Neither Perl, nor (as far as I'm aware), PDL provides a mechanism for creating banded (sparse) matrices. You could use normal rectangular matrix, and just ignore the zeros, but for large dimensions, that would waste a lot of space.
However, the "normal" way of dealing with them, is to map the active elements to an appropriately sized (smaller) rectangular matrix. The mapping is very simple & regular. A simple sub that maps the original coordinates to the reduced matrix should be pretty simple to write.
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