// F-TranslateABL_TS.js script function by Christophe Leterrier
// Translate localizations between Abbelight text file and ThunderSTORM csv

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: size of pixel on raw image sequence (for coordinates)
// ppc: photons per count to translate camera ADU to photons (for intensity)


function TranslateABLTS(inPath, outDir, pxSize, ppc){

	// Separators
	var inSep = " "; // input separator
	var sep = ","; // output separator

	// Fields of the input header
	var inHeaderList = ["x_EPI (subpix)","y_EPI (subpix)","Wx_EPI","Wy_EPI","Intensity_EPI","Background_EPI"];
//	var outHeader2DList = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"sigma [nm]\"","\"intensity [photon]\"","\"offset [photon]\"","\"bkgstd [photon]\"","\"uncertainty_xy [nm]\"", "\"chi2\"", "\"detections\""];
	var outHeader2DList = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"sigma [nm]\"","\"intensity [photon]\"","\"bkgstd [photon]\""];

	// Correspondance
	/*
	2D case:
	x [nm] = x_EPI (subpix) [0] * pxSize
	y [nm] = y_EPI (subpix) [1] * pxSize
	sigma [nm] =  average(Wx_EPI, Wy_EPI) in nm = sqrt([2]^2 +[3]^2) * pxSize , if Wx are SD - if FWHM need to divide by Wx and Wy by 2.35
	uncertainty_xy [nm] should be calculated from Intensity_EPI [4] but how?
	bkgstd [photon] can be obtained form Background_EPI [5]? but now it's constant at 1.
	*/

	// 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);

	// Pass the header lines (####)
	for (var i = 0; i < 11; i++) {
		br.readLine();
	}
	// Columns header (right now labels are separated by coma+space ", " with "# " at the beginning 0_0)
	var inHeader = br.readLine();
	//IJ.log("inHeader: " + inHeader);

	// hard coding the column numbers for used variables
	var xIndex = 0;
	var yIndex = 1;
	var sdxIndex = 2;
	var sdyIndex = 3;
	var intIndex = 4;
	var bgIndex = 5;

	// Define output extension and header for 2D
	var outSuffix = "_TS2D";
	var outHeaderList = outHeader2DList;

	// 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 = 1; // no frame info in file
		var xOut = (parseFloat(inCells[xIndex]) * pxSize).toFixed(1);
		var yOut = (parseFloat(inCells[yIndex]) * pxSize).toFixed(1);
		var sigma1Out = parseFloat(inCells[sdxIndex] * pxSize);
		var sigma2Out = parseFloat(inCells[sdyIndex] * pxSize);
		var sigmaOut = (Math.sqrt((sigma1Out * sigma1Out)  + (sigma2Out * sigma2Out))).toFixed(1);
		var intOut = (parseFloat(inCells[intIndex]) * ppc).toFixed(0);
		var bgstdOut = (parseFloat(inCells[bgIndex]) * ppc).toFixed(1);

		// Assemble output line
		var outLineArray = [fOut, xOut, yOut, sigmaOut, intOut, bgstdOut];
		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;
}