#include <SoftwareSerial.h>
#include <Wire.h>
#include <Adafruit_GFX.h>
#include <Adafruit_SSD1306.h>
#include "RTClib.h"
#include <SD.h>
#include <SPI.h>

// This code is a modification of the code found here (https://github.com/kromadg/soil-sensor)

//START LOGGER CODE HEADER
#define LOG_INTERVAL  1000 // mills between entries
#define ECHO_TO_SERIAL   1 // echo data to serial port
//END LOGGER CODE HEADER

#define SCREEN_WIDTH 128    // OLED display width, in pixels
#define SCREEN_HEIGHT 64    // OLED display height, in pixels
#define OLED_RESET -1       // Reset pin # (or -1 if sharing Arduino reset pin)
Adafruit_SSD1306 display(SCREEN_WIDTH, SCREEN_HEIGHT, &Wire, OLED_RESET);

#define RE 8
#define DE 7

//LOGGER CODE
RTC_DS1307 RTC; // define the Real Time Clock object


// for the data logging shield, we use digital pin 10 for the SD cs line
const int chipSelect = 10;

// the logging file
File logfile;

void error(char *str)
{
  Serial.print("error: ");
  Serial.println(str);
  while(1);
}
//LOGGER CODE
const byte hum_temp_ec[8] = {0x01, 0x03, 0x00, 0x00, 0x00, 0x03, 0x05, 0xCB};
byte sensorResponse[12] = {0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00};
byte sensor_values[11];

SoftwareSerial mod(2, 3); // RX, TX

void setup(void) {
    Serial.begin(9600);
    Serial.println();
    pinMode(RE, OUTPUT);
    pinMode(DE, OUTPUT);
    digitalWrite(RE, LOW);
    digitalWrite(DE, LOW);
    delay(1000);
    mod.begin(4800);
    delay(100);

    // Initializes display
    display.begin(SSD1306_SWITCHCAPVCC, 0x3C); // initialize with the I2C addr 0x3C (128x64)
    delay(500);
    display.clearDisplay();
    display.setCursor(13, 15);
    display.setTextSize(1);
    display.setTextColor(WHITE);
    display.println(" THC Soil Sensor");
    display.setCursor(21, 35);
    display.setTextSize(1);
    display.print("Initializing...");
    display.display();
    delay(5000);

    //START LOGGER CODE SETUP


  // initialize the SD card
  Serial.print("Initializing SD card...");
  // make sure that the default chip select pin is set to
  // output, even if you don't use it:
  pinMode(10, OUTPUT);

  // see if the card is present and can be initialized:
  if (!SD.begin(chipSelect)) {
    Serial.println("Card failed, or not present");
    // don't do anything more:
    return;
  }
  Serial.println("card initialized.");

  // create a new file
  char filename[] = "LOGGER00.CSV";
  for (uint8_t i = 0; i < 100; i++) {
    filename[6] = i/10 + '0';
    filename[7] = i%10 + '0';
    if (! SD.exists(filename)) {
      // only open a new file if it doesn't exist
      logfile = SD.open(filename, FILE_WRITE);
      break;  // leave the loop!
    }
  }

  if (! logfile) {
    error("couldnt create file");
  }

  Serial.print("Logging to: ");
  Serial.println(filename);

  // connect to RTC
  Wire.begin();
  if (!RTC.begin()) {
    logfile.println("RTC failed");
#if ECHO_TO_SERIAL
    Serial.println("RTC failed");
#endif  //ECHO_TO_SERIAL
  }


  logfile.println("millis,time,light,temp");
  }


   // If you want to set the aref to something other than 5v
  //analogReference(EXTERNAL);


void loop(void) {
    /************** Soil EC Reading *******************/
    digitalWrite(DE, HIGH);
    digitalWrite(RE, HIGH);
    memset(sensor_values, 0, sizeof(sensor_values));
    delay(100);

    if (mod.write(hum_temp_ec, sizeof(hum_temp_ec)) == 8) {
        digitalWrite(DE, LOW);
        digitalWrite(RE, LOW);
        for (byte i = 0; i < 12; i++) {
            sensorResponse[i] = mod.read();
            yield();
        }
    }

    delay(250);

    // get sensor response data
    float soil_hum = 0.1 * int(sensorResponse[3] << 8 | sensorResponse[4]);
    float soil_temp = 0.1 * int(sensorResponse[5] << 8 | sensorResponse[6]);
    int soil_ec = int(sensorResponse[7] << 8 | sensorResponse[8]);

    /************* Calculations and sensor corrections *************/

    float as_read_ec = soil_ec;

    // This equation was obtained from calibration using distilled water and a 1.1178mS/cm solution.
    soil_ec = 1.93*soil_ec - 270.8;
    soil_ec = soil_ec/(1.0+0.019*(soil_temp-25));

    // soil_temp was left the same because the Teros and chinese sensor values are similar

    // quadratic aproximation
    // the teros bulk_permittivity was calculated from the teros temperature, teros bulk ec and teros pwec by Hilhorst 2000 model
    float soil_apparent_dieletric_constant = 1.3088 + 0.1439 * soil_hum + 0.0076 * soil_hum * soil_hum;

    float soil_bulk_permittivity = soil_apparent_dieletric_constant;  /// Hammed 2015 (apparent_dieletric_constant is the real part of permittivity)
    float soil_pore_permittivity = 80.3 - 0.37 * (soil_temp - 20); /// same as water 80.3 and corrected for temperature

    // converting bulk EC to pore water EC
    float soil_pw_ec;
    if (soil_bulk_permittivity > 4.1)
        soil_pw_ec = ((soil_pore_permittivity * soil_ec) / (soil_bulk_permittivity - 4.1) / 1000); /// from Hilhorst 2000.
    else
        soil_pw_ec = 0;

  //LCD
      display.clearDisplay();

    display.setTextSize(1);
    display.setCursor(0, 0);
    display.print("Humi:  ");
    display.setTextSize(2);
    display.print(soil_hum);
    display.setTextSize(1);
    display.print(" %");

    display.setTextSize(1);
    display.setCursor(0, 17);
    display.print("Temp:  ");
    display.setTextSize(2);
    display.print(soil_temp);
    display.setTextSize(1);
    display.print(" C");

    display.setTextSize(1);
    display.setCursor(0, 34);
    display.print("EC:    ");
    display.setTextSize(2);
    display.print(soil_ec);
    display.setTextSize(1);
    display.print(" us/cm");

    display.setTextSize(1);
    display.setCursor(0, 50);
    display.print("pwEC:  ");
    display.setTextSize(2);
    display.print(soil_pw_ec);
    display.setTextSize(1);
    display.print(" dS/m");

    display.display();
    //LCD
  //START LOGGER CODE LOOP

DateTime now;

  // delay for the amount of time we want between readings
  delay((LOG_INTERVAL -1) - (millis() % LOG_INTERVAL));


  // log milliseconds since starting
  uint32_t m = millis();
  logfile.print(m);           // milliseconds since start
  logfile.print(", ");
#if ECHO_TO_SERIAL
  Serial.print(m);         // milliseconds since start
  Serial.print(", ");
#endif

  // fetch the time
  now = RTC.now();
  // log time
  logfile.print(now.unixtime()); // seconds since 1/1/1970
  logfile.print(", ");
  logfile.print('"');
  logfile.print(now.year(), DEC);
  logfile.print("/");
  logfile.print(now.month(), DEC);
  logfile.print("/");
  logfile.print(now.day(), DEC);
  logfile.print(" ");
  logfile.print(now.hour(), DEC);
  logfile.print(":");
  logfile.print(now.minute(), DEC);
  logfile.print(":");
  logfile.print(now.second(), DEC);
  logfile.print('"');
#if ECHO_TO_SERIAL
  Serial.print(now.unixtime()); // seconds since 1/1/1970
  Serial.print(", ");
  Serial.print('"');
  Serial.print(now.year(), DEC);
  Serial.print("/");
  Serial.print(now.month(), DEC);
  Serial.print("/");
  Serial.print(now.day(), DEC);
  Serial.print(" ");
  Serial.print(now.hour(), DEC);
  Serial.print(":");
  Serial.print(now.minute(), DEC);
  Serial.print(":");
  Serial.print(now.second(), DEC);
  Serial.print('"');
#endif //ECHO_TO_SERIAL

  //END LOGGER CODE LOOP

  Serial.print("Humidity:");
  Serial.print(soil_hum);
  Serial.print(",");
  Serial.print("Temperature:");
  Serial.print(soil_temp);
  Serial.print(",");
  Serial.print("EC:");
  Serial.print(soil_ec);
  Serial.print(",");
  Serial.print("READEC:");
  Serial.print(as_read_ec);
  Serial.print(",");
  Serial.print("pwEC:");
  Serial.print(soil_pw_ec);
  Serial.print(",");
  Serial.print("soil_bulk_permittivity:");
  Serial.println(soil_bulk_permittivity);


  logfile.print(", ");
  logfile.print(soil_hum);
  logfile.print(", ");
  logfile.print(soil_temp);
  logfile.print(", ");
  logfile.print(soil_pw_ec);
  logfile.println();
}