Mostly improvements to RELION compatibility `cryojax.data`. Also, initial implementation of the multislice algorithm in `cryojax.experimental`.
What's Changed * Multislice by geoffwoollard in https://github.com/mjo22/cryojax/pull/253 * 252 add envelope function to reliondataset by DSilva27 in https://github.com/mjo22/cryojax/pull/264 * Make it optional to read in envelopes by mjo22 in https://github.com/mjo22/cryojax/pull/268 * Fix bugs in `RelionDataset` by mjo22 in https://github.com/mjo22/cryojax/pull/269 * Simplify writer by assuming function takes in particle stack by mjo22 in https://github.com/mjo22/cryojax/pull/270 * Fix bug in new writer function by mjo22 in https://github.com/mjo22/cryojax/pull/271 * 211 starfile writer by DSilva27 in https://github.com/mjo22/cryojax/pull/266 * Small bug in how the name of the mrcs was defined inside the starfiles by DSilva27 in https://github.com/mjo22/cryojax/pull/272 * implement loading from different mrcfiles in RelionDataset by DSilva27 in https://github.com/mjo22/cryojax/pull/274 * fix bug in loading from multiple mrcs by DSilva27 in https://github.com/mjo22/cryojax/pull/275 * fix type checking in tests by mjo22 in https://github.com/mjo22/cryojax/pull/279 * get rid of AbstractStructualEnsembleBatcher by mjo22 in https://github.com/mjo22/cryojax/pull/283 * First pass at multislice implementation by mjo22 in https://github.com/mjo22/cryojax/pull/258
New Contributors * geoffwoollard made their first contribution in https://github.com/mjo22/cryojax/pull/253
Pre-release for 0.3.2 release, which adds and improves features for RELION compatibility and merges an initial pass of the multislice algorithm into `cryojax.experimental`.
0.3.1
What's Changed * Generate volumes using error functions by mjo22 in https://github.com/mjo22/cryojax/pull/233 * Touch up filter and mask interface and add more cosine masks by mjo22 in https://github.com/mjo22/cryojax/pull/238 * Cleanup the radially averaged power spectrum by mjo22 in https://github.com/mjo22/cryojax/pull/240 * Change FFT normalization convention to "ortho" by mjo22 in https://github.com/mjo22/cryojax/pull/241 * Convert back to standard FFT convention by mjo22 in https://github.com/mjo22/cryojax/pull/242 * Option to normalize signal in IndependentGaussianFourierModes distribution by mjo22 in https://github.com/mjo22/cryojax/pull/244 * Fix mac install issues by mjo22 in https://github.com/mjo22/cryojax/pull/247 * Bugfix: missing factor of 10 in loading from mdtraj by ehthiede in https://github.com/mjo22/cryojax/pull/249 * Add feature to compute images from extracting surfaces on the ewald sphere by mjo22 in https://github.com/mjo22/cryojax/pull/232 * Optionally read arrays on the CPU in `RelionDataset` by mjo22 in https://github.com/mjo22/cryojax/pull/257 * add option to only load starfile parameters in RelionDataset by DSilva27 in https://github.com/mjo22/cryojax/pull/256 * Change defocus parameter convention to mean defocus by mjo22 in https://github.com/mjo22/cryojax/pull/263
Pre-release for 0.3.1 release, which fixes install issues, creates `cryojax.experimental`, generates volumes using error functions, and adds improvements to things like whitening filters, STAR file reading, and simulating images from `cryojax.distributions`.
0.3.0
Major version release of `cryojax`. This have two major components:
- An API overhaul to support more complex scattering theories in the future - Significant advancements and documentation in computing images / volumes from atoms. In particular, a new API and massive speedups for computing voxel grids from atoms, and an implementation for computing projected potentials directly from atoms.
Additionally, a grid search API is added to `cryojax.inference`. This addition is slightly experimental and could be branched into a separate package in the future.
What's Changed * API Update in preparation for supporting more complex scattering theories. by mjo22 in https://github.com/mjo22/cryojax/pull/212 * Add a grid search API in cryojax.inference by mjo22 in https://github.com/mjo22/cryojax/pull/207 * implement centering atoms closes 220 by DSilva27 in https://github.com/mjo22/cryojax/pull/221 * API re-vamp of the atoms -> voxel grid pipeline. by mjo22 in https://github.com/mjo22/cryojax/pull/216 * implement gaussian mixture atomic potential integrator closes 224 by DSilva27 in https://github.com/mjo22/cryojax/pull/225 * Speedup in voxel grid computation by mjo22 in https://github.com/mjo22/cryojax/pull/231
New Contributors * DSilva27 made their first contribution in https://github.com/mjo22/cryojax/pull/221