3.0.0a2

What's Changed

• Remove submitit dependency by @talonchandler in #454
• Skip reconstructions of empty FOVs by @ieivanov in #457
• Instructions to install from pip and github by @talonchandler in #451
• Gui update by @amitabhverma in #458
• Documentation infrastructure by @amitabhverma in #461
• Vector prototype CLI by @talonchandler in #440
• Refactor compute_midband_power by @talonchandler in #471
• run tests on pr by @tlambert03 in #477
• simplify test ci by @tlambert03 in #478
• tests: run example tests on ci and mock show by @tlambert03 in #476
• Exclude docs/, tests/, etc. from wheel by @talonchandler in #480
• Faster tests by @talonchandler in #487
• Handle single position .zarr stores as CLI input by @talonchandler in #486
• Fixes loading default phase.yml and fluorescence.yml config files in GUI by @amitabhverma in #488
• Improve installation instructions by @talonchandler in #479
• Package layout fix by @talonchandler in #489
• Visual assets appear in plugin by @talonchandler in #495
• Bump iohub by @talonchandler in #492
• 2D fluorescence reconstruction by @talonchandler in #460

New Contributors

• @amitabhverma made their first contribution in #458
• @tlambert03 made their first contribution in #477

Full Changelog: 3.0.0a1...3.0.0a2

3.0.0a1

What's Changed

• bug in monitor by @ahillsley in #445

New Contributors

• @ahillsley made their first contribution in #445

Full Changelog: 3.0.0a0...3.0.0a1

3.0.0a0

This release features the recOrder->waveorder merge and newly fixed 3D-to-2D phase reconstructions.

What's Changed

• Fix installation by @talonchandler in #184
• Fix style by @talonchandler in #185
• Fix pytests by @talonchandler in #186
• Clean up examples and temp files by @talonchandler in #187
• Remove recorder image references by @talonchandler in #189
• Merging README by @mattersoflight in #188
• Merge recOrder into waveorder by @talonchandler in #183
• Bump iohub and pydantic by @ziw-liu in #448
• Test on click 8.2.0 by @ziw-liu in #450
• Fix 3D to 2D phase reconstruction by @talonchandler in #441
• Settings-ratio checks should give warnings, not errors by @talonchandler in #452

Full Changelog: 2.2.1...3.0.0a0

2.2.1

What's Changed

• Styling by @talonchandler in #182
• Calculate transfer functions on grids smaller than data by @talonchandler in #180

Full Changelog: 2.2.0...2.2.1

2.2.1b0

What's Changed

• Styling by @talonchandler in #182
• Calculate transfer functions on grids smaller than data by @talonchandler in #180

Full Changelog: 2.2.0...2.2.1b0

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