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Re-sync main from dev#637

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sezelt merged 71 commits intomainpy4dstem/py4DSTEM:mainfrom devpy4dstem/py4DSTEM:devCopy head branch name to clipboardMar 21, 2024

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Commits on Nov 8, 2023

• Adding more papers

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• more cites

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Commits on Dec 20, 2023

• Merge remote-tracking branch 'cophus/dev' into dev

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Commits on Jan 9, 2024

• bug fix

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Commits on Jan 12, 2024

• Revert "bug fix"

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Commits on Jan 22, 2024

• Bump tj-actions/changed-files from 41 to 42

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• Bump github/super-linter from 4 to 5

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• Bump actions/checkout from 3 to 4

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• Bump actions/setup-python from 2 to 5

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Commits on Jan 25, 2024

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

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• Merge pull request #600 from py4dstem/dependabot/github_actions/tj-actions/changed-files-42

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• Merge pull request #601 from py4dstem/dependabot/github_actions/github/super-linter-5

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• Merge pull request #602 from py4dstem/dependabot/github_actions/actions/checkout-4

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• Merge pull request #603 from py4dstem/dependabot/github_actions/actions/setup-python-5

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Commits on Jan 28, 2024

• num_probes_fit_aberrations

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Commits on Jan 31, 2024

• flip 180 option for read arina

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Commits on Feb 1, 2024

• ptycho positions offset

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Commits on Feb 2, 2024

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

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• remove 180 flip

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• tweaking amorphous fitting function

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• median_filter_masked_pixels

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Commits on Feb 6, 2024

• save polar aberrations instead

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• read-write compatibility

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• uncertainty viz bug

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• adding force_com_measured functionality to ptycho

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Commits on Feb 7, 2024

• clean up force_com_measured

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• adding DP normalization progress bar

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• moving fov_mask calc to as needed

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Commits on Feb 8, 2024

• adding detector_fourier_mask

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Commits on Feb 10, 2024

• bug fix for filtering

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Commits on Feb 26, 2024

• Friedel origin finder, various FEM tools (#607)

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

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• Default threshold should be zero

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Commits on Feb 28, 2024

• Release memory after Bayesian optimization (#599)

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• remove duplicate make_fourier_coords_2D

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• format with black

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• Added phase_contrast warning in README (#608)

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Commits on Mar 5, 2024

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

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Commits on Mar 6, 2024

• switching to non-vectorized datacube resampling

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Commits on Mar 7, 2024

• Merge pull request #611 from sezelt/fourier_coords_dedup

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• Merge pull request #610 from cophus/dev

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Commits on Mar 9, 2024

• fixing region_of_interest_shape flag

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• adding cross-correlation function

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Commits on Mar 12, 2024

• more careful array sums interpolation

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Commits on Mar 13, 2024

• Bump gdown to 5.1.0 (#617)

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

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• docstring change per Colin review

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Commits on Mar 14, 2024

• DP resampling mode to nearest

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• adding fourier_mask in forward mode, ie pre error calculation

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• Merge pull request #616 from py4dstem/phase_contrast

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Commits on Mar 15, 2024

• small bugfix, moving reset before object_type change

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Commits on Mar 18, 2024

• parallax odd pixel padding bugfix

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• parallax upsample, fit, and correct should return self

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• removing Wiener filter

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• fixing depth sectioning

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• Merge pull request #630 from py4dstem/phase_contrast

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Commits on Mar 19, 2024

• Bump tj-actions/changed-files from 42 to 43 (#629)

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Commits on Mar 21, 2024

• fixing aberration correction for odd radial symmetries. I think the sign ought to be negative, still checking with sims

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

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• ACOM module - fix for .ang file writer (#382)

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• Merge pull request #632 from py4dstem/phase_contrast

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• Fixing projection 2D thickness (#631)

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• Versioning to 0.14.10

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• Merge pull request #633 from cophus/dev

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• Revert "Versioning to 0.14.10"

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• Merge pull request #635 from py4dstem/revert-633-dev

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• Update pypi_upload.yml

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• Update pypi_upload.yml

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• Merge branch 'dev' into pypi-sync

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• Merge pull request #636 from py4dstem/pypi-sync

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• Merge branch 'main' of https://github.com/py4dstem/py4DSTEM into dev

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