release_notes.rst

Release Notes

v0.8.0 (2022-05-05)

Highlights

• New implants: :py:class:`~pulse2percept.implants.BVT44` [Petoe2021]_ (:pull:`465`)
• New models: :py:class:`~pulse2percept.models.BiphasicAxonMapModel` [Granley2021]_ (:pull:`398`) and :py:class:`~pulse2percept.models.Thompson2003Model` [Thompson2003]_ (:pull:`448`)
• New datasets: :py:func:`~pulse2percept.datasets.load_greenwald2009` [Greenwald2009]_ (:pull:`459`) and :py:func:`~pulse2percept.datasets.load_perezfornos2012` [PerezFornos2012]_ (:pull:`457`)
• New stimuli: :py:class:`~pulse2percept.stimuli.BarStimulus`, :py:class:`~pulse2percept.stimuli.GratingStimulus` (:pull:`310`)
• Python 3.10 support (:pull:`479`)

New features

• New gallery examples for visual field maps (:pull:`432`), Nanduri dataset (:pull:`452`), psychophysics stimuli (:pull:`480`), and :py:class:`~pulse2percept.models.BiphasicAxonMapModel` (:pull:`484`)
• Crop method for :py:class:`~pulse2percept.stimuli.ImageStimulus` and :py:class:`~pulse2percept.stimuli.VideoStimulus` objects (:pull:`455`)
• Specify number of OpenMP threads (:pull:`453`)
• Ignore stimuli of deactivated electrodes (:pull:`444`)
• Percepts can now have a limited number of gray levels (:pull:`443`)
• Automatic stimulus reshaping for :py:class:`~pulse2percept.stimuli.ImageStimulus` and :py:class:`~pulse2percept.stimuli.VideoStimulus` objects (:pull:`434`)
• :py:class:`~pulse2percept.implants.ElectrodeGrid` can now have different spacings in x and y direction (:pull:`430`)
• Add new plotting styles for a grid's plot method (:pull:`426`, :pull:`433`, :pull:`446`)
• Additional options for :py:func:`~pulse2percept.viz.scatter_correlation` (:pull:`422`)

API changes

Backward-incompatible changes

• RetinalCoordTransform has been renamed to VisualFieldMap (:pull:`432`)
• plot_axon_map was removed: Use :py:meth:`pulse2percept.models.AxonMapModel.plot`
• plot_implant_on_axon_map was removed: Use :py:meth:`pulse2percept.implants.ProsthesisSystem.plot` on top of :py:meth`pulse2percept.models.AxonMapModel.plot`

Deprecations

None.

Bug fixes

• Fix handling of multi-channel images for scikit-image >= 0.19 (:pull:`473`)
• Fix corrupted stimuli when created from multiple stimuli (:pull:`469`)
• :py:func:`~pulse2percept.viz.plot_argus_phosphenes` now works for sliced subsets of data (:pull:`415`)
• Fix plot window for the :py:class:`~pulse2percept.models.AxonMapModel` plot method (:pull:`414`)
• Keep metadata intact when stimuli are created from other stimuli (:pull:`396`)
• Be able to run :py:class:`~pulse2percept.models.AxonMapModel` on a single pixel (:pull:`395`)
• Mirror-flip the :py:class:`~pulse2percept.implants.BVT24` implant (:pull:`393`)

v0.7.1 (2021-06-21)

New features

• Add :py:class:`~pulse2percept.models.FadingTemporal`, a generic phosphene fading model (:pull:`378`)

Maintenance

• Various implant usability and speed upgrades (:pull:`375`, :pull:`382`, :pull:`383`, :pull:`386`)
• Various stimulus usability and speed upgrades (:pull:`382`, :pull:`383`, :pull:`384`, :pull:`385`)
• Refactor common Cython functions and move them into a utils._fast_math submodule (:pull:`382`)
• Further speed up the :py:class:`~pulse2percept.models.AxonMapModel` build process (:pull:`369`)
• Improve documentation and usability of various :py:class:`~pulse2percept.models.AxonMapModel` methods (:pull:`370`)
• Disallow lambda<10 for :py:class:`~pulse2percept.models.AxonMapModel` (:pull:`370`)
• Show a warning when :py:class:`~pulse2percept.models.ScoreboardModel` or :py:class:`~pulse2percept.models.AxonMapModel` is used with a nonzero electrode-retina distance (:pull:`368`)

Bug fixes

• Fix naming convention for :py:class:`~pulse2percept.implants.BVT24` electrodes (:pull:`380`)
• Fix issues with plotting and animating :py:class:`~pulse2percept.percepts.Percept` (:pull:`379`)
• Fix inconsistencies and missing parameters in the [Nanduri2012]_ dataset (:pull:`376`)
• Fix :py:meth:`pulse2percept.models.AxonMapModel.plot` for left eyes (:pull:`367`)
• Fix axon map visualization in :py:meth:`~pulse2percept.viz.plot_argus_phosphenes` (:pull:`366`)

v0.7.0 (2021-04-04)

Highlights

• New implants: :py:class:`~pulse2percept.implants.PRIMA`, :py:class:`~pulse2percept.implants.PRIMA75`, :py:class:`~pulse2percept.implants.PRIMA55`, :py:class:`~pulse2percept.implants.PRIMA40` (:pull:`188`)
• New electrodes: :py:class:`~pulse2percept.implants.SquareElectrode`, :py:class:`~pulse2percept.implants.HexElectrode`, :py:class:`~pulse2percept.implants.PhotovoltaicPixel` (:pull:`188`, :pull:`193`)
• New stimuli: :py:class:`~pulse2percept.stimuli.ImageStimulus` and :py:class:`~pulse2percept.stimuli.VideoStimulus` (:pull:`196`, :pull:`220`, :pull:`221`, :pull:`356`), :py:class:`~pulse2percept.stimuli.BarStimulus` and :py:class:`~pulse2percept.stimuli.GratingStimulus` (:pull:`323`)
• New datasets: :py:class:`~pulse2percept.datasets.load_nanduri2012` (:pull:`250`)
• New model selection subpackage (:pull:`311`)
• 100x speedup of building :py:class:`~pulse2percept.models.AxonMapModel` (:pull:`331`)
• OpenMP support (:pull:`260`)
• Python 3.9 support (:pull:`348`)

New features

• :py:class:`~pulse2percept.stimuli.Stimulus` objects now store stimulus parameters in their metadata (:pull:`346`)
• :py:class:`~pulse2percept.stimuli.Stimulus` objects can now be manipulated with arithmetic operators (:pull:`301`)
• Image processing methods can be directly applied to :py:class:`~pulse2percept.stimuli.ImageStimulus` and :py:class:`~pulse2percept.stimuli.VideoStimulus` objects (:pull:`241`, :pull:`253`)
• Feature matrix and phosphene visualizations (:pull:`232`)
• Percepts can be animated directly in IPython / Jupyter Notebook, and saved as a movie file (:pull:`196`, :pull:`226`, :pull:`358`)
• Electrodes, electrode arrays, and prosthesis systems now have their own plot method (:pull:`188`, :pull:`195`, :pull:`222`)

API changes

Backward-incompatible changes

• Implants rotation angles are now speicified in degrees, not radians (:pull:`357`)
• pulse2percept now requires Matplotlib 3.0.2 or newer (:pull:`223`)
• FFMPEG and scikit-video dependencies have been removed (:pull:`196`)
• TimeSeries has been removed. Please use :py:class:`~pulse2percept.stimuli.Stimulus` instead
• LegacyMonophasicPulse, LegacyBiphasicPulse and LegacyPulseTrain have been removed. Use their equivalents without the "Legacy" prefix.

Deprecations

• plot_axon_map: Use :py:meth:`pulse2percept.models.AxonMapModel.plot`
• plot_implant_on_axon_map: Use :py:meth:`pulse2percept.implants.ProsthesisSystem.plot` on top of :py:meth`pulse2percept.models.AxonMapModel.plot`

Bug fixes

• Fix metadata and plotting of Beyeler et al. (2019) dataset (:pull:`353`)
• Fix data boundaries in :py:meth:`~pulse2percept.models.AxonMapModel.plot` (:pull:`244`)
• :py:class:`~pulse2percept.models.AxonMapModel` have been drastically reduced (:pull:`215`)
• :py:class:`~pulse2percept.utils.Grid2D`: Grid now produces correct step size even when range is not divisible by step (:pull:`201`)
• :py:class:`~pulse2percept.implants.AlphaIMS`: Implant now uses :py:class:`~pulse2percept.implants.SquareElectrode` objects and has exactly 1500 electrodes (:pull:`193`)
• :py:class:`~pulse2percept.implants.ElectrodeGrid`: Alphabetic names now follow A-Z, AA-AZ, BA-BZ, etc. (:pull:`192`)
• :py:class:`~pulse2percept.implants.BVA24`: Setting a stimulus in the constructor now has the desired effect (:pull:`186`)
• Computational cost and memory usage of

v0.6.0 (2020-05-05)

Highlights

• New API (:pull:`96`, :pull:`174`, :pull:`178`)
• New implants: :py:class:`~pulse2percept.implants.BVA24` (:pull:`161`)
• New models: :py:class:`~pulse2percept.models.ScoreboardModel` (:pull:`96`), :py:class:`~pulse2percept.models.AxonMapModel` (:pull:`96`), :py:class:`~pulse2percept.models.Nanduri2012Model` (:pull:`168`), :py:class:`~pulse2percept.models.Horsager2009Model` (:pull:`180`)
• New stimuli: :py:class:`~pulse2percept.stimuli.BiphasicPulseTrain`, :py:class:`~pulse2percept.stimuli.AsymmetricBiphasicPulse`, :py:class:`~pulse2percept.stimuli.AsymmetricBiphasicPulseTrain` (:pull:`178`)
• New :py:mod:`~pulse2percept.percepts` subpackage (:pull:`174`)
• New :py:mod:`~pulse2percept.datasets` subpackage (:pull:`167`)
• New build process: Compile code and run tests via Makefile (:pull:`96`)
• Documentation now includes a tutorial, user guide, developer's guide, and a gallery
• Python 2.7 and 3.4 are no longer supported (:pull:`96`)

New features

• A visual prosthesis is now considered a :py:class:`~pulse2percept.implants.ProsthesisSystem` consisting of an :py:class:`~pulse2percept.implants.ElectrodeArray` and optionally a :py:class:`~pulse2percept.stimuli.Stimulus` (:pull:`96`).
• A :py:class:`~pulse2percept.models.Model` can be built by mix-and-matching spatial and temporal models from different publications (:pull:`174`).
• A :py:class:`~pulse2percept.stimuli.Stimulus` can be created from various source types, such as scalars, NumPy arrays, lists, and dictionaries. There are also a variety of built-in pulses and pulse trains (e.g., :py:class:`~pulse2percept.stimuli.BiphasicPulseTrain`).
• :py:class:`~pulse2percept.implants.ElectrodeArray` now stores electrodes in a dictionary (:issue:`74`).
• :py:class:`~pulse2percept.implants.ElectrodeGrid` can be used to create electrodes on a rectangular (:pull:`150`) or hexagonal grid (:pull:`160`).

API changes

Backward-incompatible changes

• Times are now specified in milliseconds.
• The Simulation object has been removed. Please directly :ref:`instantiate a model <topics-models>` instead.
• pulse2percept.retina: use :py:mod:`~pulse2percept.models` instead
• pulse2percept.files: use :py:mod:`~pulse2percept.io` instead

Deprecations

• TimeSeries: use :py:class:`~pulse2percept.stimuli.Stimulus` instead
• Old pulses got renamed to LegacyMonophasicPulse, LegacyBiphasicPulse and LegacyPulseTrain

v0.5.2 (2020-02-25)

Bug fixes

• pulse2percept.retina.Nanduri2012: improved Cython implementation

v0.5.1 (2020-02-05)

Bug fixes

• pulse2percept.retina.Nanduri2012: allow switch between FFT/Cython
• pulse2percept.retina.Horsager2009: respect use_jit option
• pulse2percept.utils.center_vector: "cannot determine Numba type"

v0.5.0 (2019-11-29)

Highlights

• New :py:mod:`pulse2percept.viz` module (:pull:`84`)
• Support for the :py:class:`~pulse2percept.implants.AlphaIMS` implant (:pull:`87`)
• Automated wheelhouse build (:pull:`130`)
• New contribution guidelines (:pull:`92`)
• New issue templates (:pull:`93`)
• New code of conduct (:pull:`95`)
• Host documentation on pulse2percept.readthedocs.io.

Bug fixes

• Fix nasal/temporal labeling for left eyes (:commit:`9c3bddc`)
• Fix :py:meth:`~pulse2percept.viz.plot_fundus` for left eyes (:commit:`a6ffdbc`)
• Fix scipy.special.factorial (:commit:`c9631ae`)

v0.4.3 (2018-05-21)

Highlights

• Cython integration:
  • The model described in Nanduri et al. (2012) now uses a finite difference method implemented in Cython as opposed to FFT-based convolutions (:pull:`83`)
  • Single-core benchmarks show a 200x speedup over a pure-Python implementation.

Bug fixes

• Python 2.7 unpacking error in :py:meth:`~pulse2percept.viz.plot_fundus` (:commit:`3dd9d1e`)

Deprecation removals

• pulse2percept.files.savemoviefiles
• pulse2percept.files.npy2movie
• pulse2percept.files.scale
• pulse2percept.stimuli.Movie2Pulsetrain
• pulse2percept.stimuli.retinalmovie2electrodtimeseries
• pulse2percept.utils.Parameters
• pulse2percept.utils.mov2npy

v0.3.0 (2018-02-20)

Highlights

• New, faster axon map calculation
• Better plotting
• Support for left/right eye