Release Notes

v0.8.0 (2022-05-05)

Highlights

• New implants: BVT44 [Petoe2021] (PR #465)
• New models: BiphasicAxonMapModel [Granley2021] (PR #398) and Thompson2003Model [Thompson2003] (PR #448)
• New datasets: load_greenwald2009 [Greenwald2009] (PR #459) and load_perezfornos2012 [PerezFornos2012] (PR #457)
• New stimuli: BarStimulus, GratingStimulus (PR #310)
• Python 3.10 support (PR #479)

New features

• New gallery examples for visual field maps (PR #432), Nanduri dataset (PR #452), psychophysics stimuli (PR #480), and BiphasicAxonMapModel (PR #484)
• Crop method for 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 objects (PR #434)
• ElectrodeGrid can now have different spacings in x and y direction (PR #430)
• Add new plotting styles for a grid’s plot method (PR #426, PR #433, PR #446)
• Additional options for scatter_correlation (PR #422)

API changes

Backward-incompatible changes

• RetinalCoordTransform has been renamed to VisualFieldMap (PR #432)
• plot_axon_map was removed: Use pulse2percept.models.AxonMapModel.plot
• plot_implant_on_axon_map was removed: Use 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 (PR #473)
• Fix corrupted stimuli when created from multiple stimuli (PR #469)
• plot_argus_phosphenes now works for sliced subsets of data (PR #415)
• Fix plot window for the AxonMapModel plot method (PR #414)
• Keep metadata intact when stimuli are created from other stimuli (PR #396)
• Be able to run AxonMapModel on a single pixel (PR #395)
• Mirror-flip the BVT24 implant (PR #393)

v0.7.1 (2021-06-21)

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)

v0.7.0 (2021-04-04)

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)

New features

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

API changes

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.

Deprecations

• plot_axon_map: Use pulse2percept.models.AxonMapModel.plot
• plot_implant_on_axon_map: Use 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 (PR #353)
• Fix data boundaries in plot (PR #244)
• AxonMapModel have been drastically reduced (PR #215)
• Grid2D: Grid now produces correct step size even when range is not divisible by step (PR #201)
• AlphaIMS: Implant now uses SquareElectrode objects and has exactly 1500 electrodes (PR #193)
• ElectrodeGrid: Alphabetic names now follow A-Z, AA-AZ, BA-BZ, etc. (PR #192)
• BVA24: Setting a stimulus in the constructor now has the desired effect (PR #186)
• Computational cost and memory usage of

v0.6.0 (2020-05-05)

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
• Python 2.7 and 3.4 are no longer supported (PR #96)

New features

• A visual prosthesis is now considered a ProsthesisSystem consisting of an ElectrodeArray and optionally a Stimulus (PR #96).
• A Model can be built by mix-and-matching spatial and temporal models from different publications (PR #174).
• A 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., BiphasicPulseTrain).
• ElectrodeArray now stores electrodes in a dictionary (issue #74).
• ElectrodeGrid can be used to create electrodes on a rectangular (PR #150) or hexagonal grid (PR #160).

API changes

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

Deprecations

• TimeSeries: use 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 pulse2percept.viz module (PR #84)
• Support for the AlphaIMS implant (PR #87)
• Automated wheelhouse build (PR #130)
• New contribution guidelines (PR #92)
• New issue templates (PR #93)
• New code of conduct (PR #95)
• Host documentation on pulse2percept.readthedocs.io.

Bug fixes

• Fix nasal/temporal labeling for left eyes (commit 9c3bddc)
• Fix 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 (PR #83)
  • Single-core benchmarks show a 200x speedup over a pure-Python implementation.

Bug fixes

• Python 2.7 unpacking error in 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