Self similarity
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It is often useful to compare the similarity of a sound to itself and see similarity of 100% (or at least close to this). There are several reasons that the similarity estimate might deviate from 100%, some are important and others can often be ignored. In the example below, we see a nice 100% diagonal similarity across all but one syllable.
Reducing the min duration with the slider will eliminate this problem, but at the cost of adding ‘noise’ of many short (and mostly meaningless) sections. Therefore, what you should have in mind is that optimizing the similarity contrast is more important than reaching 100% (as opposed to 95%) during self-similarity tests.
Another issue is setting the amplitude and Wiener entropy thresholds: if those settings differ across Sound 1 and Sound 2, self-similarity might deviate from 100% but usually not by more than 10%. Any self similarity test that gives less than 90% similarity requires a careful investigation of what went wrong.