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I would like to be able to separate the constituent color images of a Bayer focal plane, do some work on them, and then put them back together into the Bayer format. 

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You can export 16bit TIFFs of each channel from Raw Digger, using the option to fill in the missing pixels with zeros (black).  Then you can open each of the four channel TIFFs (R, G1, B, G2) and convert them to 32bit (they are linear) and stack them in linear dodge (add) mode - for each of the four layers, you can clip a recolor layer to add the CFA color that corresponds to that layer.  This will effectively give you a UniWB image - you can clip an exposure adjustment to the R and B layers and adjust the exposure of R and B to white balance the image.



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