// F-ZOLA_TS.js script function by Christophe Leterrier
// ZOLA localization file to proper ThunderSTORM file
// 06/01/2018

importClass(Packages.java.io.File);
importClass(Packages.java.io.FileReader);
importClass(Packages.java.io.FileWriter);
importClass(Packages.java.io.BufferedReader);
importClass(Packages.java.io.BufferedWriter);
importClass(Packages.ij.IJ);
importClass(Packages.java.lang.Double);

// Parameters
// inPath input file path
// outDir output directory path
// pxSize acquired sequence pixel size in nm
// sigma PSF SD in nm
// xFactor dilatation in X to compensate cylindrical lens (measured on microscope)
// zFactor factor for uncertainty in Z from uncertainty in XY

function ZolaTS(inPath, outDir, xFactor) {

	// separators (csv files)
	var inSep = ",";
	var sep = ",";

	var idHeader = "id";
	var fHeader = "frame";
	var xHeader = "x [nm]";
	var yHeader = "y [nm]";
	var zHeader = "z [nm]";
	var iHeader = "intensity";
	var bHeader = "background";
	var cHeader = "chi2";
	var cxHeader = "crlbX";
	var cyHeader = "crlbY";
	var czHeader = "crlbZ";	
//	var dHeader = "detections";

	// Define input files, folder, open it etc.
	var inFile = new File(inPath); 
	var inName = inFile.getName();
	var inNameExt = getExt("" + inName);
	
	var br = new BufferedReader(new FileReader(inFile));

	IJ.log("    inName: " + inName);

	// Get the header line and find index of Z, intensity, background and x coordinate columns
	var inHLine = br.readLine();	
	var inHeader = inHLine.split(inSep);	
	
	var idIndex = arrayFind(inHeader, idHeader);
	var fIndex = arrayFind(inHeader, fHeader);
	var xIndex = arrayFind(inHeader, xHeader);
	var yIndex = arrayFind(inHeader, yHeader);
	var zIndex = arrayFind(inHeader, zHeader);
	var iIndex = arrayFind(inHeader, iHeader);
	var bIndex = arrayFind(inHeader, bHeader);
	var cIndex = arrayFind(inHeader, cHeader);
	var cxIndex = arrayFind(inHeader, cxHeader);
	var cyIndex = arrayFind(inHeader, cyHeader);
	var czIndex = arrayFind(inHeader, czHeader);
	
	// Generate output name and path, open file writer
	var outName = inName.replace("TS3D", "TS_TS3D");
	if (outName == inName) outName = inNameExt[0] + "_TS3D." + inNameExt[1];
	var outPath = outDir + outName;
	var outFile = new File(outPath);

	if (!outFile.exists()) {
		outFile.createNewFile();
	}
	var bw = new BufferedWriter(new FileWriter(outFile));

	IJ.log("      outName: " + outName);

	// New header
	var idHTS = "id";
	var fHTS = "frame";
	var xHTS = "x [nm]";
	var yHTS = "y [nm]";
	var zHTS = "z [nm]";
	var s1HTS = "sigma1 [nm]";
	var s2HTS = "sigma2 [nm]";	
	var iHTS = "intensity [photon]";
	var oHTS = "offset [photons]";
	var bHTS = "bkgstd [photon]";
	var uxyHTS = "uncertainty_xy [nm]";
	var uzHTS = "uncertainty_z [nm]";
	var dHTS = "detections";
	
	var HTS = "" + idHTS +sep+ fHTS +sep+ xHTS +sep+ yHTS +sep+ zHTS +sep+ iHTS +sep+ bHTS +sep+ uxyHTS +sep+ uzHTS +sep ;
	
	bw.write(HTS);
		bw.newLine();

	// Write the output file line by line
	while ((inLine = br.readLine()) != null) {

		var inCells = inLine.split(inSep);
		
		
//		var idOut = parseInt(inCells[idIndex]);
//		var fOut = parseInt(inCells[fIndex]);
		
		// correct distortion in X coordinate
		var xIn = Double.parseDouble(inCells[xIndex]);
		var xInC= xIn * xFactor;
		var xOut = xInC.toFixed(1);
		
		var yIn = Double.parseDouble(inCells[yIndex]);
		var yOut = yIn.toFixed(1);
		
		var zIn = Double.parseDouble(inCells[zIndex]);
		var zOut = zIn.toFixed(1);
		
		var iIn = Double.parseDouble(inCells[iIndex]);
		var iOut = iIn.toFixed(1);
		
		var bIn = Double.parseDouble(inCells[bIndex]);
		var bOut = bIn.toFixed(1);

		// Calculate uncertainty_xy as the harmonic average of crlbX and crlbY
		var cxIn = Double.parseDouble(inCells[cxIndex]);
		var cyIn = Double.parseDouble(inCells[cyIndex]);
		var uxyIn = Math.sqrt(cxIn * cyIn);
		var uxyOut = uxyIn.toFixed(1);

		var czIn = Double.parseDouble(inCells[czIndex]);
		var uzOut = czIn.toFixed(1);
		 
		// Generate new line
//		outLine = "" + idOut +sep+ fOut +sep+ xOut +sep+ yOut +sep+ zOut +sep+ iOut +sep+ bOut +sep+ uxyOut +sep+ uzOut +sep ; 
		outLine = "" + inCells[idIndex] +sep+ inCells[fIndex] +sep+ xOut +sep+ yOut +sep+ zOut +sep+ iOut +sep+ bOut +sep+ uxyOut +sep+ uzOut +sep ; 
		
		// Write new line
		bw.write(outLine);
		bw.newLine();
	}		 
	br.close();
	bw.close();
}


function getExt(filestring){
	var namearray = filestring.split(".");
	var shortname = "";
	for (var f = 0; f < namearray.length - 1; f++) {
		shortname = shortname + namearray[f];
	}
	return [shortname, namearray[namearray.length - 1]];
}

function arrayFind(a, s){
	index = -1;
	for (var i = 0; i < a.length; i++) {
		if (a[i] == s) index = i;	
	}
	return index;
}