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version 0.14.5 release#542

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bsavitzky merged 119 commits intomainpy4dstem/py4DSTEM:mainfrom devpy4dstem/py4DSTEM:devCopy head branch name to clipboardOct 23, 2023

+7,302-773

Commits

Commits on May 12, 2023

• Adding grain clustering function

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• Fixing bugs in the grain clustering

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Commits on May 13, 2023

• More plotting tools

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• Updated viz

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• Cleaning up

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Commits on May 15, 2023

• Updating plotting function with new args

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• Merge remote-tracking branch 'py4dstem/dev' into grain_clustering

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• Fix duplicate arg

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Commits on Aug 4, 2023

• start for depth profile

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Commits on Aug 8, 2023

• adding real-space kde upsampling

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• Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast

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• more depth profile

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• saving error

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• small name changes

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Commits on Aug 17, 2023

• single slice tv denoise

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• multislice tv denoise... will test more before adding to other classes...

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Commits on Aug 21, 2023

• minor tv bugfix

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• improvements for depth plotting

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Commits on Aug 22, 2023

• tv fixes

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Commits on Aug 25, 2023

• everyone gets TV denoising

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Commits on Aug 29, 2023

• Adding moire lattice generation and plotting

  

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• run black

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• subpixel alignment phase correct, part 1

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• removing print statement

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Commits on Sep 1, 2023

• Merge remote-tracking branch 'origin/dev' into moire

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Commits on Sep 7, 2023

• parallax plotting fix

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Commits on Sep 20, 2023

• generalizing overlap tomo to orientation matrices

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• Merge branch 'phase_contrast' of github.com:py4dstem/py4DSTEM into phase_contrast

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• black formatting

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• flake8 6.1.0 found some more issues

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• adding mixed-state multi-slice ptycho class

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Commits on Sep 22, 2023

• small reset bug

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Commits on Sep 23, 2023

• fixed NaN bug

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• Merge branch 'phase_contrast' of github.com:py4dstem/py4DSTEM into phase_contrast

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• changed complex plotting

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• Merge remote-tracking branch 'origin/dev' into grain_clustering

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Commits on Sep 24, 2023

• updated complex plotting phase calls

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• adding complex CoM plotting and various dpc plotting bugs

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• Adding min angle between matches.

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Commits on Sep 27, 2023

• format with black

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• Update check_install_dev.yml

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• Merge pull request #528 from py4dstem/remove-3-12-test

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• Merge remote-tracking branch 'origin/dev' into grain_clustering

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Commits on Sep 30, 2023

• parallax descan correct

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• complex plotting improvements, formatting

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Commits on Oct 2, 2023

• Update README.md

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• update docstrings

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• replace pbar with tqdm

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Commits on Oct 4, 2023

• change to fitted intensities

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• Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast

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• tqdm-based progress bar in clustering

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• Adding docstrings and more description

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• Black formatting

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Commits on Oct 5, 2023

• move progress update step

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• Merge pull request #3 from cophus/moire

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Commits on Oct 6, 2023

• adding "sphinx_rtd_theme" to conf.py

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• adding sphinx_rtd_theme to setup.py

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• black style conf.py

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• adding sphinx_rtd_theme to docs requirements.txt

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• removing sphinx_rtd_theme from setup.py

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• Merge pull request #531 from py4dstem/docs

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• Merge pull request #525 from cophus/grain_clustering

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Commits on Oct 8, 2023

• preprocessing dtype bug

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Commits on Oct 9, 2023

• update CUDA source file location in setup.py

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• update cupy import try statements

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Commits on Oct 10, 2023

• adding tilt to propagators

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Commits on Oct 12, 2023

• single slice crop patterns

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Commits on Oct 13, 2023

• tv_denoise typo

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• revisting casting inconsistencies

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Commits on Oct 14, 2023

• Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast

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• crop pattern option for all classes

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• fix for gpu

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Commits on Oct 16, 2023

• cleaned up parallax descan

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• added support for float upsampling

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• making descan correction the default

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• Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast

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• Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast

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• removing redundant if statement

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• Merge pull request #532 from sezelt/cudakern_relocate

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• Merge pull request #533 from sezelt/cp-import

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• removed separate ctf corrections and other subpixel improvements

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• added read-write functionality to parralax

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• Apply suggestions from code review

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• format with black

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• Merge remote-tracking branch 'origin/dev' into moire

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• clean up moire

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• Fix for plotting bug

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• Merge pull request #535 from cophus/dev

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• Starting on CTF fitting

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Commits on Oct 17, 2023

• Adding more parts of parallax CTF fitting

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• added chroma_boost for show_complex

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• Working on CTF

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• It works!

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• Updating outputs

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• Adding outputs, plotting

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Commits on Oct 18, 2023

• Merge pull request #536 from cophus/phase_contrast

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Commits on Oct 19, 2023

• finally works

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• some support for aberration correct

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• small bug fixes

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Commits on Oct 20, 2023

• cleaned up parallax

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• ptycho new aberration formalism

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• adding chroma_boost defaults

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• formatted, linted, isorted

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• fixed some manual conflicts

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• fixing radial order accounting

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• make lint happy I hope!

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Commits on Oct 21, 2023

• fix extent for ms depth sectioning

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• small fixes

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• fix for ptycho aberration fit

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• black format

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Commits on Oct 22, 2023

• fixed ptycho fitting, added transpose flag in parallax

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• versions emdfile

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• Merge pull request #541 from bsavitzky/array_repr_bugfix

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• added force_transpose option for other two aberration fit methods

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• read-write device bugfix

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• Merge pull request #539 from py4dstem/phase_contrast

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• Merge pull request #514 from sezelt/moire

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Commits on Oct 23, 2023

• bugfix to update_version.py

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• Manually update version.py

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