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Releases: mjo22/cryojax

v0.3.3

15 Jan 14:57
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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

14 Jan 23:15
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v0.3.3.rc3 Pre-release
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More documentation updates and small fixes

v0.3.3rc2

14 Jan 18:02
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v0.3.3rc2 Pre-release
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Adding some documentation updates from #309

v0.3.3rc1

14 Jan 03:11
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v0.3.3rc1 Pre-release
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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

06 Dec 04:05
8de2685
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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

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

v0.3.2rc1

06 Dec 03:58
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v0.3.2rc1 Pre-release
Pre-release

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

11 Sep 15:02
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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

11 Sep 14:58
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v0.3.1rc1 Pre-release
Pre-release

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

20 May 17:55
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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

v0.3.0rc2

14 May 20:27
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v0.3.0rc2 Pre-release
Pre-release

Second pre-release for 0.3.0 major version release of cryojax. This pre-release is to test API updates that build the scattering potential.