Omnibus update

I'm sorry about this, but the time it would take to make separate pull requests and give each the review time it warrants seems unjustified in light of the very few contributors to this repository as of now. I'll do better with future PRs

Contains:
1. Some bug fixes (see commits)
2. Speedups, including the infinitely faster HDF5 data format.
3. A new data format for concatenated ptv_is files, as invented by Ron Shnapp from TAU. This format may eventually be removed, as it handles an ad-hoc format and we can do better in the future, but as long as someone needs the data I see no reason to withhold the code.