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Release into main version 0.14.10 (#634)
* Adding more papers * more cites * bug fix * Revert "bug fix" This reverts commit cbce25c. * Bump tj-actions/changed-files from 41 to 42 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 41 to 42. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v41...v42) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump github/super-linter from 4 to 5 Bumps [github/super-linter](https://github.com/github/super-linter) from 4 to 5. - [Changelog](https://github.com/github/super-linter/blob/main/docs/release-process.md) - [Commits](github/super-linter@v4...v5) --- updated-dependencies: - dependency-name: github/super-linter dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump actions/setup-python from 2 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * num_probes_fit_aberrations * flip 180 option for read arina * ptycho positions offset * remove 180 flip * tweaking amorphous fitting function * median_filter_masked_pixels * save polar aberrations instead * read-write compatibility * uncertainty viz bug * adding force_com_measured functionality to ptycho * clean up force_com_measured * adding DP normalization progress bar * moving fov_mask calc to as needed * adding detector_fourier_mask * bug fix for filtering * Friedel origin finder, various FEM tools (#607) * bug fix * Revert "bug fix" This reverts commit cbce25c. * num_probes_fit_aberrations * flip 180 option for read arina * ptycho positions offset * remove 180 flip * median_filter_masked_pixels * save polar aberrations instead * read-write compatibility * uncertainty viz bug * adding force_com_measured functionality to ptycho * clean up force_com_measured * adding DP normalization progress bar * moving fov_mask calc to as needed * adding detector_fourier_mask * Auto center finding works! * Adding center finding without a mask * Adding plot range to show_origin_fit, fixing bug * Adding local mean / variance functions for FEM * Adding symmetry analysis and plotting * Fix divide by zero in correlation origin finding function * bug fix for filtering * adding initial commit for friedel correlation origin finder * Correlation working, but mask still buggy * Fixing the masked CC * Simplifying the expression * cleaning up - still need subpixel shifts * Update origin fitting visualization * adding device arg to upsample function * First attempt to add Friedel origin finding to ptycho GPU not yet working * Adding GPU implementation warning * parabolic subpixel fitting * minor updates * Going back to dev version of phase contrast * Changing np to xp for GPU compatibility * Fixing xp = np device options * Revering phase contrast options back to dev * Cleaning up code, fixing GPU support * black formatting * black updates * Adding annular symmetry plotting function * black formatting * cleaning typos and dead code and such * Update py4DSTEM/process/polar/polar_analysis.py Co-authored-by: Steve Zeltmann <[email protected]> --------- Co-authored-by: Stephanie Ribet <[email protected]> Co-authored-by: Georgios Varnavides <[email protected]> Co-authored-by: gvarnavi <[email protected]> Co-authored-by: SE Zeltmann <[email protected]> Co-authored-by: Steve Zeltmann <[email protected]> * Default threshold should be zero * Release memory after Bayesian optimization (#599) * do not retain optimization function after finished running, to release memory * update comment * set clear_fft_cache off in optimizer defaults * Update parameter_optimize.py * format with black 24.1.1 * Update parameter_optimize.py * format with black * remove duplicate make_fourier_coords_2D * format with black * Added phase_contrast warning in README (#608) * switching to non-vectorized datacube resampling * fixing region_of_interest_shape flag * adding cross-correlation function * more careful array sums interpolation * Bump gdown to 5.1.0 (#617) * docstring change per Colin review * DP resampling mode to nearest * adding fourier_mask in forward mode, ie pre error calculation * small bugfix, moving reset before object_type change * parallax odd pixel padding bugfix * parallax upsample, fit, and correct should return self * removing Wiener filter * fixing depth sectioning * Bump tj-actions/changed-files from 42 to 43 (#629) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 42 to 43. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v42...v43) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fixing aberration correction for odd radial symmetries. I think the sign ought to be negative, still checking with sims * ACOM module - fix for .ang file writer (#382) * adding annotation import * fft normalization * upsampling limit bugs * bilinear sampling during position correction * sequential numerator-denominator pixel rolling to save memory * some useful warnings for now * add occupancy to CIF reader * add occupancy to structure factors * format with black * removing optional conda comment * adding dependencies comment * Adding correlation metrics * Correlation coefs finished * Black formatting * normalize_order = 0 bug * plotting fixes * switching to gray * allowing python 12.1 * changing python requirement to <3.13 * changing install requirements * adding initial fixes * changing how peaks are accessed * changing to PLA from BraggVectors * changing to PLA from BraggVectors * moving import to top of file * black * removing hardcoded link to sample collections * adding overwrite * typo * typo * removing accidental noteobok * back to hardcoded id * changing filename for FCU-Net file * Adding ability to force filename for collection Items * back to non hardcoded now gdrive function fixed * removing print statements * bumping allowed version of tensorflow * black * adding strain mapping back into WPF * Finishing up * Fixing minor bugs * Black formatting * removing test plotting * doc strains for visualize strain * bugs * doc string update * fixing reset=False bug * explicit bin order * some plotting preferences * fixing upsampling limits * explicit aberration orders fit * fixing abtem bug, adding conversion to polar property * adding ability to pass descan_correction_fit_function * DCT-based poisson solver phase unwrapping * constraints refactoring * fixing reshaping bugs * cleaning up calibrations * cleaning up calculate rotation * adding grid search functionality to optimize * removing tuning functions from subclasses - moved to optimizer * Update corr_kernel_size documentation * small typo * cupy numpy bug * refactoring object and probe methods * multislice plotting tweaks * moved read-only self-attribute calls up-front. Might remove all-together, especially for positions * cleaned up single-slice preprocess * cleaned up multislice preprocess * cleaned up mixedstate preprocess * underscore typos * underscore typos * huh, not how super works * cleaned up mixed-multi slice preprocess * cleaned up overlap tomography preprocess * removing redundant tune func from parallax * moved single-slice forward and adjoint to methods.py * added necessary multi-slice forward and adjoint methods * added necessary mixed-state forward and adjoint methods * added necessary mixed-state-multi-slce forward and adjoint methods * removed redundant forward and adjoint methods from overlap tomo * cleaned up single-slice reconstruct * cleaned up multi-slice reconstruct * cleaned up mixed-state reconstruct * cleaned up mixed-state multi-slice reconstruct * cleaned up overlap tomo reconstruct, different probes per tilt * moved show_transmitted probe * cleaned up self-consistency viz * oops, forgot to delete duplicate code * cleaned up position correction - is mixed state correct? * more natural location for 3D function * Bump tj-actions/changed-files from 39 to 41 in /.github/workflows Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 39 to 41. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v39...v41) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * added and cleaned up total position update functionality back in * modernized probe position correction viz * starting viz overhaul * remove redundant figax viz functions * added visualize_last functionality * visualize_all for single-slice * visualize_all for all * small np cp bugs * some figsize defaults * histogram scaling for all * added virtual detector mask * adding dependabot.yml * update to check_config workflow * black * adding dp_mask argument * renamed to ptycho-tomo, started magnetic refactoring * arina reader bug fix * reconstruct functionality for iterative magnetic * splitting up constraints * bumping python version to 3.10 * correctly handling collective updates constraints * Bugfix for forced scan sampling Correctly set scan units when `force_scan_sampling` is used * finished with magnetic ptycho * phase unwrapping bugfixes * Update py4DSTEM/io/filereaders/read_arina.py Co-authored-by: Steve Zeltmann <[email protected]> * Update py4DSTEM/process/phase/utils.py Co-authored-by: Steve Zeltmann <[email protected]> * Update py4DSTEM/process/phase/utils.py Co-authored-by: Steve Zeltmann <[email protected]> * Update py4DSTEM/process/phase/utils.py Co-authored-by: Steve Zeltmann <[email protected]> * Update py4DSTEM/process/phase/utils.py Co-authored-by: Steve Zeltmann <[email protected]> * better support for multiple measurements probe properties * broadcasting polar coordinates * Update py4DSTEM/process/phase/utils.py Co-authored-by: Steve Zeltmann <[email protected]> * Update py4DSTEM/process/phase/utils.py Co-authored-by: Steve Zeltmann <[email protected]> * docstrings * vectorized_fourier_resample docstrings * generalized show_fourier_probe, added general show_probe, added intensity reporting * visual tweaks * removed leading iterative_ from file names and trailing Reconstruction from class names * typo * FFT plotting improvements * Revert "FFT plotting improvements" This reverts commit 6669195. * Revert "typo" This reverts commit 5990942. * Revert "removed leading iterative_ from file names and trailing Reconstruction from class names" This reverts commit 9114df5. * removed leading iterative_ from file names and trailing Reconstruction from class names * typo * FFT plotting improvements * switched divergence field functions to be periodic * magnetic ptycho-tomo preprocessing * magnetic ptycho tomo constraints * magnetic ptycho tomo works * improved 3D visualizations * ragged list partitions support for complex plotting * added detector plane resampling * cleaned up cupyx.scipy imports * added storage support for singleslice. other classes likely broken, will fix tomorrow * actually enable overwriting device * fixing single-slice projection sets bugs with storage refactor * cleaning up multislice for device. changed propagator tilt convention to negative mrad * added storage support to multislice * adding mixed-state storage support * added storage to mixed-multislice * attrs copying cleanup * added storage to dpc * more dpc viz tweaks * adding vectorized flag to CoM * dp_mask can be None, dub * adding batch size in single-slice preprocess * adding to dpc, multislice, mixedstate, multislice-mixedstate * adding some basic device cleanup to parallax, no storage yer * magnetic ptycho preprocess storage support * added full storage support for magnetic ptycho * added storage to ptycho tomo * added storage support to magnetic ptycho-tomo * transferring parallax bug Steph found in phase_contrast * Update CONTRIBUTORS.md * Update CONTRIBUTORS.md * Update CONTRIBUTORS.md * Update CONTRIBUTORS.md * Update CONTRIBUTORS.md * tweaks to clear_fft_cache * Create CODE_OF_CONDUCT.md This is a suggested template that seems widely used and seems reasonable. * adding FFT-based DCT-II implementations, fixing cupy10.6 bug * small numpy bug * cleaned up cupy 12 feature guarding using try-except * restored scikit functionality * scikit-image by default, poisson as flag * various fixes discovered while making testing notebook * position update bug fix * syntax update for bug fix * complex plotting grid search * multislice grid search plotting * read/write bug fix * show hanning window fix * typo fix * mixedstate probe fourier constraint bug fix * constrain first aperture only * parallax verbosity to True * ms butterworth bug * silly George * cleaning up warnings * simplifying warnings, restructuring single slice regularization flags * one more read write bug fix * more flags more problems: multislice, mixed state, and mixed-multislice * dpc * mistake in multislice * flags to magnetic ptycho * ptycho tomo flags * magnetic ptycho tomo flags * stricter flags * perhaps i forgot an underscore * small parallax change * small read-write changes * removing switch_obj_iter * remore switch_iter from all classes * show_fft bug * Bump tj-actions/changed-files from 41 to 42 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 41 to 42. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v41...v42) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump github/super-linter from 4 to 5 Bumps [github/super-linter](https://github.com/github/super-linter) from 4 to 5. - [Changelog](https://github.com/github/super-linter/blob/main/docs/release-process.md) - [Commits](github/super-linter@v4...v5) --- updated-dependencies: - dependency-name: github/super-linter dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump actions/setup-python from 2 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * minor fixes * Friedel origin finder, various FEM tools (#607) * bug fix * Revert "bug fix" This reverts commit cbce25c. * num_probes_fit_aberrations * flip 180 option for read arina * ptycho positions offset * remove 180 flip * median_filter_masked_pixels * save polar aberrations instead * read-write compatibility * uncertainty viz bug * adding force_com_measured functionality to ptycho * clean up force_com_measured * adding DP normalization progress bar * moving fov_mask calc to as needed * adding detector_fourier_mask * Auto center finding works! * Adding center finding without a mask * Adding plot range to show_origin_fit, fixing bug * Adding local mean / variance functions for FEM * Adding symmetry analysis and plotting * Fix divide by zero in correlation origin finding function * bug fix for filtering * adding initial commit for friedel correlation origin finder * Correlation working, but mask still buggy * Fixing the masked CC * Simplifying the expression * cleaning up - still need subpixel shifts * Update origin fitting visualization * adding device arg to upsample function * First attempt to add Friedel origin finding to ptycho GPU not yet working * Adding GPU implementation warning * parabolic subpixel fitting * minor updates * Going back to dev version of phase contrast * Changing np to xp for GPU compatibility * Fixing xp = np device options * Revering phase contrast options back to dev * Cleaning up code, fixing GPU support * black formatting * black updates * Adding annular symmetry plotting function * black formatting * cleaning typos and dead code and such * Update py4DSTEM/process/polar/polar_analysis.py Co-authored-by: Steve Zeltmann <[email protected]> --------- Co-authored-by: Stephanie Ribet <[email protected]> Co-authored-by: Georgios Varnavides <[email protected]> Co-authored-by: gvarnavi <[email protected]> Co-authored-by: SE Zeltmann <[email protected]> Co-authored-by: Steve Zeltmann <[email protected]> * Release memory after Bayesian optimization (#599) * do not retain optimization function after finished running, to release memory * update comment * set clear_fft_cache off in optimizer defaults * Update parameter_optimize.py * format with black 24.1.1 * Update parameter_optimize.py * format with black * Added phase_contrast warning in README (#608) * Adding error for orix install requirements * ACOM .ang file writer fixes * format with black --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: alex-rakowski <[email protected]> Co-authored-by: Georgios Varnavides <[email protected]> Co-authored-by: bsavitzky <[email protected]> Co-authored-by: Steven Zeltmann <[email protected]> Co-authored-by: Steve Zeltmann <[email protected]> Co-authored-by: Stephanie Ribet <[email protected]> Co-authored-by: SE Zeltmann <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: gvarnavi <[email protected]> * Fixing projection 2D thickness (#631) * initial commit for projected potential * Atom coordinates mostly working Some tiling issue for image corners * Projected potential now working with bugs projection algebra definitely has a bug * minor tweak * Projected potentials fixed? * adding figsize * update docstring * Adding thickness projection * Fourier method makes boundary conditions difficult * Updated plotting * Adding robust fitting to ACOM strain mapping * Updating matching * Fixing thickness projection in 2D potentials * black * Remove testing lines. * Trying (and failing) to figure out the potential units * Black formatting * Black again * Versioning to 0.14.10 * Revert "Versioning to 0.14.10" * Update pypi_upload.yml * Update pypi_upload.yml --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Stephanie Ribet <[email protected]> Co-authored-by: Georgios Varnavides <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: gvarnavi <[email protected]> Co-authored-by: bsavitzky <[email protected]> Co-authored-by: SE Zeltmann <[email protected]> Co-authored-by: Steve Zeltmann <[email protected]> Co-authored-by: Steven Zeltmann <[email protected]> Co-authored-by: alex-rakowski <[email protected]> Co-authored-by: Stephanie Ribet <[email protected]>
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