// Get_by_Conditions.js script by Christophe Leterrier
// Takes a results table (with image name in a column, containing a string for the condition)
// Outputs one of the columns as multiple columns, one by condition
// 15-03-23

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

// Default variables
fixRepN_def = false;
repN_def = 10;
regexC_def = "C\\d";

// Dialog
var od = new OpenDialog("Choose a Results txt file", "");
var inDirectory = od.getDirectory();
var inName = od.getFileName();
var inPath = inDirectory + inName;
IJ.log("\nInput file path:" + inPath);

// Open the file
var inFile = new File(inPath); 
var inString = IJ.openAsString(inPath);

// Get the columns titles
var headerArray = getHeader(inString);
var nameTitle_def = headerArray[3]; 
var resTitle_def = headerArray[13];

// Store the file as an array
var inArray = getArray(inString);

// Options dialog
var gd = new GenericDialog("Get by Conditions: options");
gd.addCheckbox("Fixed number of replicates", fixRepN_def);
gd.addNumericField("    ", repN_def, 0, 2, " replicates");
gd.addChoice("Image Name column", headerArray, nameTitle_def);
gd.addStringField("Condition regex (escaped)", regexC_def);
gd.addChoice("Results column", headerArray, resTitle_def);
gd.showDialog();
var fixRepN = gd.getNextBoolean();
var repN = gd.getNextNumber();
var nameTitle = gd.getNextChoice();
var nameIndex = getIndex(headerArray, nameTitle);
var regexC = gd.getNextString();
var resTitle = gd.getNextChoice();
var resIndex = getIndex(headerArray, resTitle);

if (gd.wasOKed()) {

	IJ.log("Image Name column: " + nameTitle + " (column #" + nameIndex + ")");
	IJ.log("Results column: " + resTitle + " (column #" + resIndex + ")");
	var rgx = new RegExp(regexC);
	
	var nameCol = getCol(inArray, nameIndex);
	var resCol = getCol(inArray, resIndex);

	var rt = new ResultsTable();
	var p = 0;

	for (var i = 0; i < nameCol.length; i++) {	
		var currMatch = nameCol[i].match(rgx)[0];

		if (i > 0) {
			prevMatch = nameCol[i-1].match(rgx)[0];
			if (currMatch != prevMatch) p = 0;
		}
		
		rt.setValue(currMatch, p, resCol[i]);
		p++;	
	
	}

	for (var c = 0; c < rt.getLastColumn() + 1; c++) {
		l = rt.size() - 1;
		while (rt.getValue(c , l) == 0) {
			rt.setValue(c, l, Number.NaN);
			l--;
		}
		
	}
	
	// show the Profiles Table
	rt.showRowNumbers(false);
	outName = inName.replace(".txt", "_" + resTitle + ".txt");
	rt.show(outName);
}



function getHeader(st){
	var rows = st.split("\n");
	var h = rows[0].split("\t");
	return h;
}

function getArray(st) {
	var rows = st.split("\n");
	var nrows = rows.length;
	var cells = rows[1].split("\t");
	var ncols = cells.length;
	var mt = new Array (nrows-1);
	for (var i = 1; i < nrows; i++) {		
		var rowArray = new Array (ncols);
		cells = rows[i].split("\t");
		for (var j = 0; j < ncols; j++) {
			// Other columns are numbers that are parsed
			rowArray[j] = cells[j];
		}
		mt[i-1] = rowArray;
	}
	return mt;
}

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

function getCol(a, j) {
	var nrows = a.length;
	var col = new Array(nrows);
	for (var i = 0; i < nrows; i++) {
		col[i] = a[i][j];	
	}
	return col;
}