// Just open this in the Macro Editor in FIJI, click on your image, and click 'Run' 
// it should do what you want. Make sure you only do it with a 1D image. 
// it will let you pick a gaussian kernal size. I usually recommend 10-20% of your 
// image width, but definitely play around with it. 

AutoFFC();

function AutoFFC() {
	start = getTitle()
	getDimensions(width, height, channels, slices, frames); //print(height); print(width)
	getVoxelSize(vwidth, vheight, vdepth, vunit)
	blur= floor(width*0.08);
	
	Dialog.create("Set Blur Kernel")
	Dialog.addMessage("Enter Blur Kernel Size")
	Dialog.addNumber("Blur Kernel (px) = ", blur)
	Dialog.show()
	blur = Dialog.getNumber()

	if (frames>1) {		// For time series where the flat field is relatively stable
		run("Z Project...", "stop=5 projection=[Average Intensity]");
		avgBkgd = getTitle();
		run("Gaussian Blur...", "sigma=&blur");
		getStatistics(area, mean, min, max, std, histogram);
		mean = floor(mean);
		run("Calculator Plus","i1=&start i2=&avgBkgd operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=1 k2=&mean create");
		rename(start+"_bkgdSub");
		stk_bkgd = getTitle();
	}
	if (slices>1) {		// for z stacks where each image may have a different Flat field
		run("Duplicate...", "duplicate");
		avgBkgd = getTitle();
		run("Gaussian Blur...", "sigma=&blur stack");
		getStatistics(area, mean, min, max, std, histogram);
		mean = floor(mean);
		run("Calculator Plus","i1=&start i2=&avgBkgd operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=1 k2=&mean create");
		rename(start+"_bkgdSub");
		stk_bkgd = getTitle();
	}
	else {			// Single images
		run("Duplicate...", start+"_bkgdsub");
		avgBkgd = getTitle();
		run("Gaussian Blur...", "sigma=&blur");
		getStatistics(area, mean, min, max, std, histogram);
		mean = floor(mean);
		run("Calculator Plus","i1=&start i2=&avgBkgd operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=1 k2=&mean create");
		rename(start+"_bkgdSub");
		stk_bkgd = getTitle();
	}
	close(avgBkgd);
	selectWindow(stk_bkgd);
	setVoxelSize(vwidth, vheight, vdepth, vunit);
}