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I am working on a image which needs denoising (bilateral filter) and a geometric transformation. I am not sure in which order these filters should be applied. Personally I think it is better to use the transformation first because otherwise I would loose details removed by the bilateral filter. But in the same moment the transformation would amplify some of the existing noise wouldn't it? I tried it both ways and objectively it's hard to tell which one is better.

So which order is right? And how to order filters in general?

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The transform will alter the spatial spectrum of the noise, at least for most areas of the image. So denoise before the transform. More specifically, denoise in the coordinate system that the noise was generated in. This assumes, of course, your denoising algorithm is tailored for the untransformed noise.

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