Pulse2percept

Highlights

- New implants: BVT44 [[Petoe2021]](https://pulse2percept.readthedocs.io/en/latest/users/references.html#petoe2021) ([PR 465](https://github.com/pulse2percept/pulse2percept/pull/465))
- New models: [BiphasicAxonMapModel](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.models.html#pulse2percept.models.BiphasicAxonMapModel) [[Granley2021]](https://pulse2percept.readthedocs.io/en/latest/users/references.html#granley2021) ([PR 398](https://github.com/pulse2percept/pulse2percept/pull/398)) and [Thompson2003Model](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.models.html#pulse2percept.models.Thompson2003Model) [[Thompson2003]](https://pulse2percept.readthedocs.io/en/latest/users/references.html#thompson2003) ([PR 448](https://github.com/pulse2percept/pulse2percept/pull/448))
- New datasets: [load_greenwald2009](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.datasets.html#pulse2percept.datasets.load_greenwald2009) [[Greenwald2009]](https://pulse2percept.readthedocs.io/en/latest/users/references.html#greenwald2009) ([PR 459](https://github.com/pulse2percept/pulse2percept/pull/459)) and [load_perezfornos2012](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.datasets.html#pulse2percept.datasets.load_perezfornos2012) [[PerezFornos2012]](https://pulse2percept.readthedocs.io/en/latest/users/references.html#perezfornos2012) ([PR 457](https://github.com/pulse2percept/pulse2percept/pull/457))
- New stimuli: [BarStimulus](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.stimuli.html#pulse2percept.stimuli.BarStimulus), [GratingStimulus](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.stimuli.html#pulse2percept.stimuli.GratingStimulus) ([PR 310](https://github.com/pulse2percept/pulse2percept/pull/310))
- Python 3.10 support ([PR 479](https://github.com/pulse2percept/pulse2percept/pull/479))

New features

- New gallery examples for visual field maps ([PR 432](https://github.com/pulse2percept/pulse2percept/pull/432)), Nanduri dataset ([PR #452](https://github.com/pulse2percept/pulse2percept/pull/452)), psychophysics stimuli ([PR #480](https://github.com/pulse2percept/pulse2percept/pull/480)), and [BiphasicAxonMapModel](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.models.html#pulse2percept.models.BiphasicAxonMapModel) ([PR 484](https://github.com/pulse2percept/pulse2percept/pull/484))
- Crop method for [ImageStimulus](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.stimuli.html#pulse2percept.stimuli.ImageStimulus) and VideoStimulus objects (PR 455)
- Specify number of OpenMP threads (PR 453)
- Ignore stimuli of deactivated electrodes (PR 444)
- Percepts can now have a limited number of gray levels (PR 443)
- Automatic stimulus reshaping for ImageStimulus and [VideoStimulus](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.stimuli.html#pulse2percept.stimuli.VideoStimulus) objects ([PR 434](https://github.com/pulse2percept/pulse2percept/pull/434))
[ElectrodeGrid](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.implants.html#pulse2percept.implants.ElectrodeGrid) can now have different spacings in x and y direction ([PR 430](https://github.com/pulse2percept/pulse2percept/pull/430))
- Add new plotting styles for a grid’s plot method ([PR 426](https://github.com/pulse2percept/pulse2percept/pull/426), [PR #433](https://github.com/pulse2percept/pulse2percept/pull/433), [PR #446](https://github.com/pulse2percept/pulse2percept/pull/446))
- Additional options for [scatter_correlation](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.viz.html#pulse2percept.viz.scatter_correlation) ([PR 422](https://github.com/pulse2percept/pulse2percept/pull/422))

Backwards-incompatible changes

- `RetinalCoordTransform` has been renamed to `VisualFieldMap` ([PR 432](https://github.com/pulse2percept/pulse2percept/pull/432))
- `plot_axon_map` was removed: Use pulse2percept.models.AxonMapModel.plot
- `plot_implant_on_axon_map` was removed: Use [pulse2percept.implants.ProsthesisSystem.plot](https://pulse2percept.readthedocs.io/en/latest/users/_api/pulse2percept.implants.html#pulse2percept.implants.ProsthesisSystem.plot) on top of :py:meth`pulse2percept.models.AxonMapModel.plot`

New features

* Add FadingTemporal, a generic phosphene fading model (PR 378)

Maintenance

* Various implant usability and speed upgrades (PR 375, PR 382, PR 383, PR 386)
* Various stimulus usability and speed upgrades (PR 382, PR 383, PR 384, PR 385)
* Refactor common Cython functions and move them into a utils._fast_math submodule (PR 382)
* Further speed up the AxonMapModel build process (PR 369)
* Improve documentation and usability of various AxonMapModel methods (PR 370)
* Disallow lambda<10 for AxonMapModel (PR 370)
* Show a warning when ScoreboardModel or AxonMapModel is used with a nonzero electrode-retina distance (PR 368)

Bug fixes

* Fix naming convention for BVT24 electrodes (PR 380)
* Fix issues with plotting and animating Percept (PR 379)
* Fix inconsistencies and missing parameters in the [Nanduri2012] dataset (PR 376)
* Fix pulse2percept.models.AxonMapModel.plot for left eyes (PR 367)
* Fix axon map visualization in plot_argus_phosphenes (PR 366)

Highlights

* New implants: PRIMA, PRIMA75, PRIMA55, PRIMA40 (PR 188)
* New electrodes: SquareElectrode, HexElectrode, PhotovoltaicPixel (PR 188, PR 193)
* New stimuli: ImageStimulus and VideoStimulus (PR 196, PR 220, PR 221, PR 356), BarStimulus and GratingStimulus (PR 323)
* New datasets: load_nanduri2012 (PR 250)
* New model selection subpackage (PR 311)
* 100x speedup of building AxonMapModel (PR 331)
* OpenMP support (PR 260)
* Python 3.9 support (PR 348)

Backward-incompatible changes

* Implants rotation angles are now speicified in degrees, not radians (PR 357)
* pulse2percept now requires Matplotlib 3.0.2 or newer (PR 223)
* FFMPEG and scikit-video dependencies have been removed (PR 196)
* TimeSeries has been removed. Please use Stimulus instead
* LegacyMonophasicPulse, LegacyBiphasicPulse and LegacyPulseTrain have been removed. Use their equivalents without the “Legacy” prefix.

Highlights

- New API (PR 96, PR 174, PR 178)
- New implants: BVA24 (PR 161)
- New models: ScoreboardModel (PR 96), AxonMapModel (PR 96), Nanduri2012Model (PR 168), Horsager2009Model (PR 180)
- New stimuli: BiphasicPulseTrain, AsymmetricBiphasicPulse, AsymmetricBiphasicPulseTrain (PR 178)
- New percepts subpackage (PR 174)
- New datasets subpackage (PR 167)
- New build process: Compile code and run tests via Makefile (PR 96)
- Documentation now includes a tutorial, user guide, developer’s guide, and a gallery

Backward-incompatible changes

- Times are now specified in milliseconds.
- The Simulation object has been removed. Please directly instantiate a model instead.
- pulse2percept.retina: use models instead
- pulse2percept.files: use io instead

Contributions

Big thanks to all contributors, including DylanLin29, jonluntzel, ezgirmak, garethgeorge.

Bug fix:
* Restores `Nanduri2012` fast Cython implementation

Bug fixes:
- Fix "Cannot determine Numba type" error in `center_vector`
- `Horsager2009` does now respect `use_jit` option
- `Nanduri2012` now allows switch between cython/fft