ecgg.cpp

00001 /** ECG ADS1291 Test program.
00002 ADS1291 is a single channel ECG chip
00003 with a 24 bit Sigma-Delta ADC
00004  */
00005  
00006 #include "mbed.h"
00007 #include <string.h>
00008 #include <stdio.h>
00009 #include "ds3231.h"
00010 #include "SDFileSystem.h"
00011 #include "ecg_dec.h"
00012 #include "rtc.h"
00013 #include "sdcard.h"
00014 #include "ec_bp.h"
00015 
00016 #include "struct.h"  // Added on 31/5/17_Nidhin
00017 //#include "test_type.h" //Added on  31/5/17_Nidhin
00018 FILE *fpeecg1; // FILE pointer to ECG file
00019 Serial pc(USBTX,USBRX);  
00020 
00021 
00022 uint16_t ecg(int32_t pid) 
00023 //float ecg(int pid) 
00024  {
00025     
00026     uint8_t lead_reg=0;      // added on 14/06 to check lead -off 
00027     //----------------------- Structure for Bluetooth  Added Nidhin 1/6/2017-------------------//
00028     
00029     //BLUETOOTH STRUCTURE
00030     
00031     BLEMsg_info *ptr_BLEMsg_info_ecg, BLEMsg_info_ecg; // A copy of master strcuture [ "BLEMsg_info" ] by name "BLEMsg_info_ecg" is created
00032     ptr_BLEMsg_info_ecg = &BLEMsg_info_ecg;            // *ptr_BLEMsg_info_bp is the pointer to local copy;
00033     
00034     // Declaration of Date Structure
00035     DateTime_info *ptr_DateTime_info_ecg, DateTime_info_ecg; // A copy of Master Structure "DateTime_info" created, 
00036     ptr_DateTime_info_ecg = &DateTime_info_ecg;             // Structure pointer points to that copy.
00037     
00038     
00039     // RTC operations
00040     time_t epoch_time_ecg;           //A copy of time_t by name  epoch_time_bp is created 
00041     epoch_time_ecg = rtc_read();    // time is got from get epoch function.  
00042     
00043     struct tm * ptr_time_info_ecg, time_info_ecg;   // Sturucture copy of tm is created
00044     ptr_time_info_ecg = localtime(&epoch_time_ecg); // Structure accepts the time in local format from "time_t" type.
00045       
00046     //BELOW LINE IS TO CHECK Date and TIME 
00047     //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);
00048     //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);
00049     
00050     //Copying from one structure to the other using variables
00051     DateTime_info_ecg.hour = (uint8_t)(*ptr_time_info_ecg).tm_hour;
00052     DateTime_info_ecg.mins = (uint8_t)(*ptr_time_info_ecg).tm_min;
00053     DateTime_info_ecg.sec =  (uint8_t)(*ptr_time_info_ecg).tm_sec;
00054     
00055     DateTime_info_ecg.date = (uint8_t) (*ptr_time_info_ecg).tm_mday;
00056     DateTime_info_ecg.month =(uint8_t)(*ptr_time_info_ecg).tm_mon+1;
00057     DateTime_info_ecg.year = (uint8_t)(*ptr_time_info_ecg).tm_year-100;
00058     
00059     // Copying Time to Main structure
00060     BLEMsg_info_ecg.date_time.hour = DateTime_info_ecg.hour;
00061     BLEMsg_info_ecg.date_time.mins = DateTime_info_ecg.mins;
00062     BLEMsg_info_ecg.date_time.sec = DateTime_info_ecg.sec;
00063     
00064     BLEMsg_info_ecg.date_time.date = DateTime_info_ecg.date ;
00065     BLEMsg_info_ecg.date_time.month = DateTime_info_ecg.month ;
00066     BLEMsg_info_ecg.date_time.year =  DateTime_info_ecg.year ;
00067     
00068     
00069     //Checking if the structure has these values    
00070     //pc.printf("Time 2 is %d:%d:%d\n", DateTime_info_ecg.hour, DateTime_info_ecg.mins, DateTime_info_ecg.sec);
00071     //pc.printf("\t Date is %d:%d:%d\n",DateTime_info_ecg.date, DateTime_info_ecg.month, DateTime_info_ecg.year);
00072     
00073     
00074     //Loading values to of Test type
00075     test_type_info test_type_info_ecg;  // copy of " test_type_info" created  
00076     test_type_info_ecg = ECG_Test;       // Loaded value 00 to the test type 
00077     
00078     BLEMsg_info_ecg.test_type = test_type_info_ecg;
00079     //Check if 00 is getting printed
00080     //pc.printf("Test Type is : %d\n", test_type_info_ecg);
00081     
00082     
00083     // Loading values of Length ,  PID, DID, sampling frequency, number of samples, calculated data.
00084     BLEMsg_info_ecg.device_id = 01;                   // Device ID fixed
00085     BLEMsg_info_ecg.patient_id = (uint32_t)pid;       // Patient ID
00086     BLEMsg_info_ecg.sampling_freq = 500;              // sampling frrquency
00087     BLEMsg_info_ecg.length = 8022;                   //Total length of data in bytes  22 B+ 4000 data
00088     
00089     /*
00090     //Loading number of samples
00091     NumSamples_info NumSamples_info_bp;              //Copy of structure NumSamples_info
00092     NumSamples_info_bp.num_ppg_sample = 1664;        // PPG & ECG Sample number loaded in structure copy
00093     NumSamples_info_bp.num_ecg_sample = 1024;
00094     */
00095     
00096     BLEMsg_info_ecg.num_samples.num_sample_ppg_dummy =  0 ;// PPG  number of samples copied to master struct 
00097     BLEMsg_info_ecg.num_samples.num_sample_ecg_OTtyp =  2000 ; // ECG  number of samples copied to master struct
00098     
00099     //----------------------------------------END Structure for Bluetooth - Added Nidhin 1/6/2017-------
00100 
00101      uint32_t concatenate_value2 = 0;      // ORG. "int concatenate_value2 = 0;" Nidhin 1/6/17
00102     uint32_t *ecg_ptr;                   // Added 1/6/2017 Nidhin
00103     ecg_ptr = &concatenate_value2; // Pointer to pass for ECG write into SD card Nidhin 1/6/2017
00104     
00105     uint16_t count = 0; 
00106     uint16_t fs = 500;
00107     //uint32_t ecg_buf[N_ECG];
00108     Timer t;
00109     
00110     //------------------ Declaration for Peak value detection ------------------------------------
00111   uint32_t ecg_samp1[1] ; uint32_t ecg_samp2[1]; uint32_t ecg_samp3[1];  // Buff 12 &3 Stores sample 1, 2 & 10th sample
00112   uint32_t fppos;  // Variable to hold pointer position
00113   uint32_t hi_val;
00114   uint32_t pk_val[20];
00115   uint16_t pk_pos[20]={0};
00116  // unsigned int a; //uint32_t pk=0;
00117   int32_t hi_dif = 0; //diff between high value and it's consecutive value
00118   uint16_t j=0; // int count1 = N_ECG/fs, a_dif=0, fs1 = fs ,h=0;
00119   int32_t m =0;       // Variable to move the file pointer in fseek fun
00120   int32_t samp_10 = 28;       // Variable to move to 10th sampple from current
00121   char buffer3[32];
00122   
00123     // ------------------------- Declaration for Heart Rate calculation --------------------------
00124  uint8_t n=0; 
00125  float pos_dif, HR[10], HR1,t_pos_dif;
00126  uint8_t t_sec = 60; 
00127  float HR_sum = 0,HR_avg;
00128     // -------------------------------------------------------------------------------------------
00129   //  unsigned char chk = 1;
00130     pc.baud(baud_rate);
00131     freqset();               // setting the frequency
00132     setupfunc();    
00133     //ecgtestsetupfunc();          // For test set up of 1Hz square wave signal
00134    lead_reg= ecgsetupfunc();
00135  //   chk = 1;
00136  
00137  
00138    //ORIGINAL sd_open_ECGfile(pid);        // opening the ecg file  COMMENTED Nidhin 1/6/2017
00139  if (lead_reg==0)                    // checking for proper lead contact// 14/06
00140  {  
00141    sd_open_ECGfilee(pid);  // REPLACED Nidhin 1/6/2017 Nidhin 
00142    
00143   pc.printf( "Raw data is = \n"); 
00144   
00145  for(int i=0; i<N_ECG; i++)
00146    {
00147      concatenate_value2= readvalue();
00148      pc.printf( "%d\n", concatenate_value2); //ADDED Nidhin 21/6/2017
00149      
00150      sd_ecgwrite(ecg_ptr); // REPLACED Nidhin 1/6/2017
00151      
00152    } 
00153   
00154    //sd_close();          // closing the file COMMENTED Nidhin 1/6/2017
00155     sd_close_ecg();          // closing the ECG file REPLACED Nidhin 1/6/2017 Nidhin
00156     
00157     
00158 /*   
00159  // ---------- reading back SD data for processing --------------------
00160  sd_read_file(15);
00161  printf("Reading back SD data\n");
00162  for(int i=10;i<N_ECG;i++)
00163  {
00164  ecg_buf= sd_read();
00165  //printf("%d\n",ecg_buf[i]);
00166  }
00167  
00168   sd_close();    */
00169  
00170 
00171  //----------------------------- PEAK DETECTION AND HEART RATE CALCULATION ---------------------------------------------------
00172  
00173  // -------------------------------------- PEAK DETECTION -------------------------------------------------------------
00174  // ----------------------------------------- Main loop --------------------------------------------------
00175  
00176  sprintf(buffer3, "/sd/%d_ECG.csv", pid);    // For opening a specific file    
00177  fpeecg1 = fopen(buffer3, "r");
00178  
00179 for(uint16_t i=0;i<(N_ECG-10);i++){
00180     count++;
00181 rewind(fpeecg1);               // Go to start of file each time
00182 fseek(fpeecg1, m, SEEK_CUR);   // Update the count value according to move pointer //// after every calc. the pointer moves to 0th position, as we have used fseek, hence to make it jump to the respective position by "m" bytes this command is used
00183 fread(ecg_samp1, sizeof(uint32_t), 1, fpeecg1);  // Read sample 1
00184 fread(ecg_samp2, sizeof(uint32_t), 1, fpeecg1);  // Read Sample 2
00185 fseek(fpeecg1, samp_10, SEEK_CUR);   // Moving to tenth sample
00186 fread(ecg_samp3, sizeof(uint32_t), 1, fpeecg1);  // Read 3rd sample
00187 //pc.printf("ecg_samp1 = %d , ecg_samp2 = %d, ecg_samp3 = %d\n",ecg_samp1[0],ecg_samp2[0],ecg_samp3[0] ); //Test  Value held by buffer each round
00188 
00189 
00190 if(ecg_samp1[0]>ecg_samp2[0])
00191 {
00192 hi_val = ecg_samp1[0]; //To find the high value
00193 //printf("high value= %d\n",hi_val);
00194 //a = i;
00195 //printf("a= %d\n",a);
00196 hi_dif = hi_val-ecg_samp3[0];
00197 
00198   // ---------------------------- If hi_val is greater than next ten input values, then compare the hi_val with the tenth input value. 
00199   //     If the diff is greater than 10000, then it is a valid peak (pls chk the below condition)-------------------------------------
00200   //   if((hi_dif > 10000) && ((a+10) < N_ECG))
00201     if(hi_dif > 10000)
00202     {
00203    //  if(a_dif <= 0) ------------------------ add this condition if needed ----------------------
00204    //  {
00205      pk_val[j] = hi_val; //if condition satisfied, put the "pk" value into "pk_val" buffer
00206      pc.printf("peak value= %d\n",pk_val[j]);
00207      pk_pos[j]=i; // also save the peak's position
00208      pc.printf("peak position is = %d\n",pk_pos[j]);
00209      i = i+120;  // once confirmed that this is the necessary peak, skip the next 120 input values
00210      n = j; // where n is the number of peaks detected
00211      j = j+1;
00212      m = m + 480; //similar reason to considering 28, but to skip 120 samples. this cond. is satisfied only when we hit a peak - suhasini_26thjune17
00213      
00214   //   printf("j after peak detection is= %d\n",j);
00215   //   }
00216      }
00217      
00218     else
00219     {
00220      m = m+4; // this is when we do not hit a peak and have to continue searching thru, hence move to the next sample and not skip 120 samples- - suhasini_26thjune17
00221     }
00222      // store the peak value position in "pk_pos" 
00223 }
00224 else
00225 {
00226 m = m+4;
00227 }
00228 //pc.printf("i=%d",i);
00229 }
00230 n=n+1;
00231 pc.printf("n=%d\n",n);
00232 
00233  // ----------------- HEART RATE LOGIC --------------------------- 
00234  
00235  for(uint16_t i = 0;i < n-1;i++)
00236  {
00237   pos_dif = pk_pos[i+1] - pk_pos[i];                 // difference between two consequtive peaks
00238   pc.printf("peak position diff is = %f\n",pos_dif);
00239   //printf("peak position i value is = %d\n",i);
00240   t_pos_dif = pos_dif/fs;                           // sample difference between peak positions divided by sampling frequency gives the difference value in terms of actual time
00241   pc.printf("time in seconds is = %f\n",t_pos_dif);
00242   HR[i] = t_sec/t_pos_dif;                          //HR calculation
00243   pc.printf("Heart Rate is = %f\n",HR[i]);
00244  // n = i;
00245   HR1 = HR[0];
00246  }
00247  
00248  
00249  // ---------------------- To average individual HRs for higher number of samples -----------------------
00250  for(uint16_t i = 0;i < n-1;i++)
00251  {
00252  HR_sum = HR[i]+HR_sum; 
00253  }
00254  HR_avg = HR_sum/(n-1); // To find average of all the individual HRs calculated
00255  printf("Heart Rate sum is = %f\n",HR_sum);
00256  //printf("Denominator = %d\n",n);
00257  printf("Heart Rate avg is = %f\n",HR_avg);
00258  
00259  fclose(fpeecg1);
00260  pc.printf("temporary file closed\n"); 
00261  
00262 if(HR_avg>100 || HR_avg<40) 
00263     {
00264         
00265         return 1;               // out of range condition returning 1  //nikita//10/7
00266         
00267         }
00268  else 
00269      {
00270  
00271         BLEMsg_info_ecg.cal_data.cal_sbp_dummy = 0;
00272       BLEMsg_info_ecg.cal_data.cal_dbp_OTtyp = HR_avg;  //To be modified after HR code is added. // changed nikita
00273 
00274         structure_file(ptr_BLEMsg_info_ecg, pid); //copy the ECG structure to Main file  //COMMENTED Nidhin 10/6/2017 
00275         ecgfile_mainfile(pid);                        // copy raw data to the main file and ECG file is cleared. //COMMENTED Nidhin 10/6/2017
00276 
00277         pc.printf("Closed the main file\n");
00278  
00279  
00280  
00281   //return HR1;
00282         return HR_avg; 
00283   }
00284 }          
00285  else 
00286      {
00287         pc.printf("improper lead connection");
00288         return 0;                        // returning 0 for improper lead connection
00289     } 
00290 pc.printf("closing temporary file\n");
00291  // fclose(fpeecg1);
00292 //  pc.printf("temporary file closed\n");
00293 }   // End of main function