ImageJ macro not waiting for command to finish running - imagej

Question

I'm using ImageJ macro to batch process images.
Specifically, I'm trying to run a plugin called Log3D on each image.
For some reason, ImageJ macro won't wait for the command to finish running before running the next line in the script.
Is there a way around this?
Thank you!
I'm currently using "waitForUser" to manually let ImageJ know when to continue but this is quite annoying and not useful when I process hundreds of images at once.
selectWindow(file + " - C=" + chFISH);
run("LoG 3D", "sigmax=1.5 sigmay=1.5 sigmaz=1.5 displaykernel=0 volume=1");
waitForUser("Proceed when Log3D is complete");
run("Invert", "stack");
run("16-bit");
print("Saving smFIHS channel to: " + output);
saveAs("Tiff", output + File.separator + file + ".chFISH");
close();

Answer 1

You could try running Log3D over all the images first and then running the rest over the newly processed images.
openPath = getDirectory("Choose Source Directory");
files = getFileList(openPath);
savePath = getDirectory("Choose Destination Directory");
for (timePoint = 0; timePoint < (files.length); timePoint++)
{
if (indexOf(files[timePoint], chFISH) >= 0) //Screens file names for your variable
{
tempName = getTitle();
open(openPath + files[timePoint]);
run("LoG 3D", "sigmax=1.5 sigmay=1.5 sigmaz=1.5 displaykernel=0 volume=1");
saveAs("Tiff", savePath + tempName);
close();
}
}
files = getFileList(savePath);
for (timePoint = 0; timePoint < (files.length); timePoint++)
{
run("Invert", "stack");
run("16-bit");
print("Saving smFIHS channel to: " + savePath);
saveAs("Tiff", savePath + File.separator + file + ".chFISH");
close();
}

Answer 2

If your images are of a consistent file size, you could use the "wait" command, which causes ImageJ to wait "n" milliseconds before continuing.
selectWindow(file + " - C=" + chFISH);
run("LoG 3D", "sigmax=1.5 sigmay=1.5 sigmaz=1.5 displaykernel=0 volume=1");
wait(30000); //Waits for 30 seconds
run("Invert", "stack");
run("16-bit");
print("Saving smFIHS channel to: " + output);
saveAs("Tiff", output + File.separator + file + ".chFISH");
close();
You'll have to work out how long it takes for your plugin to run on a given image, but in principle this should resolve your issue.