Releases: mjo22/cryojax
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 inAbstractStructuralEnsemble
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 theAbstractAssembly
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
fromequinox
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
v0.3.3rc1
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
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
v0.3.1rc1
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
.
v0.3.0
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 #212
- Add a grid search API in cryojax.inference by @mjo22 in #207
- implement centering atoms closes #220 by @DSilva27 in #221
- API re-vamp of the atoms -> voxel grid pipeline. by @mjo22 in #216
- implement gaussian mixture atomic potential integrator closes #224 by @DSilva27 in #225
- Speedup in voxel grid computation by @mjo22 in #231
New Contributors
Full Changelog: v0.2.3...v0.3.0