NPQ 10 minutes - RG - Dark recovery


5 minutes with actinic light 250 uE, followed by 5 minutes of dark. One SP each minute
var data = json.data_raw;
var output = {};
var Fs = {};
var FmP = {};
var FmPs = {};
var PhiII = {};

var f0p = {};
var qL = {};
var NPQ = {};

var sample_cal = MathMEAN(data.slice(1,10));

// retrieve the baseline information from the data JSON and save (using measuring light 15, calibrating light 14)
for (i in json.get_ir_baseline) {	
	if (json.get_ir_baseline[i][0] == 15) {
		var slope_light = json.get_ir_baseline[i][1];
		var yint_light = json.get_ir_baseline[i][2];
	}
	if (json.get_ir_baseline[i][0] == 14) {
		var slope_cal = json.get_ir_baseline[i][1];
		var yint_cal = json.get_ir_baseline[i][2];
	}
}

// calculate the baseline
var shinyness = (sample_cal-yint_cal)/slope_cal; // where 0 is dull black electrical tape, and 1 is shiny aluminum
var baseline = slope_light*shinyness+yint_light;

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

var F0 = MathMEAN(data.slice(68,70)) - baseline;
var Fmsort = data.slice(71, 120).sort();
var Fm = MathMEAN(Fmsort.slice(45,49)) - 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 = 520; 
var Fsuma = {};
var FtotFs = {};

for (i=1 ; i<=10 ; i++) { 
  
  
  var frag = data.slice(x,x+200);
     Fs [i]  = MathMEAN(frag.slice(40,50)) - baseline;
     FmPs = frag.slice(50,100).sort();
     FmP [i] = MathMEAN(FmPs.slice(45,50));
     f0p [i] = F0 /(fvfm + (F0/FmP [i]));
  
  Fsuma [i] = MathSUM(frag.slice(100,200));
  FtotFs[i] = Fsuma [i] - (100 *  Fs [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]);   

  
    
 //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);
 
  var x= x + 200;
  
}  
for (i=1; i<=10; i++) {
output ["Fs " + i ] = MathROUND(Fs [i],0);
}
          
 
for (i=1; i<=10; i++) {

  output ["Fm' " + i] = MathROUND(FmP [i],0);
}
for (i=1; i<=10; i++) {
output ["F0' calc " + i] = MathROUND(f0p [i],0);
}
for (i=1; i<=10; i++) {
output ["PhiII " + i] = MathROUND(PhiII [i],3);
}

for (i=1; i<=10; i++) {
output ["area cola " + i] = MathROUND(FtotFs [i],3);
}
output ["baseline" ] = baseline;

return output;
{
  "time_offset": 180,
  "time": 1473793290656,
  "device_id": 109,
  "firmware_version": "0.450",
  "sample": [
    [
      {
        "time": 1473795093387,
        "protocol_id": 1,
        "get_ir_baseline": [
          [
            15,
            4.31,
            -0.1
          ],
          [
            14,
            6188.48,
            6930.63
          ]
        ],
        "light_intensity": 2.42,
        "r": 2.62,
        "g": 0.6,
        "b": 0.4,
        "relative_humidity": 41.01,
        "temperature": 26.13,
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      }
    ]
  ],
  "app_os": "win",
  "app_name": "PhotosynQ",
  "app_version": "0.3.5",
  "app_device": "x86-32",
  "location": [
    "-32.9548015",
    "-60.6433767"
  ],
  "ConsoleMacro": "221"
}
Default avatar
Created by

Rodrigo Gomez


Protocol connections:
2
Latest Update:
Sep 2016