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Compare the number of valid measurements per wavelength to the number of valid sky fibers (i.e. fibers that have some non null ivar values after the call to get_fiberbitmasked_frame_arrays) instead of comparing to the total number of sky fibers.
This feature caused sky subtraction to set ivar=0 to full frames. It happened in the first few nights after restart because many sky fibers have large positioning errors (>100 um).