Process Stack Pop Up Window?

imagej
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#1

I am trying to write a Macro that my team can use for the long term so I am trying to streamline it and make it as user friendly as possible. The Macro is for analyzing a stack of photos with a number of filters and user inputs. The issue I am having is that when I run the Macro, there are two times as it is running that I get this Pop Up window stating:
Process Stack?
“Process all images? There is no Undo if you select “Yes”.”
And then I have to select Yes, No, or Cancel to continue.

I would really like this pop up window to go away or find a way to always say yes with the macro so the user doesn’t have to click through this every time it pops up.

Any suggestions for resolving this would be greatly appreciated! Thanks!


#2

Good day,

could you please post a minimal working example code that shows this behavior.

This woud help us to help you.

Regards

Herbie


#3

Thanks Herbie,
I’ve been going through it and found that the line of code that is triggering this pop up is here:

run(“8-bit”);
run(“Threshold…”);
run(“Convert to Mask”, “method=Default background=Dark calculate black”);
run(“Fill Holes”);

Specifically it is the Fill holes function causing this… I can’t remove that because it’s integral to the Macro but maybe that can provide some context as to how I can get rid of the pop up window…


#4

In addition,
I have found under Misc. Options - the “Hide Process Stack” dialogue almost does what I need. However when this box is checked, ImageJ suppresses the dialog but then only processes the current slice. I need the dialogue box to be suppressed but need ALL slices to be processed.
Hope that makes sense. Thanks for any input:)


#5

You may use:
run("Fill Holes", "stack");

Regards

Herbie


#6

Wow thank you so much! I had been overcomplicating that lol…