pulse2percept.implants.base

ProsthesisSystem, RectangleImplant

Classes

ProsthesisSystem(earray[, stim, eye, ...])	Visual prosthesis system
RectangleImplant([x, y, z, rot, shape, r, ...])	A generic rectangular implant

class pulse2percept.implants.base.ProsthesisSystem(earray, stim=None, eye='RE', preprocess=False, safe_mode=False, raster=None, max_current=None)

Visual prosthesis system

A visual prosthesis combines an electrode array and (optionally) a stimulus. This is the base class for prosthesis systems such as ArgusII and AlphaIMS.

Added in version 0.6.

Parameters:

• earray (ElectrodeArray or) – Electrode The electrode array used to deliver electrical stimuli to the retina.

• stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

• eye ('LE' or 'RE') – A string indicating whether the system is implanted in the left (‘LE’) or right eye (‘RE’)

• preprocess (bool or callable, optional) – Either True/False to indicate whether to execute the implant’s default preprocessing method whenever a new stimulus is assigned, or a custom function (callable).

• safe_mode (bool, optional) – If safe mode is enabled, only charge-balanced stimuli are allowed. Safety is an electrical property, so this also requires the stimulus to be measured in units of current.

• raster (Raster, optional) –

  How the stimulator takes turns between electrodes that it cannot drive at the same time. If None, every electrode may fire at once.

  Added in version 0.10.0.

• max_current (float, optional) –

  The total current (uA) the stimulator can source at any one instant, summed over all electrodes. If given, assigning a stimulus that exceeds it raises. If None, no such check is performed.

  May be given as a plain number of microamps or as a unitful quantity (e.g. 0.1 * mA); see pulse2percept.units.

  Added in version 0.10.0.

Examples

A system in the left eye made from a single DiskElectrode with radius r=100um sitting at x=200um, y=-50um, z=10um:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> implant = ProsthesisSystem(DiskElectrode(200, -50, 10, 100), eye='LE')

Note

A stimulus can also be assigned later (see stim).

property raster

Raster pattern

Most implants do not set this in their constructor, so the slot backing it may never have been written to; an unset raster means all electrodes may fire at once.

property max_current

Total instantaneous current (uA) the stimulator can source

check_stim(stim)

Quality-check the stimulus

This method is executed every time a new value is assigned to stim.

If safe_mode is set to True, this function will only allow stimuli that are charge-balanced. If max_current is set, it will only allow stimuli whose total instantaneous current stays within it.

Both are questions about electricity, and neither can be answered about a stimulus that is not a current, so each raises a DimensionMismatchError on one. An implant that asks for neither does not run either check, which is why a dimensionless stimulus may still be assigned to one – preprocess has already had its chance to turn it into current, and if it did not, no safety claim is being made about it either.

The user can define their own checks in implants that inherit from ProsthesisSystem.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Raises:

• DimensionMismatchError – If an electrical check was requested and stim is not measured in units of current.

• .. versionchanged: – 0.10.0: The electrical checks verify that the stimulus really is electrical, instead of reading whatever numbers it holds as microamps.

preprocess_stim(stim)

Preprocess the stimulus

This methods is executed every time a new value is assigned to stim.

No preprocessing is performed by default, but the user can define their own method in implants that inherit from return stim ProsthesisSystem.

A custom method must return a Stimulus object with the correct number of electrodes for the implant.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Returns:

stim_out

Return type:

Stimulus object

plot(annotate=False, autoscale=True, ax=None, stim_cmap=False)

Plot

Parameters:

• annotate (bool, optional) – Whether to scale the axes view to the data

• 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.

• stim_cmap (bool, str, or matplotlib colormap, optional) – If not false, the fill color of the plotted electrodes will vary based on maximum stimulus amplitude on each electrode. The chosen colormap will be used if provided

Returns:

ax – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes

property earray

Electrode array

property stim

Stimulus

A stimulus can be created from many source types, such as scalars, NumPy arrays, and dictionaries (see Stimulus for a complete list).

A stimulus can be assigned either in the ProsthesisSystem constructor or later by assigning a value to stim.

Note

Unless when using dictionary notation, the number of stimuli must equal the number of electrodes in earray.

Examples

Send a biphasic pulse (30uA, 0.45ms phase duration) to an implant made from a single DiskElectrode:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> from pulse2percept.stimuli import BiphasicPulse
>>> implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
>>> implant.stim = BiphasicPulse(30, 0.45)

Stimulate Electrode B7 in Argus II with 13 uA:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(stim={'B7': 13})

property eye

Implanted eye

A ProsthesisSystem can be implanted either in a left eye (‘LE’) or right eye (‘RE’). Models such as AxonMapModel will treat left and right eyes differently (for example, adjusting the location of the optic disc).

Examples

Implant Argus II in a left eye:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(eye='LE')

property n_electrodes

Number of electrodes in the array

This is equivalent to calling earray.n_electrodes.

property electrodes

Return all electrode names and objects in the electrode array

Internally, electrodes are stored in an ordered dictionary. You can iterate over different electrodes in the array as follows:

for name, electrode in implant.electrodes.items():
    print(name, electrode)

You can access an individual electrode by indexing directly into the prosthesis system object, e.g. implant['A1'] or implant[0].

property electrode_names

Return a list of all electrode names in the electrode array

property electrode_objects

Return a list of all electrode objects in the array

class pulse2percept.implants.base.RectangleImplant(x=0, y=0, z=0, rot=0, shape=(15, 15), r=75.0, spacing=400.0, eye='RE', stim=None, preprocess=True, safe_mode=False)

A generic rectangular implant

Parameters:

• x (float, optional) – The x, y, z coordinates (um) of the center of the implant

• y (float, optional) – The x, y, z coordinates (um) of the center of the implant

• z (float, optional) – The x, y, z coordinates (um) of the center of the implant

• rot (float, optional) – The rotation of the implant in degrees

• shape (tuple, optional) – The number of rows and columns in the implant

• r (float, optional) – The electrode radius (um)

• spacing (float, optional) – The distance (um) between electrodes in the implant

• eye (str, optional) – The eye in which the implant is implanted

• stim (Stimulus source type) – A valid source type for a stimulus

• preprocess (bool, optional) – Whether to preprocess the stimulus

• safe_mode (bool, optional) – Whether to enforce charge balance

Notes

• Lengths may be given as plain numbers of microns or as unitful quantities (e.g. spacing=0.4 * mm). See pulse2percept.units.

check_stim(stim)

Quality-check the stimulus

This method is executed every time a new value is assigned to stim.

If safe_mode is set to True, this function will only allow stimuli that are charge-balanced. If max_current is set, it will only allow stimuli whose total instantaneous current stays within it.

Both are questions about electricity, and neither can be answered about a stimulus that is not a current, so each raises a DimensionMismatchError on one. An implant that asks for neither does not run either check, which is why a dimensionless stimulus may still be assigned to one – preprocess has already had its chance to turn it into current, and if it did not, no safety claim is being made about it either.

The user can define their own checks in implants that inherit from ProsthesisSystem.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Raises:

• DimensionMismatchError – If an electrical check was requested and stim is not measured in units of current.

• .. versionchanged: – 0.10.0: The electrical checks verify that the stimulus really is electrical, instead of reading whatever numbers it holds as microamps.

property electrode_names

Return a list of all electrode names in the electrode array

property electrode_objects

Return a list of all electrode objects in the array

property electrodes

Return all electrode names and objects in the electrode array

Internally, electrodes are stored in an ordered dictionary. You can iterate over different electrodes in the array as follows:

for name, electrode in implant.electrodes.items():
    print(name, electrode)

You can access an individual electrode by indexing directly into the prosthesis system object, e.g. implant['A1'] or implant[0].

property max_current

Total instantaneous current (uA) the stimulator can source

property n_electrodes

Number of electrodes in the array

This is equivalent to calling earray.n_electrodes.

plot(annotate=False, autoscale=True, ax=None, stim_cmap=False)

Plot

Parameters:

• annotate (bool, optional) – Whether to scale the axes view to the data

• 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.

• stim_cmap (bool, str, or matplotlib colormap, optional) – If not false, the fill color of the plotted electrodes will vary based on maximum stimulus amplitude on each electrode. The chosen colormap will be used if provided

Returns:

ax – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes

preprocess_stim(stim)

Preprocess the stimulus

This methods is executed every time a new value is assigned to stim.

No preprocessing is performed by default, but the user can define their own method in implants that inherit from return stim ProsthesisSystem.

A custom method must return a Stimulus object with the correct number of electrodes for the implant.

Parameters:

stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).

Returns:

stim_out

Return type:

Stimulus object

property raster

Raster pattern

Most implants do not set this in their constructor, so the slot backing it may never have been written to; an unset raster means all electrodes may fire at once.

property earray

Electrode array

property stim

Stimulus

A stimulus can be created from many source types, such as scalars, NumPy arrays, and dictionaries (see Stimulus for a complete list).

A stimulus can be assigned either in the ProsthesisSystem constructor or later by assigning a value to stim.

Note

Unless when using dictionary notation, the number of stimuli must equal the number of electrodes in earray.

Examples

Send a biphasic pulse (30uA, 0.45ms phase duration) to an implant made from a single DiskElectrode:

>>> from pulse2percept.implants import DiskElectrode, ProsthesisSystem
>>> from pulse2percept.stimuli import BiphasicPulse
>>> implant = ProsthesisSystem(DiskElectrode(0, 0, 0, 100))
>>> implant.stim = BiphasicPulse(30, 0.45)

Stimulate Electrode B7 in Argus II with 13 uA:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(stim={'B7': 13})

property eye

Implanted eye

A ProsthesisSystem can be implanted either in a left eye (‘LE’) or right eye (‘RE’). Models such as AxonMapModel will treat left and right eyes differently (for example, adjusting the location of the optic disc).

Examples

Implant Argus II in a left eye:

>>> from pulse2percept.implants import ArgusII
>>> implant = ArgusII(eye='LE')