A simple method would be to generate a time series stack of quality masks, and then simply multiply the two time series arrays together. Data you want masked out will now be zero. You can do that from within band math.
If your pixel reliability measure is always DN > 2, then use that expression within the spectral math tool set, or band math, and map the expression to a file rather than a single band. This will generate your quality measure time series stack.
If you wanted you could probably do the entire expression in a single band math statement, but you wouldn't get to save the intermediate masking file.
Hope that helps
Cheers
Josh
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