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It appears that the plot_masked_pixels works as expected when called in the script e.g. here as well as when it's called from the GUI in order to plot onto the GUI. When it's called from the GUI though, with plot=True no PDF-files are created since they are all empty and empty PDFs are deleted by PDFPages by choice of keep_empty=False. So essentially everything works, except for that the PDFs in this case here and here are empty which is what I do not understand. If anyone has an idea, let me know.
After reloading a session and setting the pdf output under global options to on, no pdfs are created.
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