// F-LSFtxtTranslate.js script function by Christophe Leterrier
// Translate single-channel txt localization files from Sandrine to .xls ThunderSTORM localization files

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);

function RiesCSVTranslate(inPath, outDir, outFormat, pxSize) {
	
	// is there a header?
	var inHeader = true;
	var FWHM = 2.355;
	var crlbF = 0.4; // to go from crlb to uncertainty in sigma
	var Bgstd = 25 // background standard deviation in photons (fixed because not in Ries csv file)
	var Sigma = 160 // sigma for x and y psd width (not in Ries csv file)

	
	// Header format (if exists)
    if (inHeader == true) var inHeaderNS = ["frame", "x_pix", "y_pix", "z_nm", "photons", "background", "crlb_x", "crlb_y", "crlb_z", "crlb_photons", "crlb_background", "logLikelyhood"];
	var inSep = ",";
	
	// Assign the indexes for all columns in the input format
	iF = 0;
	iXp = 1; // X coordinate in pixels
	iYp = 2; // Y coodrinate in pixels
	iZ = 3; // z coordinate in nanometrers
	iP = 4; // photon number
	iB = 5; // backgound (in photons) = offset on TS
	iUXp = 6; // crlb X uncertainty in pixels
	iUYp = 7; // crlb Y uncertainty in pixels
	iUZ = 8; // crlb Z uncertainty in nanometers
	 
	// Define input file path
	var inFile = new File(inPath); 
	var inName = inFile.getName();
	var inNameExt = getExt("" + inName);
	IJ.log("    inName: " + inName);

	// Open input File reader
	var br = new BufferedReader(new FileReader(inFile));

	// Pass header line
	if (inHeader == true) inLine = br.readLine();

	// ThunderSTORM 3D format
	if (outFormat == "csv") {
		var sep = ",";	
		var outHeader = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"z [nm]\"","\"sigma1 [nm]\"","\"sigma2 [nm]\"","\"intensity [photon]\"","\"offset [photon]\"","\"bkgstd [photon]\"","\"uncertainty_xy [nm]\"", "\"uncertainty_z [nm]\""];
			var outSuffix = "_TS3D";
		var includeHeader = true;	
		var outExt = ".csv";
	}

	// Prepare output file path
	var outName = inName.substring(0, inName.length()-4) + outSuffix + outExt;
	var outPath = outDir + outName;
	var outFile = new File(outPath);
	if (!outFile.exists()) {
		outFile.createNewFile();
	}
	IJ.log("      outName: " + outName);

	// Open output File writer
	var bw = new BufferedWriter(new FileWriter(outFile));	
	// Write new Header
	if (includeHeader == true) {
		var outLine = makeLineFromArray(outHeader, sep);
		bw.write(outLine);
		bw.newLine();
	}

	// Write the output file line by line
	var m = 0;
	while ((inLine = br.readLine()) != null) {

			m++;
			var inCells = inLine.split(inSep);

			Frame = parseInt(inCells[iF]);
			// convert X and Y coordinates in nanometers
			Xn = parseFloat(inCells[iXp]) * pxSize;
			Yn = parseFloat(inCells[iYp]) * pxSize;
			Zn = parseFloat(inCells[iZ]);
			// convert uncertainites in nanometers, and adjust them with the factor given by Jonas (0.4)
			UXn = parseFloat(inCells[iUXp]) * pxSize * crlbF;
			UYn = parseFloat(inCells[iUYp]) * pxSize * crlbF;
			UXYn = Math.max(UXn, UYn);
			UZn = parseFloat(inCells[iUZ]) * crlbF;

			Iphot = parseFloat(inCells[iP]);
			Offset = parseFloat(inCells[iB]);

			// ThunderSTORM xls format
			if (outFormat == "csv") {
			
					// Build results line
	 				// 3D case
					// peak width: TS has Wx and Wy (astigmatism-deformed PSF), but N-STORM has only one width W and an axial ratio Ax
					// so we calculate Wx and Wy from W and Ax
				
					outLine = "" + Frame + sep + Xn + sep + Yn + sep + Zn + sep + Sigma + sep + Sigma + sep + Iphot + sep + Offset + sep + Bgstd + sep + UXYn + sep + UZn;
					
			}
			if (Xn != "�") {
				bw.write(outLine);
				bw.newLine();
			}
		}	 
	br.close();
	bw.close();
}


function makeLineFromArray(ar, se) {
	ol = "" + ar[0];
	for (t = 1; t < ar.length; t++) {
		ol = ol + se + ar[t];
	}
	return ol;
}


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]];
}