plot.pde

capture.ino

// Modified sensor code for Arduino

#define bitSet(value, bit) ((value) |= (1UL << (bit)))
#define bitClear(value, bit) ((value) &= ~(1UL << (bit)))

/*
 * Macro Definitions
 */
#define SPEC_TRG         A0
#define SPEC_ST          A1
#define SPEC_CLK         A2
#define SPEC_VIDEO       A3
#define WHITE_LED        A4
#define LASER_404        A5

#define SPEC_CHANNELS    288 // New Spec Channel
uint16_t data[SPEC_CHANNELS];

inline void __attribute__((always_inline)) clockPulse()  {
//      digitalWrite(SPEC_CLK, HIGH);
//      delayMicroseconds(delayTime);
//      digitalWrite(SPEC_CLK, LOW);
//      delayMicroseconds(delayTime);
  
  // see: https://docs.google.com/spreadsheets/d/1zFkrNUWS6-ow6kGBxUObfnzK1ZsuW7VK3vRO1FoV8fc/edit#gid=0
  bitSet(PORTF, PIN5);
  bitClear(PORTF, PIN5);
}

void setup(){

  //Set desired pins to OUTPUT
  pinMode(SPEC_CLK, OUTPUT);
  pinMode(SPEC_ST, OUTPUT);
  pinMode(LASER_404, OUTPUT);
  pinMode(WHITE_LED, OUTPUT);

  //digitalWrite(WHITE_LED, HIGH); // Set SPEC_CLK High

  digitalWrite(SPEC_CLK, HIGH); // Set SPEC_CLK High
  digitalWrite(SPEC_ST, LOW); // Set SPEC_ST Low

  Serial.begin(115200); // Baud Rate set to 115200

  // Fast ADC clock (http://r6500.blogspot.com/2015/01/fast-adc-on-arduino-leonardo.html)
//  ADCSRA=(ADCSRA&0xF80)|0x04;
}

/*
 * This functions reads spectrometer data from SPEC_VIDEO
 * Look at the Timing Chart in the Datasheet for more info
 */
void readSpectrometer(){

  int delayTime = 1; // delay time

  // Start clock cycle and set start pulse to signal start
  digitalWrite(SPEC_CLK, LOW);
  
  clockPulse();

//  digitalWrite(SPEC_ST, HIGH);
//  delayMicroseconds(delayTime);
  bitSet(PORTF, PIN6);

  //Sample for a period of time
  for(int i = 0; i < 2500; i++){
     clockPulse();
  }

  //Set SPEC_ST to low
//  digitalWrite(SPEC_ST, LOW);
  bitClear(PORTF, PIN6);

  //Sample for a period of time
  for(int i = 0; i < 85; i++){
    clockPulse();
  }

  //One more clock pulse before the actual read
  clockPulse();

  //Read from SPEC_VIDEO
  for(int i = 0; i < SPEC_CHANNELS; i++){
    data[i] = analogRead(SPEC_VIDEO);
    
    clockPulse();      
  }

  digitalWrite(SPEC_CLK, HIGH);
  delayMicroseconds(delayTime);
  
}

/*
 * The function below prints out data to the terminal or 
 * processing plot
 */
void printData(){
  
  for (int i = 0; i < SPEC_CHANNELS; i++){
    
    Serial.print(data[i]);
    Serial.print(',');
    
  }
  
  Serial.print("\n");
}

void loop(){
   
  readSpectrometer();
  printData();
  delay(10);  
   
}

gistfile1.txt

//Processing sketch to display data + simple peak detector

import processing.serial.*;

Serial myPort; 
String val;    
int[] data; 
float[] summed;
int sum_count = 0;
boolean draw_sum = false;

final int dc_offset = 100; // Correct for the DC offset in the measurement

final int POINT_COUNT = 289;

// Given calibration data and a sample, determine the wavelength
float wavelength(int pix) {
  // Note; Replace these with the values for your sensr
  final double A0 = 3.062951791E+02;
  final double B1 = 2.720613040E+00;
  final double B2 = -1.302773396E-03;
  final double B3 = -7.101037823E-06;
  final double B4 = 8.279199710E-09;
  final double B5 = 5.742926217E-12;
  
  //wavelength resolution = 9.2nm
  
  double wavelength = A0 + B1*pix + B2*(pix^2) + B3*(pix^3) + B4*(pix^4) + B5*(pix^5);
  
  return (float)wavelength;
}
  

float val(int i) {
  if(draw_sum)
    return summed[i]/sum_count;
  else
    return data[i];
}

void plotdata()
{
  if(sum_count == 0)
    return;
  
  background(0);
  stroke(255);

  for (int i=0; i<data.length-1; i++) {
    line(i, height, i, height-val(i));
  }

  final int window = 10;
  final float noise_floor = 40;

  int peak_count = 0;
  
  stroke(255,0,0);
  fill(255,0,0);
  for (int i=window; i<(data.length-1-window); i++) {
    boolean top = true;

    for (int j = i-window; j < i+window; j++) {
      if ((i != j) && (val(j) >= val(i))) {
        top = false;
      }
    }

    if (top && (val(i) > noise_floor)) {
      ellipse(i, height-val(i),4,4);
      text(wavelength(i), 20, 20+20*peak_count);
      peak_count+=1;
    }
  }
}


void setup() 
{
  println(Serial.list());
  String portName = Serial.list()[1]; //This is the index into the serial list, if you only have one serial device the index is 0
  myPort = new Serial(this, portName, 115200);

  summed = new float[POINT_COUNT];

  for (int i = 0; i < POINT_COUNT; i++) 
  {
    summed[i] = 0;
  }

  // Processign design bug: can't use a constant here.
  size(289, 750);
}

void draw()
{
  if ( myPort.available() <= 0)
    return;
    
  val = myPort.readStringUntil('\n');         // read it and store it in val
  if (val == null)
    return;
    
  data = int(split(val, ','));
  for(int i = 0; i < data.length; i++) {
    data[i] = data[i] - dc_offset;
  }
  
  // Discard first frame if it is the wrong size
  if(data.length != POINT_COUNT)
    return;

  for (int i = 0; i < data.length; i++) {
    if (i<summed.length) {
      summed[i] +=  data[i];
    }
  }
  sum_count++;
    
  plotdata();
}

void keyPressed() {

  if (key == 'c' ) 
  {
    for (int i = 0; i < summed.length; i++) 
    {
      summed[i] = 0;
    }
    sum_count = 0;
  } else if (key == 't' ) 
  {
    draw_sum = !draw_sum;
  }
}