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convert LOGO: -median 3x3 m33.png
convert LOGO: -median 3 m3.png
convert LOGO: -statistic median 3x3 sm33.png
convert LOGO: -statistic median 3 sm3.png
And, maybe I missed it, documentation is not clear how 'geometry' parameter is interpreted. Is it radius? Is it a rectangular box width and height? (So, e.g., for '3x3' there are 8 pixels affecting current pixel, for '5x5' -- 24, etc. Then what about even or fractional parameters?)
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Version: ImageMagick 6.9.1-1 Q16 x86 2015-03-20 http://www.imagemagick.org