aspire - 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

- Python
Published by garrettwrong 8 months ago

aspire - 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

- Python
Published by garrettwrong 12 months ago

aspire - 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)

- Python
Published by garrettwrong over 1 year ago

aspire - 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

- Python
Published by garrettwrong over 1 year ago

aspire - 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

- Python
Published by garrettwrong over 1 year ago

aspire - 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

- Python
Published by garrettwrong about 2 years ago

aspire - 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

- Python
Published by garrettwrong about 2 years ago

aspire - 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

- Python
Published by garrettwrong over 2 years ago

aspire - 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

- Python
Published by garrettwrong almost 3 years ago

aspire - 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

- Python
Published by garrettwrong almost 3 years ago

aspire - 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

- Python
Published by garrettwrong about 3 years ago

aspire - 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

- Python
Published by garrettwrong over 3 years ago

aspire - 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.

- Python
Published by garrettwrong almost 4 years ago

aspire - 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.

- Python
Published by chris-langfield almost 4 years ago

aspire - 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

- Python
Published by garrettwrong about 4 years ago

aspire - v0.8.1

ASPIRE v0.8.1 is an early patch release.

This release provides the following features:

• New Sphinx-Gallery Documentation and Tutorial refresh
• Aligner classes supporting simple 2D class average alignments
• Conversion to GEMMI for starfile IO

Bug fixes:

• Cov2D shrinker formulas
• Cov2D noise variance estimation
• Relion Source - mrcs singleton

Systems/CI Updates:

• Ubuntu 18.04LTS Azure deprecation (now 20.04LTS)
• Tox updates - py3.{6,7,8}-dev targets
• Minor setup.py updates

Also beginning with this release ASPIRE-Python releases will begin being tracked by Zenado. A persistent DOI will become published in the next release.

- Python
Published by garrettwrong over 4 years ago

aspire - v0.8.0

ASPIRE v0.8.0 adds the following scientific features:

• Begin adding Class Averaging Components (experimental)
• Adaptive Support Radius Calculations
• Wavelet-based approximate Earth-Mover's Distance (wemd)
• Irregular (Non Square) Block Diagonal Extensions

Additionally this release includes the following updates:

• Minor Numpy Updates in preperation for Python 3.9
• ArrayImageSource should now admit numpy arrays directly
• Minor README updates
• Introduce informational Code Coverage reporting to CI (Codecov)
• Minor PIL Upstream dependency patch
• Improve corrupt mrc file handling in APPLE.picking
• ArrayImageSource Patches for use in MeanEstimator

- Python
Published by garrettwrong over 4 years ago

aspire - v0.7.0

This version adds a core backend component for CTF Estimation along with mating CLI entry point which wraps MRC file IO.

Otherwise this is mostly fixes for issues found during development:

• Bugfix covar2d shrinker and getcwfcoeffs for clean images (noise_var=0)
• Bugfix Simulation n=1 crashes
• Move some developer deps to "dev" package extension
• Demo Notebook corrections and refresh
• Bugfix in Pandas code supporting Starfile IO
• Bugfix filter eval points outside interp grid
• Add parallel test code coverage job to GitHub Actions (Codecov)
• Add tests for Rotation class

- Python
Published by garrettwrong almost 5 years ago

aspire -

v0.6.3 Mainly consists of small patches and continuous updates for dependent software and CI systems. It also extends the tutorials and notebook based documentation.

• cufinufft v1.2 Updates
• Update Example Notebooks and add a more comprehensive demonstration
• Replace Travis CI with GitHub Actions
• Migrate GitHub Pages Documentation to GitHub Actions
• FFB3D/FB3D debugging (order and dtype patches)
• Remove unused skimage dependency
• Add aspire cli entry point
• Fix ImageArraySource and add working tutorial to test suite
• Minor doc updates
• Use nufft "many" interface in 3D calls
• Add isotropic noise estimator
• Separate save function into save_metedata and save_images
• Option to load numeric backend modules

- Python
Published by garrettwrong about 5 years ago

aspire - v0.6.2

Minor update to better support pip install for ubuntu 20.04. Additions for preprocessing pipeline example and Rotations class.

- Python
Published by garrettwrong about 5 years ago

aspire - v0.6.1

Minor updates to facilitate publishing package to PyPI.

- Python
Published by garrettwrong about 5 years ago

aspire - v0.6.0

This release covers a large collection of refactoring along with cleanup:

• Bulk of code converted to Row Major from the initial Column Major port
• Automated style, import, and linting/pep compliance controls.
• Restructuring of classes
• Implementation and use of Image/Volume Classes
• Improvements to datatype handling and addition of dtype class attributes
• Now supporting pip installs for multiple Python versions under automated CI testing.
• Improved logging
• Deprecated code cleanup
• Dependency simplification and cleanup

Additionally this release includes some scientific programming feature additions: * Addition of Dirac and Polar basis classes * Include orientation estimation submodule * Unify preprocessing Pipeline * Develop new interface for normal FFT transform using Scipy, Pyfftw and Cupy * Replace old FFT functions with new FFT interface * Integration with next generation of FINUFFT Python package * Integration of cufinufft pip package for CUDA enabled devices.

More details of work can be found in the project board associated with this changeset: https://github.com/ComputationalCryoEM/ASPIRE-Python/projects/2

- Python
Published by garrettwrong over 5 years ago