v1 NPQ 5 minutes - RG


5 minutes with actinic light 250 uE
var data = json.data_raw;
var output = {};
var Fs = {};
var FmP = {};
var FmPs = {};
var PhiII = {};
var baseline = 0;
var f0p = {};
var qL = {};
var NPQ = {};


// retrieve the baseline information from the data JSON and save (using measuring light 15, calibrating light 14)

var sample_cal = json.detector_read1;//es para la luz 940

var shinyness = (sample_cal-json.recall["ir_baseline_yint[5]"])/json.recall["ir_baseline_slope[5]"]; // where 0 is dull black electrical tape, and 1 is shiny aluminum
var baseline = json.recall["ir_baseline_slope[3]"]*shinyness+json.recall["ir_baseline_yint[3]"];

if (!baseline || !json.recall["ir_baseline_yint[5]"] || sample_cal == 65535) {						// if it hasn't been calibrated or there's an error or it's maxed, set baseline == 0
  baseline = 0;
}



// initial values of F0 and Fm from dark adapted state.

var F0 = MathMEAN(data.slice(32,38)) - baseline;
var Fmsort = data.slice(40, 90).sort();
var Fm = MathMEAN(Fmsort.slice(45,50)) - baseline; // take the 4 largest values and average them
var fvfm = (Fm-F0)/Fm;
output ["F0"] = MathROUND(F0,0);
output ["Fm"] = MathROUND(Fm,0);
output ["Fv/Fm"] = MathROUND(fvfm,3);

// illumination period
var x = 290; 

for (i=1 ; i<=10 ; i++) { 
  
  
  var frag = data.slice(x,x+150);
     Fs [i]  = MathMEAN(frag.slice(40,49)) - baseline;
     FmPs = frag.slice(50,100).sort();
     FmP [i] = MathMEAN(FmPs.slice(45,50)) - baseline;
     f0p [i] = F0 /(fvfm + (F0/FmP [i]));
    
     PhiII [i] = (FmP [i] - Fs [i])/FmP[i];
  qL [i]= ((FmP [i] - Fs[i] )/(FmP [i] - f0p [i] ))*f0p[i] /Fs [i] ;
  NPQ [i] = ((Fm - FmP [i]) / FmP [i]);   

    var x= x + 150;
  
    
 //output ["Fs " + i] = MathROUND(Fs [i], 0);
 //output ["Fm' " + i] = MathROUND(FmP [i],0);
 //output ["F0' calc " + i] = MathROUND(f0p [i],0);
 //output ["PhiII " + i] = MathROUND(PhiII [i],3);
 //output ["qL " + i] = MathROUND(qL [i],4);
//output ["NPQ " + i] = MathROUND(NPQ [i],4);
 

}  
for (i=1; i<=7; i++) {
output ["Fs " + i ] = MathROUND(Fs [i],0);
}
          
 for (i=1; i<=7; i++) {

  output ["Fm' " + i] = MathROUND(FmP [i],0);
}
for (i=1; i<=7; i++) {
output ["F0' calc " + i] = MathROUND(f0p [i],0);
}
for (i=1; i<=7; i++) {
output ["PhiII " + i] = MathROUND(PhiII [i],3);
}

for (i=1; i<=7; i++) {
output ["NPQ " + i] = MathROUND(NPQ [i],3);
}
for (i=1; i<=7; i++) {
output ["qL " + i] = MathROUND(qL[i],3);
}
var thickness = json.thickness;
output ["thickness - mm "] = MathROUND(thickness , 4);

output ["baseline" ] = baseline;

return output;
{
  "time_offset": 180,
  "time": 1497548385647,
  "device_name": "MultispeQ",
  "device_version": "1",
  "device_id": "01:06:11:88",
  "device_battery": 39,
  "device_firmware": 1.17,
  "sample": [
    {
      "time": 1497548385728,
      "protocol_id": 1,
      "detector_read1": 8302,
      "light_intensity": 2,
      "r": 0,
      "g": 0,
      "b": 0,
      "light_intensity_raw": 0,
      "temperature": 22.77,
      "humidity": 72.392578,
      "pressure": 1008.725525,
      "temperature2": 23.040001,
      "humidity2": 70.757812,
      "pressure2": 1009.098999,
      "contactless_temp": 22.19,
      "thickness": 0.2,
      "compass_direction": "E",
      "compass": "90.00",
      "angle": 2.86,
      "angle_direction": "S",
      "pitch": 2.64,
      "roll": 1.09,
      "recall": {
        "time": 1497548696677,
        "colorcal_blank1[1]": 16511.5,
        "colorcal_blank1[2]": 24324.5,
        "colorcal_blank1[3]": 29277.5,
        "colorcal_blank1[4]": 37138,
        "colorcal_blank1[6]": 33194,
        "colorcal_blank1[8]": 28720.5,
        "colorcal_blank1[9]": 31100,
        "colorcal_blank1[10]": 34614,
        "colorcal_blank2[1]": 21662,
        "colorcal_blank2[2]": 18077,
        "colorcal_blank2[3]": 21188.5,
        "colorcal_blank2[4]": 18162,
        "colorcal_blank2[6]": 16493.5,
        "colorcal_blank2[8]": 17087,
        "colorcal_blank2[9]": 18622,
        "colorcal_blank2[10]": 16523.5,
        "colorcal_blank3[1]": 20515.5,
        "colorcal_blank3[2]": 9866,
        "colorcal_blank3[3]": 19621.5,
        "colorcal_blank3[4]": 13418.5,
        "colorcal_blank3[6]": 5898.5,
        "colorcal_blank3[8]": 6295.5,
        "colorcal_blank3[9]": 5582,
        "colorcal_blank3[10]": 6047,
        "colorcal_intensity1_slope[2]": 2.309,
        "colorcal_intensity1_yint[2]": 1.7,
        "colorcal_intensity2_slope[2]": 2.377,
        "colorcal_intensity2_yint[2]": 3,
        "colorcal_intensity3_slope[2]": 2.554,
        "colorcal_intensity3_yint[2]": -17.299999,
        "ir_baseline_slope[5]": 8895,
        "ir_baseline_yint[5]": 13422.5,
        "ir_baseline_slope[3]": 526.5,
        "ir_baseline_yint[3]": 738.5
      },
      "data_raw": [
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  ],
  "app_os": "win",
  "app_name": "PhotosynQ",
  "app_version": "0.3.8",
  "app_device": "x86-32",
  "location": [
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  ]
}
Img 20171030 190259
Created by

Rodrigo Gomez


Protocol connections:
2
Latest Update:
Jun 2017