print("Morphology Picker v3.2");
print("Kyle Morris, University of Sussex, 2010");
print("--------------------");

	Dialog.create("Calibration, warning: global scales will be first removed");
	Dialog.addChoice("Magnification:", newArray("50,000X", "30,000X", "20,000X", "15,000X", "10,000X", "5,000X", "Manual"));
	Dialog.show();
	run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel global");

	Mag = Dialog.getChoice();
	print(Mag);

	if (Mag=="5,000X") {
		boxwidthpx = 37.5;
		boxlengthpx = 300;
	}
		else
		if (Mag=="10,000X") {
			boxwidthpx = 75;
			boxlengthpx = 600;
		}
			else
			if (Mag=="15,000X") {
				boxwidthpx = 112.5;
				boxlengthpx = 900;
			}
				else
				if (Mag=="20,000X") {
					boxwidthpx = 150;
					boxlengthpx = 1200;
				}
					else
						if (Mag=="30,000X") {
							boxwidthpx = 225;
							boxlengthpx = 1800;
						}
							else
								if (Mag=="50,000X") {
									boxwidthpx = 375;
									boxlengthpx = 3000;
								}

//Main function is embedded in while loop such that after each measurement user is asked if they want to repeat

	repeat = 1;
	do {

//Line parameters are collected
		
		waitForUser("Make a line selection and then click OK:");
	
		getLine(x1, y1, x2, y2, lineWidth);
		if (x1==-1) {
		exit("Can't find a line :*(, please restart macro");
		}
		getPixelSize(unit, pw, ph);
		x1*=pw; y1*=ph; x2*=pw; y2*=ph;
	
//Line parameters, x-y coordinates, length and angle are calculated

		dx = x2-x1; dy = y2-y1;
		length = sqrt(dx*dx+dy*dy);
	
		if (y1==y2) {
			if (x1<x2)
			angle = 0;
			else
			angle = 180;
		}
		else {
		angle = (atan2(y2-y1,x2-x1)*-57.2957795);
		}

		print("Selection parameters:");
		print ("Angle: ", angle, "degrees", "(", angle-90, ")");
		transformangle = (angle-90);
	
//User inputs fibril  in pixels and polygon is drawn at right angle to line
//User may adjust polygon width and length incrementally and when completed select the finalise checkbox to continue
	
		finalise=1;
		do {			
			Dialog.create("");
			Dialog.addMessage("Enter fibril width:");
			Dialog.addNumber("Width/px:", boxwidthpx);
			Dialog.addNumber("Length/px:", boxlengthpx);
			Dialog.addCheckbox("Finalise:", false);
			Dialog.show();
			finalise = Dialog.getCheckbox();
			bwpx = Dialog.getNumber();
			blpx = Dialog.getNumber();;

			if (bwpx!=boxwidthpx||blpx!=boxlengthpx) {
				//print("px change");
				boxlengthpx = blpx;
				boxwidthpx = bwpx;
			}
			else {
				//print("No change");
			}

			IncX = (sin(angle/57.2957795)*boxwidthpx);
		
			if (angle==0) {
				IncY = boxwidthpx;
			}
			else {
				IncY = IncX/(tan(angle/57.2957795));
			}

			a = angle;
			b = 90 - angle;
			width = boxwidthpx/2;
			//print (width);
			length = boxlengthpx/2;
			//print (length);

			IncXnew = IncX/2;
			IncYnew = IncY/2;

			x1new = x1-(cos(b/57.2957795)*width);
			y1new = y1-(sin(b/57.2957795)*width);

			x2new = x1+(cos(angle/57.2957795)*boxlengthpx);
			y2new = y1-(sin(angle/57.2957795)*boxlengthpx);
			x2newer = x2new-(cos(b/57.2957795)*width);
			y2newer = y2new-(sin(b/57.2957795)*width);

			makePolygon(x1new,y1new,x2newer,y2newer,x2new+IncXnew,y2new+IncYnew,x1+IncXnew,y1+IncYnew);			
			getStatistics(area, mean, min, max, std);
			background = mean;
			//print (background);
			
		}  while (finalise==0);
	
		print("Length:", boxlengthpx, "pixels");
		print("Width:", boxwidthpx, "pixels");	

//Stores filename and position of extension for later renaming

name = getTitle();
//print(tmp);
ext = lastIndexOf(name, ".");
//print(ext);

//The following copies the selection made by the user and macro, copies to the internal clipboard and creates a new image with the copy rotated to normal.

run("Copy");
setBackgroundColor(background,0,0);
run("Internal Clipboard");
selectWindow("Clipboard");
run("Rotate... ", "angle=transformangle grid=1 interpolation=Bilinear fill enlarge");

//Updates new image filename with addition of "-CROP", minus extension

cropname = substring(name,0,ext);
cropname = cropname + "-CROP";
//print (cropname);
rename(cropname);

//Gets dimensions of new image

getDimensions(width, height, channels, slices, frames);
//print("x: ", width, "(", width/2, ")");
//print("y: ", height, "(", height/2, ")");

//Based on box selection calculates positions of polygon boudaries for new selection

x1 = width/2-boxwidthpx/2;
y1 = height/2-boxlengthpx/2;

x2 = width/2+boxwidthpx/2;
y2 = height/2-boxlengthpx/2;

x3 = width/2+boxwidthpx/2;
y3 = height/2+boxlengthpx/2;

x4 = width/2-boxwidthpx/2;
y4 = height/2+boxlengthpx/2;

makePolygon(x1, y1, x2, y2, x3, y3, x4, y4);

//Crops selection

run("Crop");

//Copies crop into new image, renames and runs bandpass filter with default settings

run("Copy");
run("Internal Clipboard");
selectWindow("Clipboard");

bpname = cropname + "-BP_FILTERED";
rename(bpname);

run("Bandpass Filter...", "filter_large=40 filter_small=3 suppress=None tolerance=5 autoscale saturate");

//Gives user the option of saving crop and bandpass filtered images to directory of original image
//Various overly complicated if statements figure out if the files are overwrites or not

selectWindow(name);
dir = getDirectory("image");
selectWindow(cropname);
selectWindow(bpname);

store = getBoolean("Do you want to save the cropped images to the parent directory?");

if (store==0) {
	print("--------------------");
	print("Warning: Processed images not saved");
	}
else {
	suffix = 1;
	Dialog.create("");
	Dialog.addNumber("Affix suffix to saved images?", suffix);
	Dialog.show();
	suffix = Dialog.getNumber();
	
	dir1 = dir + cropname + "-" + suffix;
	dir2 = dir + bpname + "-" + suffix;
	dir3 = dir + cropname + "-" + suffix + ".tif";
	dir4 = dir + bpname + "-" + suffix + ".tif";
	//print(dir);
	//print(dir1);
	//print(dir3);
	overwrite = File.exists(dir3);
	//print(overwrite);

	if (overwrite==1) {
		store1 = getBoolean("Suffix name exists. Overwrite?");
		//print("Overwrite=", store1);
		
		if (store1==0) {
			print(store1);
			print("--------------------");
			print("Warning: Processed images not saved");
			}
		else {
			selectWindow(cropname);
			saveAs("tiff", dir1);
		
			selectWindow(bpname);
			saveAs("tiff", dir2);
		
			print("--------------------");
			print("Processed images saved to parent directory:");
			print(dir3);
			print(dir4);
		}
			}
	else {
		selectWindow(cropname);
		saveAs("tiff", dir1);
	
		selectWindow(bpname);
		saveAs("tiff", dir2);
	
		print("--------------------");
		print("Processed images saved to parent directory:");
		print(dir3);
		print(dir4);
	}
}

print("--------------------");
print("END OF MACRO");
print("--------------------");
exit();