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Just Intonation is tricky business in terms of notation. I’ve been working on this puzzle a bit for a while now, and though there’s still some limitations to my system, it still opens up a huge number of avenues, especially when it comes to understanding what’s going on.
The way I see JI is that it’s a flexible system of relative pitch, with an emphasis on harmony (but not always necessarily so). In my opinion, you can’t really get away from two pitches implying a harmony in JI. So I think instead of fighting this, it’s important to embrace it. My system attempts to do just this.
It’s a system similar to my method for notating large equal temperaments using standard notation. I first establish a scale of justly-tuned intervals that approximates the 12-TET chromatic scale, with some important alterations. Then, I indicate which pitch on the staff goes with which tone in the system. Formerly, I kept C on the staff as the “root” location of the moving scale, and indicated which place C was to be sounding. The idea was that folks tend to be used to the system when it comes to transposing instruments in orchestras and such, but it’s becoming pretty cumbersome in my opinion, especially if you are trying to follow a melody that modulates and such. You can check out this score (nope not anymore) for an example of this, or just watch the following video with playback:
Whelp, I am going to expand this more later.