//For predoc course 2013
// mail for writer: niwayama@embl.de
// SET channel_num before use
var NUCMEM_channel_num = 1;
var Cdx2_channel_num = 2;
var fonto_no_saizu = 45;
//pre-fixed variables
var celID = 0;
var current_result = 0;
var destdir = "C:\\";
var file_name = "default_name";
var st ="";
var nuc_ave1 =  newArray(100);
var nuc_area1 = newArray(100);
var nuc_tot1 = newArray(100);


var cell_x = newArray(100);
var cell_y = newArray(100);
var cell_z = newArray(100);
var kakuno_ave = newArray(100);
var kakuno_area = newArray(100);
var kakuno_tot = newArray(100);
var pixel_length_x = 0;
var pixel_value_x = 0;
var pixel_length_y = 0;
var pixel_value_y = 0;
var cx;
var cy;

macro "fileIO [1]"{
	destdir = getDirectory("");
	file_name =getInfo("image.filename");
	//f = File.open("C:\\Users\\NIGImaris\\Desktop\\fiji-win64-20110307\\Fiji.app\\test.txt");
	f = File.open(destdir + file_name +"analysis.txt");
	print(f, "CELL_ID" +" \t" + "Cdx2_AREA" + " \t" +
		"Cdx2_AVE" + " \t" + "Cdx2_TOT" + " \t" +
		"Histone_AREA      " + " \t" + "Histonel_AVE" + " \t" +
		"Histone_TOT");
	for(i = 1; i<= celID; i++){
		print(f, i +" \t" + nuc_area1[i] + " \t" +
		nuc_ave1[i] + " \t"  + nuc_tot1[i] + " \t" +
		kakuno_area[i] + " \t" + kakuno_ave[i] + " \t" +
		kakuno_tot[i] );
	}
	File.close(f);
	
}
macro "get_NucleusSignal [7]"{
	celID = celID +1;
	Stack.setChannel(NUCMEM_channel_num);
	run("Measure");
	current_result = nResults-1;
	kakuno_area[celID] = getResult("Area",current_result);
	kakuno_ave[celID] = getResult("Mean",current_result);
	kakuno_tot[celID] = kakuno_area[celID]*kakuno_ave[celID];
	Stack.setChannel(Cdx2_channel_num);
	run("Measure");
	current_result = nResults-1;
	nuc_area1[celID] = getResult("Area",current_result);
	nuc_ave1[celID] = getResult("Mean",current_result);
	nuc_tot1[celID] = nuc_area1[celID]*nuc_ave1[celID];
	print("nucAreaPro1:" + nuc_area1[celID] + "nucAve1:" + nuc_ave1[celID]);
	roiManager("Add");
	Stack.setChannel(NUCMEM_channel_num);
	roiManager("reset");
	setFont("SansSerif", fonto_no_saizu);
 	toUnscaled(cell_x[celID],cell_y[celID]);
	setColor(255,255,255);
	setJustification("center");
	st = toString(celID);
	drawString(st, cell_x[celID], cell_y[celID]);
	Stack.setChannel(NUCMEM_channel_num);		
}