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i'm trying to run "Filter" operation using AcGIS on a stack layer of 331 bands. However, the result is always a raster of only one band. How can i get operation to be done on the whole stack?

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The filter is only applied to a single band. If you want to apply the filter on every band, you should do it on each band separately, then build a stacked image from the filtered bands. The best way to do that is to create a python program that loops over each band (when they are separated images not in stack form) to filter the images, then create a stacked image from the output filtered bands.

Based on Luke's comment, you have an option to leave bands in stack and access them individually to do the necessary filtering. But in both cases, you cannot do filtering of the 331 bands all as a single image. You should do filtering on the images individually either before or after the stacking.

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    You can leave the bands in a stack and access them individually. – user2856 May 17 '16 at 1:38
  • @Luke Thanks for your addition, I updated the answer based on your comment. – ahmadhanb May 17 '16 at 1:53

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