#include <DS3231.h>
#include <SPI.h>
#include <SD.h>
#include <max6675.h>

const int thermoDO = 12;
const int thermoCS = 2;
const int thermoCLK = 13;

MAX6675 thermocouple(thermoCLK, thermoCS, thermoDO);

File eventList;                                    // FILE pointer for eventLst file     

DS3231  rtc(SDA, SCL);                             // Define rtc

  const int Red=3;
  const int Green=5;
  const int Blue=6;

  byte nextEventFlag[13];                          // array to hold the pointer to the next event on the list aiming to impliment multiple events for all channels
  byte activeEventPointer[13];                     // ppinters to show which of the 2 d array is active for any channel
  float intensity[13];                             // array that holds the calculated intensity for each channel
  float output;                                    // variable used to calculate the normalisation setting for the overall output once scaled to each channels individual intensity setting
  long refTime[13];                                // array to hold a list of event start times
  long duration[13];                               // array to hold the duration of each event
  float maxIntensity[13];                          // array to hold a list of maximum intensities
  const char* filename = {"eventlis.csv"};         // file to hold list of events
  long startTime;
  
  int i;
  int flag = 1;

  const float pi = 3.14159;

void setup() {

  Serial.begin(9600);
 
  Serial.println("MAX6675 Initialise");

  delay(500);
        digitalWrite(thermoCS,LOW);                 // forcing CS for 6675 low although looking at MAX6675.cpp, it looks as if this is not needed

        Serial.print("C = "); 
        Serial.println(thermocouple.readCelsius());
        digitalWrite(thermoCS,HIGH);                // forcing CS for 6675 HIGH although looking at MAX6675.cpp, it looks as if this is not needed 

        delay(2000);

  pinMode(Red, OUTPUT); 
  pinMode(Green, OUTPUT);
  pinMode(Blue, OUTPUT);
  
  rtc.begin();                                     // start real time clock stream
  
  if (!SD.begin(10)) {
    Serial.println("initialization failed!");
      }
           digitalWrite(10,HIGH);                 // trying to force the sd card to release the SPI bus but making its CS pin high

           digitalWrite(thermoCS,LOW);
        Serial.print("again C = "); 
        Serial.println(thermocouple.readCelsius());
        digitalWrite(thermoCS,HIGH);
        delay(500);