// Worm Data Processing

// Written by Wilson Adams, Vanderbilt Biophotonics Center, 24 July 2019

stk = getTitle()
makeRectangle(137, 49, 906, 931);

waitForUser('Selefct general field of interest')

roiManager("Add");
run("Enhance Contrast", "saturated=0.35");
run("Duplicate...", "duplicate"); 
crop = getTitle();
//roiManager("Select", 0);
//run("Duplicate...", "duplicate"); roiManager("Show All"); roiManager("Show None");
//run("Crop");
//run("Subtract Background...", "rolling=30 sliding stack");
runMacro("AutomatedFlatfieldCorrection", "blur=35");
ffc_crop = getTitle();
close(crop)
//roiManager("Show All"); roiManager("Show None");
run("Enhance Contrast", "saturated=0.35");

//		time derivative filter
//run("FeatureJ Derivatives", "x-order=0 y-order=0 z-order=1 smoothing=1");
//zdev = getTitle();

//		StDev projection
//run("Z Project...", "projection=[Standard Deviation]");
//zdev_std = getTitle();

// 35px FFC seems to work okay

// Ext.CLIJ_blur3D("4hr_11PM_Food_Stack-3.tif_bkgdSub_bkgdSub", "CLIJ_blur3D_destination_4hr_11PM_Food_Stack-3.tif_bkgdSub_bkgdSub", 2.0, 2.0, 5.0);
// Ext.CLIJ_pull("CLIJ_blur3D_destination_4hr_11PM_Food_Stack-3.tif_bkgdSub_bkgdSub");
run("Blur3D on GPU", "cl_device=[Quadro M2000] source=&ffc_crop sigmax=4 sigmay=4 sigmaz=5");



// 2X iterative FFC
macro "FFC" {
	h = getTitle()
	for (i = 0; i < 2; i++) {
		j = getTitle();
		blur = 35;
		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=&j i2=&avgBkgd operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=1 k2=&mean create");
		rename(j+"_bkgdSub");
		stk_bkgd = getTitle();
		close(avgBkgd);	
	}
	close(h+"_bkgdSub")
}