wavetrace is great for batch processing, however it's tough to import into another project and call the methods, returning the result you need.
There are a few things that could make this easier - without making the batch processing harder, so i'll note these ideas one-per-issue;
This one is logging.
Logging instead of print statements would make it much easier for a consuming project to handle the output. Logging also makes it easy to see where and when (even what line no.) a logging call is being made from, plus you can crank up the logging level with one line change, and drop it back after you find and fix the problem.