// Batch_Warp_Channels.js script by Christophe Leterrier
// Use warping function in N-STORM.ini to apply warping correction
// 15-07-16

importClass(Packages.java.io.File);
importClass(Packages.java.nio.file.Files);
importClass(Packages.java.nio.file.Paths);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.ij.IJ);
importClass(Packages.ij.gui.GenericDialog);

// extension for input files
extFormat = "csv";
colZ = 3;
pxSizeDef = 160; // cam image pixel size in nm
ZCompDef = 1;
manShiftDef = false;
manZShiftDef = 25;


// Dialog 1: choose source directory
var dc = new DirectoryChooser("Choose a folder");
var inDir = dc.getDirectory() + File.separator;
var inDirFile = new File(inDir);
var parDir = inDirFile.getParent() + File.separator;

// Localize the SR folder to get the path to functions and ini File
var routineFolder =  "NeuroCyto" + File.separator + "added macros" + File.separator + "ChriSTORM extras" + File.separator;
var plugDir = IJ.getDirectory("imagej");
plugDir = plugDir + "scripts" + File.separator + routineFolder;

// ini File should be placed in the chriSTORM scripts folder
var iniName = "N-STORM.ini";
var iniPath = plugDir + iniName;

IJ.log("\n\n*** Batch Warp Channels started ***");
IJ.log("");
IJ.log("N-STORM.ini file path: " + iniPath);

// get the ini reader function and the warp transformation function function path and load
var Func1JS = "F-IniReadWarp.js";
var Func1Path = plugDir + Func1JS;
IJ.log("Function path:" + plugDir + Func1JS);
load(Func1Path);

var Func2JS = "F-TSWarp.js";
var Func2Path = plugDir + Func2JS;
IJ.log("Function path:" + plugDir + Func2JS);
load(Func2Path);

var iniArray = readIniWarp(iniPath);
var objArray = iniArray[0];
var repArray = iniArray[1];
var warpArray = iniArray[2];
var zShiftArray = iniArray[3];

// Dialog 2: choose objective, source string, source and destination WL
var gd = new GenericDialog("Batch warp channels: options");
gd.addNumericField("Camera pixel size", pxSizeDef, 1, 6, "nm");
gd.addChoice("Objective", objArray, objArray[0]);
gd.addStringField("String for source wavelength", "_647_");
gd.addChoice("Source wavelength (longer)", repArray, repArray[0]);
gd.addChoice("Destination wavelength (shorter)", repArray, repArray[1]);
gd.addCheckbox("3D files", true);
gd.addNumericField("Z compression (1 for none)", ZCompDef, 3, 6, "X");
gd.addCheckbox("Manual Z shift", manShiftDef);
gd.addNumericField("Z shift value", manZShiftDef, 0, 6, "nm");

gd.showDialog();

var pxSize = gd.getNextNumber();
var objName = gd.getNextChoice();
var swlString = gd.getNextString();
var objIndex = getIndex(objArray, objName);
var swlName = gd.getNextChoice();
var swlIndex = getIndex(repArray, swlName);
var dwlName = gd.getNextChoice();
var dwlIndex = getIndex(repArray, dwlName);
var is3D = gd.getNextBoolean();
var ZComp = gd.getNextNumber();
var manShift = gd.getNextBoolean();
var manZShift = gd.getNextNumber();


if (gd.wasOKed()) {
	
	// start
	var startTime = new Date().getTime();
	IJ.log("Input folder: " + inDir);
	
	// define input folder, define and create output folder
	var inDirFunc = inDir;
	var outDirFunc = parDir + "Locs TS warp" + File.separator;
	IJ.log("Function input folder: " + inDirFunc);
	IJ.log("Function output folder: " + outDirFunc);
	var outDirFuncFile = new File(outDirFunc);
	if (!outDirFuncFile.exists()) {
			outDirFuncFile.mkdir();
		}
	
	// get the file list from the input folder, batch process them
	var fileQueueS = getExtFiles(inDirFunc, extFormat);
	for (var f = 0; f < fileQueueS.length; f++) {
		inPath = fileQueueS[f];
		inName = inPath.getName();

		// only process source files defined by source WL string
		if (inName.indexOf(swlString) > 0) {			


			IJ.log("input file: " + inPath.getAbsolutePath());
			// test if 3D or 2D ThunderSTORM file
			if (is3D == true || inName.indexOf("TS3D.csv") > 0) {
				dimIndex = 1;
				IJ.log("3D file");
			}
			else {
				dimIndex = 0;
				IJ.log("2D file");
			}
			
			// build the Warp ID (in binary format, then convert it to 32-bit int)
			var fBin = dimIndex.toString(2) + padBin(dwlIndex.toString(2), 4) + padBin(swlIndex.toString(2), 4) + padBin(objIndex.toString(2), 4); 
			var fIndex = parseInt(fBin, 2);
			IJ.log("Condition index in warpDB: " + fIndex);
			// find what warp (index) corresponds to this Warp ID in the warps array
			var wIndex = getWarpIndex(warpArray, fIndex);
			// find what Z shift (index) corresponds to this Z shift ID in the Z shifts array
			if (dimIndex == 1) var zIndex = getWarpIndex(zShiftArray, fIndex);
			else zIndex = -1;
				
			//  Log the indexes found
//			IJ.log("warp ID (binary): " + fBin);
//			IJ.log("warp ID: " + fIndex);
			IJ.log("XY warp index in warpDB: " + wIndex);			
			if (dimIndex == 1) IJ.log("Z shift index in warpDB: " + zIndex);

			// Process only if Warp has been correctly identified
			if (wIndex > -1) {

				// will send the warp array
				var currWarp = warpArray[wIndex];
				// will send the z shift value or 0 if 2D file
				if (dimIndex == 1) var currZShift = zShiftArray[zIndex][1];
				else var currZShift = 0;
				
				// Log Warp ID and coeffients to check if everything was found
				IJ.log("XY warp ID: " + currWarp[0]);
				xCoefs = "X coefficients: " + currWarp[1][0];
				yCoefs = "Y coefficients: " + currWarp[2][0];
				for (w = 1; w < currWarp[1].length; w++) {
					xCoefs += ", " + currWarp[1][w];
					yCoefs += ", " + currWarp[2][w];
				}
				IJ.log(xCoefs);
				IJ.log(yCoefs);
				
				if (dimIndex == 1) {	
					currZFactor = ZComp;
					if (manShift == true) {
						currZShift = manZShift;
						IJ.log("Using Z correction: " + currZFactor + "* Z + " + currZShift + " (manual)");
					}
					else {
						IJ.log("Using Z correction: " + currZFactor + "* Z + " + currZShift + " (from ini file)");
					}			
				}
				
				// call to the transformation function
				TSWarp(inPath, outDirFunc, currWarp, dimIndex, currZFactor, currZShift, pxSize);
				IJ.log("       warped file created\n");			
			}

		}

		else {
			var inPathP = Paths.get(inPath);
			var outPathP = Paths.get(outDirFunc + inName);
			Files.copy(inPathP, outPathP);		
		}
		
	}
	
	// end
	var stopTime = new Date().getTime();
	var Time = stopTime - startTime;
	IJ.log("\n*** Batch Warp Channels end after " + Time / 1000 + " s ***");
}



// Utility functions

function getIndex(arr, str) {
	for (var f = 0; f < arr.length; f++) {
		if (arr[f] == str) return f;
	}
	return -1;
}

function getExtFiles(dirst, inext) {
        var dir = new File(dirst); 
        var allfiles = dir.listFiles(); 
        var extFiles = new Array(); 
        for (var i = 0 ; i < allfiles.length; i++) { 
                var name = allfiles[i].getName(); 
                var ext = name.substring(name.lastIndexOf(".")+1);
                if (ext == inext) { 
                        extFiles.push(allfiles[i]); 
                } 
        } 
        return extFiles; 
} 

function padBin(s, l) {
	var out = s;
	for (var i = s.length; i < l; i++) {
		out = "0" + out;
	}
	return out;
}

function getWarpIndex(ca, fi) {
	for (var i = 0; i < ca.length; i++) {
		if (ca[i][0] == fi) return i;
	}
	return -1;

}