importClass(Packages.cz.cuni.lf1.lge.ThunderSTORM.results.IJResultsTable);
importClass(Packages.java.io.File);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.ij.IJ);
importClass(Packages.ij.gui.GenericDialog);
importClass(Packages.ij.measure.ResultsTable);

// Dialog
var dc = new DirectoryChooser("Choose a folder");
var inDirSt = dc.getDirectory() + File.separator;
var inDir = new File(inDirSt);

// Start
var startTime = new Date().getTime();
IJ.log("\n\n*** Batch Localizations Stats started ***");
IJ.log("Input folder: " + inDirSt);

// Get the file list from the input folder, batch process them using the translate function
var fileQueueT = getExtFiles(inDirSt, "csv");
var nFiles = fileQueueT.length;

var ot = new ResultsTable;
var otr = -1;
var headStat = ["min", "max", "mean", "median", "SD"]

for (var f = 0; f < fileQueueT.length; f++) {
	inPath = fileQueueT[f].getPath();
	IJ.log("    Processing file #" + (f + 1) + "/" + (nFiles + 1) + ": " + fileQueueT[f].getName());

	
//	IJ.run("Import results", "filepath=[" + inPath + "] fileformat=[CSV (comma separated)] append=false startingframe=1 rawimagestack= livepreview=false");
//	var rt = IJResultsTable.getResultsTable();
//	var nRows = rt.getRowCount();
//	var Col = arrayJS(rt.getColumnAsDoubles("uncertainty"));

	rt = ResultsTable.open(fileQueueT[f].getPath());
	head = rt.getHeadings();

	if (rt.getColumnIndex("z [nm]") > 0) is3D = true;
	else is3D = false;

	if (is3D == true) {
		var indArray = [0, 4, 5, 6, 9, 10];
	}
	else {
		var indArray = [0, 3, 4, 7];
	}

	ot.incrementCounter();
	otr++;
	
	for (c = 0 ; c < indArray.length; c++) {

		var Col = arrayJS(rt.getColumn(indArray[c]));
		
		var Stats = getStats(Col);
		var SD = getSD(Col, Stats[2]);
		var Median = getMedian(Col);
		var aStat = [Stats[0], Stats[1], Stats[2], Median, SD];
	
		ot.setValue("Name", otr, fileQueueT[f].getName());
		ot.setValue("Number", otr, rt.size());	
		
		if (c == 0) {
			ot.setValue(head[indArray[c]] + " " + headStat[1], otr, aStat[1]);
		}
		else {
			for (t = 0; t < aStat.length; t++) {
				ot.setValue(head[indArray[c]] + " " + headStat[t], otr, aStat[t]);
			}
		}
	}
}

// End

ot.show(inDir.getName() + "_Results");
var stopTime = new Date().getTime();
var Time = stopTime - startTime;
IJ.log("\n*** Batch Localizations Stats ended after " + Time / 1000 + " s ***");





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 arrayJS(arr) {
		var arrJS = new Array(arr.length);
		for (var r = 0 ; r < arr.length; r++) {
			arrJS[r] = parseFloat(arr[r]);
		}
		return arrJS;
}

function getStats(arr){
	var min = arr[0];
	var max = arr[0];
	var sum = 0;
	for( var i = 0; i < arr.length; i++ ){
    	if (arr[i] < min) min = arr[i];
		if (arr[i] > max) max = arr[i];
    	sum += arr[i];
	}
	var avg = sum / arr.length;
	return [min, max, avg];
}

function getSD(val, meanval){;
	var sumdiff = 0;
	for( var j = 0; j < val.length; j++ ){
		var diff = val[j] - meanval;
		var sqdiff = diff * diff;
		sumdiff += sqdiff;
	}
	var avsqdiff = sumdiff / val.length;
	var stddev = Math.sqrt(avsqdiff);
	return stddev;
}

function getMedian(val) {
    val.sort( function(a,b) {return a - b;} );
    var half = Math.floor(val.length/2);
    if(val.length % 2)
        return val[half];
    else
        return (val[half-1] + val[half]) / 2.0;
}