v1.2.0

What's changed

New features

• Allowing using total intensity for probe centering constraint
• PIE now supports multislice
• Added device module and symbol wrapper to support Intel GPUs

API changes

• Users can now export/import settings from/to Options objects as JSON
• OptimizationPlan is now a subclass of Options and is moved to api.options.base
• Removed depreciated Options classes
• OPRModeWeightsSmoothingOptions.method now has a default value

v1.1.0

What's changed

Bug fixes

• Fixed affine transformation matrix fitting.
• Corrected sign in get_max_batch_size.
• Fixed an in-place update in propagators which caused an issue in AD backpropagation.
• Fixed AD's device transfer bug when using multiple GPUs with DataParallel.

Algorithm changes

• Probe update magnitude limit is further clipped by mean absolute deviation of update.

UI changes

• Default setting of image differentiation method for probe position correction was changed to FOURIER_DIFFERENTIATION; step size default was changed to 0.3; update magnitude limit default was changed to 0.1.
• Spelling of ASYMMETRY in affine transformation constraint's degrees of freedom was corrected.
• Added LSQML preconditioning damping factor to API.

Build-related changes

• Added requirements.txt generated by uv.
• Use uv for environment management in CI.

Experimental features

• Synthetic sparse dictionary learning for probe optimization (#33)

v1.0.0

What's Changed

New fetures

• Save movies of arrays by @hruth in #31
• Deep image prior (experimental) by @mdw771 in #32
• Adding the Bilinear Hessian method for reconstruction by @nikitinvv in #27
• Non-square pixel size support
• Slice spacing optimization (AD only)
• Affine transformation constraint on probe positions​
• Allow choosing the slice for probe position correction​

Bug fixes

• Allow choosing alternative ways of defining object-frame pixel coordinates of position origin
• Fixed performance issue in uniform batching
• Fixed performance issue in automatic differentiation

Full Changelog: v0.1.0...v1.0.0

v0.1.0

What's changed

• The reconstruction quality of LSQML is significantly improved on data with low overlap and large illumination variation.
• New difference map reconstructor.
• Reconstruction speed is now 2--3x faster; further speedup can be obtained by setting reconstruction_options.use_double_precision_for_fft to False (less tested; use with caution).
• New profiling utility.
• Added new constraint routines including remove_object_probe_ambiguity and opr_weight_smoothing, and improved multislice_regularization.
• Added documentation.
• Allow switching between faster yet non-deterministic and slower yet deterministic algorithms.

v0.0.1-alpha

Features

Reconstruction engines

• LSQML
• PIE (including ePIE and rPIE)
• Difference map
• Automatic differentiation

Major correction features

• Probe position correction: gradient-based and cross correlation-based
• Multislice (only in LSQML and AD)
• Orthogonal probe relaxation (only in LSQML and AD)
• Mixed-state probe
• Compact batching

Other features

• Multi-GPU (only in AD)