Scico

----------------------------

• No changes yet.

----------------------------

• 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.

----------------------------

• 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.

----------------------------

• 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.

----------------------------

• 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.

----------------------------

• 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.