// At the moment the macro does not check if the largest possible circle is used.
// If the ring is not more or less centred a smalller ROI could be measured.

answer = 1;
title = getTitle();
title1 = File.nameWithoutExtension();
run("Duplicate...", " ");
run("Split Channels");
selectWindow(title1+"-1.JPG (blue)");
close();
selectWindow(title1+"-1.JPG (red)");
close();

// Threshold and clean up to find ring
selectWindow(title1+"-1.JPG (green)");
setAutoThreshold("Intermodes dark");
setOption("BlackBackground", false);
run("Convert to Mask");
run("Despeckle");
run("Remove Outliers...", "radius=5 threshold=50 which=Bright");
run("Erode");
run("Dilate");
run("Dilate");
run("Erode");
run("Erode");
run("Despeckle");

// Make circle and find ring edge
a=1080;
b=255;
c=2874;
d=2874;
makeOval(a, b, c, d);
best = 0;
for (i=1; i<25; i++){
	run("Make Band...", "band=25");
	getStatistics(area, mean, min, max, std, histogram);
	if ((max==255)&&(std>100)&&(std > best)){
		i = 25;
		a = a-25;
		c = c+50;
		b = b-25;
		d = d+50;
	}else{
		best = std;
		a = a-25;
		c = c+50;
		b = b-25;
		d = d+50;
		makeOval(a, b, c, d);
	}
}
// Now the ROI should move to check if it should grow further
// Not implemented.

// Move ROI to check for better overlap with threshold ring
while (answer==1){
	makeOval(a, b, c, d);
	roiManager("Add");
	run("Make Band...", "band=25");
	getHistogram(values, counts, 256);
	p0=(counts[255]);

	a = a+25;
	makeOval(a, b, c, d);
	run("Make Band...", "band=25");
	getHistogram(values, counts, 256);
	p1=(counts[255]);
	roiManager("Add");

	a = a-50;
	makeOval(a, b, c, d);
	run("Make Band...", "band=25");
	getHistogram(values, counts, 256);
	p2=(counts[255]);
	roiManager("Add");

	a = a+25;
	b = b+25;
	makeOval(a, b, c, d);
	run("Make Band...", "band=25");
	getHistogram(values, counts, 256);
	p3=(counts[255]);
	roiManager("Add");

	b = b-50;
	makeOval(a, b, c, d);
	run("Make Band...", "band=5");

	getHistogram(values, counts, 256);
	p4 = (counts[255]);
	roiManager("Add");

	b = b+25; // ROI back to middle position

	// check for best circle overlap.  
	if ((p0>p1)&&(p0>p2)&&(p0>p3)&&(p0>p4)) answer = 0;
	if ((p1>p0)&&(p1>p2)&&(p1>p3)&&(p1>p4)) {a = a+25; p0 = p1;}
	if ((p2>p0)&&(p2>p1)&&(p2>p3)&&(p2>p4)) {a = a-25; P0 = p2;}
	if ((p3>p0)&&(p3>p1)&&(p3>p2)&&(p3>p4)) {b = b+25; p0 = p3;}
	if ((p4>p0)&&(p4>p1)&&(p4>p2)&&(p4>p3)) {b = b-25; p0 = p4;}
}
roiManager("select", (roiManager("count")-5));
setBackgroundColor(255, 255, 255);
run("Clear Outside");
setForegroundColor(0, 0, 0);
run("Fill");
run("Analyze Particles...", "size=4-Infinity summarize add");
selectWindow(title);
roiManager("select", (roiManager("count"))-1);
setBackgroundColor(255, 255, 255);
run("Clear Outside");
run("Color Threshold...");

// Color Thresholder 2.0.0-rc-30/1.49t
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
rename("0");
selectWindow("Saturation");
rename("1");
selectWindow("Brightness");
rename("2");
min[0]=46;
max[0]=144;
filter[0]="pass";
min[1]=32;
max[1]=255;
filter[1]="pass";
min[2]=0;
max[2]=255;
filter[2]="pass";
for (i=0;i<3;i++){
  selectWindow(""+i);
  setThreshold(min[i], max[i]);
  run("Convert to Mask");
  if (filter[i]=="stop")  run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (i=0;i<3;i++){
  selectWindow(""+i);
  close();
}
selectWindow("Result of 0");
close();
selectWindow("Result of Result of 0");
rename(a);
// Colour Thresholding-------------

roiManager("Delete");
run("Analyze Particles...", "size=4-Infinity summarize add");

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