// F-SMAPTranslate.js script function by Christophe Leterrier
// Translate single-channel txt localization files from .csv SMAP to .csv 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 SMAPTranslate(inPath, outDir) {

	var inSep = ","; // separator for the input file
	var sep = ","; // separator for the output file
	var sigpara = 0.4; // factor for uncertainty
	var bgdefault = 25 // background standard deviation in photons (fixed because not in Ries csv file)

	// Fields of the input header
	var inHeaderList = ["xnm","ynm","znm","layer","PSFxnm","PSFypix","bg","frame","locprecnm","locprecznm","logLikelihood","numberInGroup","phot","LLrel","PSFxpix","PSFynm","channel","colorfield","filenumber","groupindex","iterations","photerr","xnmerr","xpix","xpixerr","ynmerr","ypix","ypixerr"];
	var outHeader2DList = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"sigma [nm]\"","\"intensity [photon]\"","\"offset [photon]\"","\"bkgstd [photon]\"","\"uncertainty_xy [nm]\"", "\"chi2\"", "\"detections\""];
	var outHeader3DList = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"z [nm]\"","\"sigma1 [nm]\"","\"sigma2 [nm]\"","\"intensity [photon]\"","\"offset [photon]\"","\"bkgstd [photon]\"","\"uncertainty_xy [nm]\"","\"uncertainty_z [nm]\"", "\"chi2\"", "\"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 inHeader = br.readLine();
	//IJ.log("inHeader: " + inHeader);
	var inHeaderArray = inHeader.split(inSep);

	// get the indexes of the columns needed in input file from its header
	var fIndex = arrayFind(inHeaderArray, inHeaderList[7]);
	var xIndex = arrayFind(inHeaderArray, inHeaderList[0]);
	var yIndex = arrayFind(inHeaderArray, inHeaderList[1]);
	var sdxIndex = arrayFind(inHeaderArray, inHeaderList[4]);
	var sdyIndex = arrayFind(inHeaderArray, inHeaderList[15]);
	var unxIndex = arrayFind(inHeaderArray, inHeaderList[22]);
	var unyIndex = arrayFind(inHeaderArray, inHeaderList[25]);
	var unxyIndex = arrayFind(inHeaderArray, inHeaderList[8]);
	var intIndex = arrayFind(inHeaderArray, inHeaderList[12]);
	var bgIndex = arrayFind(inHeaderArray, inHeaderList[6]);
	var chi2Index = arrayFind(inHeaderArray, inHeaderList[10]);
	var detecIndex = arrayFind(inHeaderArray, inHeaderList[11]);

	var zIndex = arrayFind(inHeaderArray, inHeaderList[2]);
	var unzIndex = arrayFind(inHeaderArray, inHeaderList[9]);

	// Define output extension and header depending on 2D or 3D
	if (zIndex == -1) {
		var is3D = false;
		var outSuffix = "_TS2D";
		var outHeaderList = outHeader2DList;
	}
	else {
		var is3D = true;
		var outSuffix = "_TS3D";
		var outHeaderList = outHeader3DList;
	}

	// Generate output name and path, open file writer

	var outName = inName.replace("." + inNameExt[1], outSuffix + ".csv");
	if (outName == inName) outName = inNameExt[0] + outSuffix + "." + inNameExt[1]; // in the case we are processing CSV files
	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);

	// Write the header
	var outHeader = makeLineFromArray(outHeaderList, sep);
	bw.write(outHeader);
	bw.newLine();

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

		// Processing of individual values from input file lines, split by inSep
		var inCells = inLine.split(inSep);

		var fOut = inCells[fIndex];
		var xOut = parseFloat(inCells[xIndex]).toFixed(1);
		var yOut = parseFloat(inCells[yIndex]).toFixed(1);
		var sigma1Out = parseFloat(inCells[sdxIndex]);
		var sigma2Out = parseFloat(inCells[sdyIndex]);
		if (is3D == false) var sigmaOut = (Math.sqrt((sigma1Out * sigma1Out)  + (sigma2Out * sigma2Out))).toFixed(1);
//		var unxOut = parseFloat(inCells[unxIndex]);
//		var unyOut = parseFloat(inCells[unyIndex]);
		var unxyOut = (parseFloat(inCells[unxyIndex]) * sigpara).toFixed(1);

		var intOut = parseFloat(inCells[intIndex]).toFixed(0);
		var offOut = parseFloat(inCells[bgIndex]).toFixed(0);
		var bgstdOut = bgdefault;
		var chi2Out = parseFloat(inCells[chi2Index]).toFixed(2);
		var detecOut = inCells[detecIndex];

		if (is3D == true) {
			var zOut = parseFloat(inCells[zIndex]).toFixed(1);
			var unzOut = (parseFloat(inCells[unzIndex]) * sigpara).toFixed(1);
		}

		// Assemble output line
		// 1 at the end is for the detection number (linked localization accross several frames) that are not reported by DOM
		if (is3D == false) var outLineArray = [fOut, xOut, yOut, sigmaOut, intOut, offOut, bgstdOut, unxyOut, chi2Out, detecOut];
		else var outLineArray = [fOut, xOut, yOut, zOut, sigma1Out, sigma2Out, intOut, offOut, bgstdOut, unxyOut, unzOut, chi2Out, detecOut];
		var outLine = makeLineFromArray(outLineArray, 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){
	for (var i = 0; i < a.length; i++) {
		testS = a[i];
		if (testS.indexOf(s)>-1 && testS.indexOf(s)<3) return i;
	}
	return -1;
	}

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