I always use the raw weight.
Calorie counting is, in a very real sense, a series of educated guesses. The calories in a tomato, for example, will depend on it's size, sure, but also it's level of ripeness, relative moisture content, the soil it was grown in, and how much sun it got...all of those things effect sugar and water levels, and therefore the total calories. So you're always looking at an estimate no matter how you slice it. But being "close" is better than having no idea, right? And it all evens out in the end.
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