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;
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]));
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);
}
output ["baseline" ] = baseline;
return output;{
"time_offset": 180,
"time": 1472671959928,
"device_id": 109,
"firmware_version": "0.450",
"sample": [
[
{
"time": 1472671959934,
"protocol_id": 1,
"get_ir_baseline": [
[
15,
4.31,
-0.1
],
[
14,
6188.48,
6930.63
]
],
"light_intensity": 0,
"r": 0,
"g": 0,
"b": 0,
"relative_humidity": 49.6,
"temperature": 27.17,
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