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Hi Scott,
To get the ball rolling on getting the waterfaller into PRESTO, I put the code into presto and did a little bit of testing to make sure it works. A lot of the credit should go to Patrick since he wrote spectra.py, the updated psrfits.py, and the original waterfaller.py.
There are still more I'd like to do, e.g. add a filterbank.py (from Patrick's pypulsar) that uses spectra.py so that the waterfaller can run on .fil files. But, that will take more work and testing since the current filterbank.py in presto is used in injectpsr.py and I'd like to not break that script.
Let me know if you have any questions!