Fluorescence and reflectance with PAR-test-AK


Workaround
//============================================
// Macro for data evaluation on PhotosynQ.org
// created: 4/17/2016
//============================================

//Define the output object here
var output = {};

// Number of pixel per spectrum 
var pixels = 256;

// Number of spectra collected
var specNum = 7;

// Background Spectrum
var bgspec = 5;
var bg = 0

// Integration times for each spectrum
// The integration times are currently taken from the protocol
var intTimes = [
			1600,
			1600,
			50,
			50,
			800,
			800,
			80,
			80,
			80
];

// Pixel reflecting 730 nm
var pix = 80;
var A0 = 3.2e2;
var B1 = 2.4;
var B2 = -9e-4;
var B3 = -4e-6;
var B4 = -3e-9;
var B5 = 2e-11;

var nm = {};
var nms = [];
var pixel = {};
for(i=0;i<256;i++){
   var pix = i+1;
   var wl = A0 + B1*pix + B2*Math.pow(pix,2) + B3*Math.pow(pix,3) + B4*Math.pow(pix,4) + B5*Math.pow(pix,5);
   nm[MathROUND(wl,0)] = pix;
   nms.push(MathROUND(wl,0));
   pixel[pix] = [MathROUND(wl,0)];
}


// Now we fill up the array to make sure the is no undefiend when we enter a wavelength
var min = MathMIN(nms);
var max = MathMAX(nms);
var nms = {};
var tmp = 0;
for(var i = min;i<max;i++){
	if(nm[i] !== undefined){
      nms[i] = nm[i];
		tmp	= i;
    }
    else{
		nms[i] = nm[tmp];
    }
}
var nm = nms;


// Split the rawtrace up into separate spectra
// The number of spectra is set in specNum.
// The traces gets devided by the number of pixels for a spectrum
// defined by pixels
var spectra = [];
for (i=0,j=json.data_raw.length; i<j; i+=pixels) {
    spectra.push(json.data_raw.slice(i,i+pixels));   
}


// Normalize spectra to integration times
for(var i=0;i<bgspec+1;i++){
  for(var j=0;j<pixels;j++){
	spectra[i][j] = spectra[i][j] / intTimes[i];
  }
}

// Substract background spectrum from all other spectra
for(var i=0;i<bgspec;i++){
  for(var j=0;j<pixels;j++){
	spectra[i][j] -= spectra[bg][j]; 
  }
}

var ms = [];
//Substract drift
for(var i=0;i<bgspec;i++){
  var len = spectra[i].length;
  var m = (spectra[i][nm[650]] - spectra[i][0]) / (nm[650] - 0);
  var b = spectra[i][nm[650]] - (m * nm[650]);
  for(var j=0;j<len;j++){
	spectra[i][j] -= (m * j) + b;
  }
}

//Substract drift
for(var i=0;i<bgspec;i++){
  var len = spectra[i].length;
  var m = (spectra[i][len-1] - spectra[i][nm[650]]) / (len - nm[650]);
  var b = spectra[i][nm[650]] - (m * nm[650]);
  for(var j=nm[650];j<len;j++){
	spectra[i][j] -= (m * j) + b;
  }
}

var m = spectra[2].slice(nm[420],nm[525]);
var min = MathMIN( m );
var max = MathMAX( m );

var lower = 420;
for(i=420;i<525;i++){
	var IntInPercent = ((spectra[2][nm[i]] - min) / max)  * 100;
	if(IntInPercent < 15)
		lower = i;
    else
		break;
}


var higher = 525;
for(i=525;i>420;i--){
	var IntInPercent = ((spectra[2][nm[i]] - min) / max)  * 100;
	if(IntInPercent < 15)
		higher = i;
    else
		break;
}



//Normalize to 410-490 better 510-530
for(var i=1;i<bgspec;i++){
  var n = spectra[i].slice(nm[425],nm[430]);
  var m = spectra[i].slice(nm[495],nm[505]);
  var o = spectra[i].slice(nm[425],nm[505]);
  var norm = MathMEAN(n) + MathMEAN(m);
  var norm = spectra[i][nm[420]];
  for(var j=0;j<pixels;j++){
	spectra[i][j] = spectra[i][j] / norm;
  }
}

var nmMin = 650;
var nmMax = 780;

// Fm' is derived from the last spectrum 
output.Fmp = MathSUM(spectra[2].slice(nm[nmMin],nm[nmMax]));

output.Fmp = MathROUND(output.Fmp,3);

output.spectra = spectra[2].slice(nm[nmMin],nm[nmMax])

// In case the number of spectra in specNum and the number after the
// trace got split didn't match up, a warning is triggered
if(spectra.length != specNum)
	danger('Insufficent number of spectra collected!',output);


//Return data
return output;
{
  "id": 222091,
  "user_id": 156,
  "status": "submitted",
  "api_version": "3",
  "location": [
    "42.72262750",
    "-84.47466530"
  ],
  "user_answers": {
    "10710": "Porites C2 27.2C",
    "10711": "Brown"
  },
  "sample": [
    [
      {
        "time": 1454602151817,
        "protocol_id": 1,
        "light_intensity": 8.01,
        "r": 3.21,
        "g": 3.21,
        "b": 1.6,
        "data_raw": [
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  "firmware_version": "0.46",
  "device_id": 252,
  "time": 1454602151809,
  "time_offset": 300
}
Sebastian kuhlgert square
Created by

Sebastian


Protocol connections:
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Latest Update:
Jun 2016