v0.3.1

What's Changed

In this release, we have restructured and added new examples in k-wave-python. All examples now include colab notebook links for faster exploration. We have made some enhancements as well thanks in part to our new community contributer @guillefix. Minor bugfixes are also included in this release.

Improved examples

• Ivp photo acoustic waveforms by @djps in #237
• Migrate examples to notebooks by @waltsims in #229
• Add example as a notebook: example_na_controlling_the_pml by @faridyagubbayli in #217

Enhancements

• Add type and shape annotations by @faridyagubbayli in #249
• Update record_reader.py to remove warnings by @waltsims in #211
• non-copying operation to improve speed for large matrices (useful for 3D simulation) by @guillefix in #269

Bug fixes

• 250 bug phantom data cannot be downloaded from google drive by @waltsims in #251
• 238 bug attributeerror kwavesimulation object has no attribute record u split field by @waltsims in #242

Dependency updates

Updated

• Bump sphinx-toolbox from 3.4.0 to 3.5.0 by @dependabot in #181
• Bump furo from 2023.8.19 to 2023.9.10 by @dependabot in #207
• Bump deepdiff from 6.3.1 to 6.7.1 by @dependabot in #241
• Bump h5py from 3.9.0 to 3.10.0 by @dependabot in #240
• Bump opencv-python from 4.8.0.76 to 4.8.1.78 by @dependabot in #239
• Bump sphinx-tabs from 3.4.1 to 3.4.4 by @dependabot in #243
• Bump opencv-python from 4.8.1.78 to 4.9.0.80 by @dependabot in #247
• Update numpy requirement from <1.25.0,>=1.22.2 to >=1.22.2,<1.27.0 by @dependabot in #209
• Bump gdown from 4.6.0 to 4.7.3 by @dependabot in #266

Added

• Added beartype and nptyping #249

Removed

• Drop scikit-image dependency by @waltsims in #268

Project maintenance

• Update issue templates by @waltsims in #230
• Cache generated matlab references by @faridyagubbayli in #260
• Bump pytest coverage 3.11 by @waltsims in #206
• Bump python version for pages test by @waltsims in #234

New Contributors

• @guillefix made their first contribution in #269

Full Changelog: v0.3.0...v0.3.1

v0.3.0

What's Changed

This release includes new interface improvements, updates to reach functional and testing parity with k-Wave v1.4.0, improved documentation, performance improvements, and fixes to k-Wave-python. We are happy to say that this release was also supported by new community contributors including @djps, @bvale1 , @talg2324! Thanks to everyone for their work and support. We hope this release accelerates your work and look forward to hearing from you.

⚠️ This release contains breaking changes ⚠️

Interface refactoring

• Refactor kSpaceFirstOrder inputs by @faridyagubbayli in #107
• Replace Array class with numpy-based Vector class by @faridyagubbayli in #118
• Vectorize variables by @faridyagubbayli in #124

k-Wave v1.4.0 changes

This release extends functional and testing coverage to k-Wave v1.4.0 MATLAB release. This includes migrating matlab functions to k-Wave-python and testing for correctness. These include:

• Python implementation of makeCartRect by @faridyagubbayli in #126
• Add trim_zeros function and test by @waltsims in #128
• Python implementation of trimCartPoints by @faridyagubbayli in #134
• New funcs: get_affine_matrix() and compute_linear_transform() by @faridyagubbayli in #146
• Update fwhm return values for v1.4.0 by @waltsims in #148
• Add makeCartArc and tests by @waltsims in #149
• Add get_delta_BLI and test by @waltsims in #150
• Update focus_bowl_oneil to return complex axial pressure by @waltsims in #154
• MATLAB data collector for testing kWaveArray by @faridyagubbayli in #161
• Add make_cart_bowl by @waltsims in #164
• Add make_cart_disc by @waltsims in #165
• Add make_cart_spherical_segment and test by @waltsims in #166
• Python implementation of kWaveArray & get_off_grid_points(...) by @faridyagubbayli in #168
• Update pytest.yml to run on PRs as well by @waltsims in #197
• Add custom element by @bvale1 in #212
• Test nearest neighbor mode of resize function by @faridyagubbayli in #216

Documentation updates

We have updated and extended the documentation of k-Wave by porting the documentation to readthedocs.

• rename pages to publish_pages by @waltsims in #119
• Update README.md to fix broken docs link by @waltsims in #123
• Create ruff.yml by @waltsims in #131
• Migrate documentation to Readthedocs by @waltsims in #152
• Clean up documentation by @waltsims in #158
• Update README.md by @waltsims in #170

More examples 🍾

• Example script refactor and added testing by @waltsims in #108
• Examples/at linear array transducer by @waltsims in #174
• Example of karray source by @waltsims in #193

Performance improvements

• Auto chunking for HDF5 by @djps in #222
• Accelerate computations by @djps in #223

Fixes

• Update conversion.py - fix ordering in tolStar by @djps in #172
• Clean up extra GOLDEN_ANGLES by @waltsims in #178
• Update kwave_array.py removing discretization by @djps in #195
• lower library verbosity by @talg2324 in #196
• Update workflow checkout to v4 by @waltsims in #200
• Update filters.py by @djps in #202
• Update save_to_disk_func.py - fix dtype error by @djps in #204
• fix typo by @djps in #214

Dependency updates

• Bump sphinx-toolbox from 3.2.0 to 3.4.0 by @dependabot in #99
• Bump deepdiff from 5.2.3 to 6.2.3 by @dependabot in #87
• Bump gdown from 4.6.0 to 4.6.4 by @dependabot in #110
• Bump k-Wave test version to v1.4.0 by @waltsims in #116
• Bump m2r2 from 0.3.2 to 0.3.3.post2 by @dependabot in #98
• Bump matplotlib from 3.6.3 to 3.7.1 by @dependabot in #114
• Bump sphinx-copybutton from 0.5.1 to 0.5.2 by @dependabot in #121
• Bump opencv-python from 4.7.0.68 to 4.7.0.72 by @dependabot in #112
• Bump scipy from 1.7.3 to 1.10.1 by @dependabot in #109
• Bump h5py from 3.6.0 to 3.8.0 by @dependabot in #113
• Bump gdown from 4.6.4 to 4.7.1 by @dependabot in #143
• Bump scikit-image from 0.19.3 to 0.21.0 by @dependabot in #147
• Bump deepdiff from 6.2.3 to 6.3.1 by @dependabot in #169
• Bump matplotlib from 3.7.1 to 3.7.2 by @dependabot in #179
• Bump furo from 2022.12.7 to 2023.8.19 by @dependabot in #189
• Bump h5py from 3.8.0 to 3.9.0 by @dependabot in #186
• Bump opencv-python from 4.7.0.72 to 4.8.0.76 by @dependabot in #198

New Contributors

• @djps made their first contribution in #172
• @talg2324 made their first contribution in #196
• @bvale1 made their first contribution in #212

Full Changelog: v0.2.1...v0.3.0

v0.2.1

• ensure download path is absolute

v0.2.0

Hey all,

this is a pretty big release with extended testing and improved GPU support. Let us know if you encounter any challenges.

Thanks,
Walter

What's Changed

• GitHub workflow by @waltsims in #15
• Update for Windows binary test compatibility by @Redstonemaster29 in #19
• Added Windows compatibility by @ktritz in #20
• Address warning in kspaceFirstOrder by @waltsims in #22
• Matlab ci artifacts by @waltsims in #25
• Build rebuild by @waltsims in #37
• Re-add requirement files for sphinx-build and dependabot by @waltsims in #39
• Update development documentation by @waltsims in #45
• [WIP] Added testing by @waltsims in #38
• Fix docs for pyproject.toml support by @waltsims in #53
• Bump gdown from 4.4.0 to 4.5.3 by @dependabot in #47
• Refactor camel-case method names to snake case by @waltsims in #54
• Tests fail after un-skipping cart2grid test by @waltsims in #56
• Unskip tests by @waltsims in #65
• Utils cleanup by @waltsims in #55
• add docs dependency version requirements by @waltsims in #66
• Options refactor by @waltsims in #64
• kWaveGrid tests & TestRecorder by @faridyagubbayli in #62
• remove all import-alls by @waltsims in #76
• angular_spectrum: implementation & test by @faridyagubbayli in #83
• [WIP] Docs cleanup by @waltsims in #82
• Update License by @waltsims in #90
• Bump gdown from 4.5.3 to 4.6.0 by @dependabot in #63
• Update numpy requirement from ~=1.22.2 to >=1.22.2,<1.25.0 by @dependabot in #68
• Angular Spectrum CW: implementation & test by @faridyagubbayli in #95
• Misssing collectors cleanup by @waltsims in #80
• Bump matplotlib from 3.6.1 to 3.6.3 by @dependabot in #91
• Attention Compensation: implementation & test by @faridyagubbayli in #96
• [WIP] Lazy binary install strategy by @waltsims in #89
• V0.2.0 release by @waltsims in #101
• Bump opencv-python from 4.6.0.66 to 4.7.0.68 by @dependabot in #92
• v0.2.0 release by @waltsims in #103

New Contributors

• @waltsims made their first contribution in #15
• @Redstonemaster29 made their first contribution in #19
• @ktritz made their first contribution in #20
• @dependabot made their first contribution in #47

Full Changelog: v0.1.0...0.2.0

v0.1.0

The first official release of k-Wave-python 🎉 🎉 🎉 !

What's New

• Simulation runner by @faridyagubbayli in #7
• BMode Linear Scan & Reconstruction example by @faridyagubbayli in #5
• Script to run tests in a Docker Container by @faridyagubbayli in #8

New Contributors

• @faridyagubbayli made their first contribution in #7

Full Changelog: https://github.com/waltsims/k-wave-python/commits/v0.1.0