v1 NPQ 5 min light acclimation 20 dark recovery JRP


5 minutes with actinic light 800 uE, and 20 minutes of dark recovery
var data = json.data_raw;
var output = {};
var Fs = {};
var FmP = {};
var FmPs = {};
var PhiII = {};
var baseline = 0;
var f0p = {};
var qL = {};
var NPQ = {};
var f0pFR = [];
var diff0p = [];
var FsD = {};
var FmPD = {};
var FmPsD = {};
var PhiIID = {};
var f0pD = {};
var qLD = {};
var NPQD = {};
var f0pFRD = [];
var diff0pD = [];



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

var sample_cal = json.detector_read1;

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.

Fo = data.slice(40,80);



var F0 = MathMEAN(Fo) - baseline;
var Fmsort = data.slice(130,200).sort();
//output["Fmsort "] = data.slice(130,200);
var Fm = MathMEAN(Fmsort.slice(65,70)) - baseline; // take the 4 largest values and average them
var fvfm = (Fm-F0)/Fm;



//output ["baseline"] = baseline;

output ["F0"] = MathROUND(F0,0);
output ["Fm"] = MathROUND(Fm,0);
output ["Fv/Fm"] = MathROUND(fvfm,3);

// illumination period flashes

var x = 400; 



for (i=1 ; i<=5 ; i++) { 
    var frag = data.slice(x,x+200);
     Fs [i]  = MathMEAN(frag.slice(0,60)) - baseline;
     FmPs = frag.slice(60,140).sort();
     FmP [i] = MathMEAN(FmPs.slice(70,80)) - 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]);   
  if (i <= 5) {
  var valsmed = frag.slice(101,150).sort();
  f0pFR [i]= MathMEAN(valsmed.slice(0,5)) - baseline;
    diff0p [i] = f0pFR[i] - f0p [i];
    
}
  
  var x= x + 200;
    var r = 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);
 

} 




// dark period flashes

var x2 = 1460;



for (i=1 ; i<=5 ; i++) { 
    var frag2 = data.slice(x2,x2+180);
     FsD [i]  = MathMEAN(frag2.slice(0,40)) - baseline;
     FmPsD = frag2.slice(41,120).sort(); /// full peak
     FmPD [i] = MathMEAN(FmPsD.slice(60,79))- baseline;// save last 29 pulses for mean
     f0pD [i] = F0 /(fvfm + (F0/FmPD [i]));
     PhiIID [i] = (FmPD [i] - FsD [i])/FmPD[i];
  qLD [i]= ((FmPD [i] - FsD[i] )/(FmPD [i] - f0p [i] ))*f0p[i] /FsD [i] ;
  NPQD [i] = ((Fm - FmPD [i]) / FmPD [i]);   
  if (i <= 5) {
  var valsmed = frag2.slice(121,180).sort();
  f0pFRD [i]= MathMEAN(valsmed.slice(50,59)) - baseline;
    diff0pD [i] = f0pFRD[i] - f0pD [i];
    
}
  
  var x2= x2 + 180;
    var r2 = 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 qE =  (Fm/FmP[5])  - (Fm/FmPD[3]);
//output ["qE"] = qE;


//var qT =  (qLD[3]  - qE);
//output ["qT"] = qT;

//// light period Fs
for (i=1; i<=r; i++) {
output ["Fs " + i ] = MathROUND(Fs [i],0);
}
//// Dark period Fs
for (i=1; i<=r2; i++) {
output ["FsD " + i ] = MathROUND(FsD [i],0);
}
 


//// light period Fm
 for (i=1; i<=r; i++) {

  output ["Fm' " + i] = MathROUND(FmP [i],0);
}

//// dark period Fm
 for (i=1; i<=r2; i++) {

  output ["FmD' " + i] = MathROUND(FmPD [i],0);
}


for (i=1; i<=r; i++) {
output ["F0' calc " + i] = MathROUND(f0p [i],0);
  if (i <= 5) {
  output ["F0' med " + i] = MathROUND(f0pFR [i],0);
  output ["diff F0p med - calc " + i ] = MathROUND(diff0p [i],0);
  }
}


//// light period PhiII
for (i=1; i<=r; i++) {
output ["PhiII " + i] = MathROUND(PhiII [i],3);
}

//// dark period PhiII
for (i=1; i<=r2; i++) {
output ["PhiIID " + i] = MathROUND(PhiIID [i],3);
}


//// light period NPQ
for (i=1; i<=r; i++) {
output ["NPQ " + i] = MathROUND(NPQ [i],3);
}

//// dark period NPQ
for (i=1; i<=r2; i++) {
output ["NPQD " + i] = MathROUND(NPQD [i],3);
}


//// light period qL
for (i=1; i<=r; i++) {
output ["qL " + i] = MathROUND(qL[i],3);
}


//// dark period qL
for (i=1; i<=r2; i++) {
output ["qLD " + i] = MathROUND(qLD[i],3);
}



var thickness = json.thickness;
output ["thickness - mm "] = MathROUND(thickness , 4);

output ["baseline" ] = baseline;


return output;
{
  "time_offset": 300,
  "time": 1518702584133,
  "device_name": "MultispeQ",
  "device_version": "1",
  "device_id": "01:12:70:99",
  "device_battery": 67,
  "device_firmware": 1.17,
  "sample": [
    {
      "time": 1518702584160,
      "protocol_id": 1,
      "detector_read1": 9401,
      "temperature": 21.26,
      "humidity": 34.357422,
      "pressure": 987.563416,
      "contactless_temp": 21.3,
      "thickness": 0.66,
      "recall": {
        "time": 1518704094296,
        "ir_baseline_slope[5]": 10425,
        "ir_baseline_yint[5]": 15385.5,
        "ir_baseline_slope[3]": 684.5,
        "ir_baseline_yint[3]": 913
      },
      "data_raw": [
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      ]
    }
  ],
  "app_os": "mac",
  "app_name": "PhotosynQ",
  "app_version": "0.3.9",
  "app_device": "x86-64",
  "location": [
    "43.0087370",
    "-78.7837400"
  ],
  "ConsoleMacro": "382"
}
Default avatar
Created by

Jonathan R Pleban


Protocol connections:
3
Latest Update:
Feb 2018