea9c7 177 // {
suhasini 13:5d3b478ea9c7 178 pk_val[j] = hi_val; //if condition satisfied, put the "pk" value into "pk_val" buffer
suhasini 13:5d3b478ea9c7 179 pc.printf("peak value= %d\n",pk_val[j]);
suhasini 13:5d3b478ea9c7 180 pk_pos[j]=a; // also save the peak's position
suhasini 13:5d3b478ea9c7 181 pc.printf("peak position is = %d\n",pk_pos[j]);
suhasini 13:5d3b478ea9c7 182 i = a+120; // once confirmed that this is the necessary peak, skip the next 120 input values
suhasini 13:5d3b478ea9c7 183 n = j; // where n is the number of peaks detected
suhasini 13:5d3b478ea9c7 184 j = j+1;
suhasini 13:5d3b478ea9c7 185
suhasini 13:5d3b478ea9c7 186 // printf("j after peak detection is= %d\n",j);
suhasini 13:5d3b478ea9c7 187 // }
suhasini 13:5d3b478ea9c7 188 }
suhasini 13:5d3b478ea9c7 189 else
suhasini 13:5d3b478ea9c7 190 {
suhasini 13:5d3b478ea9c7 191 //h = a+1;
suhasini 13:5d3b478ea9c7 192 i = a+1;
suhasini 13:5d3b478ea9c7 193 // printf("i if peak not found is= %d\n",i);
suhasini 13:5d3b478ea9c7 194 }
suhasini 13:5d3b478ea9c7 195 // store the peak value position in "pk_pos"
suhasini 13:5d3b478ea9c7 196
suhasini 13:5d3b478ea9c7 197 }
suhasini 13:5d3b478ea9c7 198 }
suhasini 13:5d3b478ea9c7 199 // ----------------- HEART RATE LOGIC ---------------------------
nikitateggi 3:9a06c2bed650 200
suhasini 13:5d3b478ea9c7 201 for(int i = 0;i < n-1;i++)
suhasini 13:5d3b478ea9c7 202 {
suhasini 13:5d3b478ea9c7 203 pos_dif = pk_pos[i+1] - pk_pos[i]; // difference between two consequtive peaks
suhasini 13:5d3b478ea9c7 204 pc.printf("peak position diff is = %f\n",pos_dif);
suhasini 13:5d3b478ea9c7 205 //printf("peak position i value is = %d\n",i);
suhasini 13:5d3b478ea9c7 206 t_pos_dif = pos_dif/fs; // sample difference between peak positions divided by sampling frequency gives the difference value in terms of actual time
suhasini 13:5d3b478ea9c7 207 pc.printf("time in seconds is = %f\n",t_pos_dif);
suhasini 13:5d3b478ea9c7 208 HR[i] = t_sec/t_pos_dif; //HR calculation
suhasini 13:5d3b478ea9c7 209 pc.printf("Heart Rate is = %f\n",HR[i]);
suhasini 13:5d3b478ea9c7 210 // n = i;
suhasini 13:5d3b478ea9c7 211 HR1 = HR[0];
suhasini 13:5d3b478ea9c7 212
suhasini 13:5d3b478ea9c7 213 }
suhasini 13:5d3b478ea9c7 214 // ---------------------- To average individual HRs for higher number of samples -----------------------
suhasini 13:5d3b478ea9c7 215 /* for(int i = 0;i < 5;i++)
suhasini 13:5d3b478ea9c7 216 {
suhasini 13:5d3b478ea9c7 217 HR_sum = HR[i]+HR_sum;
suhasini 13:5d3b478ea9c7 218 }
suhasini 13:5d3b478ea9c7 219 HR_avg = HR_sum/5; // To find average of all the individual HRs calculated
suhasini 13:5d3b478ea9c7 220 printf("Heart Rate sum is = %f\n",HR_sum);
suhasini 13:5d3b478ea9c7 221 printf("Denominator = %d\n",n);
suhasini 13:5d3b478ea9c7 222 printf("Heart Rate = %f\n",HR_avg);
suhasini 13:5d3b478ea9c7 223 */
nidhinvarghese 14:f5c62d30c6fc 224
nidhinvarghese 14:f5c62d30c6fc 225 //ADDED Nidhin 1/6/2017
nidhinvarghese 14:f5c62d30c6fc 226
nidhinvarghese 14:f5c62d30c6fc 227 BLEMsg_info_ecg.cal_data.cal_sbp_dummy = 0;
nidhinvarghese 14:f5c62d30c6fc 228 BLEMsg_info_ecg.cal_data.cal_dbp_OTtyp = (uint16_t)HR1; //To be modified after HR code is added.
nidhinvarghese 14:f5c62d30c6fc 229
nidhinvarghese 14:f5c62d30c6fc 230 structure_file(ptr_BLEMsg_info_ecg, pid); //copy the ECG structure to Main file
nidhinvarghese 14:f5c62d30c6fc 231 ecgfile_mainfile(pid); // copy raw data to the main file and ECG file is cleared.
nidhinvarghese 14:f5c62d30c6fc 232
nidhinvarghese 14:f5c62d30c6fc 233 pc.printf("Closed the main file\n");
nidhinvarghese 14:f5c62d30c6fc 234
nidhinvarghese 14:f5c62d30c6fc 235
nidhinvarghese 14:f5c62d30c6fc 236
suhasini 13:5d3b478ea9c7 237 return HR1;
suhasini 13:5d3b478ea9c7 238 // return HR_avg;
suhasini 13:5d3b478ea9c7 239
suhasini 13:5d3b478ea9c7 240 } // End of main function
suhasini 13:5d3b478ea9c7 241