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

Full Changelog: https://github.com/mehta-lab/waveorder/compare/2.2.1...3.0.0a0

- Python
Published by talonchandler 9 months ago

waveorder - 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...2.2.1

- Python
Published by talonchandler 11 months ago

waveorder - 2.2.1b0

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

- Python
Published by talonchandler 12 months ago

waveorder - 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 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

- Python
Published by talonchandler about 1 year ago

waveorder - 2.2.0rc0

2.2.0 release candidate.

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

- Python
Published by ziw-liu over 1 year ago

waveorder - 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 https://github.com/mehta-lab/waveorder/pull/160

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

- Python
Published by talonchandler almost 2 years ago

waveorder - 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 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

- Python
Published by talonchandler almost 2 years ago

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

New Contributors

• @ziw-liu made their first contribution in https://github.com/mehta-lab/waveorder/pull/108

Full Changelog: https://github.com/mehta-lab/waveorder/compare/1.0.0rc0...1.0.0

- Python
Published by talonchandler almost 3 years ago