2.2.0

Vector optics birefringence reconstruction.

Release supports arxiv preprint.

What's Changed

• fix bug finding focus in stack with only one slice by @ieivanov in #162
• Authorship and release updates by @talonchandler in #165
• Bump Python by @ziw-liu in #168
• Merge alg-dev into main ahead of release by @talonchandler in #171
• Pin numpy <2 by @ziw-liu in #173
• Bump torch to unpin numpy by @ziw-liu in #176
• Wrap-safe transfer functions by @talonchandler in #175
• Vector-optics birefringence reconstruction prototype by @talonchandler in #170

Full Changelog: 2.1.0...2.2.0

2.2.0rc0

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 #162
• Authorship and release updates by @talonchandler in #165
• Bump Python by @ziw-liu in #168
• Merge alg-dev into main ahead of release by @talonchandler in #171
• Pin numpy <2 by @ziw-liu in #173

Full Changelog: 2.1.0...v2.2.0rc0

2.1.0

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 #160

Full Changelog: 2.0.0...2.1.0

2.0.0

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

Full Changelog: 1.0.0...2.0.0

1.0.0

Overview

Ths first major release of waveorder is a well-tested and stable version of phase, birefringence, and fluorescence simulation and reconstruction algorithms.

Key changes
Since waveorder==1.0.0rc0, we have:

• moved all I/O functionality to iohub.
• curated and updated the /examples/ folder, and added the most important example scripts to CI/CD testing for maintenance through the upcoming refactoring.
• added focus finding algorithms
• dropped support for 3.7 and bumped to 3.8-3.10

What's Changed

• Bump version to 1.0.0rc0 by @ieivanov in #82
• BSD 3-clause by @talonchandler in #84
• Don't delete test data by @talonchandler in #83
• improve readability of waveOrder by @mattersoflight in #85
• Drop 3.7 and add 3.8, 3.9, 3.10 by @talonchandler in #99
• Find focus by optimizing a transverse spatial frequency band by @talonchandler in #92
• Improve README.md by @talonchandler in #101
• uPTI -> PTI; black formatting; improved comments by @talonchandler in #104
• README copy edits by @talonchandler in #105
• Replace OpenCV with pillow by @ziw-liu in #108
• Add .git-blame-ignore-revs by @talonchandler in #109
• Prepare for waveorder==1.0.0 release by @talonchandler in #114
• Fix link to example by @talonchandler in #115
• Pin README links by @talonchandler in #116

New Contributors

• @ziw-liu made their first contribution in #108

Full Changelog: 1.0.0rc0...1.0.0