v0.4.0rc1

Pre-release for new major release of cryoJAX

v0.3.4

Version release v0.3.4.

What's Changed

• Implement transfer theory for ewald sphere by @mjo22 in #314
• create CustomOperator in cryojax.image.operators by @mjo22 in #315
• Backend API updates for initial version of ewald sphere code by @mjo22 in #316
• Implement error function evaluation in gaussians-to-atoms projections and debug projection upsampling by @mjo22 in #318
• fix small bug in batched_map functions by @DSilva27 in #320
• Adjust PDBReader by @mjo22 in #326
• set mdtraj as interface for pdb reading by @DSilva27 in #324
• Drop Biopython in favor of MDTraj for PDB reading by @mjo22 in #333
• removed b factor as default relion stack option by @Miro-Astore in #323
• Simulating images for an AbstractAssembly does not hit a memory error anymore by @mjo22 in #336
• More cleanups to PDB reader by @mjo22 in #335
• set jittable default to false for writing image starfile by @Miro-Astore in #338
• One particle in stack by @Miro-Astore in #337

Full Changelog: v0.3.3...v0.3.4

v0.3.4rc1

Some PDB reader fixes, STAR file reader and writer updates, ...

v0.3.3

API updates for simulator (the pose, structural ensemble, and CTF) and relion datasets. Create cryojax.utils submodule for useful features for working with JAX/Equinox. Fix deprecation of equinox.internal.if_mapped so that cryojax works with newest versions of equinox.

What's Changed

• Add IndependentGaussianPixels distribution by @mjo22 in #289
• Get rid of conformational_space abstract attribute in AbstractStructuralEnsemble by @mjo22 in #293
• update ewald branch by @mjo22 in #300
• Remove extra definition of voltage in the CTF by @mjo22 in #295
• Merge relion refactoring with assembly + offset_z_in_angstroms refactoring by @mjo22 in #301
• Remove offset_z_in_angstroms. Required a refactoring of the AbstractAssembly by @mjo22 in #302
• Refactor RelionDataset into two cases, one for reading metadata and another for images + metadata by @mjo22 in #298
• Ewald sphere initial attempt in cryojax.experimental by @mjo22 in #296
• Refactor transforms interface by @mjo22 in #306
• Change vmap recommendations to remove if_mapped from equinox by @mjo22 in #307
• Lift error if underfocus is passed by @mjo22 in #308
• Document cryojax.coordinates and create API directory for docs by @mjo22 in #309
• Documentation and bugfixes for cryojax.constants by @mjo22 in #312

Full Changelog: v0.3.2...v0.3.3

v0.3.3.rc3

More documentation updates and small fixes

v0.3.3rc2

Adding some documentation updates from #309

v0.3.3rc1

API updates for the pose, structural ensemble, and CTF. Create cryojax.utils submodule for useful features for working with JAX/Equinox. Fix deprecation of equinox.internal.if_mapped.

v0.3.2

Mostly improvements to RELION compatibility cryojax.data. Also, initial implementation of the multislice algorithm in cryojax.experimental.

What's Changed

• Multislice by @geoffwoollard in #253
• 252 add envelope function to reliondataset by @DSilva27 in #264
• Make it optional to read in envelopes by @mjo22 in #268
• Fix bugs in RelionDataset by @mjo22 in #269
• Simplify writer by assuming function takes in particle stack by @mjo22 in #270
• Fix bug in new writer function by @mjo22 in #271
• 211 starfile writer by @DSilva27 in #266
• Small bug in how the name of the mrcs was defined inside the starfiles by @DSilva27 in #272
• implement loading from different mrcfiles in RelionDataset by @DSilva27 in #274
• fix bug in loading from multiple mrcs by @DSilva27 in #275
• fix type checking in tests by @mjo22 in #279
• get rid of AbstractStructualEnsembleBatcher by @mjo22 in #283
• First pass at multislice implementation by @mjo22 in #258

New Contributors

• @geoffwoollard made their first contribution in #253

Full Changelog: v0.3.1...v0.3.2

v0.3.2rc1

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.

v0.3.1

What's Changed

• Generate volumes using error functions by @mjo22 in #233
• Touch up filter and mask interface and add more cosine masks by @mjo22 in #238
• Cleanup the radially averaged power spectrum by @mjo22 in #240
• Change FFT normalization convention to "ortho" by @mjo22 in #241
• Convert back to standard FFT convention by @mjo22 in #242
• Option to normalize signal in IndependentGaussianFourierModes distribution by @mjo22 in #244
• Fix mac install issues by @mjo22 in #247
• Bugfix: missing factor of 10 in loading from mdtraj by @ehthiede in #249
• Add feature to compute images from extracting surfaces on the ewald sphere by @mjo22 in #232
• Optionally read arrays on the CPU in RelionDataset by @mjo22 in #257
• add option to only load starfile parameters in RelionDataset by @DSilva27 in #256
• Change defocus parameter convention to mean defocus by @mjo22 in #263

Full Changelog: v0.3.0...v0.3.1