v1 NPQ 5 min light acclimation 20 dark recovery JRP


5 minutes with actinic light 800 uE, and 20 minutes of dark recovery uses mPF
var data = json.data_raw;
var output = {};
var Fs = {};
var FmP = {};
var FmPs = {};

var baseline = 0;

var Fs1 = {};
var Fs2 = {};
var Fs3 = {};

var FmP1 = {};
var FmP2 = {};
var FmP3 = {};

var PhiII_1 = {};
var PhiII_2 = {};
var PhiII_3 = {};

var PhiII_init = {};

var FsD1 = {};
var FsD2 = {};
var FsD3 = {};
var FsD4 = {};

var FmPD1 = {};
var FmPD2 = {};
var FmPD3 = {};
var FmPD4 = {};

var PhiIID_1 = {};
var PhiIID_2 = {};
var PhiIID_3 = {};
var PhiIID_4 = {};





// 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);
//output["FOsort "] = data.slice(40,80);


var F0 = MathMEAN(Fo) - baseline;
var Fmsort = data.slice(80,172).sort();
//output["Fmsort "] = data.slice(80,172);
//output["Fmsort_2 "] = Fmsort(1,100);
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 ["baseline "] = MathROUND(baseline,2);
output ["F0 "] = MathROUND(F0,0);
output ["Fm "] = MathROUND(Fm,0);
output ["Fv/Fm"] = MathROUND(fvfm,3);

// illumination period flashes
// output["look "] = data.slice(230,250);

Fs1sort= data.slice(230,250);
Fs1= MathMEAN(Fs1sort.slice(10,19)) - baseline;
output["Fs1 "]=MathROUND(Fs1,3);
Fs2sort= data.slice(340,460);
Fs2= MathMEAN(Fs2sort.slice(115,120)) - baseline;
output["Fs2 "]=MathROUND(Fs2,3);
Fs3sort= data.slice(550,670);
Fs3= MathMEAN(Fs3sort.slice(115,120)) - baseline;
output["Fs3 "]=MathROUND(Fs3,3);


FmP1sort= data.slice(251,340);
FmP1= MathMEAN(FmP1sort.slice(85,90)) - baseline;
output["FmP1 "]=MathROUND(FmP1,3);
FmP2sort= data.slice(461,550);
FmP2= MathMEAN(FmP2sort.slice(85,90)) - baseline;
output["FmP2 "]=MathROUND(FmP2,3);
FmP3sort= data.slice(671,760);
FmP3= MathMEAN(FmP3sort.slice(85,90)) - baseline;
output["FmP3 "]=MathROUND(FmP3,3);


PhiII_1 = (FmP1 - Fs1)/FmP1;
output["PhiII_1 "]=MathROUND(PhiII_1,3);
PhiII_2 = (FmP2 - Fs2)/FmP3;
output["PhiII_2 "]=MathROUND(PhiII_2,3);
PhiII_3 = (FmP3 - Fs3)/FmP3;
output["PhiII_3 "]=MathROUND(PhiII_3,3);


PhiII_init = (Fm - Fs3)/Fm;
output["PhiII_init "]=MathROUND(PhiII_init,3);
// dark period

FsD1sort= data.slice(820,910);
FsD1= MathMEAN(FsD1sort.slice(85,90)) - baseline;
output["FsD1 "]=MathROUND(FsD1,3);
FsD2sort= data.slice(1010,1480);
FsD2= MathMEAN(FsD2sort.slice(465,470)) - baseline;
output["FsD2 "]=MathROUND(FsD2,3);
FsD3sort= data.slice(1600,1870);
FsD3= MathMEAN(FsD3sort.slice(265,270)) - baseline;
output["FsD3 "]=MathROUND(FsD3,3);


FmPD1sort= data.slice(251,340);
FmPD1= MathMEAN(FmPD1sort.slice(85,90)) - baseline;
var FmX =MathROUND(FmPD1,3);
output["FmX "]=MathROUND(FmPD1,3);

FmPD2sort= data.slice(461,550);
FmPD2= MathMEAN(FmPD2sort.slice(85,90)) - baseline;
output["FmPP "]=MathROUND(FmPD2,3);
var FmPP =MathROUND(FmPD2,3);

FmPD3sort= data.slice(671,760);
FmPD3= MathMEAN(FmPD3sort.slice(85,90)) - baseline;
output["FmY "]=MathROUND(FmPD3,3);
var FmY =MathROUND(FmPD3,3);


PhiIID_1 = (FmPD1 - FsD1)/FmPD1;
output["PhiIID_1 "]=MathROUND(PhiIID_1,3);
PhiIID_2 = (FmPD2 - FsD2)/FmPD3;
output["PhiIID_2 "]=MathROUND(PhiIID_2,3);
PhiIID_3 = (FmPD3 - FsD3)/FmPD3;
output["PhiIID_3 "]=MathROUND(PhiIID_3,3);


/// energy paritioning paramters following Guadagno 2010 

var Phi_qE ={};
Phi_qE = ((FmX -FmP3)/FmX)*(Fs3/FmX) ;
output["Phi_qE "]=MathROUND(Phi_qE,3);

var Phi_qT ={};
Phi_qT = ((FmY - FmX)/FmX)*(Fs3/FmY) ;
output["Phi_qT "]=MathROUND(Phi_qT,3);

var Phi_qI ={};
Phi_qI = ((Fm - FmY)/FmY)*(Fs3/Fm) ;
output["Phi_qI "]=MathROUND(Phi_qI,3);

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



return output;
{
  "time_offset": 240,
  "time": 1533059466292,
  "device_name": "MultispeQ",
  "device_version": "1",
  "device_id": "01:12:38:86",
  "device_battery": 79,
  "device_firmware": 1.17,
  "sample": [
    {
      "time": 1533059466336,
      "protocol_id": 1,
      "detector_read1": 8102,
      "temperature": 25.02,
      "humidity": 57.180664,
      "pressure": 998.049072,
      "contactless_temp": 23.29,
      "thickness": 0.81,
      "recall": {
        "time": 1533060975545,
        "ir_baseline_slope[5]": 7773.5,
        "ir_baseline_yint[5]": 12514,
        "ir_baseline_slope[3]": 562,
        "ir_baseline_yint[3]": 801
      },
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    }
  ],
  "app_os": "mac",
  "app_name": "PhotosynQ",
  "app_version": "0.3.9",
  "app_device": "x86-64",
  "location": [
    "43.0086949",
    "-78.7836925"
  ],
  "ConsoleMacro": "453"
}
Default avatar
Created by

Jonathan R Pleban


Protocol connections:
3
Latest Update:
Aug 2018