Arduino project with pulsesensor and microSD shield.

pulse_irq.ino

volatile int rate[10];                    // used to hold last ten IBI values
volatile unsigned long sampleCounter = 0;          // used to determine pulse timing
volatile unsigned long lastBeatTime = 0;           // used to find the inter beat interval
volatile int P =512;                      // used to find peak in pulse wave
volatile int T = 512;                     // used to find trough in pulse wave
volatile int thresh = 512;                // used to find instant moment of heart beat
volatile int amp = 100;                   // used to hold amplitude of pulse waveform
volatile boolean firstBeat = true;        // used to seed rate array so we startup with reasonable BPM
volatile boolean secondBeat = true;       // used to seed rate array so we startup with reasonable BPM

void interruptSetup(){     
  // Initializes Timer2 to throw an interrupt every 2mS.
  TCCR2A = 0x02;     // DISABLE PWM ON DIGITAL PINS 3 AND 11, AND GO INTO CTC MODE
  TCCR2B = 0x06;     // DON'T FORCE COMPARE, 256 PRESCALER 
  OCR2A = 0X7C;      // SET THE TOP OF THE COUNT TO 124 FOR 500Hz SAMPLE RATE
  TIMSK2 = 0x02;     // ENABLE INTERRUPT ON MATCH BETWEEN TIMER2 AND OCR2A
  sei();             // MAKE SURE GLOBAL INTERRUPTS ARE ENABLED      
} 

// THIS IS THE TIMER 2 INTERRUPT SERVICE ROUTINE. 
// Timer 2 makes sure that we take a reading every 2 miliseconds
ISR(TIMER2_COMPA_vect){                         // triggered when Timer2 counts to 124
  cli();                                      // disable interrupts while we do this
  sd.service();
  Signal = analogRead(pulsePin);              // read the Pulse Sensor 
  sampleCounter += 2;                         // keep track of the time in mS with this variable
  int N = sampleCounter - lastBeatTime;       // monitor the time since the last beat to avoid noise

  // find the peak and trough of the pulse wave
  if(Signal < thresh && N > (IBI/5)*3){       // avoid dichrotic noise by waiting 3/5 of last IBI
    if (Signal < T){                        // T is the trough
      T = Signal;                         // keep track of lowest point in pulse wave 
    }
  }

  if(Signal > thresh && Signal > P){          // thresh condition helps avoid noise
    P = Signal;                             // P is the peak
  }                                        // keep track of highest point in pulse wave
    
  // NOW IT'S TIME TO LOOK FOR THE HEART BEAT
  // signal surges up in value every time there is a pulse
  if (N > 250){                                   // avoid high frequency noise
    if ( (Signal > thresh) && (Pulse == false) && (N > (IBI/5)*3) ){        
      Pulse = true;                               // set the Pulse flag when we think there is a pulse
      digitalWrite(blinkPin,HIGH);                // turn on pin 13 LED
      IBI = sampleCounter - lastBeatTime;         // measure time between beats in mS
      lastBeatTime = sampleCounter;               // keep track of time for next pulse

      if(firstBeat){                         // if it's the first time we found a beat, if firstBeat == TRUE
        firstBeat = false;                 // clear firstBeat flag
        return;                            // IBI value is unreliable so discard it
      }   
      if(secondBeat){                        // if this is the second beat, if secondBeat == TRUE
        secondBeat = false;                 // clear secondBeat flag
        for(int i=0; i<=9; i++){         // seed the running total to get a realisitic BPM at startup
          rate[i] = IBI;                      
        }
      }
 
      // keep a running total of the last 10 IBI values
      word runningTotal = 0;                   // clear the runningTotal variable    

      for(int i=0; i<=8; i++){                // shift data in the rate array
        rate[i] = rate[i+1];              // and drop the oldest IBI value 
        runningTotal += rate[i];          // add up the 9 oldest IBI values
      }

      rate[9] = IBI;                          // add the latest IBI to the rate array
      runningTotal += rate[9];                // add the latest IBI to runningTotal
      runningTotal /= 10;                     // average the last 10 IBI values 
      BPM = 60000/runningTotal;               // how many beats can fit into a minute? that's BPM!
      QS = true;                              // set Quantified Self flag 
      // QS FLAG IS NOT CLEARED INSIDE THIS ISR
    }
  }

  if (Signal < thresh && Pulse == true){     // when the values are going down, the beat is over
    digitalWrite(blinkPin,LOW);            // turn off pin 13 LED
    Pulse = false;                         // reset the Pulse flag so we can do it again
    amp = P - T;                           // get amplitude of the pulse wave
    thresh = amp/2 + T;                    // set thresh at 50% of the amplitude
    P = thresh;                            // reset these for next time
    T = thresh;
  }

  if (N > 2500){                             // if 2.5 seconds go by without a beat
    thresh = 512;                          // set thresh default
    P = 512;                               // set P default
    T = 512;                               // set T default
    lastBeatTime = sampleCounter;          // bring the lastBeatTime up to date        
    firstBeat = true;                      // set these to avoid noise
    secondBeat = true;                     // when we get the heartbeat back
  }
  
  sei();                                     // enable interrupts when youre done!
}// end isr

pulse_sd.ino

#include <integer.h>
#include <diskio.h>
#include <ffconf.h>
#include <ff.h>
#include <mmc.h>
#include <stdio.h>
// SD imports
#include <SDcard.h>
// RTC imports
#include <DS1307.h>
#include <Wire.h>

//  VARIABLES
int pulsePin = 0;                 // Pulse Sensor purple wire connected to analog pin 0
int blinkPin = 13;                // pin to blink led at each beat
int fadePin = 5;                  // pin to do fancy classy fading blink at each beat
int fadeRate = 0;                 // used to fade LED on with PWM on fadePin

SDcard sd;
DS1307 rtc;
char fileName[12];

uint8_t sec, min, hour, day, month;
uint16_t year;

// these variables are volatile because they are used during the interrupt service routine!
volatile int BPM;                   // used to hold the pulse rate
volatile int Signal;                // holds the incoming raw data
volatile int IBI = 600;             // holds the time between beats, the Inter-Beat Interval
volatile boolean Pulse = false;     // true when pulse wave is high, false when it's low
volatile boolean QS = false;        // becomes true when Arduoino finds a beat.

void setup(){
  pinMode(blinkPin,OUTPUT);         // pin that will blink to your heartbeat!
  pinMode(fadePin,OUTPUT);          // pin that will fade to your heartbeat!
  Serial.begin(115200);             // we agree to talk fast!
  Serial.println("Setting up...");
  //rtc.set(0, 0, 18, 6, 3, 2013);
  rtc.start();                      // start real-time clock
  sd.init(4); //spi-clk = Fcpu/4    // set up SDcard
  interruptSetup();                 // sets up to read Pulse Sensor signal every 2mS 
  // UN-COMMENT THE NEXT LINE IF YOU ARE POWERING The Pulse Sensor AT LOW VOLTAGE, 
  // AND APPLY THAT VOLTAGE TO THE A-REF PIN
  //analogReference(EXTERNAL);
  //get time from RTC
  rtc.get(&sec, &min, &hour, &day, &month, &year);
  sprintf(fileName, "%04d%02d%02d.csv", year, month, day, hour, min, sec);
  if(sd.mount() == 0){
    Serial.println("SDcard available.");
    Serial.print("Using file ");
    Serial.println(fileName);
  } else {
    Serial.println("SDcard unavailable.");
  }
  Serial.println("Setup done.");
}

void loop(){
  if (QS == true){                       // Quantified Self flag is true when arduino finds a heartbeat
    fadeRate = 255;                  // Set 'fadeRate' Variable to 255 to fade LED with pulse
    Serial.println("B" + String(BPM) + " Q" + String(IBI));
    // write new line to file
    WriteFile();
    QS = false;                      // reset the Quantified Self flag for next time
  }
  
  delay(5000);                             //  take a break
  //TODO when to sd.unmount()?
}

void WriteFile(){
  FIL fdst;     //file objects
  FRESULT res;  //result code

  //get time from RTC
  rtc.get(&sec, &min, &hour, &day, &month, &year);

  res = f_open(&fdst, fileName, FA_OPEN_ALWAYS | FA_WRITE);
  if(res == FR_OK){
    // seek to EOF
    f_lseek(&fdst, f_size(&fdst));
    // write data - remember to "#define _USE_STRFUNC 1" in ffconf.h
    f_printf(&fdst, "%04d%02d%02d-%02d%02d%02d B%04d Q%04d", year, month, day, hour, min, sec, BPM, IBI);
    f_close(&fdst);
    return;
  }

  Serial.println("Error!");
}