test_new_spad_2


test of new spad process
/**
 * Macro for data evaluation on PhotosynQ.org
 * by: David M. Kramer
 * created: 2017-06-21 @ 10:36:29
 var lights = [1,2,3,4,5,6,8,9,10];// define the lights to have absorbance measured
var wavelengths = ["530","650","605","420","940","940","850","730","880"];// define the lights to have absorbance measured
var detectors = [3,3,3,3,3,1,1,1,1,1];// define the lights to have absorbance measured
 
 */

// Define the output object here
var output = {};
var wavelengths = ["530","650","605","420","940","940","850","730","880"];
// Check if the key time exists in json

if (json.time !== undefined){

	// Add key time and value to output
	output.time = json.time;
}

for (var i in json.set){
	output["t_"+i]=json.set[i].data_raw;
}

output["tt_"+i]=json.set[i].data_raw;
//output.test=json.set[1].data_raw[0];

var n_traces=json.set.length;
output.n_traces=n_traces-1;

var len_traces=json.set[1].data_raw.length;
	output.trace_length=len_traces;

var n_cycles=20; 
output.n_cycles=n_cycles;
var n_lights=len_traces/n_cycles; //figure out how many lights were used

output.n_lights=n_lights;

// set up a matrix, s, to hold results


var ss = new Array; //holds the successive values of transmission for each light


for (var i = 0; i < n_lights+1; i++) { 
   sss = new Array;  //set up a new array  
  	for (var j = 1; j < n_traces; j++) {
      var temp_val=0;
      for (var k=0; k < n_cycles; k++){
        lp=(k*n_lights)+i-1;
        temp_val+=json.set[j].data_raw[lp];
      }
      sss.push(temp_val);

    }
	ss.push(sss); 
}

output.ss=ss[2].join(", ");

var offset=1000.0;

var abs = new Array; //holds the successive values of transmission for each light
for (var i in ss){  //loop through the lights
  var ab = new Array; //holds the successive values of transmission for each light
    for (var ii in ss[i]){ //loop through the traces
		ab.push(MathLOG(ss[i][0]-offset)-MathLOG(ss[i][ii]-offset));
    }
  abs.push(ab);
}

var wavelengths = ["530","650","605","420","940","650","850","730","880"];// define the lights to have absorbance measured
var detectors = [3,3,3,3,3,1,1,1,1,1];// define the lights to have absorbance measured

var reference=6;
var sample_number=3;

var abs_dif = new Array; //holds the successive values of transmission for each light
for (var i in ss){  //loop through the lights
  var ab_dif = new Array; //holds the successive values of transmission for each light
    for (var ii in ss[i]){ //loop through the traces
		ab_dif.push(MathROUND(abs[i][ii]-abs[reference][ii]));
    }
  abs_dif.push(ab_dif);
}



output.abs=abs[sample_number];
output.ref=abs[reference];
output.diff=abs_dif[sample_number];

output.diff_nums=abs_dif[sample_number].join(",  ");


/*
var out_x = new Array(n_traces);

var lp=0;
var abs = new Array(n_traces);
for (var j=1; j< n_traces-1; j++){
	out_x[j]=0.1;
 }


var out_x_all = new Array(n_traces);

for (var i = 1; i < n_lights+1; i++) {  //iterate through the lights
  for (var j=1; j< n_traces; j++){//iterate through the traces
    out_x[j]=0;
      for (var k=0; k < n_cycles; k++){
         lp=(k*n_lights)+i-1;
          out_x[j]+=json.set[j].data_raw[lp]/n_cycles;
      }
    abs[j]=MathLOG(out_x[j]);
  }
  out_x_all=out_x;
  output["intensity #"+i]=out_x.slice(1,n_traces+1);
  output["absorbance #"+i]=abs;
  output[i]=abs;
}


var reference_light=5;
var dif = new Array(n_traces);

for (var i = 1; i < n_lights+1; i++) {  //iterate through the lights
	for (var j=1; j< n_traces; j++){//iterate through the traces
		var temp1=i; //output[i][j];
      ii=5;
      	var temp2=j; //output[ii][j];
        dif[j]=output[i][j]-output[1][j]; //-temp2;
}
	output["diff=#"+i]=dif;

}
/*

for (var i = 1; i < n_lights+1; i++) {  //iterate through the lights
	var abs = new Array(n_traces);
	for (var j=1; j< n_traces; j++){
		abs=MathLOG(out_x_all[i][j]); //-MathLOG(out_x_all[i][]);
	}
  output["abs :" + i]=abs;
}


//output.out_x=out_x.slice(0,n_traces);

/*

for (var i = 1; i < n_lights-1; i++) {  //iterate through the lights
  for (var j=1; j< n_traces-1; j++){//iterate through the traces
		for (var k=0; k < n_cycles; k++){
        	 lp=(k*n_lights)+i;
          		temp2+=2.0; //json.set[2].data_raw[3];
        }
	}  
} 


/*
ss[2][2]=json.set[2].data_raw[4];
ss[2][2]+=json.set[2].data_raw[4];
ss[2][2]+=json.set[2].data_raw[4];

output.ss=ss;

output.testit=json.set[2].data_raw[5];
var k=1;
var i=2;
output.testit2=(k*n_cycles)+i;

/*
for (var i = 0; i < n_lights; i++) {  //iterate through the lights
	output["intensity #"+i]=s[i];
}


for (var i=1; i< n_traces; i++){
	output["trace_ #" + i]=json.set[i].data_raw;
}

for (var j=0; j<n_lights; j++){
	for (var i=1; i< n_traces; i++){
		for (var k=0; k<n_cycles; k++){
        }
	}
}



/*
for (i in json.set[2]){
	output["lab:"+i]=json.set[1][i];
}

/*
var number_spads=8;
for (var i=1; i< number_spads; i++){
	output["t_"+i]=json.set[i].data_raw;
}

var i_sample = new Array(number_spads-1);
var i_ref = new Array(number_spads-1);
var spad_out = new Array(number_spads-1);

var sample_led=2;
var ref_led=3;
var num_pulses = 10;
var offset=100;
//var i_1_3_0=MathMEAN(json.set[1].data_raw.slice(1,9));
for (var i=1; i< number_spads; i++){
	i_ref[i-1]=MathMEAN(json.set[i].data_raw.slice((ref_led)*num_pulses,(ref_led)*num_pulses+1));
	i_sample[i-1]=MathMEAN(json.set[i].data_raw.slice((sample_led)*num_pulses,(sample_led+1)*num_pulses));
	spad_out[i-1]=MathROUND(MathLOG(i_ref[i-1]-offset)-MathLOG(i_sample[i-1]-offset), 2);
}
output.i_ref=i_ref;
output.i_sample=i_sample;
output.spad_out=spad_out;

output.spad_out=spad_out.join(",");


/*
var i_1_3_0=MathMEAN(json.set[1].data_raw.slice(1,9));
var i_2_3_0=MathMEAN(json.set[1].data_raw.slice(11,19));
var i_3_3_0=MathMEAN(json.set[1].data_raw.slice(21,29));
var i_6_1_0=MathMEAN(json.set[1].data_raw.slice(31,39));
var i_7_1_0=MathMEAN(json.set[1].data_raw.slice(41,49));

var i_1_3=MathMEAN(json.set[2].data_raw.slice(0,9));
var i_2_3=MathMEAN(json.set[2].data_raw.slice(11,19));
var i_3_3=MathMEAN(json.set[2].data_raw.slice(21,29));
var i_6_1=MathMEAN(json.set[2].data_raw.slice(31,39));
var i_7_1=MathMEAN(json.set[2].data_raw.slice(41,49));

var DA_1_3=MathLOG(i_1_3_0/i_1_3);
var DA_2_3=MathLOG(i_2_3_0/i_2_3);
var DA_3_3=MathLOG(i_3_3_0/i_3_3);
var DA_6_1=MathLOG(i_6_1_0/i_6_1);
var DA_7_1=MathLOG(i_7_1_0/i_7_1);

output.DA_1_3=DA_1_3;
output.DA_2_3=DA_2_3;
output.DA_3_3=DA_3_3;
output.DA_6_1=DA_6_1;
output.DA_7_1=DA_7_1;

var DA_2_3=MathLOG(i_2_3_0/i_2_3);
var DA_3_3=MathLOG(i_3_3_0/i_3_3);
var DA_6_1=MathLOG(i_6_1_0/i_6_1);
var DA_7_1=MathLOG(i_7_1_0/i_7_1);


var DA_array=[DA_1_3,DA_2_3,DA_3_3,DA_6_1,DA_7_1];
output.DA_array=DA_array;



var i_1_3=MathMEAN(json.set[3].data_raw.slice(0,9));
var i_2_3=MathMEAN(json.set[3].data_raw.slice(11,19));
var i_3_3=MathMEAN(json.set[3].data_raw.slice(21,29));
var i_6_1=MathMEAN(json.set[3].data_raw.slice(31,39));
var i_7_1=MathMEAN(json.set[3].data_raw.slice(41,49));

var DA_1_3=MathLOG(i_1_3_0/i_1_3);
var DA_2_3=MathLOG(i_2_3_0/i_2_3);
var DA_3_3=MathLOG(i_3_3_0/i_3_3);
var DA_6_1=MathLOG(i_6_1_0/i_6_1);
var DA_7_1=MathLOG(i_7_1_0/i_7_1);

output.DA_1_3_2=DA_1_3;
output.DA_2_3_2=DA_2_3;
output.DA_3_3_2=DA_3_3;
output.DA_3_3_2=DA_3_3;
output.DA_6_1_2=DA_6_1;
output.DA_7_1_2=DA_7_1;

var DA_1_3_2=MathLOG(i_2_3_0/i_2_3);
var DA_2_3_2=MathLOG(i_2_3_0/i_2_3);
var DA_3_3_2=MathLOG(i_3_3_0/i_3_3);
var DA_6_1_2=MathLOG(i_6_1_0/i_6_1);
var DA_7_1_2=MathLOG(i_7_1_0/i_7_1);

var DA_array_2=[DA_1_3_2,DA_2_3_2,DA_3_3_2,DA_6_1_2,DA_7_1_2];
//output.DA_array_2=DA_array_2;

var number_leds=5;
var number_spads=5;
var leds=[1,2,3,6,7];
var lambda=[535,650,590,940,655];            
var start_pt=[1,101,201,301,401];
var end_pt=[91,191,291,391,491];
var spad_val=[7.9,15,30.3,24.9];

var ttp = new Array(number_spads);
for (var i = 0; i < number_leds; i++) {
  ttp[i] = new Array(number_spads);
  	for (var j = 0; j < number_leds; j++) {
     ttp[i][j]=i*j; 
    }
}
for (i = 0; i < number_leds; i++) {
	for (j = 0; j < number_spads; j++) {      	
  	  i_zero=MathMEAN(json.set[1].data_raw.slice(start_pt[j],end_pt[j]));
  	  i_l=MathMEAN(json.set[i+1].data_raw.slice(start_pt[j],end_pt[j]));
	  a=MathLOG(i_zero/i_l);
      ttp[j][i]=a;  
    }
}

var spad_outputs_1 = new Array(number_spads);
for (j = 0; j < number_spads; j++) { 
  spad_outputs_1[j]=ttp[2][j] - ttp[3][j];
}

output.so=spad_outputs_1;

var spad_outputs_2 = new Array(number_spads);
for (j = 0; j < number_spads; j++) { 
  spad_outputs_2[j]=ttp[0][j] - ttp[3][j];
}

output.so_2=spad_outputs_2;


var spad_outputs_3 = new Array(number_spads);
for (j = 0; j < number_spads; j++) { 
  spad_outputs_3[j]=ttp[4][j] - ttp[3][j];
}

output.so_3=spad_outputs_3;



//output.trial=ttp[3];
//for (i = 0; i < number_spads; i++) {
//	output["res"+i]=ttp[i];
//}

for (i = 0; i < number_leds; i++) {
	output["delta_A_"+lambda[i]]=ttp[i]; //.slice(1,5);
	//output["delta_A_"+i]=ttp[i];
}


output.spads=spad_val;

//output.DA1=ttp[2];

//output.d530=ttp[1];

/*
var d=0.0;
var c=(66.5); //(2*45.6);
var i_650_0=MathMEAN(json.set[1].data_raw.slice(0,90));
var i_940_0=MathMEAN(json.set[1].data_raw.slice(100,190));
output.i_650_0=i_650_0;
output.i_940_0=i_940_0;


i_650=MathMEAN(json.set[5].data_raw.slice(0,99));
i_940=MathMEAN(json.set[5].data_raw.slice(100,199));
var i_650_black=0; //i_650;
var i_940_black=0; //i_940;
output.i_650_black=i_650;
output.i_940_black0=i_940;

var s=1;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);

spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.trace_1=json.set[1].data_raw;

//spad=-1*MathLOG(T_650);

output.T_650_1=T_650;
output.T_940_1=T_940;
output.spad1=spad;
output.trace_1=json.set[s].data_raw;

var s=2;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);
spad=c*(d*MathLOG(T_940)-MathLOG(T_650));

output.T_650_2=T_650;
output.T_940_3=T_940;
//spad=-1*MathLOG(T_650);

output.spad2=spad;
output.trace_2=json.set[2].data_raw;

var s=3;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
var spad=(41/62.0)*100*MathLOG(((i_650_0)/(i_650))/((i_940_0-i_94_black0)/(i_940-i_94_black0)));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);

//T_940=(i_940-i_940_black)/(i_940_0-i_940_black);
spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.T_650_3=T_650;
output.T_940_3=T_940;
//spad=-1*MathLOG(T_650);

output.spad3=spad;
output.trace_3=json.set[s].data_raw;


var s=4;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);

spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.T_650_4=T_650;
output.T_940_4=T_940;
//spad=-1*MathLOG(T_650);

output.spad4=spad;
output.trace_4=json.set[s].data_raw;

var s=5;

var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);

spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.T_650_5=T_650;
output.T_940_5=T_940;
//spad=-1*MathLOG(T_650);

output.spad5=spad;
output.trace_5=json.set[s].data_raw;


var s=6;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);
spad=c*(d*MathLOG(T_940)-MathLOG(T_650));

output.T_650_6=T_650;
output.T_940_6=T_940;
//spad=-1*MathLOG(T_650);

output.spad6=spad;
output.trace_6=json.set[s].data_raw;


var s=7;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);

spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.T_650_7=T_650;
output.T_940_7=T_940;
//spad=-1*MathLOG(T_650);
output.spad7=spad;
output.trace_7=json.set[s].data_raw;


var s=8;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));
T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);

output.T_650_8=T_650;
output.T_940_8=T_940;
//spad=-1*MathLOG(T_650);
spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.spad8=spad;
output.trace_8=json.set[s].data_raw;

var s=9;
var i_650=MathMEAN(json.set[s].data_raw.slice(0,99));
var i_940=MathMEAN(json.set[s].data_raw.slice(100,199));

T_650=(i_650-i_650_black)/(i_650_0-i_650_black);
T_940=(i_940-i_940_black)/(i_940_0-i_940_black);
spad=c*(d*MathLOG(T_940)-MathLOG(T_650));
output.T_650_9=T_650;
output.T_940_9=T_940;
//spad=-1*MathLOG(T_650);

output.spad9=spad;
// Return data
output.trace_9=json.set[s].data_raw;
*/

return output;
{
  "time": "1498164125988",
  "device_name": "MultispeQ",
  "device_version": "1",
  "device_id": "01:12:53:21",
  "device_battery": 86,
  "device_firmware": 1.18,
  "sample": [
    [
      {
        "time": "1498164125988",
        "light_intensity_raw": 0,
        "data_raw": [

        ],
        "protocol_id": 1,
        "set": [
          {
            "time": "1498164125988",
            "blank:": "blank"
          },
          {
            "time": "1498164126000",
            "data_raw": [
              50099,
              51,
              53145,
              51071,
              1727,
              50725,
              497,
              49841,
              49283,
              50081,
              48,
              53144,
              51079,
              1725,
              50712,
              496,
              49828,
              49278,
              50071,
              51,
              53138,
              51073,
              1728,
              50711,
              494,
              49840,
              49269,
              50091,
              52,
              53138,
              51067,
              1731,
              50711,
              491,
              49838,
              49270,
              50071,
              51,
              53130,
              51097,
              1730,
              50739,
              493,
              49842,
              49272,
              50087,
              52,
              53131,
              51076,
              1728,
              50726,
              494,
              49847,
              49270,
              50045,
              52,
              53137,
              51093,
              1731,
              50719,
              491,
              49827,
              49275,
              50069,
              47,
              53129,
              51049,
              1728,
              50717,
              493,
              49837,
              49275,
              50067,
              50,
              53129,
              51069,
              1726,
              50719,
              498,
              49842,
              49280,
              50068,
              49,
              53143,
              51073,
              1729,
              50723,
              497,
              49835,
              49281,
              50091,
              48,
              53130,
              51067,
              1724,
              50733,
              499,
              49839,
              49268,
              50103,
              48,
              53123,
              51062,
              1727,
              50727,
              499,
              49846,
              49270,
              50097,
              52,
              53128,
              51050,
              1731,
              50733,
              505,
              49838,
              49278,
              50053,
              52,
              53126,
              51071,
              1731,
              50722,
              499,
              49826,
              49264,
              50080,
              52,
              53130,
              51090,
              1729,
              50719,
              496,
              49824,
              49277,
              50105,
              54,
              53129,
              51071,
              1727,
              50717,
              495,
              49837,
              49275,
              50063,
              48,
              53127,
              51071,
              1731,
              50731,
              498,
              49832,
              49279,
              50094,
              54,
              53127,
              51065,
              1726,
              50713,
              499,
              49835,
              49271,
              50108,
              46,
              53127,
              51058,
              1728,
              50725,
              500,
              49834,
              49272,
              50121,
              56,
              53111,
              51064,
              1727,
              50725,
              496,
              49825,
              49261
            ]
          },
          {
            "time": "1498164129661",
            "data_raw": [
              35577,
              48,
              31930,
              15389,
              1688,
              49538,
              389,
              48762,
              32375,
              35509,
              49,
              31912,
              15382,
              1689,
              49534,
              382,
              48751,
              32362,
              35533,
              48,
              31917,
              15380,
              1693,
              49535,
              387,
              48746,
              32362,
              35528,
              50,
              31915,
              15383,
              1684,
              49545,
              389,
              48754,
              32369,
              35505,
              49,
              31911,
              15390,
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}
Dave in cap img 4615
Created by

David M. Kramer


Protocol connections:
0
Latest Update:
Jun 2017