waspx_dirkECS combo gradual


waspx_dirkECS combo gradual
/**
 * Macro for data evaluation of RIDES1_light_potential 
 * data on PhotosynQ.org
 * by: David M. Kramer 
 * created: 2017-05-09 @ 18:15:27     
 *                   
 * 
        
/* Note: Special thanks to Sebastian Kuhlgert for the curve fitting routines!
*     
* The following variables are for fitting the ECS decay curves when the 
* procedure written by Kevin and Greg often fails. Fortunately, Sebastian added 
* a really important new feature that allows for very flexible and useful 
* nonlinear curve fitting.  
*/       
  
// Define the output object here 
var output = {}; //dictionary to hold results
n_sets=json.set.length; 
//output.n_sets=json.set.length;
var details=1;   
var PAR=[]; //json.v_arrays[0];
//output.PAR=PAR;

var DIRK_ECS=GetProtocolByLabel( "dirk_ecs", json, true ); 

var WASP_ECS=GetProtocolByLabel( "ecs_wasp", json, true ); 

var number_traces = WASP_ECS.length;
var WASP_ECS_Decon=[];  
var ECS_only_traces=[]; 
var ECS_w_WASP=[];  
var Fluor = [];
var Phi2=[];
var wasp_vals=[];
var ESC_dirk_traces=[];
var LEF=[]; 
var vHwasp = []; 

output.number_traces=number_traces; 
wasp_only_vals=[];

var preillumination = [];
for (var i=0; i<number_traces; i++) {
 
  PAR.push(DIRK_ECS[i].pre_illumination[1]); 
}
output.PAR=PAR;

var wasp_only_traces=[];
var dirk_linear=[];
for (var i=0; i<number_traces; i++) {
    var dirk = DIRK_ECS[i].data_raw.slice(31,60);
  	dirk = TransformTrace( "abs", dirk );
  	dirk_linear.push(MathROUND(-1000*dirk[7],3));
  	ESC_dirk_traces.push(dirk); 
    WASP_traces = WASP_ECS[i].data_raw; 
    output.WASP_traces_composite=WASP_traces[i].data_raw; 
  	
    ECS_WASP = ArrayNth( WASP_traces, 4, 1 );// sub trace with both the ECS and the WASP pulse (I, not A)
    output.ECS_WASP=ECS_WASP;
  	ECS_w_WASP.push(ECS_WASP);
    ECS_only = ArrayNth( WASP_traces, 4, 0 ); // sub trace with the ECS but NO WASP pulse (I, not A)
    output.ECS_only=ECS_only;
    WASP_only = ArrayNth( WASP_traces, 4, 2 ); // sub trace with WASP but NO ECS pulse (I, not A)
    output.WASP_only=WASP_only;
  	wasp_only_traces.push(WASP_only);
    wasp_only_vals.push( MathMEAN(WASP_only.slice(3,29))-MathMEAN(WASP_only.slice(31,59)));
    var FLUOR = ArrayNth( WASP_traces, 4, 3 ); // sub trace with WASP but NO ECS pulse (I, not A)
    output.FLUOR=FLUOR;
    Fluor.push(FLUOR); 
	output.bleed=DIRK_ECS[i].bleed;
	output.wasp_only_traces=wasp_only_traces;
  
  //output.XXXX=TransformTrace("subtract", ECS_WASP, ECS_only);
   
  output.wasp_only_vals=wasp_only_vals;
    
    var ECS_WASP_m_WASP = TransformTrace( "subtract", ECS_WASP, WASP_only); //ECS_wasp_diff, ECS_no_wasp);
    //output.ECS_WASP_m_WASP=ECS_WASP_m_WASP;  // difference between the trace with ECS and WASP and just the WASP 
                                             // should get rid of the WASP component,
                                             // leaving only the ECS with the actinic effect of the WASP pulse
     
    var ECS_WASP_m_ECS_only = TransformTrace( "subtract", ECS_WASP_m_WASP, ECS_only); //ECS_wasp_diff, ECS_no_wasp);
                                            // Differnece between the corrected ECS trace that
                                            // has actinic effect of WASP and the trace with 
                                            // no WASP actinic. This means that
                                            // if the WASP pulse induces an increase
                                            // in ECS (by inducing charge separation)
                                            // the increase in absorbance should decrease
                                            // the ECS_WASP_m_ECS_only signal. 
	//output.ECS_WASP_m_ECS_only=ECS_WASP_m_ECS_only; 
     
  var baseline = MathMEAN(ECS_WASP_m_ECS_only.slice(32,59) );
    
      
  	ECS_WASP_m_ECS_only = TransformTrace( "subtract", ECS_WASP_m_ECS_only, baseline);
    //output["ECS_WASP_m_ECS_only:" + i]=ECS_WASP_m_ECS_only; 
 	ECS_WASP_m_ECS_only[0]=0; 
 	ECS_WASP_m_ECS_only[30]=0;  
  	ECS_WASP_m_ECS_only[60]=0;  
     
  WASP_ECS_Decon.push(ECS_WASP_m_ECS_only);  
  var wasp_ss=MathMEAN(ECS_WASP_m_ECS_only.slice(1,29));
  var wasp_sp=MathMEAN(ECS_WASP_m_ECS_only.slice(31,59)); 
  var we=MathROUND(wasp_sp-wasp_ss,3); 
  wasp_vals.push(MathROUND(we,2)); //    
       
  var b = ECS_only[0]; 
  var ECS_only_m_b=TransformTrace( "subtract", ECS_only, b); 
  ECS_only_traces.push(ECS_only);
  var Fs=MathMEAN(FLUOR.slice(1,29));
  var Fmp=MathMAX(FLUOR.slice(31,59));
  var fi2= (Fmp-Fs)/Fmp;
  Phi2.push(MathROUND(fi2,3)); 
  LEF.push(MathROUND(fi2*PAR[i],2));
  
} 


dirk_time=[];

for (var i=0; i< ESC_dirk_traces[0].length; i++) {
  dirk_time.push(i+1);
}

ECSt=[];
gProton=[];
vProton=[];
for (var i=0; i< ESC_dirk_traces.length; i++) {
    var values=ArrayZip( dirk_time, ESC_dirk_traces[i] );

    // decay_model=MathEXPINVREG(values);
    var dirk_fit=MathEXPINVREG(values); 
        output["a_" + i]=MathROUND(-1000*dirk_fit.asymptote,3);
        output["t_" + i]=MathROUND(dirk_fit.lifetime,1);
        output["r2_" + i]=MathROUND(dirk_fit.rsquared,4);
    //     control_array.push(dirk_fit.lifetime);
	ECSt.push(MathROUND(-1000*dirk_fit.asymptote,3));
	gProtonv=1000/dirk_fit.lifetime;
  gProton.push(gProtonv);
  var vProtonv=-1000*gProtonv*dirk_fit.asymptote; //dirk_fit.asymptote; ///dirk_fit.lifetime;
  	vProton.push(vProtonv);
    // output.decay=decay_model.t
}
output.ECSt=ECSt;
output.gProton=gProton;
output.vProton=vProton;
output.LEF=LEF;

output.ESC_dirk_traces=ESC_dirk_traces;
output.dirk_linear=dirk_linear;
output.WASP_ECS_Decon=WASP_ECS_Decon; 
output.ECS_only_traces=ECS_only_traces;
output.ECS_w_WASP=ECS_w_WASP;
output.Fluor=Fluor;

//output.wasp=wasp_vals;
//output.wasp_vals=".append([" + wasp_vals.join() + "])";

output.wasp_cor=[];
var Fpmf=[];
for (var i=0; i<wasp_vals.length;i++){
  var wasp_cor_v=wasp_vals[i]-wasp_only_vals[i]; 
  output.wasp_cor.push(MathROUND(wasp_vals[i]-wasp_only_vals[i],2));
  Fpmf.push(MathROUND(0.001*wasp_cor_v*PAR[i],2)); 
}

output.Fpmf=Fpmf;

output.Phi2=Phi2;
//output.zPhi2vals=".append([" + Phi2.join() + "])";

output.wasp_corr=".append([" + output.wasp_cor.join() + "])";

output.zpython="{";
output.zpython += "\"Phi2\":[" + Phi2.join() + "]";
output.zpython += ",\"wasp_vals\":[" + wasp_vals.join() + "]";
output.zpython += ",\"wasp_corr\":[" + output.wasp_cor.join() + "]";
output.zpython += ",\"LEF\":[" + output.LEF.join() + "]";
output.zpython += ",\"Fpmf\":[" + Fpmf.join() + "]";
output.zpython += ",\"vHplus\":[" + output.dirk_linear.join() + "]";
output.zpython += ",\"PAR\":[" + PAR.join() + "]";

output.zpython += "}";

return output;

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  "device_id": "32:11:48:18",
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  "device_firmware": 2.0091,
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Dave in cap img 4615
Created by

David M. Kramer


Protocol connections:
0
Latest Update:
Jan 2019