Waveorder

What's Changed
* Styling by talonchandler in https://github.com/mehta-lab/waveorder/pull/182
* Calculate transfer functions on grids smaller than data by talonchandler in https://github.com/mehta-lab/waveorder/pull/180


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/2.2.0...2.2.1

What's Changed
* Styling by talonchandler in https://github.com/mehta-lab/waveorder/pull/182
* Calculate transfer functions on grids smaller than data by talonchandler in https://github.com/mehta-lab/waveorder/pull/180


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/2.2.0...2.2.1b0

Vector optics birefringence reconstruction.

Release supports [arxiv preprint](https://arxiv.org/abs/2412.09775).

What's Changed
* fix bug finding focus in stack with only one slice by ieivanov in https://github.com/mehta-lab/waveorder/pull/162
* Authorship and release updates by talonchandler in https://github.com/mehta-lab/waveorder/pull/165
* Bump Python by ziw-liu in https://github.com/mehta-lab/waveorder/pull/168
* Merge `alg-dev` into main ahead of release by talonchandler in https://github.com/mehta-lab/waveorder/pull/171
* Pin numpy <2 by ziw-liu in https://github.com/mehta-lab/waveorder/pull/173
* Bump torch to unpin numpy by ziw-liu in https://github.com/mehta-lab/waveorder/pull/176
* Wrap-safe transfer functions by talonchandler in https://github.com/mehta-lab/waveorder/pull/175
* Vector-optics birefringence reconstruction prototype by talonchandler in https://github.com/mehta-lab/waveorder/pull/170


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/2.1.0...2.2.0

2.2.0 release candidate.

This release features phase reconstruction that is invariant to voxel size (164).

What's Changed
* fix bug finding focus in stack with only one slice by ieivanov in https://github.com/mehta-lab/waveorder/pull/162
* Authorship and release updates by talonchandler in https://github.com/mehta-lab/waveorder/pull/165
* Bump Python by ziw-liu in https://github.com/mehta-lab/waveorder/pull/168
* Merge `alg-dev` into main ahead of release by talonchandler in https://github.com/mehta-lab/waveorder/pull/171
* Pin numpy <2 by ziw-liu in https://github.com/mehta-lab/waveorder/pull/173


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/2.1.0...v2.2.0rc0

PTI documentation and example scripts release in preparation for PTI paper.

What's Changed
* PTI example jupyter notebook to script and .pdf by talonchandler in https://github.com/mehta-lab/waveorder/pull/160


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/2.0.0...2.1.0

Overview

This major release of `waveorder` is a well-tested and stable version of phase, birefringence, and fluorescence simulation and reconstruction algorithms, **now running in `torch`, with each reconstruction factored into an precalculation and an (typically less-expensive) reconstruction**.

**Key changes:**
- phase, birefringence, and fluorescence reconstruction use `torch`
- these reconstructions are factored into an expensive precalculation and an inexpensive reconstruction
- Key PTI reconstruction code paths are conserved through the refactor, with automated example scripts on synthetic data and one data-based jupyter notebook

What's Changed
* Remove `__init__` imports by talonchandler in https://github.com/mehta-lab/waveorder/pull/134
* Add optional parameters `plot_path` and `threshold_FWHM` to `focus_from_transverse_band` by talonchandler in https://github.com/mehta-lab/waveorder/pull/132
* Fix threshold-free focus-finding edge case by talonchandler in https://github.com/mehta-lab/waveorder/pull/135
* close figure after saving by ieivanov in https://github.com/mehta-lab/waveorder/pull/136
* **Major changes:** `alg-dev` branch merge to `main` by talonchandler in https://github.com/mehta-lab/waveorder/pull/121
* Specify meshgrid indexing order by talonchandler in https://github.com/mehta-lab/waveorder/pull/138
* Fix readme figure by talonchandler in https://github.com/mehta-lab/waveorder/pull/141
* Simplify dependencies by talonchandler in https://github.com/mehta-lab/waveorder/pull/147
* Add rotate and flip orientation options to `waveorder` options by talonchandler in https://github.com/mehta-lab/waveorder/pull/148
* `waveorder` handles all rotational quantities (including retardance) in radians by talonchandler in https://github.com/mehta-lab/waveorder/pull/149
* Device agnostic compute for polarization by ziw-liu in https://github.com/mehta-lab/waveorder/pull/150
* Document order-dependent scripts by talonchandler in https://github.com/mehta-lab/waveorder/pull/155
* M1 installation documentation by talonchandler in https://github.com/mehta-lab/waveorder/pull/156
* Prepare README for 2.0.0 by talonchandler in https://github.com/mehta-lab/waveorder/pull/157
* Link BIA data next to examples by talonchandler in https://github.com/mehta-lab/waveorder/pull/158
* Update a single PTI example notebook by talonchandler in https://github.com/mehta-lab/waveorder/pull/159


**Full Changelog**: https://github.com/mehta-lab/waveorder/compare/1.0.0...2.0.0