// ThunderSTORM Transform Locs script by Christophe Leterrier
// Calls F-TransformLocs.js to rotate the localizations in a ThunderSTORM file
// See https://github.com/cleterrier/ChriSTORM/blob/master/Readme.md

importClass(Packages.ij.io.OpenDialog)
importClass(Packages.java.io.File)
importClass(Packages.ij.IJ);
importClass(Packages.ij.gui.GenericDialog);

// Default values
var xTdef = 0; // coordinates translation (in nm) for X
var yTdef = 0; // coordinates translation (in nm) for Y
var zTdef = 0; // coordinates translation (in nm) for Z
var xFdef = 1; // coordinates scaling for X
var yFdef = 1; // coordinates scaling for Y
var zFdef = 1; // coordinates scaling for Z
var xCdef = 20480; // X coordinate (in nm) of rotation center
var yCdef = 20480; // Y coordinate (in nm) of rotation center
var rotAdef = 0; // Rotation angle (in degrees)
var fvdef = false; // flip vertically
var fhdef = false; // flip horizontally
var zUdef = 2; // scaling factor to calculate Z uncertainty from XY uncertainty using Z = zU * xyU

// Where to find the routine JS in the plugins folder
var routineFolder =  "NeuroCyto Lab" + File.separator + "ChriSTORM" + File.separator + "Routines" + File.separator;

// Name of the routine JS that will be called
var routineJS = "F-TransformLocs.js";

// Name of the output folder (added to the name of the input folder)
var addFolder = "transfo";

// Choose file or folder dialog
var od = new OpenDialog("Choose a ThunderSTORM csv file or a folder for batch", "");
var path = od.getPath();
var directory = od.getDirectory();
var name = od.getFileName();
var inFile = new File(path);
var parDir = inFile.getParent() + File.separator; // parent Directory
var isBatch = inFile.isDirectory(); // test if file is directory to decide single file or batch processing

// Log
IJ.log("*** Transform ThunderSTORM csv localizations ***");
IJ.log("Input path:" + path);
IJ.log("Input directory:" + directory);
IJ.log("Input name:" + name);
if (isBatch == 0) IJ.log("Processing a single file, path:" + path);
else IJ.log("Batch processing a folder, path:" + path);

// Options dialog
var gd = new GenericDialog("Process ThunderSTORM csv: options");
gd.addMessage("Coordinates translation");
gd.addNumericField("X translation:", xTdef, 0, 6, "nm (0 for none)");
gd.addNumericField("Y translation:", yTdef, 0, 6, "nm  (0 for none)");
gd.addNumericField("Z translation:", zTdef, 0, 6, "nm (0 for none)");
gd.addMessage("Coordinates scaling\nFor NSTORM scope cylindrical lens correction, X scaling is 1.0369");
gd.addNumericField("X scaling:", xFdef, 4, 6, "X (1 for none)");
gd.addNumericField("Y scaling:", yFdef, 4, 6, "X (1 for none)");
gd.addNumericField("Z scaling:", zFdef, 4, 6, "X (1 for none)");
gd.addMessage("Coordinates rotation\nFor NSTORM scope, center of FoV is (20480 nm,20480 nm)");
gd.addNumericField("Center X:", xCdef, 0, 6, "nm");
gd.addNumericField("Center Y:", yCdef, 0, 6, "nm");
gd.addNumericField("Angle:", rotAdef, 0, 6, "deg (0 for none)");
gd.addCheckbox("Flip horizontally", fhdef);
gd.addCheckbox("Flip vertically", fvdef);
gd.addMessage("Z uncertainty creation (by scaling XY uncertainty)");
gd.addNumericField("Scaling factor:", zUdef, 0, 6, "X (0 for none)");
gd.showDialog();
var xT = gd.getNextNumber();
var yT = gd.getNextNumber();
var zT = gd.getNextNumber();
var xF = gd.getNextNumber();
var yF = gd.getNextNumber();
var zF = gd.getNextNumber();
var xC = gd.getNextNumber();
var yC = gd.getNextNumber();
var rotA = gd.getNextNumber();
var fh = gd.getNextBoolean();
var fv = gd.getNextBoolean();
var zU = gd.getNextNumber();

if (gd.wasOKed()) {

	// Start timer
	var startTime = new Date().getTime();

	// Get routine path and load the routine JS
	var plugDir = IJ.getDirectory("plugins"); 
	plugDir = plugDir + routineFolder;
	var routinePath = plugDir + routineJS;
	IJ.log("Routine path:" + routinePath);
	load(routinePath);

	if (isBatch == 0) {
		// Process the single file
		TransformLocs(path, directory, xT, yT, zT, xF, yF, zF, xC, yC, rotA, fh, fv, zU);
	}
	else {
		// Define input folder, define and create output folder
		// input folder for translation is the output folder from previous step (split)
		var outDir = parDir + name + addFolder + File.separator;
		IJ.log("Transform input folder: " + inDir);
		IJ.log("Transform output folder: " + outDir);
		var outDirFile = new File(outDir);
		if (!outDirFile.exists()) {
				outDirFile.mkdir();// Name of the routine JS that will be called
var routineJS = "F-TransformLocs.js";
			}
	
		// Get the file list from the input folder, batch process them using the translate function
		var fileQueue = getExtFiles(inDir, "csv");
		for (var f = 0; f < fileQueue.length; f++) {
			inPath = fileQueue[f];
			TransformLocs(inpath, directory, xT, yT, zT, xF, yF, zF, xC, yC, rotA, fh, fv, zU);
		}
	}
	
	// Stops timer
	var stopTime = new Date().getTime();
	var Time = stopTime - startTime;

	// Log end
	IJ.log("*** Transform ThunderSTORM csv localizations ended after " + Time / 1000 + " s  ***");
}