pulse2percept.models.cortex.dynaphos

DynaphosModel

Classes

DynaphosModel(**params) Adaptation of the Dynaphos model from [Grinten2023]
class pulse2percept.models.cortex.dynaphos.DynaphosModel(**params)[source]

Adaptation of the Dynaphos model from [Grinten2023]

The original and official implementation is available at https://github.com/neuralcodinglab/dynaphos.

Implements the Dynaphos model. Percepts from each electrode are Gaussian blobs, with the size dictated by a magnification factor M determined by the electrode’s position in the visual cortex.

Parameters:
  • dt (float, optional) – Sampling time step of the simulation (ms)
  • regions (list of str, optional) – The visual regions to simulate. Options are ‘v1’, ‘v2’, or ‘v3’. Default : [‘v1’]
  • rheobase (float, optional) – Rheobase current constant (uA)
  • tau_trace (float, optional) – Trace decay constant (ms)
  • kappa_trace (float, optional) – Stimulus input effect modifier constant for memory trace
  • excitability (float, optional) – Excitability constant for current spread (uA/mm^2)
  • tau_act (float, optional) – Activation decay constant (ms)
  • sig_slope (float, optional) – Slope of the sigmoidal brightness curve
  • a_thr (float, optional) – Activation threshold value, under which a phosphene is not generated
  • a50 (float, optional) – Activation value for which a phosphene reaches half of its maximum brightness
  • freq (float, optional) – Default stimulus frequency (Hz)
  • p_dur (float, optional) – Default stimulus pulse duration (ms)
  • xrange ((x_min, x_max), optional) – A tuple indicating the range of x values to simulate (in degrees of visual angle). Negative values correspond to the right hemisphere of visual cortex, and positive values correspond to the left hemisphere.
  • yrange ((y_min, y_max), optional) – A tuple indicating the range of y values to simulate (in degrees of visual angle).
  • xystep (int, double, tuple, optional) – Step size for the range of (x,y) values to simulate (in degrees of visual angle). For example, to create a grid with x values [0, 0.5, 1] use x_range=(0, 1) and xystep=0.5.
  • grid_type ({'rectangular', 'hexagonal'}, optional) – Whether to simulate points on a rectangular or hexagonal grid.
  • vfmap (VisualFieldMap, optional) – An instance of a VisualFieldMap object that provides visual field mappings. By default, Polimeni2006Map is used.
  • n_gray (int, optional) – The number of gray levels to use. If an integer is given, k-means clustering is used to compress the color space of the percept into n_gray bins. If None, no compression is performed.
  • noise (float or int, optional) – Adds salt-and-pepper noise to each percept frame. An integer will be interpreted as the number of pixels to subject to noise in each frame. A float between 0 and 1 will be interpreted as a ratio of pixels to subject to noise in each frame.

Important

If you change important model parameters outside the constructor (e.g., by directly setting model.xrange = (-10, 10)), you will have to call model.build() again for your changes to take effect.

build(**build_params)[source]

Build the model

Performs expensive one-time calculations, such as building the spatial grid used to predict a percept. You must call build before calling predict_percept.

Parameters:build_params (additional parameters to set) – You can overwrite parameters that are listed in get_default_params. Trying to add new class attributes outside of that will cause a FreezeError. Example: model.build(param1=val)
get_default_params()[source]

Returns all settable parameters of the Dynaphos model

is_built

A flag indicating whether the model has been built

plot(use_dva=False, style=None, autoscale=True, ax=None, figsize=None, fc=None)[source]

Plot the model :param use_dva: Plot points in visual field. If false, simulated points will be

plotted in cortex
Parameters:
  • style ({'hull', 'scatter', 'cell'}, optional) –

    Grid plotting style: * ‘hull’: Show the convex hull of the grid (that is, the outline of

    the smallest convex set that contains all grid points).
    • ’scatter’: Scatter plot all grid points
    • ’cell’: Show the outline of each grid cell as a polygon. Note that this can be costly for a high-resolution grid.
  • autoscale (bool, optional) – Whether to adjust the x,y limits of the plot to fit the implant
  • ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None, will either use the current axes (if exists) or create a new Axes object.
  • figsize ((float, float), optional) – Desired (width, height) of the figure in inches
Returns:

ax (matplotlib.axes.Axes) – Returns the axis object of the plot
predict_percept(implant, t_percept=None)[source]

Predict the spatiotemporal response

Parameters:
  • implant (ProsthesisSystem) – A valid prosthesis system. A stimulus can be passed via stim.
  • t_percept (float or list of floats, optional) – The time points at which to output a percept (ms). If None, implant.stim.time is used.
Returns:

percept (Percept) – A Percept object whose data container has dimensions Y x X x T. Will return None if implant.stim is None.
set_params(**params)[source]

Set the parameters of this model