// F-TSRotate.js script function by Christophe Leterrier
// Rotate ThunderSTORM txt localization files coordinate of a given angle
// See https://github.com/cleterrier/ChriSTORM/blob/master/Readme.md

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 TSRotate(inPath, outDir, angle, h, v) {


	// separators (csv files)
	inSep = ",";
	sep = ",";
	
	// Center of rotation (in nm, center of the 256x256, 160 nm/pixel field of view)
	Xc = 20480;
	Yc = 20480;

	// Define input and output files, folder etc.
	var inFile = new File(inPath); 
	var inName = inFile.getName();
	var inNameExt = getExt("" + inName);

	var outString = "";
	if (h == true) outString = outString + "H";
	if (v == true) outString = outString + "V";
	
	var outName = inName.replace("TS3D", "rot" + angle + outString + "_TS3D");
	var outName = outName.replace("TS2D", "rot" + angle + outString + "_TS2D");
	var outPath = outDir + outName;
	var outFile = new File(outPath);

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

	if (!outFile.exists()) {
		outFile.createNewFile();
	}

	var br = new BufferedReader(new FileReader(inFile));
	var bw = new BufferedWriter(new FileWriter(outFile));

	IJ.log("  outName: " + outName);
	
	// Write header
	inLine = br.readLine();
	bw.write(inLine);
	bw.newLine();
	
	var m = 0;

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

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

			var X = inCells[1];
			var Y = inCells[2];

			var XYn = rotateXY(X, Y, Xc, Yc, angle);
			var Xn = XYn[0];
			var Yn = XYn[1];
			
			if (h == true) {
				XYn = flipH(Xn, Yn, Yc);
				Xn = XYn[0];
				Yn = XYn[1];
			}
			
			if (v == true) {
				XYn = flipV(Xn, Yn, Xc);
				Xn = XYn[0];
				Yn = XYn[1];
			}			
			
			outLine = inCells[0] + sep + Xn + sep + Yn;
			for (var t= 3; t < inCells.length; t++) {
				outLine = outLine + sep + inCells[t]; 
			}
			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 rotateXY(x, y, xm, ym, a){
	// Convert to radians because that's what JavaScript likes
	a = a * Math.PI / 180, 

    // Subtract midpoints, so that midpoint is translated to origin
    // and add it in the end again
    xr = (x - xm) * Math.cos(a) - (y - ym) * Math.sin(a)   + xm,
    yr = (x - xm) * Math.sin(a) + (y - ym) * Math.cos(a)   + ym;

    return [xr, yr];
}

function flipH(x, y, m) {
	xf = m - (x-m);
	return [xf, y];
}

function flipV(x, y, m) {
	yf = m - (y-m);
	return [x, yf];
}