How to exclude the transparent parts which are not rectangles when conducting Fourier analyses on PNG images?

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Some PNG images have transparent backgrounds. We can get maps of transparent degree from PNG images through imread.
It's easy to exclude the transparent parts in Fourier analysis if they are rectangles. However, how to exclude the transparent parts which are not rectangles in Fourier analysis (using fft2)?

See one of my images with transparent background that is not rectangle.

In this case, how to use the maps of transparent degree in conducting Fourier analysis?

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