pulse2percept.implants.cortex¶

Orion, Cortivis, ICVP, EllipsoidElectrode, NeuralinkThread, LinearEdgeThread, Neuralink

`orion`	`Orion`
`cortivis`	`Cortivis`
`icvp`	`ICVP`
`neuralink`	`EllipsoidElectrode`, `LinearEdgeThread`, `NeuralinkThread`

See also

Basic Concepts > Visual Prostheses

class pulse2percept.implants.cortex.Orion(x=15000, y=0, z=0, rot=0, stim=None, preprocess=False, safe_mode=False)[source]¶

Create a Orion array.

This function creates a Orion array and places it on the visual cortex such that the center of the base of the array is at 3D location (x,y,z) given in microns, and the array is rotated by angle rot, given in degrees.

Orion contains 60 electrodes in a hex shaped grid inspired by Argus II.

Note

By default the implant is in right hemisphere, use negative x-values to shift it to left hemisphere

Parameters:

x/y/z (double) – 3D location of the center of the electrode array. z can either be a list with 35 entries or a scalar that is applied to all electrodes.
rot (float) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.
stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).
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.

Examples

Create an Orion array, by default centered 15mm to the right of fovea in V1:

>>> from pulse2percept.implants.cortex import Orion
>>> Orion() # doctest: +NORMALIZE_WHITESPACE
Orion(earray=ElectrodeGrid, preprocess=False,
      safe_mode=False, shape=(10, 7), stim=None)

Get access to electrode ‘96’:

>>> orion = Orion()
>>> orion['96'] # doctest: +NORMALIZE_WHITESPACE
DiskElectrode(activated=True, name='96', r=1000.0,
              x=3450.0, y=-9640.928378532848, z=0.0)

check_stim(stim)[source]¶

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.

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).

earray¶: Electrode array

electrode_names¶: Return a list of all electrode names in the electrode array

electrode_objects¶: Return a list of all electrode objects in the array

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].

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')

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)[source]¶

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 (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)[source]¶

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 (`Stimulus` object)

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})

class pulse2percept.implants.cortex.Cortivis(x=20000, y=-5000, z=0, rot=0, stim=None, preprocess=False, safe_mode=False)[source]¶

Create a Cortivis array.

This function creates a Cortivis array and places it on the visual cortex such that the center of the base of the array is at 3D location (x,y,z) given in microns, and the array is rotated by angle rot, given in degrees.

Cortivis is a Utah electrode array containing 96 electrodes in a 10x10 array with 400 um spacing, and electrode diameter of 80 um at the base.

Note

By default the implant is in right hemisphere, use negative x-values to shift it to left hemisphere

Parameters:

x/y/z (double) – 3D location of the center of the electrode array. z can either be a list with 35 entries or a scalar that is applied to all electrodes.
rot (float) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.
stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).
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.

Examples

Create an Cortivis array, by default centered 20mm to the right of fovea in V1:

>>> from pulse2percept.implants.cortex import Cortivis
>>> Cortivis() # doctest: +NORMALIZE_WHITESPACE
Cortivis(earray=ElectrodeGrid, preprocess=False,
     safe_mode=False, shape=(10, 10), stim=None)

Get access to electrode ‘11’:

>>> cortivis = Cortivis()
>>> cortivis['11'] # doctest: +NORMALIZE_WHITESPACE
DiskElectrode(activated=True, name='11', r=40.0, x=21400.0,
              y=-6000.0, z=-1500.0)

check_stim(stim)[source]¶

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.

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).

earray¶: Electrode array

electrode_names¶: Return a list of all electrode names in the electrode array

electrode_objects¶: Return a list of all electrode objects in the array

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].

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')

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)[source]¶

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 (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)[source]¶

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 (`Stimulus` object)

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})

class pulse2percept.implants.cortex.ICVP(x=15000, y=0, z=0, rot=0, stim=None, preprocess=False, safe_mode=False)[source]¶

Create an ICVP array.

This function creates a ICVP array and places it on the visual cortex such that the center of the base of the array is at 3D location (x,y,z) given in microns, and the array is rotated by angle rot, given in degrees.

ICVP (Intracortical Visual Prosthesis Project) is an electrode array containing 16 Parylene-insulated (and 2 uninsulated reference and counter) iridium shaft electrodes in a 4 column array with 400 um spacing. The electrodes have a diameter of 15 um at the laser cut. They are inserted either 650 um or 850 um into the cortex.

Note

By default the implant is in right hemisphere, use negative x-values to shift it to left hemisphere

Parameters:

x/y/z (double) – 3D location of the center of the electrode array. z can either be a list with 35 entries or a scalar that is applied to all electrodes.
rot (float) – Rotation angle of the array (deg). Positive values denote counter-clock-wise (CCW) rotations in the retinal coordinate system.
stim (Stimulus source type) – A valid source type for the Stimulus object (e.g., scalar, NumPy array, pulse train).
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.

Examples

Create an ICVP array, by default centered 15mm to the right of fovea in V1:

>>> from pulse2percept.implants.cortex import Orion
>>> ICVP() # doctest: +NORMALIZE_WHITESPACE
ICVP(earray=ElectrodeGrid, preprocess=False,
     safe_mode=False, shape=(5, 4), stim=None)

Get access to electrode ‘11’:

>>> icvp = ICVP()
>>> icvp['11'] # doctest: +NORMALIZE_WHITESPACE
DiskElectrode(activated=True, name='11', r=50.0,
              x=15173.205080756888, y=100.0, z=-650.0)

check_stim(stim)[source]¶

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.

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).

earray¶: Electrode array

electrode_names¶: Return a list of all electrode names in the electrode array

electrode_objects¶: Return a list of all electrode objects in the array

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].

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')

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)[source]¶

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 (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)[source]¶

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 (`Stimulus` object)

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})

class pulse2percept.implants.cortex.EllipsoidElectrode(x=0, y=0, z=0, rx=7, ry=7, rz=12, orient=array([0, 0, 1]), orient_mode='direction', name=None, activated=True)[source]¶

plot(autoscale=False, ax=None)[source]¶

Plot

Parameters:	autoscale (bool, optional) – Whether to adjust the x,y limits of the plot ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None given, a new one will be created.
Returns:	ax (`matplotlib.axes.Axes`) – Returns the axis object of the plot

plot3D(ax=None, **kwargs)[source]¶

Plot the electrode in 3D space

Parameters:	ax (matplotlib.axes.Axes) – Axes to plot on. If None, a new figure and axes will be created.

class pulse2percept.implants.cortex.NeuralinkThread(earray, stim=None, eye='RE', preprocess=False, safe_mode=False)[source]¶

Base class for Neuralink threads

check_stim(stim)[source]¶

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.

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).

earray¶: Electrode array

electrode_names¶: Return a list of all electrode names in the electrode array

electrode_objects¶: Return a list of all electrode objects in the array

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].

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')

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)[source]¶

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 (matplotlib.axes.Axes) – Returns the axis object of the plot

preprocess_stim(stim)[source]¶

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 (`Stimulus` object)

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})

class pulse2percept.implants.cortex.LinearEdgeThread(x=0, y=0, z=0, orient=array([0, 0, 1]), orient_mode='direction', r=5, n_elecs=32, spacing=50, insertion_depth=0, electrode=<class 'pulse2percept.implants.cortex.neuralink.EllipsoidElectrode'>, stim=None, preprocess=False, safe_mode=False)[source]¶

check_stim(stim)[source]¶

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.

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).

earray¶: Electrode array

electrode_names¶: Return a list of all electrode names in the electrode array

electrode_objects¶: Return a list of all electrode objects in the array

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].

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')

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)[source]¶

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 (matplotlib.axes.Axes) – Returns the axis object of the plot

plot3D(ax=None, **kwargs)[source]¶

Plot the thread in 3D space

Parameters:	ax (matplotlib.axes.Axes) – Axes to plot on. If None, a new figure and axes will be created.

preprocess_stim(stim)[source]¶

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 (`Stimulus` object)

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})

class pulse2percept.implants.cortex.Neuralink(threads, stim=None, preprocess=False, safe_mode=False)[source]¶

check_stim(stim)[source]¶

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.

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).

earray¶: Electrode array

electrode_names¶: Return a list of all electrode names in the electrode array

electrode_objects¶: Return a list of all electrode objects in the array

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].

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')

classmethod from_coords(implant_type, locs=None, xrange=None, yrange=None, xystep=None)[source]¶

Create an ensemble implant using physical (cortical or retinal) coordinates.

Parameters:	implant_type (type) – The type of implant to create for the ensemble. locs (np.ndarray with shape (n, 2), optional) – Array of physical locations (um) to create implants at. Not needed if using xrange, yrange, and xystep. yrange (xrange,) – Range of x and y coordinates to create implants at. xystep (float, optional) – Spacing between implant centers.

classmethod from_cortical_map(implant_type, vfmap, locs=None, xrange=None, yrange=None, xystep=None, region='v1')[source]¶

Override of parent class from cortical map method. Uses from_neuropythy instead of from_cortical_map if the provided vfmap is a NeuropythyMap.

Parameters:

implant_type (p2p.implants.ProsthesisSystem) – Type of implant to create. Currently only NeuralinkThread is supported.
vfmap (p2p.topography.CorticalMap) – Cortical map to create implant from.
locs (np.ndarray with shape (n, 2), optional) – Array of visual field locations to create threads at. Not needed if using xrange, yrange, and xystep.
yrange (xrange,) – Range of x and y coordinates to create threads at.
xystep (float, optional) – Spacing between threads.
region (str, optional) – Region of cortex to create implant in.

Returns:

Neuralink (p2p.implants.Neuralink) – Neuralink ensemble implant created from the visual field map.

classmethod from_neuropythy(vfmap, locs=None, xrange=None, yrange=None, xystep=None, rand_insertion_angle=None, region='v1', Thread=<class 'pulse2percept.implants.cortex.neuralink.LinearEdgeThread'>)[source]¶

Create a neuralink implant from a neuropythy visual field map.

The implant will be created by creating a NeuralinkThread for each visual field location specified either by locs or by xrange, yrange, and xystep. Each thread will be inserted perpendicular to the cortical surface at the corresponding location in cortex, with up to rand_insertion_angle degrees of azimuthal rotation.

Parameters:

vfmap (p2p.topography.NeuropythyMap) – Visual field map to create implant from.
locs (np.ndarray with shape (n, 2), optional) – Array of visual field locations to create threads at. Not needed if using xrange, yrange, and xystep.
yrange (xrange,) – Range of x and y coordinates to create threads at.
xystep (float, optional) – Spacing between threads.
rand_insertion_angle (float, optional) – If not none, insert threads at a random offset from perpendicular, with a maximum azimuthal rotation of rand_insertion_angle degrees.
region (str, optional) – Region of cortex to create implant in.
Thread (NeuralinkThread, optional) – Thread class to use for the implant. Must accept x, y, z, and orient parameters.

Returns:

Neuralink (p2p.implants.Neuralink) – Neuralink ensemble implant created from the visual field map.

implants¶: Dict of implants

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)[source]¶

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 (matplotlib.axes.Axes) – Returns the axis object of the plot

plot3D(ax=None, **kwargs)[source]¶

Plot the implant in 3D space

Parameters:	ax (matplotlib.axes.Axes) – Axes to plot on. If None, a new figure and axes will be created.

preprocess_stim(stim)[source]¶

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 (`Stimulus` object)

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})