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