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

v0.11.0

ASPIRE v0.11.0 is minor release, adding several scientific and API changes.

This release provides the following features:

• Extensible ClassAvgSource framework
• Ab-initio modeling for Cn symmetry (CLSymmetryCn)
• FLE Basis (FLEBasis2d)
• IndexedSource for source slicing and remapping
• Immutable source API migration
• Image and Volume API cleanup (return types)
• asnumpy as immutable views
• Additional RELION 3.1 STAR file support
• SNR Estimation and Simulation utilities
• Improved whiten syntax
• Immutable Source API

Documentation and Logging:

• Tutorial Gallery restructuring
• Lecture Feature Demo updates
• Class Averaging API documentation and UML
• Introductory API documentation and UML (gallery)
• Continued filtering of log messages
• CTF forward model validation and tutorial

Bug fixes:

• Redundant Image conversion bug in denoised_src
• Fixed eval_coords clustering (adjusted Rand score)
• Negative Image index slicing (wraparound bug)
• Polar Fourier Row Major cleanup

Systems/CI Updates:

• conda BLAS accelerated numerical backends (mkl, openblas, accelerate)
• Relaxed pip version requirements
• Long running test suite on review-ready
• CI documentation and gallery build on push
• Windows CI patches
• Resolve deprecation warnings (pandas, scipy)
• Partial removal of parameterized_class
• black 23.1.0 updates

v0.10.1

ASPIRE v0.10.1 is a patch release focused on adding several API improvements, bug fixes, and CI updates.

This release provides the following features:

• Synthetic volume generators (Legacy and compact Asymmetric, Cn, Dn, T, O)
• confuse based ASPIRE config
• Multi dimensional stack axis for Image and Volume
• Parallel and batched BFR and BFSR alignment
• Scale colorbar for Image.show utilities
• Implement and check top level imports (import aspire)
• Restores ability to use cufinufft via config
• NoiseAdder framework and updates

Documentation and Logging:

• User configuration tutorial
• Dramatically reduced console log spam
• Replaced some logging with tqdm progress bars
• Support user/runtime logger and tqdm configuration
• Updated simulation docstring
• Docstring formatting
• Pipeline demo gallery

Bug Fixes and Cleanup:

• Updates rotation convention to be counter-clockwise
• Real coefficient rotations
• Normalize background dtype
• Fourier Bessel zero finding cleanup
• im_translate and preprocessing cleanup/deprecation
• CTFEstimator and voltage_to_wavelength unit fixes
• CTF starfile output column name
• Unit test fixes for averagers
• Pytest parallel processing limits
• Added missing paramatrized test cases
• Gaussian 2D and 3D util cleanup
• Unified transpose and flip for Volume and Image
• covar2d ells mask bug fix
• Consistently use recent about_axis() and Volume.load()
• ImageSource.save() dict return
• Remove Micrograph and MrcStack in favor of ImageSource
• Consistent use of fft module
• Dtype updates (Basis, Simulation, Volume, CLOrient3D, nufft)
• Filter indices bug fix
• Migration to Image.Resolution from Image.res (via DeprecationWarning)
• Workaround for scipy==v0.10.0 2D interpolation
• importlib resources updates

Systems/CI Updates:

• GPU CI
• Daily documentation build testing (develop)
• CI config and additional logging
• Disable ray on Azure for OSX and Windows
• Adds pytest-xdist plugin for developers
• Support building docs without running gallery
• Updates for latest scikit-learn release
• Began migration towards pure pytests
• tox v4 support
• Azure OSX 12 updates
• Github actions v3/v4 updates

v0.10.0

ASPIRE v0.10.0 is large release adding a wide range of features and fixes.

This release provides the following features:

• Common Lines Method for C3/C4 Symmetry (CLSymmetryC3C4, experimental)
• Image Accessor API for ImageSource
• Parallelized BFSReddyChatterjiAverager2D and ReddyChatterjiAverager2D class averaging image aligners
• Support Nonsequential ImageSource.images
• Improved RIRClass2D batching
• crop_pad_3d
• Replace 2D Downsample algorithm (includes 1-pixel scaling bugfix)
• ClassSelector API and RandomClassSelector (now randomized as default)
• gaussian_* helper functions
• Filter.sign method
• Integrate CTF estimator with CoordinateSource

Bug fixes:

• Improved dtype passthrough
• Volume.flip default axis change
• Rectangular micrograph axes
• Fix crash in BatchedRotCov2D when invoked without CTF details
• Volume.dtype mismatches and checks

Systems/CI Updates:

• Refresh Azure pipeline Ubuntu images
• Deprecate Azure OSX 10.15 CI in favor of OSX 11

Cleanup and Documentation Updates:

• Logical (F)FBBasis3D tests
• Documentation format cleanup (fixes broken parsing)
• Top level submodule imports (API improvement)
• .rots ~> .rotations attribute cleanup
• 3D Downsampling cleanup
• Improved Getting Started page
• Improved Gallery Tutorials and Experiments examples
• Sphinx language patch
• Implement lower bound checks for FSPCA components
• Fourier-Bessel Mixin class (FBBasisMixin)
• Resolve PIL package deprecations
• Update ComplexPCA scikit workaround for upstream releases
• Improve evaluate and evaluate_t API standards
• Improve Zenodo affiliation integration

v0.9.2

ASPIRE v0.9.2 is a patch release.

This release adds the following new features:

Bug fixes:

Resolves deprecation warning for PIL.
Patches ComplexPCA for newer sklearn.
Updates Zenodo references.

v0.9.1

ASPIRE v0.9.1 is a patch release.

This release adds the following new features:

• crop_pad_2d() in aspire.utils.coor_trans

Bug fixes:

• Some images appeared flipped by 180 degrees in Reddy Chatterji image registration.
• Basis objects did not stop the user from expanding images that did not match the size of the basis.
• ArrayImageSource should have integer filter indices.

Code cleanup:

• Basis objects can be instantiated with an integer instead of a tuple when creating square or cubic bases.
• More descriptive commenting and docstrings added to Bessel function zero-finding code.
• Testing for Downsampling and Fourier-Bessel 2D basis that used to depend on hardcoded results and output files now instead test expected mathematical properties.
• Improvements to the gallery section of the documentation page include grammar fixes, updates to the author page, and a consistent color map for all images in experiment demonstrations.

v0.9.0

ASPIRE v0.9.0 is a minor release, adding many scientific features and software improvements.

This release provides the following new features:

• Adds simulated and experimental abinitio pipeline gallery experiments
• Adds ImageSource subclasses supporting whole-micrograph/particle-coordinate sources
• Refactor and add Cn symmetry to Gaussian blob volume generation
• extract-particles preprocessing
• Adds Reddy Chetterji based image registration
• Refactors class averaging towards Averager2D framework
• Volume .mrc loading and saving functions
• Adds Volume projection gallery tutorial

Bug fixes:

• FB3D and FFB3D fixes (norm legendre factorial and quadrature points)
• cov2d shrinker formula
• Redundant Whitening for Simulation sources
• PolarBasis2D default initialization
• Improve handling empty result sets in APPLE
• Default cov2d noise estimation
• cov2d denoising matrix normalization
• RelionSource with a single image
• DenoisedImageSource batching
• CTF estimation CLI output_dir

Code Cleanup:

• Standardize use of Rotation class
• PSWF and FPSWF cleanup, minor performance improvements
• Force finufft signals to be complex
• Replace CTF estimation log files with STAR
• Refactor and cleanup grid indexing
• Remove APPLE settings from site configuration
• Add APPLE settings as class and command line options
• Removes orientation estimation settings from site configutation
• Replace importlib_resources with importlib.resources
• Deprecates ensure
• Tutorial gallery updates
• Updates code contributors
• Minor logging and documentation improvements

Systems/CI Updates:

• Roll default Python to 3.7
• Deprecates Python 3.6
• Adds Python 3.10
• Update formatting to Black 22.1.0
• Roll stable MacOS tests to 10.15 from 10.14