////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////TRUEHEME CODE V0.1.4 - BETA Version (To be Tested)/////////////////////////////////////////////////////////////////////
//////////NEW Changes: All LED warmup function Added; Limit Switch added;EEPROM storage of DAC values; Stray light sensing; Turing on any one LED///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
#include "ADS1X15.h"
#include <EEPROM.h>
#include <SPI.h>
#include <Wire.h>
/////////////////////////////////////////////////////////////////////PLEASE UPDATE DEVICE ID BEFORE UPLOADING TO ANY DEVICE/////////////////////////////////////////////////////////////////
String Device_ID = "SNS HCV-00X-6XXX SNE";                        // Device ID SNS HPP1-000-5001 SNE
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
const int LED_available[] = {1,2,3,4};                            // List of LEDs available. All Variables with 4 columns (other than ones controlling the LED turning ON sequence) must be filled in this order
int LED_sequence[] = {1,2,3,4};                                   // LED turning ON sequence
int Detector_sequence[] = {1,1,1,1};                              // Detector sequence (if hardware supports dual pathlength)
int LED_dac[] = {1792,2304,2048,1920};                            // Preset DAC values for the device
int LED_sample_size[] = {50,50,50,50};                            // No. of ADC readings to use for Average ADC calculation
int LED_DS_threshold[] = {22000,18000,18000,22000};               // DAC sweep upperlimit for each LED
int LED_settling_time[] = {20000,20000,20000,20000};              // Settling time given to each LED
int ADC_reading_delay[] = {0,0,0,0};                              // Delay for each ADC reading while averaging
int led_warmup_DAC[] = {3000,3000,3000,3000};                     // DAC value at which all the LEDs will be powered during LED warmup
int DAC_Sweep_start_limit[] = {1000,1000,1000,1000};              // Lower limit for DAC sweep
int DAC_Sweep_end_limit[] = {4000,4000,4000,4000};                // Upper limit for DAC sweep
int DacSweep_gain_combinations[] = {0,0,0,0};                     // Gain to be used for DAC sweep

int incr=8;                                                       // DAC sweep increment
int del=1000;                                                     // Delay between each interval of the DAC sweep
int appmode=1;                                                    // if =1, it removes most of the unwanted serial prints
int raw_ADC_print=0;                                              // if =1, it will serialprint raw ADC values (even during LED warmup and settling)
int timestamp_printer=0;                                          // if =1, will print timestamp at regular intervals
int limit_switch_active=0;                                        // If there is a limit switch in the device, make it 1

int Blank_gain_combinations[] = {0,0,0,0};                        // Programmable gain to be used while blanking
int Sample_gain_combinations[5][4] = {{0,0,0,0},{1,1,1,1},{2,2,2,2},{4,4,4,4},{8,8,8,8}}; // Programmable gain to be used while taking sample readings

///////////////////////////////////////////DO NOT CHANGE ANY VALUES BELOW //////////////////////////////////////////////////////////////////////////////////////////////
const int PIN_CS_DAC1 = 10;                                       // Chip select pin for DAC 1
const int PIN_CS_DAC2 = 9;                                        // Chip select pin for DAC 2
const int GAIN_1 = 0x1;                                           // DAC 1X gain (output between 0 - 2.048 Volts)
const int GAIN_2 = 0x0;                                           // DAC 2X gain (output between 0 - 4.096 Volts)

const int PD1G1 = 6;                                              // Programmable gain resistor _______ X gain
const int PD1G2 = 8;                                              // Programmable gain resistor _______ X gain
const int PD2G1 = 5;                                              // Programmable gain resistor _______ X gain
const int PD2G2 = 7;                                              // Programmable gain resistor _______ X gain

const int LEDR = A2;                                              // Red indicator LED
const int LEDB = A0;                                              // Blue indicator LED
const int LEDG = A1;                                              // Green indicator LED

const int Limit_Switch = 2;                                       // Limit switch for cuvette sensing
const int Buzzer_pin = 3;                                         // Buzzer connection for alert

ADS1115 ADS(0x48);                                                // 
const char compile_date[] = __DATE__ " " __TIME__;                // Stores date and time when the firmware was uploaded on the arduino
String Firmware_location_Auto =__FILE__;                          // Stores location of the firmware on the computer used for uploading
String Firmware_version_Auto =__FILE__;                           // Stores the firmware version uploaded
///////////////////////////////////////////DO NOT CHANGE ANY VALUES ABOVE //////////////////////////////////////////////////////////////////////////////////////////////

int DAC_lower_limit[] = {0,0,0,0};                                //
int DAC_upper_limit[] = {4096,4096,4096,4096};                    //
unsigned long long intensity_storage = 0;                         //
int temp_counter = 0;                                             //
const int detector_settling_time = 2000;                          //
const int detector_settling_time_DACsweep = 1000;
int initialRGBstate = 0;

float average_readings = 0;
float avg_blank[] = {0,0,0,0};
float avg_sample[] = {0,0,0,0};
int LED_on_status[] = {0,0,0,0};
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void setup()
{
  Serial.begin(9600);
  pinMode(PIN_CS_DAC1, OUTPUT);
  pinMode(PIN_CS_DAC2, OUTPUT);
  pinMode(PD1G1, OUTPUT);
  pinMode(PD1G2, OUTPUT);
  pinMode(PD2G1, OUTPUT);
  pinMode(PD2G2, OUTPUT);
  pinMode(LEDR, OUTPUT);
  pinMode(LEDG, OUTPUT);
  pinMode(LEDB, OUTPUT);
  pinMode(Limit_Switch, INPUT);
  pinMode(Buzzer_pin, OUTPUT);
  digitalWrite(LEDR, LOW);
  digitalWrite(LEDG, HIGH);
  digitalWrite(LEDB, HIGH);
  SPI.begin();
  SPI.setClockDivider(SPI_CLOCK_DIV2);
  ADS.begin();  
  if(appmode==0)
  {
    Serial.print("Process: Setup End; Timestamp: ");Serial.println(millis());
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void buzzer(int mode = 1)
{
  for(int i=0;i<mode;i++)
  {
    tone(Buzzer_pin, 2730, 1000);
    delay(500);
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void all_LEDs_turnoff()
{  
  setOutput(GAIN_1, 0, 1);
  setOutput(GAIN_1, 0, 2);
  setOutput(GAIN_1, 0, 3);
  setOutput(GAIN_1, 0, 4);
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void secondary_gain_select(int gain_combo)
{
  bool gain_choice1=bitRead(gain_combo, 0);
  bool gain_choice2=bitRead(gain_combo, 1);
  bool gain_choice3=bitRead(gain_combo, 2);
  bool gain_choice4=bitRead(gain_combo, 3);
  digitalWrite(PD1G1, gain_choice1);
  digitalWrite(PD1G2, gain_choice2);
  digitalWrite(PD2G1, gain_choice3);
  digitalWrite(PD2G2, gain_choice4);
  if(appmode==0)
  {
    Serial.print("Gains Used\t G1:");Serial.print(gain_choice1);Serial.print("\t G2:");Serial.print(gain_choice2);Serial.print("\t G3:");Serial.print(gain_choice3);Serial.print("\t G4:");Serial.println(gain_choice4);
  }  
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void setOutput(byte gain, unsigned int val, int LEDselect)
{
  byte channel = 0;
  byte shutdown = 1;
  if(LEDselect%2 == 0)
  {
    channel = 1;
  }
  else
  {
    channel = 0;
  }
  byte lowByte = val & 0xff;
  byte highByte = ((val >> 8) & 0xff) | channel << 7 | gain << 5 | shutdown << 4;
  if (LEDselect <= 2)
  {
    PORTB &= 0xfb;
    SPI.transfer(highByte);
    SPI.transfer(lowByte);
    PORTB |= 0x4;
  }
  else
  {
    PORTB &= 0xfd;
    SPI.transfer(highByte);
    SPI.transfer(lowByte);
    PORTB |= 0x2;
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void indicator_LED(char statusLED)
{
  digitalWrite(LEDR,LOW);
  digitalWrite(LEDG,LOW);
  digitalWrite(LEDB,LOW);
  digitalWrite(LEDR,(statusLED=='R'));
  digitalWrite(LEDG,(statusLED=='G'));
  digitalWrite(LEDB,(statusLED=='B'));
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int setDAC_LED()
{  
  int LED_flags[]={0,0,0,0};
  int flags_combined=0;
  if(appmode==0)
  {
    Serial.println("#DAC Sweep Start");  
  }  
  all_LEDs_turnoff();
  delay(1000);
  ////////////////////////////////////////FIRST FORLOOP TO DISCARD STARTS/////////////////////////////////////////////////
  for (int i=3000;i<4096;i+=incr)
  {
    setOutput(GAIN_1, i, 1);
    delay(del);
    int16_t val_0 = ADS.readADC(0);    
    if((val_0>24000))
    {
      break;
    }
  }
  all_LEDs_turnoff();
  delay(2000);
  ////////////////////////////////////////FIRST FORLOOP TO DISCARD ENDS/////////////////////////////////////////////////  
  for (int j=0;j<4;j++)
  {
    all_LEDs_turnoff();
    secondary_gain_select(DacSweep_gain_combinations[j]);
    for (int i=DAC_Sweep_start_limit[j];i<DAC_Sweep_end_limit[j];i+=incr)
    {
      setOutput(GAIN_1, i, j+1);
      delay(del);
      int16_t val_0 = ADS.readADC(0);   
      if((val_0>LED_DS_threshold[j])&&(LED_flags[j]==0))
      {
        LED_dac[j]=i;
        LED_flags[j]=1;
        break;
      }
    } 
    all_LEDs_turnoff();
    if (appmode==0)
    {
      Serial.print("LED ");Serial.print(j+1);Serial.print(" DACsweep Completed");Serial.print("\t");Serial.print("NEW DAC VALUE : ");Serial.println(LED_dac[j]);
    }
    delay(1000);   
  }
  all_LEDs_turnoff();
  flags_combined=(LED_flags[3]*1)+(LED_flags[2]*10)+(LED_flags[1]*100)+(LED_flags[0]*1000);
  if(appmode==0)
  {
    Serial.println("#DAC Sweep End");  
  }  
  return flags_combined;    
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void eeprom_DAC_write()
{
  int led_dac_split[]= {0,0,0,0,0,0,0,0};
  Serial.println("#GS"); 
  led_dac_split[0] = LED_dac[0]/100;
  led_dac_split[1] = LED_dac[0]-(led_dac_split[0]*100);
  led_dac_split[2] = LED_dac[1]/100;
  led_dac_split[3] = LED_dac[1]-(led_dac_split[2]*100);
  led_dac_split[4] = LED_dac[2]/100;
  led_dac_split[5] = LED_dac[2]-(led_dac_split[4]*100);
  led_dac_split[6] = LED_dac[3]/100;
  led_dac_split[7] = LED_dac[3]-(led_dac_split[6]*100);
  if(appmode==0)
  {
    Serial.print(led_dac_split[0]);Serial.print("\t");Serial.println(led_dac_split[1]);
    Serial.print(led_dac_split[2]);Serial.print("\t");Serial.println(led_dac_split[3]);
    Serial.print(led_dac_split[4]);Serial.print("\t");Serial.println(led_dac_split[5]);
    Serial.print(led_dac_split[6]);Serial.print("\t");Serial.println(led_dac_split[7]);
  }   
  for (int i=0;i<8; i++)
  {
    EEPROM.write(i, led_dac_split[i]);
  }  
  Serial.println("#GC"); 
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void eeprom_DAC_read()
{
  int led_dac_split[]= {0,0,0,0,0,0,0,0};
  Serial.println("#RS"); 
  for(int i=0;i<8;i++)
  {
    led_dac_split[i] = EEPROM.read(i);
  }
  for(int i=0;i<4;i++)
  {
    LED_dac[i] = (led_dac_split[i*2]*100)+led_dac_split[(i*2)+1];
  }
  if(appmode==0)
  {
    Serial.print(led_dac_split[0]);Serial.print("\t");Serial.println(led_dac_split[1]);
    Serial.print(led_dac_split[2]);Serial.print("\t");Serial.println(led_dac_split[3]);
    Serial.print(led_dac_split[4]);Serial.print("\t");Serial.println(led_dac_split[5]);
    Serial.print(led_dac_split[6]);Serial.print("\t");Serial.println(led_dac_split[7]);
    Serial.print(LED_dac[0]);Serial.print("\t");Serial.print(LED_dac[1]);Serial.print("\t");Serial.print(LED_dac[2]);Serial.print("\t");Serial.println(LED_dac[3]);
  }
  Serial.println("#R C");     
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void eeprom_DeviceID_write()
{
  int deviceID_split[]= {0,0,0,0};
  int D_ID_temp[]={000,0000};
  Serial.println("#GS"); 
  deviceID_split[0] = D_ID_temp[0]/100;
  deviceID_split[1] = D_ID_temp[0]-(deviceID_split[0]*100);
  deviceID_split[2] = D_ID_temp[1]/100;
  deviceID_split[3] = D_ID_temp[1]-(deviceID_split[2]*100);
  if(appmode==0)
  {
    Serial.print(deviceID_split[0]);Serial.print("\t");Serial.println(deviceID_split[1]);
    Serial.print(deviceID_split[2]);Serial.print("\t");Serial.println(deviceID_split[3]);
  }   
  for (int i=0;i<4;i++)
  {
    EEPROM.write(i+8, deviceID_split[i]);
  }  
  Serial.println("#GC"); 
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void eeprom_DeviceID_read()
{
  int led_DeviceID_split[]= {0,0,0,0};
  int Device_version[]={0,0,0};
  int Dev_ID[]={0,0,0,0};
  String Dev_version="000";
  String D_ID="0000";
  //Serial.println("#NS"); 
  for(int i=8;i<12;i++)
  {
    led_DeviceID_split[i-8] = EEPROM.read(i);
  }
  Device_version[0] = led_DeviceID_split[0]%10;
  Device_version[1] = (led_DeviceID_split[1]-(led_DeviceID_split[1]%10))/10;
  Device_version[2] = led_DeviceID_split[1]%10;
  Dev_ID[0] = (led_DeviceID_split[2]-(led_DeviceID_split[2]%10))/10;
  Dev_ID[1] = led_DeviceID_split[2]%10;
  Dev_ID[2] = (led_DeviceID_split[3]-(led_DeviceID_split[3]%10))/10;
  Dev_ID[3] = led_DeviceID_split[3]%10;
  Dev_version = String(Device_version[0])+String(Device_version[1])+String(Device_version[2]);
  D_ID = String(Dev_ID[0])+String(Dev_ID[1])+String(Dev_ID[2])+String(Dev_ID[3]);
  if(appmode==0)
  {
    Serial.print("Device Version: ");Serial.println(Dev_version);
    Serial.print("Device ID: ");Serial.println(D_ID);
  }
  Device_ID = "SNS HCV-" + Dev_version + "-" + D_ID + " SNE";
  //Serial.println("#NC");     
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

void LED_warmup(int warmup_time)
{
  Serial.println("#YS");
  int warmup_start=millis();
  int current_time=millis();
  while((current_time-warmup_start)<warmup_time)
  {
    setOutput(GAIN_1, led_warmup_DAC[0], 1);
    setOutput(GAIN_1, led_warmup_DAC[1], 2);
    setOutput(GAIN_1, led_warmup_DAC[2], 3);
    setOutput(GAIN_1, led_warmup_DAC[3], 4);
    current_time=millis();
  }  
  all_LEDs_turnoff();
  Serial.println("#YC");
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
float ten_ADC_averager(int detector_select, int reading_delay)
{
  long temp_storage=0;
  float temp_average_storage=0;
  for (int i=0;i<10;i++)
  {
    delay(reading_delay);
    int16_t val_0 = ADS.readADC(detector_select-1);
    if(raw_ADC_print==1)
    {
      Serial.println(val_0);      
    }
    temp_storage+=val_0;
  }
  temp_average_storage=temp_storage/10;
  return temp_average_storage;
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
float detector(int number_of_readings, int detector_select, int gain_combo, int settling_time, int reading_delay)
{
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Detector Start for any one LED; Timestamp: ");Serial.println(millis());
  }
  secondary_gain_select(gain_combo);
  temp_counter = 0;
  intensity_storage = 0;
  int16_t detector_val = 0;
  int start_time=millis();
  int current_time=millis();
  int lower_limit=0;
  int upper_limit=0;
  //limit_average_storage=0;
  while((current_time-start_time)<settling_time)
  {
    int16_t val_0 = ADS.readADC(detector_select-1);
    if(raw_ADC_print==1)
    {
      Serial.println(val_0);
    }
    current_time=millis();
  }
  for (int i=0;i<(number_of_readings/10);i++)
  {      
    intensity_storage+=ten_ADC_averager(detector_select, reading_delay);
    temp_counter++;
  }
  all_LEDs_turnoff();
  average_readings = intensity_storage/temp_counter;
  if(appmode==0)
  {
    if (timestamp_printer==1)
    {
      Serial.print("Process: Detector Start for any one LED; Timestamp: ");Serial.println(millis());
    }    
  }
  return average_readings;
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
int limit_switch_check()
{
  int switch_state = digitalRead(Limit_Switch);
  return switch_state;
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void loop()                                                                         
{
  ADS.setGain(0);
  all_LEDs_turnoff();
  if(initialRGBstate==0)
  {
    indicator_LED('R');
    initialRGBstate=1;
  }  
  if (Serial.available()) 
  {
    char data = Serial.read();
    if ((data == 'C')||(data == 'D'))
    {
      if(data == 'C')
      {
        Serial.println("#CS");
        int flags=setDAC_LED();
        if(flags!=1111)
        {
          if(appmode==0)
          {
            Serial.println("Unable to reach MAX ADC Limit for atleast one LED");
          }        
        }
        Serial.print("LED1_DAC: ");Serial.println(LED_dac[0]);
        Serial.print("LED2_DAC: ");Serial.println(LED_dac[1]);
        Serial.print("LED3_DAC: ");Serial.println(LED_dac[2]);
        Serial.print("LED4_DAC: ");Serial.println(LED_dac[3]);
        Serial.println("#CC");
        buzzer(1);
      }
      else if(data == 'D') 
      {
        startTask3(); 
        buzzer(1);       
      }      
    }
    else if (data == 'B') 
    {
      indicator_LED('G');
      startTask1();
      indicator_LED('B');
      buzzer(1);
    }
    else if ((data == 'S')||(data == 'T')||(data == 'U')||(data == 'V')||(data == 'W')) 
    {
      indicator_LED('G');
      if(data == 'S')
      {
        startTask2(1);
      }
      else if(data == 'T')
      {
        startTask2(2);
      }
      else if(data == 'U')
      {
        startTask2(3);
      }
      else if(data == 'V')
      {
        startTask2(4);
      }
      else if(data == 'W')
      {
        startTask2(5);
      }
      indicator_LED('R');
      buzzer(1);
    }
    else if (data == 'O')
    {
      startTask4();
      buzzer(1);
    }
    else if ((data == 'I')||(data == 'F')||(data == 'X'))
    {      
      if(data == 'I')
      {
        //Serial.println(Device_ID);                       //Remove code or comment it out
        //eeprom_DeviceID_write();                         //Remove code or comment it out
        eeprom_DeviceID_read();     
        Serial.println(Device_ID);
      }
      else if (data == 'F')
      {
        int location=0;
        for (int i=0;i<Firmware_location_Auto.length();i++)
        {
          if(Firmware_location_Auto[i]=='\\')
          {
            location=i;
          }
        }
        Firmware_version_Auto.remove(0,location+1);
        if (appmode==0)
        {
          Serial.print("Firmware Location: ");Serial.println(Firmware_location_Auto);
        }        
        Serial.print("Firmware Version: ");Serial.println(Firmware_version_Auto);
        Serial.print("Date and Time of Firmware Upload : ");Serial.println(compile_date);
      }      
      else if (data =='X')
      {
        Serial.println(F("Command 'C' will do : Slow DAC sweep, stop the sweep once required ADC is reached, update DAC value"));
        Serial.println(F("Command 'D' will do : Fast DAC sweep, will sweep from 0 to 4096, prints ADC values"));
        Serial.println(F("Command 'B' will do : Blank readings"));
        Serial.println(F("Command 'S/T/U/V/W' will do : Sample readings with pre-defined secondary gain"));
        Serial.println(F("Command 'O' will do : Blank readings without turning on the LED"));
        Serial.println(F("Command 'I' will do : Print Device Serial No."));
        Serial.println(F("Command 'F' will do : Print the firmware version and upload date and time"));
        Serial.println(F("Command 'X' will do : Print all available commands"));
        Serial.println(F("Command 'Y' will do : LED warmup for 5 seconds"));
        Serial.println(F("Command 'G' will do : Write DAC values temporarily set into permanent EEPROM"));
        Serial.println(F("Command 'E' will do : Read EEPROM stored DAC values and store in temporary memory"));
        Serial.println(F("Command 'N' will do : Read EEPROM stored Device ID values and store in temporary memory"));
        Serial.println(F("Command 'P' will do : Print all ADC values (blank and sample)"));
        Serial.println(F("Command 'R' will do : Print DAC values stored in temporary memory"));
        Serial.println(F("Command 'L' will do : Print the status of the limit switch"));
        Serial.println(F("Command '1/2/3/4' will do : Turen ON LED 1/2/3/4 if pressed ODD number of times, Turen OFF LED 1/2/3/4 if pressed EVEN number of times"));
      }
    }    
    else if (data == 'Y')
    {
      Serial.println("#YS");
      LED_warmup(5000);
      Serial.println("#YC");
    }
    else if ((data == 'G')||(data == 'E')||(data == 'N'))
    {
      if(data == 'G')
      {
        eeprom_DAC_write();
      }
      else if(data == 'E')
      {
        eeprom_DAC_read();
      }      
      else if(data == 'N')
      {
        eeprom_DeviceID_read();
      }
    }
    else if ((data == 'P')||(data == 'R'))
    { 
      if(data == 'P')
      {
        Serial.print("RESULT"); Serial.println(" "); 
        Serial.print("LB1 "); Serial.println(avg_blank[0]); Serial.print("LB2 "); Serial.println(avg_blank[1]);
        Serial.print("LB3 "); Serial.println(avg_blank[2]); Serial.print("LB4 "); Serial.println(avg_blank[3]);
        Serial.print("LS1 "); Serial.println(avg_sample[0]); Serial.print("LS2 "); Serial.println(avg_sample[1]); 
        Serial.print("LS3 "); Serial.println(avg_sample[2]); Serial.print("LS4 "); Serial.println(avg_sample[3]);  
        Serial.println("REND");
        delay(100);
      }
      else if (data == 'R')
      {
        Serial.println("#RS");
        int dac_print=0;
        for (int i=0;i<4;i++)
        {
          Serial.print("LED");Serial.print(i+1);Serial.print(" DAC : ");Serial.println(LED_dac[i]);
        }
        Serial.println("#RC");
      }
    }
    else if (data == 'L')
    {
      int switch_state = digitalRead(Limit_Switch);
      if (switch_state == LOW)
      {
        Serial.println("#CIN");
      }
      else
      {
        Serial.println("#AIN");
      }
    }
    else if ((data == '1')||(data == '2')||(data == '3')||(data == '4'))
    {
      int LED_ID = data-'0';
      String ON_msg= "#L" + String(LED_ID) + "ON";
      String OFF_msg= "#L" + String(LED_ID) + "OF";
      if(LED_on_status[LED_ID-1]==0)
      {
        setOutput(GAIN_1, LED_dac[LED_ID-1], LED_ID);
        LED_on_status[LED_ID-1]=1;
        Serial.println(ON_msg);
      }
      else
      {
        setOutput(GAIN_1, 0, LED_ID);
        LED_on_status[LED_ID-1]=0;
        Serial.println(OFF_msg);
      }
    }
  }    
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void startTask1() 
{
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Buffer start; Timestamp: ");Serial.println(millis());
  }
  all_LEDs_turnoff();
  delay(100);
  all_LEDs_turnoff();
  Serial.println("#BS");
  for (int i=0;i<4;i++)
  {
    setOutput(GAIN_1, LED_dac[i], LED_sequence[i]);
    delay(100);
    avg_blank[i] = detector(LED_sample_size[LED_sequence[i]-1], Detector_sequence[LED_sequence[i]-1], Blank_gain_combinations[LED_sequence[i]-1], LED_settling_time[LED_sequence[i]-1], ADC_reading_delay[LED_sequence[i]-1]);
    all_LEDs_turnoff();
    delay(1000);
  }
  if (appmode==0)
  {
    Serial.print(millis());Serial.print("\t");Serial.print("LED1B : "); Serial.print(avg_blank[0]); Serial.print("\t"); Serial.print("LED2B : "); Serial.print(avg_blank[1]); Serial.print("\t"); Serial.print("LED3B : "); Serial.print(avg_blank[2]); Serial.print("\t"); Serial.print("LED4B : "); Serial.println(avg_blank[3]);
  }
  Serial.println("#BC");
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Buffer end; Timestamp: ");Serial.println(millis());
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void startTask2(int selector) 
{
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Sample start; Timestamp: ");Serial.println(millis());
  }
  all_LEDs_turnoff();
  delay(100);
  all_LEDs_turnoff();
  Serial.print("#SS");Serial.println(selector);
  for (int i=0;i<4;i++)
  {
    setOutput(GAIN_1, LED_dac[i], LED_sequence[i]);
    delay(100);
    avg_sample[i] = detector(LED_sample_size[LED_sequence[i]-1], Detector_sequence[LED_sequence[i]-1], Sample_gain_combinations[selector-1][LED_sequence[i]-1],LED_settling_time[LED_sequence[i]-1], ADC_reading_delay[LED_sequence[i]-1]);
    all_LEDs_turnoff();
    delay(1000);
  }
  if (appmode==0)
  {
    Serial.print(millis());Serial.print("\t");Serial.print("LED1S : "); Serial.print(avg_sample[0]); Serial.print("\t"); Serial.print("LED2S : "); Serial.print(avg_sample[1]); Serial.print("\t"); Serial.print("LED3S : "); Serial.print(avg_sample[2]); Serial.print("\t"); Serial.print("LED4S : "); Serial.println(avg_sample[3]);
  }
  Serial.print("#SC");Serial.println(selector);
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Sample end; Timestamp: ");Serial.println(millis());
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void startTask3() 
{
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Diagnostics start; Timestamp: ");Serial.println(millis());
  }
  int16_t val_0 =0;
  int reading_increment=128;
  int lowerlimit_dac=0;
  int upperlimit_dac=0;
  all_LEDs_turnoff();
  Serial.println("#DS");
  
  for (int j=0;j<4;j++)
  {
    all_LEDs_turnoff();
    int start_time=millis();
    int current_time=millis();
    while (((current_time-start_time)<(detector_settling_time*2)))
    {
      val_0 = ADS.readADC((Detector_sequence[LED_sequence[j]-1])-1); 
      current_time=millis();      
    }
    if((val_0 > 10)&&(appmode==0))
    {
      Serial.println("Error: stray light interference or LED partly ON ");
    }
    int flag=0;    
    secondary_gain_select(DacSweep_gain_combinations[j]);
    for (int i = 0; i <=4096; i+= reading_increment)
    {
      setOutput(GAIN_1, i, j+1);
      int start_time=millis();
      int current_time=millis();
      while ((current_time-start_time)<detector_settling_time_DACsweep)
      {
        val_0 = ADS.readADC((Detector_sequence[LED_sequence[j]-1])-1); 
        current_time=millis();
      }           
      if((val_0>LED_DS_threshold[LED_sequence[j]-1])&&(flag==0))
      {
        lowerlimit_dac= i-(reading_increment*2);
        upperlimit_dac= i+(reading_increment*2);
        if (lowerlimit_dac<0)
        {
          lowerlimit_dac=0;
        }
        if(upperlimit_dac>4095)
        {
          upperlimit_dac=4095;
        }
        DAC_lower_limit[j]=lowerlimit_dac;
        DAC_upper_limit[j]=upperlimit_dac;
        flag=1;
      }
      Serial.print("LED:");Serial.print(j+1);Serial.print("__DAC:");Serial.print(i);Serial.print("__ADC:");Serial.println(val_0);      
    }
    if (appmode==0)
    {
      Serial.print("LED:");Serial.print(j+1);Serial.print("__DAC LOWER LIMIT:");Serial.println(DAC_lower_limit[j]);  
      Serial.print("LED:");Serial.print(j+1);Serial.print("__DAC UPPER LIMIT:");Serial.println(DAC_upper_limit[j]);  
    }
    secondary_gain_select(0);    
    all_LEDs_turnoff();
  }
  Serial.println("#DC");
  all_LEDs_turnoff();
  delay(1000);
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Diagnostics end; Timestamp: ");Serial.println(millis());
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void startTask4() 
{
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Buffer start; Timestamp: ");Serial.println(millis());
  }
  all_LEDs_turnoff();
  delay(100);
  all_LEDs_turnoff();
  Serial.println("#OS");
  for (int i=0;i<4;i++)
  {
    setOutput(GAIN_1, 0, LED_sequence[i]);
    delay(100);
    avg_blank[i] = detector(LED_sample_size[LED_sequence[i]-1], Detector_sequence[LED_sequence[i]-1], Blank_gain_combinations[LED_sequence[i]-1], 2000, ADC_reading_delay[LED_sequence[i]-1]);
    all_LEDs_turnoff();
    delay(1000);
  }
  if (appmode==0)
  {
    Serial.print(millis());Serial.print("\t");Serial.print("LED1B : "); Serial.print(avg_blank[0]); Serial.print("\t"); Serial.print("LED2B : "); Serial.print(avg_blank[1]); Serial.print("\t"); Serial.print("LED3B : "); Serial.print(avg_blank[2]); Serial.print("\t"); Serial.print("LED4B : "); Serial.println(avg_blank[3]);
  }
  Serial.println("#OC");
  if((appmode==0)&&(timestamp_printer==1))
  {
    Serial.print("Process: Buffer end; Timestamp: ");Serial.println(millis());
  }
}
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////