float[] tempx,tempdata,weights,errs;

double[][] constraints;

String function,exdef,weightfunction;

boolean checkc2,redirect;

int iterations,series;

int hitcounter;

float c2;

//ScriptEngineManager manager;

ScriptEngine engine;

Compilable ce;

CompiledScript cs;

PlotWindow4 pw;

TextWindow tw;

public void run(String arg) {

ImageWindow iw=WindowManager.getCurrentWindow();

pw=jutils.getPW4SelCopy(iw);

String title=pw.getTitle();

float[][] yvals=pw.getYValues();

float[][] xvals=pw.getXValues();

int length=yvals[0].length;

if(pw.getShowErrors()) errs=pw.getErrors(0,false);

int[] colors=pw.getColors();

colors[0]=0;

ScriptEngineManager manager=new ScriptEngineManager();

engine=manager.getEngineByName("js");

ce=(Compilable)engine;

//hitcounter=0;

c2=0.0f;

iterations=0;

checkc2=false;

double[] stats=new double[3];

tempx=new float[length]; tempdata=new float[length];

System.arraycopy(xvals[0],0,tempx,0,length);

System.arraycopy(yvals[0],0,tempdata,0,length);

pw.addPoints(tempx,new float[tempx.length],false);

series=pw.getNpts().length-1;

double[] params=new double[10];

int[] fixes={0,0,0,1,1,1,1,1,1,1};

init_options(params,fixes);

if(!init_functions()){return;}

while(showoptions(params,fixes)){

NLLSfit_v2 fitclass;

if(checkc2){

fitclass=new NLLSfit_v2(this,0);

} else {

fitclass=new NLLSfit_v2(this,0.0001,50,0.1);

}

float[] fit=fitclass.fitdata(params,fixes,constraints,yvals[0],weights,stats,true);

pw.updateSeries(fit,series,false);

c2=(float)stats[1];

iterations=(int)stats[0];

}

IJ.log("Chi Squared = "+(float)stats[1]);

IJ.log("Iterations = "+(int)stats[0]);

for(int i=0;i<10;i++){

IJ.log("P"+(i+1)+" = "+(float)params[i]+" fixed = "+fixes[i]);

}

IJ.log("AIC = "+(float)stats[2]);

//IJ.log("hits = "+hitcounter);

set_options(params,fixes);

}

boolean init_functions(){

GenericDialog gd=new GenericDialog("Fitting Options");

gd.addStringField("Extra Definitions",exdef,50);

gd.addCheckbox("Weight Using Plot Errors",false);

gd.addStringField("Weighting Equation (y is for data)",weightfunction,50);

gd.addStringField("Fit_Equation",function,50);

gd.showDialog(); if(gd.wasCanceled()){return false;}

exdef=gd.getNextString();

boolean errweights=gd.getNextBoolean();

weightfunction=gd.getNextString();

function=gd.getNextString();

//first initialize the weights

weights=new float[tempdata.length];

if(errweights || weightfunction.equals("") || weightfunction==null || weightfunction=="1.0"){

if(errweights){

for(int i=0;i<tempdata.length;i++) weights[i]=1.0f/(errs[i]*errs[i]);

} else {

for(int i=0;i<tempdata.length;i++) weights[i]=1.0f;

}

} else {

for(int i=0;i<tempdata.length;i++){

String script="y ="+tempdata[i]+"; "+

"x ="+tempx[i]+"; "+

"retval="+weightfunction+";";

Double temp=new Double(0.0);

try{

temp=(Double)engine.eval(script);

}catch(Exception e){

IJ.log(e.getMessage());

}

if(!(temp.isInfinite() || temp.isNaN())){

weights[i]=temp.floatValue();

}

}

}

//now compile the function script

try{

String script1=exdef+"; retval="+function+";";

cs=ce.compile(script1);

}catch(Exception e){

IJ.log(e.toString());

return false;

}

return true;

}

boolean showoptions(double[] params,int[] fixes){

//GenericDialog gd=new NonBlockingGenericDialog("Options");

GenericDialog gd=new GenericDialog("Options");

gd.addCheckbox("Check Chi Squared",checkc2);

for(int i=0;i<10;i++){

gd.addNumericField("P"+(i+1),params[i],5,10,null);

gd.addCheckbox("Fix?",(fixes[i]==1));

}

gd.addCheckbox("Get_Errors",false);

gd.addCheckbox("Set_Constraints",false);

gd.addNumericField("Iterations",iterations,0,10,null);

gd.addNumericField("chi squared",c2,5,10,null);

gd.addDialogListener(this);

gd.showDialog(); if(gd.wasCanceled()){return false;}

checkc2=gd.getNextBoolean();

for(int i=0;i<10;i++){

params[i]=gd.getNextNumber();

if(gd.getNextBoolean()){fixes[i]=1;}

else{fixes[i]=0;}

}

boolean geterrors=gd.getNextBoolean();

boolean setconstraints=gd.getNextBoolean();

for(int i=0;i<10;i++){

if(function.indexOf("P"+(i+1))<0){fixes[i]=1;}

}

if(geterrors){

if(!get_errors(params,fixes)){return false;}

}

if(setconstraints) constraints=get_constraints(params);

return true;

}

public boolean dialogItemChanged(GenericDialog gd, AWTEvent e){

checkc2=gd.getNextBoolean();

double[] params=new double[10];

int[] fixes=new int[10];

for(int i=0;i<params.length;i++){

params[i]=gd.getNextNumber();

if(gd.getNextBoolean()){fixes[i]=1;}

else{fixes[i]=0;}

}

gd.getNextBoolean();

gd.getNextNumber();

gd.getNextNumber();

NLLSfit_v2 fitclass=new NLLSfit_v2(this,0);

double[] stats=new double[2];

float[] fit=fitclass.fitdata(params,fixes,null,tempdata,null,stats,true);

pw.updateSeries(fit,series,false);

c2=(float)stats[1];

return true;

}

public boolean get_errors(double[] params,int[] fixes){

GenericDialog gd=new GenericDialog("Error Options");

String[] methods={"Support Plane","Monte Carlo"};

gd.addChoice("Method",methods,methods[0]);

float conf=0.67f;

gd.addNumericField("SP_Confidence Limit (%)",(int)(conf*100.0f),5,10,null);

String[] labels={"P1","P2","P3","P4","P5","P6","P7","P8","P9","P10"};

gd.addChoice("SP_Parameter",labels,labels[0]);

double spacing=0.01;

gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?",spacing*100.0,2,10,null);

int ntrials=100;

gd.addNumericField("MC_#_Trials",ntrials,0);

gd.showDialog(); if(gd.wasCanceled()){return false;}

int methodindex=gd.getNextChoiceIndex();

conf=0.01f*(float)gd.getNextNumber();

int paramindex=gd.getNextChoiceIndex();

spacing=0.01*gd.getNextNumber();

ntrials=(int)gd.getNextNumber();

if(methodindex==0){

support_plane_errors_v2 erclass=new support_plane_errors_v2(this,0.0001,50,false,0.1);

int errindex=paramindex;

int nfit=0;

for(int i=0;i<labels.length;i++){

if(fixes[i]==0){

nfit++;

}

}

int npts=tempdata.length;

int dofnum=npts-(nfit-1)-1;

int dofden=npts-nfit-1;

double flim=(new jdist()).FLimit(dofnum,dofden,(double)conf);

IJ.log("FLimit = "+(float)flim);

if(flim==Double.NaN && flim < 1.0){IJ.showMessage("Invalid Limiting F Value"); return false;}

double truespacing=Math.abs(params[errindex]*spacing);

double[][] c2plot=erclass.geterrors(params,fixes,constraints,tempdata,weights,flim,truespacing,errindex);

IJ.log("upper limit = "+c2plot[1][0]+" lower limit = "+c2plot[0][0]);

IJ.log("upper error = "+(c2plot[1][0]-params[errindex])+" lower error = "+(params[errindex]-c2plot[0][0]));

int templength=c2plot[0].length;

float[][] c2plotf=new float[2][templength-1];

for(int i=0;i<(templength-1);i++){

c2plotf[0][i]=(float)c2plot[0][i+1];

c2plotf[1][i]=(float)c2plot[1][i+1];

}

new PlotWindow4("c2 plot",labels[errindex],"Chi^2",c2plotf[0],c2plotf[1]).draw();

} else {

StringBuffer sb=new StringBuffer();

sb.append("Trial\t");

for(int i=0;i<labels.length;i++){

if(fixes[i]==0) sb.append(labels[i]+"\t");

}

sb.append("chi^2");

tw=new TextWindow("Monte Carlo Results",sb.toString(),"",400,400);

redirect=true;

monte_carlo_errors_v2 erclass=new monte_carlo_errors_v2(this,0.0001,50,false,0.1);

double[][] errors=erclass.geterrors(params,fixes,constraints,tempdata,weights,ntrials);

sb=new StringBuffer();

sb.append("StDev\t");

for(int i=0;i<errors.length;i++){

float[] ferr=new float[errors[0].length];

for(int j=0;j<ferr.length;j++) ferr[j]=(float)errors[i][j];

float stdev=jstatistics.getstatistic("StDev",ferr,null);

sb.append(""+stdev);

if(i<(errors.length-1)) sb.append("\t");

}

tw.append(sb.toString());

redirect=false;

}

return true;

}

public double[][] get_constraints(double[] params){

//here we populate the constraints

GenericDialog gd=new GenericDialog("Constraints");

for(int i=0;i<10;i++){

if(constraints==null){

gd.addNumericField("P"+(i+1)+"_upper",params[i],5,10,null);

gd.addNumericField("P"+(i+1)+"_lower",params[i],5,10,null);

} else {

gd.addNumericField("P"+(i+1)+"_upper",constraints[1][i],5,10,null);

gd.addNumericField("P"+(i+1)+"_lower",constraints[0][i],5,10,null);

}

}

gd.showDialog(); if(gd.wasCanceled()){return null;}

double[][] constraints=new double[2][10];

for(int i=0;i<10;i++){

constraints[1][i]=gd.getNextNumber();

constraints[0][i]=gd.getNextNumber();

}

return constraints;

}

public double[] fitfunc(double[] fitparams){

Bindings b=engine.createBindings();

for(int i=0;i<10;i++) b.put("P"+(i+1),fitparams[i]);

/*String script1="P1="+fitparams[0]+"; "+

"P2="+fitparams[1]+"; "+

"P3="+fitparams[2]+"; "+

"P4="+fitparams[3]+"; "+

"P5="+fitparams[4]+"; "+

"P6="+fitparams[5]+"; "+

"P7="+fitparams[6]+"; "+

"P8="+fitparams[7]+"; "+

"P9="+fitparams[8]+"; "+

"P10="+fitparams[9]+"; "+

exdef+"; x=";

String script2="; retval="+function+";";*/

try{

double[] temp=new double[tempx.length];

for(int i=0;i<tempx.length;i++){

//temp[i]=((Double)engine.eval(script1+(double)tempx[i]+script2)).doubleValue();

b.put("x",tempx[i]);

b.put("y",tempdata[i]);

temp[i]=(Double)cs.eval(b);

}

return temp;

}catch(Exception e){

IJ.log(e.getMessage());

return null;

}

}

public void showresults(String results){

if(redirect) tw.append(results);

else IJ.log(results);

}

public void init_options(double[] params,int[] fixes){

String[] initvals=jutils.get_plugin_options("fit_custom_function_jru_v1",23+21);

if(initvals==null){

function="P1*Math.exp(-x/P2)+P3";

for(int i=0;i<10;i++) params[i]=0.0;

for(int i=0;i<10;i++) fixes[i]=1;

fixes[0]=0; fixes[1]=0; fixes[2]=0;

weightfunction="1.0/y";

exdef="";

constraints=null;

} else {

function=initvals[0];

int counter=1;

for(int i=0;i<10;i++){

params[i]=Double.parseDouble(initvals[counter]);

counter++;

fixes[i]=Integer.parseInt(initvals[counter]);

counter++;

}

weightfunction=initvals[counter]; counter++;

exdef=initvals[counter]; counter++;

int hasconstraints=Integer.parseInt(initvals[counter]); counter++;

if(hasconstraints==1){

constraints=new double[2][10];

for(int i=0;i<10;i++){

constraints[0][i]=Double.parseDouble(initvals[counter]); counter++;

constraints[1][i]=Double.parseDouble(initvals[counter]); counter++;

}

} else {

constraints=null;

}

}

}

public void set_options(double[] params,int[] fixes){

String[] initvals=new String[23+21];

initvals[0]=function;

int counter=1;

for(int i=0;i<10;i++){

initvals[counter]=""+params[i];

counter++;

initvals[counter]=""+fixes[i];

counter++;

}

initvals[counter]=weightfunction; counter++;

initvals[counter]=exdef; counter++;

if(constraints!=null){

initvals[counter]="1"; counter++;

for(int i=0;i<10;i++){

initvals[counter]=""+constraints[0][i]; counter++;

initvals[counter]=""+constraints[1][i]; counter++;

}

} else {

initvals[counter]="0"; counter++;

for(int i=0;i<10;i++){

initvals[counter]="0"; counter++;

initvals[counter]="0"; counter++;

}

}

jutils.set_plugin_options("fit_custom_function_jru_v1",initvals);

}