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added 14 commits
March 25, 2026 19:09
…ith PySlice logic and preallocation of arrays
…ection via environment variable
…ice_abtem.ipynb looks good for NumPy and PyTorch CPU backend.
…ntial problems overloading default Python operators
Claude and Github Copilot made the majority of changes. The backend is now much more compartmentalized and fully testable. Need to verify the correctness of calculations more.
… functions to trajectory deleted by mistake
1. Removed parameter store_all_slices from MultisliceCalculator 2. Added force_rerun parameter to MultisliceCalculator.run in order to force recalculation even if tacaw.npy exists. 3. Fixed bug regarding chunk_size_time handling in TACAWData if chunkFFT=True 4. Added force_rerun parameter to TACAWData class to force recalculation even if tacaw.npy exists in the cache. Now tests/test_pyslice_abtem.ipynb runs successfully!
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This PR introduces a new backend implementation, which allows for a very clean handling of the arrays without relying on global module variables. Backends can now be freely mixed and matched in the same process. Furthermore the backend is easily testable as shown in the script
tests/test_backend.py.Most of the rewriting was done using Github Copilot and Claude Code. Most testing has focused on the Jupyter notebook
tests/test_pyslice_abtem.ipynb. It runs successfully and compares favorably with an abTEM calculation.We will need to test this more rigorously than I was able to do. Specifically, we should make sure all of the tests in the tests directory work. I could not verify a lot of them due to memory issues. Will try on a cluster in the near future.