Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 20 additions & 0 deletions docs/abtem/changelog.md
Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,26 @@ Bugfixes:
- Warnings replace silent fallbacks: multi-GPU requested but declined (with the reason), a missing
`if __name__ == "__main__"` guard, and a grid size that forces the Bluestein fallback (naming the
next fast size)
- Distribution weights (`gaussian`, `lorentzian`, `voigtian`, `pseudo_voigtian`, `from_values`) are now
applied as probabilities when an ensemble is reduced
([PR #466](https://github.com/abTEM/abTEM/pull/466), [issue #305](https://github.com/abTEM/abTEM/issues/305)).
They previously multiplied the wave amplitude, which gave wrong partial-coherence results:
- **STEM probes ignored the weights.** Each ensemble member was normalized after weighting, so
`Probe(defocus=gaussian(σ))` averaged its samples equally, as if the distribution were a top-hat.
For a 200 kV, α = 25 mrad probe, the peak of the reduced intensity is 1.76× the old value at
σ = 2.5 nm (25 Å) and 2.21× at σ = 5 nm (50 Å). STEM results with a defocus distribution are
worth repeating
- **HRTEM spreads were too narrow.** Weights on the amplitude entered the intensity squared, so a
Gaussian of standard deviation σ acted as one of σ/√2, and Lorentzian and Voigt spreads gained
$x^{-4}$ tails
- The weights of tilt, energy and aperture distributions were ignored
- Each ensemble member is now the unweighted wave function for its parameter value, the ensemble axis
carries the weights, and `reduce_ensemble()` returns $\sum_i p_i I_i / \sum_i p_i$. Frozen-phonon
results are unchanged. `reduce_ensemble(axis=...)` reduces an axis kept with `ensemble_mean=False`,
and `.sum()`/`.mean()` over a weighted axis warn that they ignore the weights
- The `.weights` of the distributions now sum to one (previously their squares did), and
`normalize="intensity"`/`"amplitude"` are deprecated. A `gaussian(σ)` defocus spread corresponds to
the 1/e focal-spread width `focal_spread = √2·σ` of the temporal envelope

Documentation:

Expand Down
82 changes: 44 additions & 38 deletions docs/user_guide/appendix/ensembles.ipynb

Large diffs are not rendered by default.

167 changes: 84 additions & 83 deletions docs/user_guide/examples/notebooks/hrtem_quickstart.ipynb

Large diffs are not rendered by default.

Binary file modified docs/user_guide/examples/thumbnails/hrtem_quickstart.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
156 changes: 136 additions & 20 deletions docs/user_guide/tutorials/partial_coherence.ipynb

Large diffs are not rendered by default.

Loading