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A lot of IR thermometry requires the use of protective windows - they keep atmospheres inside a furnace, reactor, or whatever - or keep it out! But there are a lot to choose from. And, you need to recognise that the wrong material could cause large errors.
Apart from the obvious - that except for ratio pyrometers, you must keep windows clean (dirt attenuates radiation) - remember also that all windows reduce the signal. Reflections at window/air interfaces reduce signals - but there need be little or no absorption loss if you choose the right material.
In fact, you can correct for losses by adjusting emissivity. For example, if the loss is 2% for each surface, you …