You need to set multiaperture.automode to true to run MA via a macro. You'll also want to wait for MA to finish by watching multiaperture.finished to be true. If you cancel the MA run, you'll want to make sure to reset automode to false so you can run MA manually.
This should work:
call("ij.Prefs.set","multiaperture.automode","true");
run("MultiAperture ", "use_previous_apertures=true pause_at_each_image=false centroid_apertures=true save_measurements_file=true");
waiting = true;
while (waiting) {
wait(1000);
finished = call("ij.Prefs.get","multiaperture.finished","false");
if(finished == "true") {
waiting = false;
call("ij.Prefs.set","multiaperture.automode","false");
call("ij.Prefs.set","multiaperture.finished","false");
print ("Multi Aperture analysis finished");
}
}
Locked
