BatchKalmanFilter.txt

// This macro will 


// File handling
// file="/Users/aostrov/Desktop/nm20110921c2_005-005.tif";
// open(file);
// current=getTitle();

// Batch File Handling
file = getArgument;
arg = split(file,","); //useful if I want to start having multiple arguements 
open(arg[0]);
current=getTitle();


// Kalman filter
print("before") //error checking
run("Kalman Stack Filter MBF", "variance=0.05 bias=0.80");
// run("Median...", "radius=1.5 stack");
print("after") //error checking

// Rename filtered Stack
kf="Kalman Stack Filter";
selectWindow(kf);
kf="kf-" + current;
rename(kf);


// Save filtered image in same directory
// as original file
kfsave=arg[1] + kf;
save(kfsave);


//clean up
close();
close();