// Remove_Overscan_Bias.txt
//
// FVH (2008-12-17)

getDateAndTime(year,month,dow,day,h,m,s,msec);
t = ""+year+"-"+month+"-"+day+"T"+h+":"+m+":"+s;

// IS THERE A STACK/IMAGE READY?

ni = nImages();
if (ni == 0) exit("Please input an image or stack to be processed!");

// ----- START LOGGING

print("\n-------------------- "+t+" --------------------");
print("Remove Overscan Bias :");

ns = nSlices();
title = getTitle();
run("32-bit");
setTool(0);

x1 = -1;
x2 = -1;
y1 = -1;
y2 = -1;

w = getWidth();
h = getHeight();

// ----- GET PREFERENCES

print("     * getting preferences ...");
overcorr = call("ij.Prefs.get","ccd.overcorr","false");
overscan = call("ij.Prefs.get","ccd.overscan","-1,-1,-1,-1");	// Java notation: 0 <= pix < N !!
log(overscan);
i1 = indexOf(overscan,",");
i2 = indexOf(overscan,",",i1+1);
x1 = substring(overscan,0,i1);
x2 = substring(overscan,i1+1,i2);
i1 = i2;
i2 = indexOf(overscan,",",i1+1);
y1 = substring(overscan,i1+1,i2);
y2 = substring(overscan,i2+1);

// DIALOG

print("     * user dialogue ...");
Dialog.create("Remove Overscan Bias");
Dialog.addMessage("Measures and removes overscan bias level in "+title);
Dialog.addNumber("From column",x1);
Dialog.addNumber("to column",x2);
Dialog.addNumber("From row",y1);
Dialog.addNumber("to row",y2);
s1 = 1;
s2 = ns;
if (ns > 1) {
	Dialog.addNumber("From slice",s1);
	Dialog.addNumber("to slice",s2);
}
Dialog.addMessage("Note:");
Dialog.addMessage("     0 (left) <= x < "+w+" (right)");
Dialog.addMessage("     0 (top) <= y < "+h+" (bottom)");
if (ns > 1) Dialog.addMessage("     1 <= slice <= "+ns);
Dialog.show();
x1 = Dialog.getNumber();
x2 = Dialog.getNumber();
y1 = Dialog.getNumber();
y2 = Dialog.getNumber();
if (ns > 1) {
	s1 = Dialog.getNumber();
	s2 = Dialog.getNumber();
}

if (x1 <  0 || x2 < 0 || y1 < 0 || y2 < 0) {
	exit("Pixel range below bounds!");
}
if (x1 >= w || x2 >= w || y1 >= h || y2 >= h) {
	exit("Pixel range above bounds!");
}
if (x1 > x2) {
	x = x1;
	x1 = x2;
	x2 = x;
}
if (y1 > y2) {
	y = y1;
	y1 = y2;
	y2 = y;
}
if (s1 <  1 || s2 < 1 || s1 > ns || s2 > ns) {
	exit("Slice range out of bounds!");
}
if (s1 > s2) {
	s = s1;
	s1 = s2;
	s2 = s;
}

// START LOG

print("     * removing overscan bias from area "+x1+" <= col <= "+x2+", "+y1+" <= row <= "+y2);
if (ns > 1) print("        ..."+s1+" <= slice <= "+s2);

// MEASURE & PROCESS

run("Set Measurements...", "  mean standard modal min bounding median slice display redirect=None decimal=2");
for (i=1; i <= ns; i++) {
	setSlice(i);

	makeRectangle(x1,y1,x2-x1+1,y2-y1+1);
	run("Measure");
	n = nResults();
	median = getResult("Median",n-1);

	makeRectangle(-1,-1,-1,-1);
	print("       "+i+": subtracting "+median);
	run("Subtract...","value="+median);
	makeRectangle(x1,y1,x2-x1+1,y2-y1+1);
}
run("Enhance Contrast", "saturated=0.5");

// SAVE PREFERENCES

print("     * saving preferences ...");
call("ij.Prefs.set","ccd.overcorr",overcorr);
call("ij.Prefs.set","ccd.overscan",""+x1+","+x2+","+y1+","+y2);

print("FINISHED!");