Well, the typical phototransistor has two modes, kind of like most garden-variety transistors: Switch mode and active mode. Switch mode is easy to work with, but active mode means you are dealing with current that ranges over four or five orders of magnitude, from a few microamps to milliamps or even tens of milliamps.
Driving a digital input in switch mode is no problem; it's just like saturating a transistor. Active mode, especially in low light levels, requires some massaging--playing with the emitter resistor (in a common collector configuration), then amplifying.
What I was trying to do was end up with a light sensor that gave me two things at the same time, an analog signal (intensity/signal strength) and a digital signal (is light present, yes or no, regardless of intensity).
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