v0.14.1

ASPIRE v0.14.1 is patch release focused on reproducing MATLAB results and bringing in some bug fixes.

This release provides the following features:

• Fix RelionSource image loading bug (large speedup)
• legacy_ preprocessing methods, (deprecates legacy=True flags)
• Reproduce MATLAB CTF Filter
• Reproduce MATLAB Crop
• Reproduce MATLAB Phaseflip
• Reproduce MATLAB Normalize Background
• Reproduce MATLAB Whitening
• Default to DiracBasis3D for recons
• Migrate pixel_size out of filter init
• Migrate towards Relion _rlnOriginX(Y)Angst offsets convention
• Add pixel_size to Coef class

Bug fixes:

• Polar cross corr FFT axis fix
• pixel_size passthrough for ClassAvgSource and DenoisedSource
• Downsample pixel_size bug fix

Documentation:

• Ribosome Legacy Preprocess Example
  • Reproduces MATLAB preprocessing to single precision

v0.14.0

ASPIRE v0.14.0 is minor release, adding scientific features, bug fixes, and many updates.

This release provides the following features:

• Fast Polar Fourier Rotational Alignment for 2D class averages
• IRLS Common Lines Algorithm
• LUD Common Lines Algorithm
• MATLAB reproducing legacy downsample flag option
• MATLAB reproducing legacy normalize_background flag option
• Load pixel_size from STAR file for RelionSource
• Add optional pixel_size to initializer CoordinateSource
• Icosahedral I symmetry
• Migrate from error to warning on incorrect Volume.rotate dtypes
• Permit corrupt MRC files in RelionSource and CoordinateSource

Bug fixes:

• Fix flaky LUD unit test
• Admit rectangular micrographs in CoordinateSource
• Fix flakey BOT_align unit test
• Fix OrientedSource save_mode=single
• Continuous patching of evolving Numpy2 casting behavior changes
• Resolve ambiguous dtype in image.downsample

Updates and Cleanup:

• Remove Numpy2 experimental feature warning
• Update registry hash for emdb_14621
• Add scheduled downloader unit test
• Deduplicate coor_trans and rotation code
• Use scipy's create_group for SymmetryGroups
• Migrate finufft and cufinufft to v2.4.0
• Pipeline demo tutorial updates

Systems/CI Updates:

• Flake8 updates
• PyProject packaging updates
• Ubuntu OS CI platform upgrade
• Windows CI platform upgrade

v0.13.2

ASPIRE v0.13.2 is a patch release, adding multiple fixes, updates, and new supporting features.

This release provides the following features:

• legacy_whitening isotropic noise estimator
• sph_harm updates/optimizations
• grid and Filter caching
• Batched (GPU) class average BFR alignment

Bug fixes and cleanup:

• Large scale image stacking OOM
• nearest_rotation patch
• CTFFilter correction
• SymmetryGroup warnings
• more dtype cleanup
• Remove all remaining legacy m_ usage
• Support mrcs file extension
• IndexedSource filter mapping

Systems/CI Updates:

• Numpy 2 support
• Scipy 1.15 support
• Remove deprecated cufinufft workaround
• Migrate gallery loggers toward print
• CI downloader caching

v0.13.1

ASPIRE v0.13.1 is patch release, adding optimizations, increasing GPU
Common Lines acceleration, updating systems/platform and fixing several bugs.

This release provides the following features:

• CUDA Common Lines Matrix kernel (CLOrient3D)
• CUDA Estimate Initial Rotations kernel (CLSync3N)
• CUDA Euler angle to rotation matrix kernel(CLSync3N)
• Added internal common line class caching
• Improve default saving overwrite behavior
• Adds DiracBasis2D and DiracBasis3D

Bug fixes:

• Whiten/PowerFilter extremal values
• Estimate shifts validation and patches
• Simulation amplitude/offset resampling

Systems/CI Updates:

• Drop Python 3.8, add Python 3.12
• Improve CI GPU code coverage
• tox updates and minor linting updates
• Restore codecov reporting
• Extend codecov report to include GPU job
• Windows specific conda environment (workaround MKL 2022 issues)

v0.13.0

ASPIRE v0.13.0 is minor release, adding new scientific features, GPU basis acceleration, updates and bug fixes.

This release provides the following features:

• CLSync3N Common Lines algorithm
• CLSymmetryD2 Common Lines algorithm
• GPU Acceleration of FFBBasis2D and FLEBasis2D
• GPU Acceleration of FFBBasis3D
• Pixel size attributes for Image, Volume, and ImageSource
• Optimized spherical harmonic computations
• Adds Sinogram GPU accelerated line projection class

Bug fixes:

• Reconcile rotation estimation with legacy MATLAB
• Reconcile shift estimation with legacy MATLAB
• Fix fuzzy_mask defaults and adds low pixel patch
• Relion/ASPIRE image offset conventions
• whiten filter thresholds
• Remove FINUFFT workarounds for old releases
• SymmetryGroup pass-through
• wemd centering patch
• MeanEstimator defaults
• Minor 10081 gallery udpates

Testing:

• Long running workflow speedups (fixture reuse)
• Reduced batched covar2D test variability
• Warnings cleanup (Linux 3.8-3.11, M1 3.9)
• Adds initial tests for common line algorithms with shifts

Systems/CI Updates:

• Native Apple Silicon support
• Remove pyshtools dependency
• Adds OSX ARM CI platform
• FINUFFT/cuFINUFFT major release updates
• Update CodeCov Auth

v0.12.3

ASPIRE v0.12.3 is patch release adding several fixes and updates.

This release provides the following features:

• Symmetry boosting for MeanEstimator
• SymmetryGroup parsing
• MeanEstimator checkpointing
• Double precision RelionSource
• Codify default 3D basis for Estimator (FFB3D).

Bug fixes:

• Update Projection-Backprojection conventions
• J-Sync index bug
• Circular import fix
• CLOrient3D Lazy Eval
• evaluate_src_filters_on_grid initializer
• IndexedSource caching

Systems/CI Updates:

• FFT swap
• Fix pydantic dependency for ray>2.9
• Bump OSX runner images
• Begin updates for Numpy 2 (WIP)
• sklearn package updates
• pytest updates
• Github Actions checkout and setup-python updates
• Github Actions setup-miniconda updates
• gemmi release updates
• CUDA 12 support and extension environment updates
• finufft 2.2.0 updates
• cufinufft 2.2.0 updates
• black style updates
• scipy updates for 1.14.0

Documentation:

• Minor documentation updates
• Progress bars for common lines methods

v0.12.2

This is a small patch release to update several dependent packages with recent versions.

It includes commits for the following:

• Enforcing the latest version of gemmi and the associated code change
• Very minor doc updates
• Symmetry Boosting in MeanEstimator
• finufft version updates
• cufinufft version updates
• Ability to load RelionSources as double precision
• MeanEstimator volume coef checkpointing
• Minor flake/black style updates

v0.12.1

ASPIRE v0.12.1 is bugfix release, adding a mix of new features and cleanup.

This release provides the following features:

• Interoperable 2D basis (covar2d, class averaging)
• Improved Relion interoperability
• Common Line SDP method
• Shared 2D Basis tests
• Common Lines optional fuzzy mask
• Add Coef class
• Nearest rotation (SVD) util method
• FRC and FSC plotting option (disable cutoff)

Bug fixes:

• Enforce grid conventions
• FLE expand unit test convergence
• Sync voting unit test patch
• Whitening extremal value patch
• Adds improved image projection tests
• Adds improved volume rotation tests
• FBBasis3D NaN values for large resolution
• {F}PSWF basis float32 patch
• Extend eval_coords to many volumes
• Enforce block dtypes on assignment
• Reduce package import resource util

Systems/CI Updates:

• Flake8 Style Updates
• Add public Issue template
• Docstring cleanup
• Adds docstring linting util to CI
• Additional pytest conversions
• Removes parameterized_class
• Workaround Ray/pydantic dependency conflict

Documentation:

• Adds Relion interoperability gallery
• Adds Weighted spectral volume gallery
• Update public facing Code of Conduct
• Add K2 camera note to CTF estimator module
• Removes deprecated legacy example scripts

v0.12.0

ASPIRE v0.12.0 is minor release, adding new scientific features, components, and several improvements.

This release provides the following features:

• MicrographSimulation component
• MicrographSources with CoordinateSource integration
• Data Downloader utility (via pooch)
• WeightedVolumesEstimator for heterogeneous 3D reconstruction
• TIFF Image loading support
• Common Lines method for C2 symmetry
• DiagMatrix operator

Bug fixes:

• clean_image caching
• Apple unit test patch (following numpy updates)
• Rename PolarBasis2D to PolarFT and consistently use compact (real symmetric) representation

Systems/CI Updates:

• Add Python 3.11, drop Python 3.7
• Modernize Python packaging via pyproject.toml
• Warnings cleanup
• Migrate several tests towards pytest.fixture
• Modular and pytest.fixture based tests for Common Lines methods
• Reduce APPLE unit test time
• Apple M1/M2 arm-64 install documentation
• cufinufft v1.3 final adoption
• GRPC dependency updates

v0.11.1

ASPIRE v0.11.1 is patch release, mainly for minor demo updates.

This release provides the following features:

• FourierRingCorrelation and FourierShellCorrelation

Bug fixes:

• Tutorial MRC file download path
• Reorders FLE indices to aid in compatibility with FB
• Exposes class indices attributes in more places (after Source slicing)
• Improved CL logging messages

Systems/CI Updates:

• Simplifies install instructions