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In the current version (v0.5), saving a structure then loading back to MATLAB does not yield the same struct because loadh5.m, originally written by Pauli Virtanen, reads objects instead of links.
I've already asked saveh5.m to track the creation order in this commit 66de6e2
but this alone is not sufficient, need also to use H5L interface to read links in loadh5.m, which I haven't figured out.
If you know how to do it, please fork and modify, thanks