Timelapse option in transform
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…ukai/BaSiCpy into timelapse_option_in_transform
…pse_option_in_transform
…ai/BaSiCpy into timelapse_option_in_transform
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I also set the |
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Docstring examples are also changed (closes #86 ) |
…pse_option_in_transform
…ukai/BaSiCpy into timelapse_option_in_transform
Nicholas-Schaub
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Jul 29, 2022
Nicholas-Schaub
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Dec 2, 2022
* Add badges to README * Update .gitignore * Add noxfile * Move files to src * Add config files * Placeholder dct functions * Update gitignore * Add class for settings * Update setup.cfg * Update requirements.txt * Add docstring to settings class * Add validation to Settings input * Update github CI * Add gpu option to init * Update README formatting * Rename 'figures' folder to 'resources' * Update gitignore * Update gitignore * Move API from README to docs * Refactor, update docstrings * Change folder ExampleData to data * Remove environment file * API development * Read the docs config * Remove png from output formats * Update Profile docs * Update docstrings * Fix imports * Fix docs... again * Update tests * Update workflow * Fix workflow * Fix workflows * Fix tests * Delete requirements.txt * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Revert "Added benchmark library asv" This reverts commit d067f04. * Deleted CONTRIBUTING.rst * Create VERSION * Update README.md * Settings becomes pydantic dataclass * Update dependencies * Update types * Update pre-commit * Update types, variable names * Rename variables * Add properties to Profile class * Add properties for getting/setting BaSiC settings * Add dct types to docs * Add abstract base class for DCT * Feat/benchmarks (#7) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Delete CONTRIBUTING.rst * Changed project/repository names * Changed to BaSiCPy * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Converted `BaSiC` to a pydantic class (#23) * Converted BaSiC to pydantic class. * Changed get_dark to get_darkfield * Added CLI parsing (#26) * Converted BaSiC to pydantic class. * Created command line inputs. * Added metavar indicator to input arguments. * Check package installed before making DCT class * Remove unused import * Added abstract base class for DCT (#25) * Add abstract base class for DCT * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Update inexact_alm_rspca_l1.py (#1) - optimise SVD choice - small other cleanup * Check package installed before making DCT class * Remove unused import Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> * Added predict method, does not include baseline estimation (#29) * Implemented shading model fit algorithm from main branch (#27) * Implemented shading model fit algorithm from main branch * Fixed idct in inexact_alm.py * Fix/fit (#34) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Revert "Added benchmark library asv" This reverts commit d067f04. * Deleted CONTRIBUTING.rst * Set score values to object attributes * Added caching to `predict` method (#35) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Revert "Added benchmark library asv" This reverts commit d067f04. * Deleted CONTRIBUTING.rst * Set score values to object attributes * Added caching for resizing of flatfield/darkfield * Feat/autodoc pydantic (#38) * Add abstract base class for DCT * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Update inexact_alm_rspca_l1.py (#1) - optimise SVD choice - small other cleanup * Check package installed before making DCT class * Remove unused import * Implement autodoc_pydantic Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> * Feat/cleanup (#39) * Add abstract base class for DCT * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Update inexact_alm_rspca_l1.py (#1) - optimise SVD choice - small other cleanup * Check package installed before making DCT class * Remove unused import * Remove Profiles class and methods from basic Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> * Convert relative to absolute imports * Add pytest-benchmark * Update noxfile for pytest-benchmark * ignored python-version * Update .gitignore * switched to commented line * refactor name to basicpy * further refactored... * changed dir name * refactor `predict` to `transform` * Update README.md change PyBaSiC to BaSiCPy * Implement logging (#44) * added logging package to all * trying to fix logging in main * initial attempt to add logger logging to each files * fixed typo * fixed main logger typo * fixed import style * added actual logs in the calculation * changed logger to class-level * added log for inexact_alm * fixed main.py logging level and added warning in dct2d_tools. * made BaSiC logger to file-level * Feat/jax dct (#46) * Add custom JAX idct function * Refactor idct * Fix tests Co-authored-by: Fukai Yohsuke <[email protected]> * Add save and load methods (#43) * Add save and load methods * Update docstring * Update load_model test * Add overwrite option and tests to save_model * Update save/load tests Co-authored-by: Fukai Yohsuke <[email protected]> * Update README.md (#49) * Update README.md * Update README.md * removed dropbox link from the link * Update README.md Co-authored-by: Fukai Yohsuke <[email protected]> * fixed pydantic version lower bound to get test_basic_save_model succeeded * set the license to MIT * removed pydantic version * Testing fit method with synthetic data (#53) * added logging package to all * trying to fix logging in main * initial attempt to add logger logging to each files * fixed typo * fixed main logger typo * fixed import style * added actual logs in the calculation * changed logger to class-level * added log for inexact_alm * added synthesized fit test * changed threshold for error * fixed typo for sign * added pooch for Zenodo datasets * some fix... * fixed pooch data bug * Revert "added pooch for Zenodo datasets" This reverts commit 4fdf0d7. * removed logger from class * refactor and added code for debug plotting in test_basic_fit_synthesized * Data in package (#57) * added files * added fetch code to data module * formatted data... * added data download function * added docstring * updated comment * added docstring for all * added test download * added pooch for dependency * typo fix... * fixed typo... * parametrized tests * disabled hash checking * fixed bug * Revert "fixed bug" This reverts commit 6b24503. * Revert "disabled hash checking" This reverts commit d0dbd8a. * added data and tests * changed data url to the dev branch * added tests * added pydantic version to get test_basic_save_model succeed * added tests for original dataset * added code for original fetch * added exception for invalid data cases * reference commit with * switched to dev branch * Fixed typo for data.py comments * Major update with LADMAP implementation (#62) * added logging package to all * trying to fix logging in main * initial attempt to add logger logging to each files * fixed typo * fixed main logger typo * Add custom JAX idct function * Refactor idct * fixed import style * added actual logs in the calculation * changed logger to class-level * added log for inexact_alm * added synthesized fit test * changed threshold for error * fixed typo for sign * added pooch for Zenodo datasets * some fix... * fixed pooch data bug * Revert "added pooch for Zenodo datasets" This reverts commit 4fdf0d7. * wrote tests for experimental data * added files * added fetch code to data module * formatted data... * added data download function * added docstring * updated comment * added docstring for all * added test download * added pooch for dependency * typo fix... * fixed typo... * parametrized tests * disabled hash checking * fixed bug * Revert "fixed bug" This reverts commit 6b24503. * Revert "disabled hash checking" This reverts commit d0dbd8a. * added jax experimental code and tested tingying's implementation * experimental implementation wroking to approximate darkfield * at least jit version is working * deleted old version codes * refactor to include D_R and D_Z * added darkfield 1 * experimental code working * loop jit * fixed package name * merged Tim's idct * jax impl working with Tim's idct * ladmap code is fed into the basicpy class (still a bit slow?) * converted _fit_ladmap_single to the member method * class method working... * refactored jnp.newaxis * in-class version working without jit * trying to add pytree property to the model but aborting this approach * writing jitted routine with new pydantic classes * added fields to jax routines * jit working * all jax working!! * apprioximate method not working with jax * confirmed approximate fit working in jax * organized files * import organize * single fit is working, but reweighting iteration is not working * reweighting loops is working! * still working example * still running... * resize implemented * fixed resize in transform * added _step_only_baseline for approximate fit * custom weight calc working * removed logger from class * approximate fit optimization changed to original imp. * working version with custom weight * working before baseline calculation * baseline calc working except approximate cases * trying to get baseline work for approximate fit * dropped python 3.7 * still approximate version not working... * some working version * approximate version working except baseline * baseline calc not working for approximate cases * sort_intensity option working for approximate fit! * removed comments * analyzing difference b/w original implementation * refactor and added code for debug plotting in test_basic_fit_synthesized * added data and tests * changed data url to the dev branch * added tests * added pydantic version to get test_basic_save_model succeed * added tests for original dataset * added code for original fetch * added exception for invalid data cases * reference commit with * switched to dev branch * added comparison w/ reference implementation at this time * Fixed typo for data.py comments * updated notebook * at least original impl is reproduced to some extent * slightly changed transform tests to get them working * Revert "Merge branch 'data_in_package' into jax_implementation" This reverts commit 9d30051, reversing changes made to a3d35ff. * deleted experimental note * added relative fitting weight argment * added fitting results at commit 11b0747 for testing * test rewriting but still failing * test working * added test with experimental data * added pytest-datadir in nox * migrated to pytest-datadir * made darkfield sparsity coef tunable * Revert "made darkfield sparsity coef tunable" This reverts commit 2b8cd5d. * loosen the isclose torelance * fixed typo in tests * deleted reference results * removed reference results * added additional darkfield coef and test passing * trying to modify dimensions * rewriting notebooks * deleted previous notebooks * notebook working * readme updated * example notebook added * fixed type * at least approximate method is working! * fixed some bugs * tests are running with loosened checks for experimental data * added 3D DCT * loosen the torelance for approximate fit * loosen darkfield torelance for approximate fit * changed DCT from 2D to 3D in ladmap fit * loosen torelance for ladmap * small modification * added constraint for S mean * get the test working * before adding positivity constraint * changed initial config * added naive mean S regularization * rewrote organizing test data notebook * added value_diff for update torelance * fixed convergence bug * ladmap working with modified stopping cond * working with modified stopping cond. (still harmonic ones not added) * added test data * removed cell output for jupyter notebook * removed cell output for jupyter notebook * updated test * loosened the darkfield test constraint * added guard for S==0 * updated example for lambda_flatfield_coef=100 * lambda_flatfield_coef=100 example update * updated flatfield and darkfield dimension for 3d images * updating organize test notebook * updated notebook path * notebook updated * re-added python 3.7 * added 3D test * refactored synthetic test * fixed tests * reduced z size in test * added rescue for RESOURCE_EXHAUSTED: Out of memory * updated enum type to str, Enum Co-authored-by: Tim Morello <[email protected]> Co-authored-by: Nicholas-Schaub <[email protected]> * Update contribution notes (#66) * initial draft * added git version for the original * 👥 Add @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Add @tying84 as a contributor * 👥 Update @tying84 as a contributor * 👥 Update @tying84 as a contributor * 👥 Add @tdmorello as a contributor * 👥 Update @tdmorello as a contributor * 👥 Update @tdmorello as a contributor * 👥 Add @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * trying to see how all-contributors works * reordered contributors * regenerated readme * commenting on contrinbution * organized README * updated nick email, added contributions to Tingying * removed experimental_code reference * updated jaxlib version to avoid importerror (#69) * Merge Yu's docs * deleting files not used at this point * enab * re-added autoflake and isort * removed opencv * Feat/release (#72) * setup.cfg * Create release pipeline * Updated config and added new details to README * Fixed build pipeline, added MANIFEST * Fixed formatting issues * Fixed typo in README * Moved bumpversion config to separate file * Fixed whitespace in bumpversion config * Exclude bumpversion config from whitespace checks * Bump version: 0.1.0-dev0 → 0.2.0-dev0 * Fix/release (#75) * setup.cfg * Create release pipeline * Updated config and added new details to README * Fixed build pipeline, added MANIFEST * Fixed formatting issues * Fixed typo in README * Moved bumpversion config to separate file * Fixed whitespace in bumpversion config * Exclude bumpversion config from whitespace checks * Bump version: 0.1.0-dev0 → 0.2.0-dev0 * Modified config, updated VERSION * Bump version: 0.2.0-dev0 → 0.2.0-dev1 * Update secrets environment * Bump version: 0.2.0-dev1 → 0.2.0-dev2 * Updated twine upload command * Bump version: 0.2.0-dev2 → 0.2.0-dev3 * Updated CI pipeline * Bump version: 0.2.0-dev3 → 0.2.0-dev4 * Use pypa publishing container * Bump version: 0.2.0-dev4 → 0.2.0-dev5 * Update build * Bump version: 0.2.0-dev5 → 0.2.0-dev6 * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @tdmorello as a contributor * 👥 Add @YuLiu-web as a contributor * update readme * 👥 Update @tying84 as a contributor * add tingying organizing meetings * Fix `lambda flatfield` bug (#74) * fixed bug for 3d images and lambda_flatfield calc * reorganized test data * Bump version: 0.2.0-dev6 → 0.2.1-dev0 * fixed save bug for 3D images and added tests (#77) * updated jaxlib dependency * updated notebooks * 👥 Update @tdmorello as a contributor * some update * fixed typos * Update docs * fixed typos * changed default parameters * updated examples * Add comments for notebook gallery * Update notebooks * compared lagrangian with the origin implementation * notebook update * formatted notebooks with black * added markdowns to notebooks * ifurther updated notebooks * Add contributing guide to docs * Add autoenum to docs * updated notebooks * updated thumbnail data for docs * updated readme * ignored package lock file for yarm * fixed type * added windows instruction * 👥 Update @YuLiu-web as a contributor * fixed notebook folder * fixed typo * added macos and windows tests * test falling back to ubuntu * added jax installation in noxfile for windows * migrated contribution details to the docs * update badges * fixed badges * a bit more update... * fixed readme * fixed badgee stype * further fix... * Timelapse option in `transform` (#80) * udpated transform method * fixed tests * fixed typo * solving problems with tests * fixed transform bug * removed tests for rescaling-fitting * removed resized transform example * added dask test * set baseline type to optinal * updated testdata * deleted notebook outputs * Update timelapse * re-organized transform part * tests running... * made the resize method changable * resize method tested * tested resize method * added comments for the transform function * minor fix * fixed fitting_weight shape bug Co-authored-by: Tim Morello <[email protected]> * Update example data (#92) * updating notebooks * updated rescaled data * updated test data * update notebooks * Fixed most unit tests * re-added reference comparison notebook * re-added test data Co-authored-by: Nicholas-Schaub <[email protected]> * Fix `fit` bug for dask array inputs (#93) * udpated transform method * fixed tests * fixed typo * solving problems with tests * fixed transform bug * removed tests for rescaling-fitting * removed resized transform example * added dask test * set baseline type to optinal * updated testdata * deleted notebook outputs * Update timelapse * re-organized transform part * tests running... * made the resize method changable * resize method tested * tested resize method * added comments for the transform function * minor fix * fixed fitting_weight shape bug * fixed dask-related bug Co-authored-by: Tim Morello <[email protected]> * Update hashes (#95) * Minor change before beta release (#96) * DCT tools update (#98) * updated hashes to newer ones * changed source to main * ci experiment with dev branch * updated branch * added tests for wrong argments * updated classifier to beta * updated copyright * just added spaces * updated downsampled data to Zenodo * renamed data to datasets * typo fix... * deleted depricated tools * fixed package names ... * import fix * 👥 Update @yfukai as a contributor * added my contribution for ci... * removed deprecated routines from old DCT2d * updated tests and fixed jax version to solve problems * Update coef definitions (#103) * updated hashes to newer ones * changed source to main * ci experiment with dev branch * updated branch * added tests for wrong argments * updated classifier to beta * updated copyright * just added spaces * updated downsampled data to Zenodo * renamed data to datasets * typo fix... * deleted depricated tools * fixed package names ... * import fix * 👥 Update @yfukai as a contributor * added my contribution for ci... * removed deprecated routines from old DCT2d * trying to add darkfield weight and changing weight for ladmap * fixed typo * added attribute * updated tests and fixed jax version to solve problems * rewrite ladmap to normalize B * working ver? * updated test data * udpated weight for darkfield * updated test data * removed print * fixed normalization const * added test to show basic does not depend on the intensity scale * small update * Update config names (#106) * updated hashes to newer ones * changed source to main * ci experiment with dev branch * updated branch * added tests for wrong argments * updated classifier to beta * updated copyright * just added spaces * updated downsampled data to Zenodo * renamed data to datasets * typo fix... * deleted depricated tools * fixed package names ... * import fix * 👥 Update @yfukai as a contributor * added my contribution for ci... * removed deprecated routines from old DCT2d * trying to add darkfield weight and changing weight for ladmap * fixed typo * added attribute * updated tests and fixed jax version to solve problems * rewrite ladmap to normalize B * working ver? * updated test data * udpated weight for darkfield * updated test data * removed print * fixed normalization const * added test to show basic does not depend on the intensity scale * small update * updated coefs * updated field names * fixed typo in log * updated the definition for self._sparse_cost_darkfield in approximate * Update documents (#107) * updated hashes to newer ones * changed source to main * ci experiment with dev branch * updated branch * added tests for wrong argments * updated classifier to beta * updated copyright * just added spaces * updated downsampled data to Zenodo * renamed data to datasets * typo fix... * deleted depricated tools * fixed package names ... * import fix * 👥 Update @yfukai as a contributor * added my contribution for ci... * removed deprecated routines from old DCT2d * trying to add darkfield weight and changing weight for ladmap * fixed typo * added attribute * updated tests and fixed jax version to solve problems * rewrite ladmap to normalize B * working ver? * updated test data * udpated weight for darkfield * updated test data * removed print * fixed normalization const * added test to show basic does not depend on the intensity scale * small update * updated coefs * updated field names * fixed typo in log * updated parameters for notebooks * added docs_build * added ci for docs * changed the notebooks so that it only installs basicpy for colab * updated docs * added pandoc in ci * fixed error typo * Cleaned up code and logging. * Changed error message comment * Add single-step convergence warning after the loop * Cleanup (#109) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Revert "Added benchmark library asv" This reverts commit d067f04. * Deleted CONTRIBUTING.rst * Cleaned up code and logging. * Changed error message comment * Add single-step convergence warning after the loop Co-authored-by: Yohsuke T. Fukai <[email protected]> * Change default log level to warning * removed device variable from the basic object (#110) Co-authored-by: Nicholas-Schaub <[email protected]> * fixed requirements for gallery fix (#112) * Bump version: 0.2.1-dev0 → 1.0.0 * Bump version: 0.2.1-dev0 → 1.0.0 * Updated docs version and bumpversion config * Bump version: 1.0.0 → 1.0.1 Co-authored-by: Tim Morello <[email protected]> Co-authored-by: Tim Morello <[email protected]> Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> Co-authored-by: Tingying Peng <[email protected]> Co-authored-by: YuLiu-web <[email protected]>
Nicholas-Schaub
added a commit
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Dec 15, 2022
* Add badges to README * Update .gitignore * Add noxfile * Move files to src * Add config files * Placeholder dct functions * Update gitignore * Add class for settings * Update setup.cfg * Update requirements.txt * Add docstring to settings class * Add validation to Settings input * Update github CI * Add gpu option to init * Update README formatting * Rename 'figures' folder to 'resources' * Update gitignore * Update gitignore * Move API from README to docs * Refactor, update docstrings * Change folder ExampleData to data * Remove environment file * API development * Read the docs config * Remove png from output formats * Update Profile docs * Update docstrings * Fix imports * Fix docs... again * Update tests * Update workflow * Fix workflow * Fix workflows * Fix tests * Delete requirements.txt * Create VERSION * Update README.md * Settings becomes pydantic dataclass * Update dependencies * Update types * Update pre-commit * Update types, variable names * Rename variables * Add properties to Profile class * Add properties for getting/setting BaSiC settings * Add dct types to docs * Add abstract base class for DCT * Feat/benchmarks (#7) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Delete CONTRIBUTING.rst * Changed project/repository names * Changed to BaSiCPy * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Converted `BaSiC` to a pydantic class (#23) * Converted BaSiC to pydantic class. * Changed get_dark to get_darkfield * Added CLI parsing (#26) * Converted BaSiC to pydantic class. * Created command line inputs. * Added metavar indicator to input arguments. * Check package installed before making DCT class * Remove unused import * Added abstract base class for DCT (#25) * Add abstract base class for DCT * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Update inexact_alm_rspca_l1.py (#1) - optimise SVD choice - small other cleanup * Check package installed before making DCT class * Remove unused import Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> * Added predict method, does not include baseline estimation (#29) * Implemented shading model fit algorithm from main branch (#27) * Implemented shading model fit algorithm from main branch * Fixed idct in inexact_alm.py * Fix/fit (#34) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Revert "Added benchmark library asv" This reverts commit d067f04. * Deleted CONTRIBUTING.rst * Set score values to object attributes * Added caching to `predict` method (#35) * Added benchmark library asv * Revert "Delete CONTRIBUTING.rst" This reverts commit 01d8fe1. * Revert "Added benchmark library asv" This reverts commit d067f04. * Deleted CONTRIBUTING.rst * Set score values to object attributes * Added caching for resizing of flatfield/darkfield * Feat/autodoc pydantic (#38) * Add abstract base class for DCT * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Update inexact_alm_rspca_l1.py (#1) - optimise SVD choice - small other cleanup * Check package installed before making DCT class * Remove unused import * Implement autodoc_pydantic Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> * Feat/cleanup (#39) * Add abstract base class for DCT * Update pre-commit * Add dct backends and tests * Update setup.cfg * Quickfix for failing tests * Update inexact_alm_rspca_l1.py (#1) - optimise SVD choice - small other cleanup * Check package installed before making DCT class * Remove unused import * Remove Profiles class and methods from basic Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> * Convert relative to absolute imports * Add pytest-benchmark * Update noxfile for pytest-benchmark * ignored python-version * Update .gitignore * switched to commented line * refactor name to basicpy * further refactored... * changed dir name * refactor `predict` to `transform` * Update README.md change PyBaSiC to BaSiCPy * Implement logging (#44) * added logging package to all * trying to fix logging in main * initial attempt to add logger logging to each files * fixed typo * fixed main logger typo * fixed import style * added actual logs in the calculation * changed logger to class-level * added log for inexact_alm * fixed main.py logging level and added warning in dct2d_tools. * made BaSiC logger to file-level * Feat/jax dct (#46) * Add custom JAX idct function * Refactor idct * Fix tests Co-authored-by: Fukai Yohsuke <[email protected]> * Add save and load methods (#43) * Add save and load methods * Update docstring * Update load_model test * Add overwrite option and tests to save_model * Update save/load tests Co-authored-by: Fukai Yohsuke <[email protected]> * Update README.md (#49) * Update README.md * Update README.md * removed dropbox link from the link * Update README.md Co-authored-by: Fukai Yohsuke <[email protected]> * fixed pydantic version lower bound to get test_basic_save_model succeeded * set the license to MIT * removed pydantic version * Testing fit method with synthetic data (#53) * added logging package to all * trying to fix logging in main * initial attempt to add logger logging to each files * fixed typo * fixed main logger typo * fixed import style * added actual logs in the calculation * changed logger to class-level * added log for inexact_alm * added synthesized fit test * changed threshold for error * fixed typo for sign * added pooch for Zenodo datasets * some fix... * fixed pooch data bug * Revert "added pooch for Zenodo datasets" This reverts commit 4fdf0d7. * removed logger from class * refactor and added code for debug plotting in test_basic_fit_synthesized * Data in package (#57) * added files * added fetch code to data module * formatted data... * added data download function * added docstring * updated comment * added docstring for all * added test download * added pooch for dependency * typo fix... * fixed typo... * parametrized tests * disabled hash checking * fixed bug * Revert "fixed bug" This reverts commit 6b24503. * Revert "disabled hash checking" This reverts commit d0dbd8a. * added data and tests * changed data url to the dev branch * added tests * added pydantic version to get test_basic_save_model succeed * added tests for original dataset * added code for original fetch * added exception for invalid data cases * reference commit with * switched to dev branch * Fixed typo for data.py comments * Major update with LADMAP implementation (#62) * added logging package to all * trying to fix logging in main * initial attempt to add logger logging to each files * fixed typo * fixed main logger typo * Add custom JAX idct function * Refactor idct * fixed import style * added actual logs in the calculation * changed logger to class-level * added log for inexact_alm * added synthesized fit test * changed threshold for error * fixed typo for sign * added pooch for Zenodo datasets * some fix... * fixed pooch data bug * Revert "added pooch for Zenodo datasets" This reverts commit 4fdf0d7. * wrote tests for experimental data * added files * added fetch code to data module * formatted data... * added data download function * added docstring * updated comment * added docstring for all * added test download * added pooch for dependency * typo fix... * fixed typo... * parametrized tests * disabled hash checking * fixed bug * Revert "fixed bug" This reverts commit 6b24503. * Revert "disabled hash checking" This reverts commit d0dbd8a. * added jax experimental code and tested tingying's implementation * experimental implementation wroking to approximate darkfield * at least jit version is working * deleted old version codes * refactor to include D_R and D_Z * added darkfield 1 * experimental code working * loop jit * fixed package name * merged Tim's idct * jax impl working with Tim's idct * ladmap code is fed into the basicpy class (still a bit slow?) * converted _fit_ladmap_single to the member method * class method working... * refactored jnp.newaxis * in-class version working without jit * trying to add pytree property to the model but aborting this approach * writing jitted routine with new pydantic classes * added fields to jax routines * jit working * all jax working!! * apprioximate method not working with jax * confirmed approximate fit working in jax * organized files * import organize * single fit is working, but reweighting iteration is not working * reweighting loops is working! * still working example * still running... * resize implemented * fixed resize in transform * added _step_only_baseline for approximate fit * custom weight calc working * removed logger from class * approximate fit optimization changed to original imp. * working version with custom weight * working before baseline calculation * baseline calc working except approximate cases * trying to get baseline work for approximate fit * dropped python 3.7 * still approximate version not working... * some working version * approximate version working except baseline * baseline calc not working for approximate cases * sort_intensity option working for approximate fit! * removed comments * analyzing difference b/w original implementation * refactor and added code for debug plotting in test_basic_fit_synthesized * added data and tests * changed data url to the dev branch * added tests * added pydantic version to get test_basic_save_model succeed * added tests for original dataset * added code for original fetch * added exception for invalid data cases * reference commit with * switched to dev branch * added comparison w/ reference implementation at this time * Fixed typo for data.py comments * updated notebook * at least original impl is reproduced to some extent * slightly changed transform tests to get them working * Revert "Merge branch 'data_in_package' into jax_implementation" This reverts commit 9d30051, reversing changes made to a3d35ff. * deleted experimental note * added relative fitting weight argment * added fitting results at commit 11b0747 for testing * test rewriting but still failing * test working * added test with experimental data * added pytest-datadir in nox * migrated to pytest-datadir * made darkfield sparsity coef tunable * Revert "made darkfield sparsity coef tunable" This reverts commit 2b8cd5d. * loosen the isclose torelance * fixed typo in tests * deleted reference results * removed reference results * added additional darkfield coef and test passing * trying to modify dimensions * rewriting notebooks * deleted previous notebooks * notebook working * readme updated * example notebook added * fixed type * at least approximate method is working! * fixed some bugs * tests are running with loosened checks for experimental data * added 3D DCT * loosen the torelance for approximate fit * loosen darkfield torelance for approximate fit * changed DCT from 2D to 3D in ladmap fit * loosen torelance for ladmap * small modification * added constraint for S mean * get the test working * before adding positivity constraint * changed initial config * added naive mean S regularization * rewrote organizing test data notebook * added value_diff for update torelance * fixed convergence bug * ladmap working with modified stopping cond * working with modified stopping cond. (still harmonic ones not added) * added test data * removed cell output for jupyter notebook * removed cell output for jupyter notebook * updated test * loosened the darkfield test constraint * added guard for S==0 * updated example for lambda_flatfield_coef=100 * lambda_flatfield_coef=100 example update * updated flatfield and darkfield dimension for 3d images * updating organize test notebook * updated notebook path * notebook updated * re-added python 3.7 * added 3D test * refactored synthetic test * fixed tests * reduced z size in test * added rescue for RESOURCE_EXHAUSTED: Out of memory * updated enum type to str, Enum Co-authored-by: Tim Morello <[email protected]> Co-authored-by: Nicholas-Schaub <[email protected]> * Update contribution notes (#66) * initial draft * added git version for the original * 👥 Add @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Update @yfukai as a contributor * 👥 Add @tying84 as a contributor * 👥 Update @tying84 as a contributor * 👥 Update @tying84 as a contributor * 👥 Add @tdmorello as a contributor * 👥 Update @tdmorello as a contributor * 👥 Update @tdmorello as a contributor * 👥 Add @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @Nicholas-Schaub as a contributor * trying to see how all-contributors works * reordered contributors * regenerated readme * commenting on contrinbution * organized README * updated nick email, added contributions to Tingying * removed experimental_code reference * updated jaxlib version to avoid importerror (#69) * Merge Yu's docs * deleting files not used at this point * enab * re-added autoflake and isort * removed opencv * Feat/release (#72) * setup.cfg * Create release pipeline * Updated config and added new details to README * Fixed build pipeline, added MANIFEST * Fixed formatting issues * Fixed typo in README * Moved bumpversion config to separate file * Fixed whitespace in bumpversion config * Exclude bumpversion config from whitespace checks * Bump version: 0.1.0-dev0 → 0.2.0-dev0 * Fix/release (#75) * setup.cfg * Create release pipeline * Updated config and added new details to README * Fixed build pipeline, added MANIFEST * Fixed formatting issues * Fixed typo in README * Moved bumpversion config to separate file * Fixed whitespace in bumpversion config * Exclude bumpversion config from whitespace checks * Bump version: 0.1.0-dev0 → 0.2.0-dev0 * Modified config, updated VERSION * Bump version: 0.2.0-dev0 → 0.2.0-dev1 * Update secrets environment * Bump version: 0.2.0-dev1 → 0.2.0-dev2 * Updated twine upload command * Bump version: 0.2.0-dev2 → 0.2.0-dev3 * Updated CI pipeline * Bump version: 0.2.0-dev3 → 0.2.0-dev4 * Use pypa publishing container * Bump version: 0.2.0-dev4 → 0.2.0-dev5 * Update build * Bump version: 0.2.0-dev5 → 0.2.0-dev6 * 👥 Update @Nicholas-Schaub as a contributor * 👥 Update @tdmorello as a contributor * 👥 Add @YuLiu-web as a contributor * update readme * 👥 Update @tying84 as a contributor * add tingying organizing meetings * Fix `lambda flatfield` bug (#74) * fixed bug for 3d images and lambda_flatfield calc * reorganized test data * Bump version: 0.2.0-dev6 → 0.2.1-dev0 * fixed save bug for 3D images and added tests (#77) * updated jaxlib dependency * updated notebooks * 👥 Update @tdmorello as a contributor * some update * fixed typos * Update docs * fixed typos * changed default parameters * updated examples * Add comments for notebook gallery * Update notebooks * compared lagrangian with the origin implementation * notebook update * formatted notebooks with black * added markdowns to notebooks * ifurther updated notebooks * Add contributing guide to docs * Add autoenum to docs * updated notebooks * updated thumbnail data for docs * updated readme * ignored package lock file for yarm * fixed type * added windows instruction * 👥 Update @YuLiu-web as a contributor * fixed notebook folder * fixed typo * added macos and windows tests * test falling back to ubuntu * added jax installation in noxfile for windows * migrated contribution details to the docs * update badges * fixed badges * a bit more update... * fixed readme * fixed badgee stype * further fix... * Timelapse option in `transform` (#80) * udpated transform method * fixed tests * fixed typo * solving problems with tests * fixed transform bug * removed tests for rescaling-fitting * removed resized transform example * added dask test * set baseline type to optinal * updated testdata * deleted notebook outputs * Update timelapse * re-organized transform part * tests running... * made the resize method changable * resize method tested * tested resize method * added comments for the transform function * minor fix * fixed fitting_weight shape bug Co-authored-by: Tim Morello <[email protected]> * Update example data (#92) * updating notebooks * updated rescaled data * updated test data * update notebooks * Fixed most unit tests * re-added reference comparison notebook * re-added test data Co-authored-by: Nicholas-Schaub <[email protected]> * Fix `fit` bug for dask array inputs (#93) * udpated transform method * fixed tests * fixed typo * solving problems with tests * fixed transform bug * removed tests for rescaling-fitting * removed resized transform example * added dask test * set baseline type to optinal * updated testdata * deleted notebook outputs * Update timelapse * re-organized transform part * tests running... * made the resize method changable * resize method tested * tested resize method * added comments for the transform function * minor fix * fixed fitting_weight shape bug * fixed dask-related bug Co-authored-by: Tim Morello <[email protected]> * Update hashes (#95) * Minor change before beta release (#96) * DCT tools update (#98) * updated hashes to newer ones * changed source to main * ci experiment with dev branch * updated branch * added tests for wrong argments * updated classifier to beta * updated copyright * just added spaces * updated downsampled data to Zenodo * renamed data to datasets * typo fix... * deleted depricated tools * fixed package names ... * import fix * 👥 Update @yfukai as a contributor * added my contribution for ci... * removed deprecated routines from old DCT2d * updated tests and fixed jax version to solve problems * Update coef definitions (#103) * updated hashes to newer ones * changed source to main * ci experiment with dev branch * updated branch * added tests for wrong argments * updated classifier to beta * updated copyright * just added spaces * updated downsampled data to Zenodo * renamed data to datasets * typo fix... * deleted depricated tools * fixed package names ... * import fix * 👥 Update @yfukai as a contributor * added my contribution for ci... * removed deprecated routines from old DCT2d * trying to add darkfield weight and changing weight for ladmap * fixed typo * added attribute * updated tests and fixed jax version to solve problems * rewrite ladmap to normalize B * working ver? * updated test data * udpated weight for darkfield * updated test data * removed print * fixed normalization const * added test to show basic does not depend on the intensity scale * small update * added installation doc for M1 chips * updated installation instruction for M1 mac * reverted some merge changes * Update README.md Co-authored-by: Tim Morello <[email protected]> Co-authored-by: Tim Morello <[email protected]> Co-authored-by: Nicholas-Schaub <[email protected]> Co-authored-by: Mahdi Lamb <[email protected]> Co-authored-by: Tingying Peng <[email protected]> Co-authored-by: YuLiu-web <[email protected]>
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An attempt to add
timelapseoption intransform. Also did some refactoring of comments and examples.