Hi Mike,
Thanks for the reply. I have round-about evidence that the master flat is normalized by the mean of the entire master flat, irrespective of color channels. Plus, since there isn't an option to tell the Master Flat section of the ImageCalibration process that it is working with a CFA image, then it is likely normalizing by the whole master flat.
My main concern is if normalizing by the entire flat frame will cause any harm if I execute the ImageCalibration process with narrowband images taken with a OSC camera. I see what you are saying that if the master flat is normalized by a factor containing those unused channels then it shouldn't necessarily add noise into the good channel. I have seen it cause a strong color cast appear when applying the master flat to images taken with a CLS-CCD filter which was my initial concern. The cast is easily repairable with BackgroundNeutralization, so I guess that normalizing the master flat by the entire master flat irrespective of OSC channels should not matter even if narrowband of LP filters are used.
Of course, the alternative (discussed in an active thread right now) is to extract the relevant channels prior to calibration which makes this a moot point. If it is desirable to treat each Bayer pane independently when normalizing the master flat, I wonder if adding a CFA checkbox to the Master Flat section of the ImageCalibration process would make this easier. That way, narrowband images taken with OSC cameras could be run through ImageCalibration without the relevant channels being extracted beforehand. They would just be extracted afterward. But, if normalizing the master flat by the mean of the entire flat frame irrespective of color channels does not matter, then this too is a moot point (I'm full of 'em tonight!).
Thanks,
Jason