Releases · lanl/scico · GitHub

19 Dec 02:14

bwohlberg

Version 0.0.5 Latest

Latest

Change Summary

New functionals functional.AnisotropicTVNorm and functional.ProximalAverage with proximal operator approximations.
New integrated Radon/X-ray transform linop.XRayTransform.
New operators operator.DiagonalStack and operator.VerticalStack.
Rename modules radon_astra and radon_svmbir to xray.astra and xray.svmbir respectively, and rename TomographicProjector classes to XRayTransform.
Rename AbelProjector to AbelTransform.
Rename solver.ATADSolver to solver.MatrixATADSolver.
Rename some __init__ parameters of linop.DiagonalStack and linop.VerticalStack.
Support jaxlib and jax versions 0.4.3 to 0.4.23.
Support flax versions up to 0.7.5.
Use orbax for checkpointing flax models.

Changes in Detail

Prepare for development of version 0.0.5 by @bwohlberg in #436
Add a jax-based X-ray projector by @Michael-T-McCann in #433
Bump maximum jaxlib/jax versions by @bwohlberg in #452
Resolve warnings with jaxlib/jax 0.4.16 by @bwohlberg in #454
Make bm3d and bm4d optional by @bwohlberg in #458
Resolve #445 by @bwohlberg in #459
Rename linear problem solver and add parameter type checking by @bwohlberg in #457
Address deprecation warning in scico.flax by @bwohlberg in #455
Updates required by recent changes in ray by @bwohlberg in #462
Remove ensure_on_device function by @bwohlberg in #463
Various improvements related to the new X-ray transform implemementation. by @bwohlberg in #461
Added a new Functional for TV Norm by @shnaqvi in #456
Clean up some example scripts and rerun some notebooks by @bwohlberg in #464
Resolve obstacles to jitting of some functionals by @bwohlberg in #467
Add proximal average implementation by @bwohlberg in #469
Resolve #468 by @bwohlberg in #470
Fix fractional centers in CircularConvolve by @Michael-T-McCann in #471
Update the SCICO x-ray projector by @Michael-T-McCann in #473
Miscellaneous changes by @bwohlberg in #475
Update data submodule to point to data's current main by @Michael-T-McCann in #476
Flax checkpoint updates by @crstngc in #472
Add Operator versions of DiagonalStack and VerticalStack by @bwohlberg in #477
Resolve #479 by @bwohlberg in #480
Resolve #478 by @bwohlberg in #481
Bump maximum supported jaxlib/jax version by @bwohlberg in #482
Resolve #483 by @bwohlberg in #484
Resolve numerous deprecation warnings by @bwohlberg in #485
Various changes by @bwohlberg in #487
Release 0.0.5 by @bwohlberg in #488

New Contributors

@shnaqvi made their first contribution in #456

Full Changelog: v0.0.4...v0.0.5

Contributors

shnaqvi, bwohlberg, and 2 other contributors

Assets 2

04 Aug 01:18

bwohlberg

Version 0.0.4

Change Summary

Add new Function class for representing array-to-array mappings with more than one input.
Add new methods and a function for computing Jacobian-vector products for Operator objects.
Add new proximal ADMM solvers.
Add new ADMM subproblem solvers for problems involving a sum-of-convolutions operator.
Extend support for other ML models including UNet, ODP and MoDL.
Add functionality for training Flax-based ML models and for data generation.
Enable diagnostics for ML training loops.
Support jaxlib and jax versions 0.4.3 to 0.4.14.
Change required packages and version numbers, including more recent version for flax.
Drop support for Python 3.7.
Add support for 3D tomographic projection with the ASTRA Toolbox.

Changes in Detail

Bump version for next release by @bwohlberg in #347
Resolve conflicts in merging main into cristina/more-flax by @bwohlberg in #348
Resolve #283 by @bwohlberg in #352
Resolve #152 by @bwohlberg in #351
Resolve issue #291 by @bwohlberg in #355
Resolve issue #240 by @bwohlberg in #354
Indicator documentation notation by @tbalke in #353
Remove jaxlib/jax version tests in scico/__init__.py by @bwohlberg in #358
Add references to JOSS paper by @bwohlberg in #362
Resolve issue #356 by @bwohlberg in #360
Fix support for building docs offline by @bwohlberg in #359
Remove deprecated numpy function and bump jaxlib/jax versions by @bwohlberg in #365
Minor docstring fixes by @bwohlberg in #366
Improve operator support for Jacobian-vector products by @bwohlberg in #367
Update dependencies by @bwohlberg in #369
Resolve test failures by @bwohlberg in #370
Add DnCNN with noise level input by @wjgancn in #349
Add proximal ADMM solvers by @bwohlberg in #371
Make compatible with jax_0.4.1 by @Michael-T-McCann in #372
Create common base class for optimizer classes. by @bwohlberg in #375
Additional CNN methods by @Michael-T-McCann in #325
Various improvements, mainly related to cleaning up example scripts by @bwohlberg in #379
Clean up docs source files by @bwohlberg in #381
Add checking for unrecognized keyword arguments by @bwohlberg in #382
Update favicon and fix pre-commit hook helper script by @bwohlberg in #384
Suppress annoying jax device warning by @bwohlberg in #385
Miscellaneous docs fixes by @bwohlberg in #386
Resolve some typing errors by @bwohlberg in #389
Fix a few typos in docstrings and an example by @Sibgatulin in #391
Reduce github pytest workflow runtime using pytest-split by @bwohlberg in #390
Fix unit test status badge and link by @bwohlberg in #393
Resolve issue #395 by @bwohlberg in #396
Add ipython extensions and requirements to fix #397 by @tbalke in #398
Drop support for Python 3.7 by @bwohlberg in #403
Replace generic Exception with more specific exceptions where possible by @bwohlberg in #405
Address #400 by @bwohlberg in #401
Rewrite of scico.ray.tune by @bwohlberg in #402
Bump jaxlib/jax minimum versions by @bwohlberg in #399
Transition from DeviceArray to jax.Array by @bwohlberg in #410
Add ADMM subproblem solvers by @bwohlberg in #411
Make adjoint and gram get auto set separately by @Michael-T-McCann in #414
Resolve #261 by @bwohlberg in #416
Resolve #165 by @bwohlberg in #415
Resolve #83 by @bwohlberg in #417
Resolve #377 by @bwohlberg in #418
Add broadcast_block_shapes by @Michael-T-McCann in #419
Remove Edit on Github button (again) by @bwohlberg in #422
Docs fixes by @bwohlberg in #420
Resolve #173 by @bwohlberg in #425
Add ADMM subproblem solver for matrix operators by @bwohlberg in #426
Resolve #412 by @bwohlberg in #428
Add support for 3D tomographic projection with astra by @Michael-T-McCann in #427
Docs improvements by @bwohlberg in #430
Cristina/docs flax by @crstngc in #429
Bump max jax version by @bwohlberg in #434
Changes for release 0.0.4 by @bwohlberg in #435

New Contributors

@wjgancn made their first contribution in #349
@Sibgatulin made their first contribution in #391

Full Changelog: v0.0.3...v0.0.4

Contributors

Sibgatulin, bwohlberg, and 4 other contributors

Assets 2

22 Sep 03:54

bwohlberg

Version 0.0.3

Change Summary

Change required packages and version numbers, including more recent version requirements for numpy, scipy, svmbir, and ray.
Package bm4d removed from main requirements list due to issue #342.
Support jaxlib versions 0.3.0 to 0.3.15 and jax versions 0.3.0 to 0.3.17.
Rename linear operators in radon_astra and radon_svmbir modules to TomographicProjector.
Add support for fan beam CT in radon_svmbir module.
Add function linop.linop_from_function for constructing linear operators from functions.
Enable addition operator for functionals.
Completely new implementation of BlockArray class.
Additional solvers in scico.solver.
New Huber norm (HuberNorm) and set distance functionals (SetDistance and SquaredSetDistance).
New loss functions loss.SquaredL2AbsLoss and loss.SquaredL2SquaredAbsLoss for phase retrieval problems.
Add interface to BM4D denoiser.
Change interfaces of linop.FiniteDifference and linop.DFT.
Change filenames of some example scripts (and corresponding notebooks).
Add support for Python 3.7.
New DiagonalStack linear operator.
Add support for non-linear operators to optimize.PDHG optimizer class.
Various bug fixes.

Changes in Detail

Preparation for next release by @bwohlberg in #226
Miscellaneous changes by @bwohlberg in #227
Check for blockarray inputs in from_operator by @Michael-T-McCann in #229
Revert SVD workaround by @Michael-T-McCann in #230
Make user-facing code use scico.random instead of np.random by @Michael-T-McCann in #235
Add loss functions for phase retrieval by @bwohlberg in #236
Fix bug and add example by @smajee in #246
Make bm3d dependency optional by @bwohlberg in #243
Fix readthedocs build failure by @bwohlberg in #248
Add doctest of modules to workflow, fix modules so they pass by @Michael-T-McCann in #247
Address missing examples in docs by @bwohlberg in #251
Minor clean up and packaging fix by @bwohlberg in #254
Add a mechanism to create linear operators from functions by @Michael-T-McCann in #249
Fix bugs in loss module by @bwohlberg in #255
svmbir refactor by @smajee in #252
Make SCICO compatible with jax 0.3.4 by @Michael-T-McCann in #256
Docs style fixes by @bwohlberg in #257
Add support for addition of functionals by @bwohlberg in #258
Sphinx autodoc configuration changes by @bwohlberg in #260
Update and fix conda environment construction script by @bwohlberg in #262
Solver and functional extensions by @bwohlberg in #264
Add BM4D by @smajee in #263
Misc bug fix by @smajee in #266
Bump pinned black version by @bwohlberg in #268
Bug fix by @bwohlberg in #267
Improve documentation for linop.optics by @bwohlberg in #233
Minor docs fix by @bwohlberg in #269
Minor additional improvements to conda script by @bwohlberg in #270
Make compatible with jax v0.3.5 by @Michael-T-McCann in #273
Change development version number structure by @bwohlberg in #271
Reduce test run time by @bwohlberg in #275
Improve SquaredL2SquaredAbsLoss by @bwohlberg in #278
Simplify BlockArray implementation by @Michael-T-McCann in #259
Fix typing errors and set up mypy workflow action by @bwohlberg in #176
Fix parameter name in example script by @bwohlberg in #286
Restore missing BlockArray docs by @bwohlberg in #285
Fix bugs introduced by BlockArray changes by @Michael-T-McCann in #282
Various improvements by @bwohlberg in #290
Improve docs by @Michael-T-McCann in #289
Bump maximum jax version and address imageio warnings by @bwohlberg in #294
Improve example checking script by @bwohlberg in #295
Modify FiniteDifference linop by @bwohlberg in #296
Clean up examples by @bwohlberg in #297
Improve handling of h_center parameter in linop.CircularConvolve by @bwohlberg in #299
Improve notebook build script by @bwohlberg in #300
Resolve import error by @bwohlberg in #302
Add Python 3.7 compatibility by @Michael-T-McCann in #301
Fix variable getting code for strings by @Michael-T-McCann in #303
Clean up ray.tune interface by @bwohlberg in #304
Improve script and resolve context-dependent test failure by @bwohlberg in #305
Update change summary by @bwohlberg in #306
Add google colab badge by @bwohlberg in #308
Add separable Huber norm and minor docs improvements. by @bwohlberg in #307
Added the name of the BlockArray class to repr by @FernandoDavis in #293
Extend interface of linop.DFT by @bwohlberg in #309
Extend L21Norm to support multiple l2 axes by @bwohlberg in #313
Update type checking command by @Michael-T-McCann in #314
Add block diagonal linear operator by @Michael-T-McCann in #315
Bump test tolerance by @Michael-T-McCann in #318
Make compatible with jax 0.3.15 by @Michael-T-McCann in #320
Miscellaneous changes by @bwohlberg in #321
Add PDHG solver with support for non-linear operators by @bwohlberg in #322
Minor improvements to scico.optimize docs by @bwohlberg in #328
Clean up Operator and LinearOperator module structure by @bwohlberg in #329
Address #335 by @bwohlberg in #336
Significant docs extension and restructuring by @bwohlberg in #332
Bump maximum jax version and some other small changes by @bwohlberg in #338
Address #324 by @bwohlberg in #339
Replaced gpu<->cpu copies with host_callback in minimize. by @FernandoDavis in #253
Resolve some components of #228 by @bwohlberg in #340
Various changes by @bwohlberg in #341
Mitigate impact of #342 by @bwohlberg in #343
Fix conda script and work around #344 by @bwohlberg in #345
Changes for 0.0.3 release by @bwohlberg in #346

Full Changelog: v0.0.2...v0.0.3

Contributors

bwohlberg, smajee, and 2 other contributors

Assets 2

18 Feb 01:20

bwohlberg

Version 0.0.2

Change Summary

Additional optimization algorithms: Linearized ADMM and PDHG.
Additional Abel transform and array slicing linear operators.
Additional nuclear norm functional.
New module scico.ray.tune providing a simplified interface to Ray Tune.
Move optimization algorithms into optimize subpackage.
Additional iteration stats columns for iterative ADMM subproblem solvers.
Renamed "Primal Rsdl" to "Prml Rsdl" in displayed iteration stats.
Move some functions from util and math modules to new array module.
Bump pinned jaxlib and jax versions to 0.3.0.

Changes in Detail

Add optional relaxation to ADMM solver by @bwohlberg in #118
Add codefactor badge by @bwohlberg in #120
Docstring cleanup and improvement of style guide compliance by @bwohlberg in #119
Added Markup section. by @FernandoDavis in #121
Clean up scico.solver module by @bwohlberg in #125
New optimization algorithms by @bwohlberg in #117
A collection of small docs updates by @Michael-T-McCann in #77
Run pytest on latest jax version by @Michael-T-McCann in #126
Add ray.tune interface and example script by @bwohlberg in #128
Improve iteration statistics mechanism by @bwohlberg in #130
Move optimizers into optimize package by @bwohlberg in #129
Bump jax version by @Michael-T-McCann in #134
Fix bugs in linop.optics by @bwohlberg in #131
Address codefactor complaints by @bwohlberg in #135
Changes to examples scripts by @bwohlberg in #137
Modify cg_kwargs mechanism in admm.LinearSubproblemSolver by @bwohlberg in #140
Add pylint to pre-commit by @SauravMaheshkar in #141
Miscellaneous changes by @bwohlberg in #143
Make pylint skip scico/test, docs/, and examples/ by @Michael-T-McCann in #145
Allow Diagonal to use broadcasting by @Michael-T-McCann in #144
Move common functions in example scripts into new module by @bwohlberg in #151
Remove problematic array copy operations by @bwohlberg in #156
Address some docs build warnings by @bwohlberg in #157
Fix explanation of weight in weighted CT example by @Michael-T-McCann in #158
Update installation instructions by @smajee in #154
Address readthedocs build failure by @bwohlberg in #169
Bump sphinx-autodoc-typehints version to avoid readthedocs build error by @Michael-T-McCann in #171
Address TODO in code by @Michael-T-McCann in #150
Silence docs build warnings by @bwohlberg in #174
Add array slicing LinearOperator by @bwohlberg in #162
Move some functions to different modules by @bwohlberg in #175
Make prox notation consistent by @Michael-T-McCann in #180
Add center_offset to svmbir interface by @smajee in #177
Fix some problems in DnCNN implementation and example by @bwohlberg in #185
Correct __module__ for wrapped functions by @Michael-T-McCann in #186
Make output types jax-array by @smajee in #187
Make pytest-latest-jax workflow get latest jax even with SCICO jax version pinned by @Michael-T-McCann in #189
Update conda install scripts by @bwohlberg in #178
Split pytest and pytest-latest by @Michael-T-McCann in #190
Refactor svmbir loss by @smajee in #191
Remove is_smooth attribute (#89) by @tbalke in #184
Fix scico.random failure with latest jax version by @bwohlberg in #194
Add Robust PCA example by @bwohlberg in #192
Poisson Example by @tbalke in #197
Replace tabs with spaces by @bwohlberg in #201
Add docs for scico.solver module by @bwohlberg in #202
Update notebooks by @tbalke in #206
Remove double spacing instances by @bwohlberg in #207
Improve ray.tune usage example. by @bwohlberg in #209
Miscellaneous minor improvements by @bwohlberg in #210
Change svd call to avoid compute_uv=False by @Michael-T-McCann in #214
Move denoiser implementations out of functional sub-module by @bwohlberg in #213
Add Abel linear operator by @smajee in #208
Add parameter documentation for h_center in CircularConvolve by @Michael-T-McCann in #217
Address excessive memory usage in functional.NuclearNorm.__call__ by @bwohlberg in #218
Fix type annotations in pgm by @tbalke in #219
Add check for A not linop in prox by @tbalke in #220
Add new example script by @bwohlberg in #221
Minor conda script changes by @bwohlberg in #222
Fix some typing and docstring issues by @bwohlberg in #223
Bump jaxlib, jax, and flax versions by @bwohlberg in #224
Final changes for 0.0.2 release. by @bwohlberg in #225

New Contributors

@SauravMaheshkar made their first contribution in #141

Full Changelog: v0.0.1...v0.0.2

Contributors

bwohlberg, smajee, and 4 other contributors

Assets 2

18 Feb 01:23

bwohlberg

Version 0.0.1

Change Summary

Initial release.

Changes in Detail

Set test_radon tolerances based on CPU/GPU by @lukepfister in #4
Add inital CI jobs by @lukepfister in #6
Add new loss with prox computed by svmbir.recon by @Michael-T-McCann in #5
Rename radon.py -> radon_astra.py by @lukepfister in #9
Switch to lukes personal email by @lukepfister in #12
Update ci-build.yml by @lukepfister in #13
Lukepfister/optics improvements by @lukepfister in #10
Fix up biconvolve docstring by @lukepfister in #14
Address docs build warnings by @bwohlberg in #18
Docs fixes by @bwohlberg in #21
Update svmbir install instructions by @bwohlberg in #24
Added additional information to error when data submodule is not present by @FernandoDavis in #20
Docs improvements by @bwohlberg in #28
Add 2D support to radon_svmbir by @Michael-T-McCann in #30
ADMM extensions by @bwohlberg in #29
Clean up example scripts by @bwohlberg in #26
Minor api docs improvements by @bwohlberg in #16
Allow ADMM f to be a Functional by @bwohlberg in #25
Add method for computing prox of convex conjugate of functional by @bwohlberg in #33
Minor test improvements by @bwohlberg in #39
Make random wrapping more robust to changes in jax.random by @Michael-T-McCann in #43
Fix scaling bug in CG by @tbalke in #45
Improve ADMM tests by @bwohlberg in #46
Add svmbir examples by @tbalke in #40
Improve notebooks build system by @bwohlberg in #51
Example script clean up by @bwohlberg in #50
Add features to PGM solver classes by @bwohlberg in #56
Mike's docs readthrough by @Michael-T-McCann in #53
Fixed SSLCertificate Error in Get_URL by @FernandoDavis in #58
Add a style guide for grammar to our style documentation by @Michael-T-McCann in #49
Additional improvements to the notebooks build system by @bwohlberg in #55
Print device info in example scripts by @bwohlberg in #59
Address user warnings in tests by @FernandoDavis in #54
Minor docs edits by @bwohlberg in #65
Rename usage examples by @bwohlberg in #67
Replace objax with flax by @crstngc in #68
Docstring cleanup by @bwohlberg in #70
Improve LinearOperator adjoint tests by @bwohlberg in #72
Pin jax version and update pip install instructions by @Michael-T-McCann in #73
Microscopy example scripts by @bwohlberg in #74
Improve usage overview docs by @bwohlberg in #76
Check todo in docs by @FernandoDavis in #71
Add function to compute operator norm by @bwohlberg in #79
Consistent notation for Hermitian conjugate by @bwohlberg in #87
Add tests for DnCNN by @bwohlberg in #85
Problem with W^1/2 weight exponent by @tbalke in #78
Skip test based on content of scico/data/examples by @bwohlberg in #99
Changes to admm and svmbir wrapper to address issue #57 by @smajee in #88
Rebuild examples by @Michael-T-McCann in #102
Add deterministic flag for DnCnn GPU-based tests by @Michael-T-McCann in #105
Add pylint check for missing docstrings by @Michael-T-McCann in #106
Stop codecov checking the patch by @Michael-T-McCann in #114
Fix ASTRA test in GPU issue #103 by @smajee in #107
Clean up notebooks build script by @bwohlberg in #108
Add missing requirement by @tbalke in #115
Modified SquareL2Loss to inherit from WeightedSquareL2Loss by @FernandoDavis in #112
Final changes for release 0.0.1 by @bwohlberg in #101

New Contributors

@lukepfister made their first contribution in #4
@crstngc made their first contribution in #68

Full Changelog: https://github.com/lanl/scico/commits/v0.0.1

Contributors

lukepfister, bwohlberg, and 5 other contributors

Assets 2