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From 2014.igem.org

1. include <stdint.h>
2. include <Wire.h>
3. include <LiquidCrystal_I2C.h>

LiquidCrystal_I2C lcd(0x27,16,2); // set the LCD address to 0x27 for a 16 chars and 2 line display

1. define LIGHT_TO_FREQ_F 2
2. define LIGHT_TO_FREQ_OD 3
3. define BUTTON 8

1. define LED_P0 9
2. define LED_P1 10

1. define LED_P2 11 // OD

1. define F_LED_BRIGHT 255
2. define OD_LED_BRIGHT 255

// volatile to be stored as close to the µC as possible volatile unsigned long cntF = 0; unsigned long oldcntF = 0; unsigned long tF = 0; unsigned long lastF;

volatile unsigned long cntOD = 0; unsigned long oldcntOD = 0; unsigned long tOD = 0; unsigned long lastOD;

// this is the recorded frequency. The average window is used to get more stable results unsigned long hz_refF; // blank frequency unsigned long hz_ref_avgF; unsigned long hz_refOD; // blank frequency unsigned long hz_ref_avgOD;

1. define AVERAGE_WINDOW 5

// this determines the output

1. define DEBUG_MODE 1
2. define OD_DIGITS 3

unsigned long hz_avgF[AVERAGE_WINDOW]; unsigned long hz_windowF = 0; unsigned long iCountF = 0; unsigned long hz_avgOD[AVERAGE_WINDOW]; unsigned long iCountOD = 0; unsigned long hz_windowOD = 0;

// this is for selection either OD or F measurement

1. define F_MODE 0
2. define OD_MODE 1
3. define ODF_PIN 5

bool odf_mode;

void irqOD() {

 cntOD++;

}

void irqF() {

 cntF++;

}

void blank() {

 iCountOD = 0;
 
 uint8_t i = 0;
 for (i = 0; i < AVERAGE_WINDOW; ++i)
 {
   unsigned long start = millis();
   oldcntOD = cntOD;
   
   while( millis()-start<=1000 ){}
   
   unsigned long t = cntOD;
   hz_refOD = t - oldcntOD;
   
   hz_avgOD[iCountOD++ % AVERAGE_WINDOW] = hz_refOD;
   
   //oldcnt = t;
   cntOD = 0;
   oldcntOD = 0;
 }
 hz_refOD = 0;
 for (i = 0; i < AVERAGE_WINDOW; ++i)
 {
   hz_refOD += hz_avgOD[i];
 }
 
 hz_refOD = hz_refOD / AVERAGE_WINDOW;
 
   cntOD = 0;
   oldcntOD = 0;
   lastOD = millis();

}

void setup() {

 Serial.begin(9600);
 
 pinMode(BUTTON, INPUT);
 digitalWrite(BUTTON, HIGH);
 delay(500);

 pinMode(LIGHT_TO_FREQ_F, INPUT);
 digitalWrite(LIGHT_TO_FREQ_F, HIGH);
 attachInterrupt(0, irqF, RISING); //interrupt 0 is on PIN 2
 
 pinMode(LIGHT_TO_FREQ_OD, INPUT);
 digitalWrite(LIGHT_TO_FREQ_OD, HIGH);
 attachInterrupt(0, irqOD, RISING); //interrupt 0 is on PIN 2
   
 lcd.init();
 
 lcd.backlight();
 lcd.setCursor(0,0);
 lcd.print("Optical Density");
 lcd.setCursor(0,1);
 lcd.print("Fluorescence");
   
 analogWrite(LED_P0, F_LED_BRIGHT);
 analogWrite(LED_P1, F_LED_BRIGHT);
 analogWrite(LED_P2, OD_LED_BRIGHT);

 // this is needed for OD :)
 blank();

}

 int getMeasurement(volatile unsigned long *cnt, unsigned long *oldcnt, unsigned long* hz_avg, unsigned long* hz, unsigned long* hz_win, unsigned long* iCount, unsigned long* last, int wait)
 {
   
   if (millis() - *last < wait)
   return 0;
   
   unsigned long t = *cnt;
   *hz = t - *oldcnt;

   hz_avg[*iCount % AVERAGE_WINDOW] = *hz;
   *iCount = *iCount + 1;

   unsigned long hz_window = 0;
   for (uint8_t i = 0; i < AVERAGE_WINDOW; ++i)
   {
     hz_window += hz_avg[i];
   }
   
   *hz_win = hz_window / AVERAGE_WINDOW; // windows average frequency
   *oldcnt = t;
   
   *last = millis();
   *cnt = 0;
   *oldcnt = 0;
   
   return 1;
   
 }

int button_in;

void loop() {

 uint64_t j;
 
 button_in = digitalRead(BUTTON);
 
 if( button_in == HIGH)
 {
   lcd.clear();
   lcd.setCursor(0, 0);
   lcd.print("OD:");
   lcd.setCursor(0, 1);
   lcd.print("setting blank");
   
   blank();
 }
 
 analogWrite(LED_P0, F_LED_BRIGHT);
 analogWrite(LED_P1, F_LED_BRIGHT);
 delay(100);

 unsigned long hzF, hzOD; //current frequency

   getMeasurement(&cntF, &oldcntF, hz_avgF,&hzF, &hz_windowF, &iCountF, &lastF, 4000);
   getMeasurement(&cntOD, &oldcntOD, hz_avgOD,&hzOD, &hz_windowOD, &iCountOD, &lastOD, 1000);
   //Serial.print((hz+50)/100);  // +50 == rounding last digit
   
   analogWrite(LED_P0, F_LED_BRIGHT);
   analogWrite(LED_P1, F_LED_BRIGHT);
   delay(500);
   
   Serial.print(0);
   Serial.print("#;");
   Serial.print(0);
   Serial.print(";");
   Serial.print(0);
   Serial.print(";");
   Serial.print(0);
   Serial.print(";");
   Serial.print(hz_refOD);
   Serial.print(";");
   Serial.print(hzOD);
   Serial.print(";");
   Serial.print(hzF);
   Serial.print("\n");

   lcd.clear();
   lcd.setCursor(0, 0);
   lcd.print("OD:");
   lcd.print(hz_windowOD);
     
     // since frequency is linear to transmission, this is transmittance      
   lcd.print(" T :");
   lcd.print(hz_windowF);
     
   if (DEBUG_MODE)
   {
     lcd.setCursor(0, 1);
     lcd.print("OD0: "); // blank value - interesting for OD
     lcd.print(hz_refOD);
     lcd.print(" Tc:"); // current value
     lcd.print(hzF);
   }

}