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Recent Releases of Scientific Computational Imaging Code (SCICO)

Scientific Computational Imaging Code (SCICO) - Version 0.0.6

Change Summary

• Significant changes to linop.xray.astra API. • Rename integrated 2D X-ray transform class to linop.xray.XRayTransform2D and add filtered back projection method fbp. • New integrated 3D X-ray transform via linop.xray.XRayTransform3D. • New functional functional.IsotropicTVNorm and faster implementation of functional.AnisotropicTVNorm. • New linear operators linop.ProjectedGradient, linop.PolarGradient, linop.CylindricalGradient, and linop.SphericalGradient. • Rename scico.numpy.util.parse_axes to scico.numpy.util.normalize_axes. • Rename scico.flax.save_weights and scico.flax.load_weights to scico.flax.save_variables and scico.flax.load_variables respectively. • Support jaxlib and jax versions 0.4.13 to 0.4.35. • Support flax versions 0.8.0 to 0.10.0.

Changes in Detail

  • Post-release preparation for next release by @bwohlberg in https://github.com/lanl/scico/pull/489
  • Resolve some packaging issues by @bwohlberg in https://github.com/lanl/scico/pull/490
  • Resolve packaging error by @bwohlberg in https://github.com/lanl/scico/pull/491
  • Various changes, primarily testing-related by @bwohlberg in https://github.com/lanl/scico/pull/492
  • Update conda installation instructions by @bwohlberg in https://github.com/lanl/scico/pull/494
  • Fix readthedocs build by @bwohlberg in https://github.com/lanl/scico/pull/495
  • Clean up and extend linop.xray.astra interface by @bwohlberg in https://github.com/lanl/scico/pull/496
  • Various improvements to scico.flax and related example scripts by @bwohlberg in https://github.com/lanl/scico/pull/498
  • Correctly check for nested tuple in mapfuncovertupleof_tuples by @Michael-T-McCann in https://github.com/lanl/scico/pull/500
  • Reduce memory requirements of Identity linop by @bwohlberg in https://github.com/lanl/scico/pull/501
  • Improve GPU handling in linop.xray.astra by @bwohlberg in https://github.com/lanl/scico/pull/505
  • Fix L21Norm handling of BlockArray input by @bwohlberg in https://github.com/lanl/scico/pull/506
  • Fixed minor documentation mistake by @Danaroth83 in https://github.com/lanl/scico/pull/508
  • Resolve dependency problems by @bwohlberg in https://github.com/lanl/scico/pull/511
  • Add support for approximate isotropic TV norm by @bwohlberg in https://github.com/lanl/scico/pull/507
  • Update black version requirement and apply latest version to source by @bwohlberg in https://github.com/lanl/scico/pull/514
  • Fix badge layout in main README by @bwohlberg in https://github.com/lanl/scico/pull/516
  • Rearrange ray initialization to avoid RuntimeWarning by @bwohlberg in https://github.com/lanl/scico/pull/515
  • Bump maximum jaxlib / jax version by @bwohlberg in https://github.com/lanl/scico/pull/504
  • Add support for np.newaxis to indexing syntax supported by linop.Slice by @bwohlberg in https://github.com/lanl/scico/pull/517
  • Bump jaxlib/jax and flax max versions by @bwohlberg in https://github.com/lanl/scico/pull/518
  • Fix minor error in linop.xray.astra docs by @bwohlberg in https://github.com/lanl/scico/pull/520
  • Minor docs fixes by @bwohlberg in https://github.com/lanl/scico/pull/522
  • Resolve some deprecation warnings by @bwohlberg in https://github.com/lanl/scico/pull/523
  • Move Sphinx API submodule table to top of module summary by @bwohlberg in https://github.com/lanl/scico/pull/525
  • Alternative version of indexed_shape with a different name by @bwohlberg in https://github.com/lanl/scico/pull/527
  • Improve TVNorm implementation by @bwohlberg in https://github.com/lanl/scico/pull/526
  • Resolve #528 by @bwohlberg in https://github.com/lanl/scico/pull/532
  • Resolve #530 by @bwohlberg in https://github.com/lanl/scico/pull/531
  • Improve docs for linop.xray subpackage by @bwohlberg in https://github.com/lanl/scico/pull/533
  • Add diagonal operator mapping base operator over an array axis by @bwohlberg in https://github.com/lanl/scico/pull/521
  • Fix typo in docs by @bwohlberg in https://github.com/lanl/scico/pull/538
  • Fix 2D X-ray projector bugs by @Michael-T-McCann in https://github.com/lanl/scico/pull/537
  • Update examples by @bwohlberg in https://github.com/lanl/scico/pull/540
  • Add linear operators computing gradients in non-Cartesian coordinates by @bwohlberg in https://github.com/lanl/scico/pull/536
  • Improve docs for 3D astra X-ray transform by @bwohlberg in https://github.com/lanl/scico/pull/544
  • Fix bug in tests and avoid variability in numerical precision across devices by @bwohlberg in https://github.com/lanl/scico/pull/545
  • Resolve #535 by @crstngc in https://github.com/lanl/scico/pull/541
  • Bump maximum supported jax version to 0.4.31 by @bwohlberg in https://github.com/lanl/scico/pull/546
  • Fix docs figure display in furo theme "dark" mode by @bwohlberg in https://github.com/lanl/scico/pull/547
  • Fix minor bug in scico.functional.TVNorm by @bwohlberg in https://github.com/lanl/scico/pull/548
  • Various changes by @bwohlberg in https://github.com/lanl/scico/pull/549
  • Resolve some sphinx build warnings by @bwohlberg in https://github.com/lanl/scico/pull/550
  • Add JAX 3D X-ray CT projector by @Michael-T-McCann in https://github.com/lanl/scico/pull/529
  • Point data to correct branch by @Michael-T-McCann in https://github.com/lanl/scico/pull/552
  • Add caveat on 3D X-ray projector by @Michael-T-McCann in https://github.com/lanl/scico/pull/554
  • Transition to Read the Docs Addons by @bwohlberg in https://github.com/lanl/scico/pull/556
  • Changes required to support jax version 0.4.33 by @bwohlberg in https://github.com/lanl/scico/pull/555
  • Fix XRayTransform2D projection dtype and docs by @Michael-T-McCann in https://github.com/lanl/scico/pull/557
  • Fix XRayTransform boundary conditions by @Michael-T-McCann in https://github.com/lanl/scico/pull/561
  • Add filtered back projection for 2D projector by @bwohlberg in https://github.com/lanl/scico/pull/558
  • Switch ML examples to integrated X-ray transform by @bwohlberg in https://github.com/lanl/scico/pull/562
  • Clean up CT examples by @bwohlberg in https://github.com/lanl/scico/pull/563
  • Changes for release 0.0.6 by @bwohlberg in https://github.com/lanl/scico/pull/565

New Contributors

  • @Danaroth83 made their first contribution in https://github.com/lanl/scico/pull/508

Full Changelog: https://github.com/lanl/scico/compare/v0.0.5...v0.0.6

Scientific Software - Peer-reviewed - Python
Published by bwohlberg over 1 year ago

Scientific Computational Imaging Code (SCICO) - Version 0.0.5

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

New Contributors

  • @shnaqvi made their first contribution in https://github.com/lanl/scico/pull/456

Full Changelog: https://github.com/lanl/scico/compare/v0.0.4...v0.0.5

Scientific Software - Peer-reviewed - Python
Published by bwohlberg over 2 years ago

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

New Contributors

  • @wjgancn made their first contribution in https://github.com/lanl/scico/pull/349
  • @Sibgatulin made their first contribution in https://github.com/lanl/scico/pull/391

Full Changelog: https://github.com/lanl/scico/compare/v0.0.3...v0.0.4

Scientific Software - Peer-reviewed - Python
Published by bwohlberg almost 3 years ago

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

Full Changelog: https://github.com/lanl/scico/compare/v0.0.2...v0.0.3

Scientific Software - Peer-reviewed - Python
Published by bwohlberg over 3 years ago

Scientific Computational Imaging Code (SCICO) - Version 0.0.1

Change Summary

  • Initial release.

Changes in Detail

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

New Contributors

  • @lukepfister made their first contribution in https://github.com/lanl/scico/pull/4
  • @crstngc made their first contribution in https://github.com/lanl/scico/pull/68

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

Scientific Software - Peer-reviewed - Python
Published by bwohlberg over 4 years ago

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

New Contributors

  • @SauravMaheshkar made their first contribution in https://github.com/lanl/scico/pull/141

Full Changelog: https://github.com/lanl/scico/compare/v0.0.1...v0.0.2

Scientific Software - Peer-reviewed - Python
Published by bwohlberg over 4 years ago