K-wave-python

What's Changed

We are excited to announce another release of k-wave-python! This release adds minor enhancements and improvements to k-wave-python along with a new example for phased-array transducers contributed by talg2324.

Enhancements
* Add ruff pre-commit-hook by waltsims in https://github.com/waltsims/k-wave-python/pull/316
* Update simulation_options.py - ensure that a 2d pml can be set by djps in https://github.com/waltsims/k-wave-python/pull/328
* Update CITATION.cff with doi by waltsims in https://github.com/waltsims/k-wave-python/pull/337
* phased array example by talg2324 in https://github.com/waltsims/k-wave-python/pull/341
* Make cart arc by djps in https://github.com/waltsims/k-wave-python/pull/343
* Metadata for lazy installation by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/347
* Use jaxtyping by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/351
* update colors for colab by waltsims in https://github.com/waltsims/k-wave-python/pull/357

Fixes
* 310 bug two times log compression in the example us bmode linear transducer by waltsims in https://github.com/waltsims/k-wave-python/pull/356
* 344 karray 2d weights dimension by waltsims in https://github.com/waltsims/k-wave-python/pull/346
* Remove deprecation warning in write attributes by waltsims in https://github.com/waltsims/k-wave-python/pull/352
Dependencies

* Bump gdown from 4.6.0 to 5.1.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/313
* Bump coverage from 7.4.3 to 7.4.4 by dependabot in https://github.com/waltsims/k-wave-python/pull/345
* Bump jaxtyping from 0.2.25 to 0.2.28 by dependabot in https://github.com/waltsims/k-wave-python/pull/354
* Bump beartype from 0.16.4 to 0.17.2 by dependabot in https://github.com/waltsims/k-wave-python/pull/331
* Bump pre-commit from 3.6.2 to 3.7.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/355


**Full Changelog**: https://github.com/waltsims/k-wave-python/compare/v0.3.2...v0.3.3

What's Changed
We're excited to announce k-wave-python v0.3.2! This release brings with it many improvements and fixes listed below. Importantly, we drop support for Python 3.8 and add support for Python 3.12. We have added development documentation on testing workflows and improved the overall documentation readability. Test coverage has also been added to the project. Furthermore, David Sinden (djps) has joined the project as our third maintainer! 🎉

Lastly, we have added a citation file to the project. If you are enjoying k-Wave-python, please cite it in your work!

Breaking Changes
* 233 drop python 38 support by waltsims in https://github.com/waltsims/k-wave-python/pull/246
Improvements
* Check if color_map is usable by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/287
* Add code coverage by waltsims in https://github.com/waltsims/k-wave-python/pull/275
* Upgrade setup-python action & use pip cache by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/280
* Remove module name from object names in the documentation. by waltsims in https://github.com/waltsims/k-wave-python/pull/285
* Remove legacy mode from write attributes by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/289
* create CITATION.cff proposal by waltsims in https://github.com/waltsims/k-wave-python/pull/290
* Update pyproject.toml by waltsims in https://github.com/waltsims/k-wave-python/pull/296
* Improve logging when checking for the presence of binaries by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/320
* Update mapgen.py to include focused annulus oneil by djps in https://github.com/waltsims/k-wave-python/pull/284
* Clean up examples and add more colab buttons by waltsims in https://github.com/waltsims/k-wave-python/pull/298
* Remove duplicate write_attributes_typed function by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/318
* Add test coverage for tol_star by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/324
* Improved typing and testing for temperature dependency functions by djps in https://github.com/waltsims/k-wave-python/pull/309
* Update make_cart_spherical_segment types to floating point values by waltsims in https://github.com/waltsims/k-wave-python/pull/315
* Add CodeCov config by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/334
* Bump python support to 3.12 by waltsims in https://github.com/waltsims/k-wave-python/pull/267
* Update local testing workflow instructions by waltsims in https://github.com/waltsims/k-wave-python/pull/291
Fixes
* 262 Fix stdout logic on exceptions by waltsims in https://github.com/waltsims/k-wave-python/pull/297
* update argument types of focused_bowl_oneil by waltsims in https://github.com/waltsims/k-wave-python/pull/317
* Fix colab link for controlling the pml by waltsims in https://github.com/waltsims/k-wave-python/pull/333

Dependencies
* Bump pre-commit from 3.5.0 to 3.6.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/278
* Bump coverage from 7.4.0 to 7.4.1 by dependabot in https://github.com/waltsims/k-wave-python/pull/294
* Bump gdown from 4.7.3 to 5.1.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/295
* Bump pre-commit from 3.6.0 to 3.6.1 by dependabot in https://github.com/waltsims/k-wave-python/pull/300
* Bump furo from 2023.9.10 to 2024.1.29 by dependabot in https://github.com/waltsims/k-wave-python/pull/299
* Bump matplotlib from 3.7.2 to 3.8.3 by dependabot in https://github.com/waltsims/k-wave-python/pull/325
* Bump scipy from 1.10.1 to 1.12.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/276
* Bump coverage from 7.4.1 to 7.4.3 by dependabot in https://github.com/waltsims/k-wave-python/pull/330
* Bump pre-commit from 3.6.1 to 3.6.2 by dependabot in https://github.com/waltsims/k-wave-python/pull/329


**Full Changelog**: https://github.com/waltsims/k-wave-python/compare/v0.3.1...v0.3.2

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 https://github.com/waltsims/k-wave-python/pull/237
* Migrate examples to notebooks by waltsims in https://github.com/waltsims/k-wave-python/pull/229
* Add example as a notebook: example_na_controlling_the_pml by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/217

Enhancements
* Add type and shape annotations by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/249
* Update record_reader.py to remove warnings by waltsims in https://github.com/waltsims/k-wave-python/pull/211
* non-copying operation to improve speed for large matrices (useful for 3D simulation) by guillefix in https://github.com/waltsims/k-wave-python/pull/269

Bug fixes
* 250 bug phantom data cannot be downloaded from google drive by waltsims in https://github.com/waltsims/k-wave-python/pull/251
* 238 bug attributeerror kwavesimulation object has no attribute record u split field by waltsims in https://github.com/waltsims/k-wave-python/pull/242

Dependency updates
Updated
* Bump sphinx-toolbox from 3.4.0 to 3.5.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/181
* Bump furo from 2023.8.19 to 2023.9.10 by dependabot in https://github.com/waltsims/k-wave-python/pull/207
* Bump deepdiff from 6.3.1 to 6.7.1 by dependabot in https://github.com/waltsims/k-wave-python/pull/241
* Bump h5py from 3.9.0 to 3.10.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/240
* Bump opencv-python from 4.8.0.76 to 4.8.1.78 by dependabot in https://github.com/waltsims/k-wave-python/pull/239
* Bump sphinx-tabs from 3.4.1 to 3.4.4 by dependabot in https://github.com/waltsims/k-wave-python/pull/243
* Bump opencv-python from 4.8.1.78 to 4.9.0.80 by dependabot in https://github.com/waltsims/k-wave-python/pull/247
* Update numpy requirement from <1.25.0,>=1.22.2 to >=1.22.2,<1.27.0 by dependabot in https://github.com/waltsims/k-wave-python/pull/209
* Bump gdown from 4.6.0 to 4.7.3 by dependabot in https://github.com/waltsims/k-wave-python/pull/266

Added
* Added `beartype` and `nptyping` [249](https://github.com/waltsims/k-wave-python/pull/249)
Removed
* Drop scikit-image dependency by waltsims in https://github.com/waltsims/k-wave-python/pull/268

Project maintenance
* Update issue templates by waltsims in https://github.com/waltsims/k-wave-python/pull/230
* Cache generated matlab references by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/260
* Bump pytest coverage 3.11 by waltsims in https://github.com/waltsims/k-wave-python/pull/206
* Bump python version for pages test by waltsims in https://github.com/waltsims/k-wave-python/pull/234

New Contributors
* guillefix made their first contribution in https://github.com/waltsims/k-wave-python/pull/269

**Full Changelog**: https://github.com/waltsims/k-wave-python/compare/v0.3.0...v0.3.1

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 https://github.com/waltsims/k-wave-python/pull/107
* Replace Array class with numpy-based Vector class by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/118
* Vectorize variables by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/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 https://github.com/waltsims/k-wave-python/pull/126
* Add trim_zeros function and test by waltsims in https://github.com/waltsims/k-wave-python/pull/128
* Python implementation of `trimCartPoints` by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/134
* New funcs: get_affine_matrix() and compute_linear_transform() by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/146
* Update fwhm return values for v1.4.0 by waltsims in https://github.com/waltsims/k-wave-python/pull/148
* Add makeCartArc and tests by waltsims in https://github.com/waltsims/k-wave-python/pull/149
* Add get_delta_BLI and test by waltsims in https://github.com/waltsims/k-wave-python/pull/150
* Update focus_bowl_oneil to return complex axial pressure by waltsims in https://github.com/waltsims/k-wave-python/pull/154
* MATLAB data collector for testing kWaveArray by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/161
* Add make_cart_bowl by waltsims in https://github.com/waltsims/k-wave-python/pull/164
* Add make_cart_disc by waltsims in https://github.com/waltsims/k-wave-python/pull/165
* Add make_cart_spherical_segment and test by waltsims in https://github.com/waltsims/k-wave-python/pull/166
* Python implementation of `kWaveArray` & `get_off_grid_points(...)` by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/168
* Update pytest.yml to run on PRs as well by waltsims in https://github.com/waltsims/k-wave-python/pull/197
* Add custom element by bvale1 in https://github.com/waltsims/k-wave-python/pull/212
* Test nearest neighbor mode of resize function by faridyagubbayli in https://github.com/waltsims/k-wave-python/pull/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 https://github.com/waltsims/k-wave-python/pull/119
* Update README.md to fix broken docs link by waltsims in https://github.com/waltsims/k-wave-python/pull/123
* Create ruff.yml by waltsims in https://github.com/waltsims/k-wave-python/pull/131
* Migrate documentation to Readthedocs by waltsims in https://github.com/waltsims/k-wave-python/pull/152
* Clean up documentation by waltsims in https://github.com/waltsims/k-wave-python/pull/158
* Update README.md by waltsims in https://github.com/waltsims/k-wave-python/pull/170

More examples 🍾
* Example script refactor and added testing by waltsims in https://github.com/waltsims/k-wave-python/pull/108
* Examples/at linear array transducer by waltsims in https://github.com/waltsims/k-wave-python/pull/174
* Example of karray source by waltsims in https://github.com/waltsims/k-wave-python/pull/193

Performance improvements

* Auto chunking for HDF5 by djps in https://github.com/waltsims/k-wave-python/pull/222
* Accelerate computations by djps in https://github.com/waltsims/k-wave-python/pull/223

Fixes
* Update conversion.py - fix ordering in tolStar by djps in https://github.com/waltsims/k-wave-python/pull/172
* Clean up extra GOLDEN_ANGLES by waltsims in https://github.com/waltsims/k-wave-python/pull/178
* Update kwave_array.py removing discretization by djps in https://github.com/waltsims/k-wave-python/pull/195
* lower library verbosity by talg2324 in https://github.com/waltsims/k-wave-python/pull/196
* Update workflow checkout to v4 by waltsims in https://github.com/waltsims/k-wave-python/pull/200
* Update filters.py by djps in https://github.com/waltsims/k-wave-python/pull/202
* Update save_to_disk_func.py - fix dtype error by djps in https://github.com/waltsims/k-wave-python/pull/204
* fix typo by djps in https://github.com/waltsims/k-wave-python/pull/214

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

New Contributors
* djps made their first contribution in https://github.com/waltsims/k-wave-python/pull/172
* talg2324 made their first contribution in https://github.com/waltsims/k-wave-python/pull/196
* bvale1 made their first contribution in https://github.com/waltsims/k-wave-python/pull/212

**Full Changelog**: https://github.com/waltsims/k-wave-python/compare/v0.2.1...v0.3.0

* ensure download path is absolute

New Contributors
* waltsims made their first contribution in https://github.com/waltsims/k-wave-python/pull/15
* Redstonemaster29 made their first contribution in https://github.com/waltsims/k-wave-python/pull/19
* ktritz made their first contribution in https://github.com/waltsims/k-wave-python/pull/20
* dependabot made their first contribution in https://github.com/waltsims/k-wave-python/pull/47

**Full Changelog**: https://github.com/waltsims/k-wave-python/compare/v0.1.0...0.2.0