pulse2percept.implants.alpha

AlphaIMS, AlphaAMS

Classes

AlphaAMS([x, y, z, rot, eye, stim, ...])

Alpha-AMS

AlphaIMS([x, y, z, rot, eye, stim, ...])

Alpha-IMS
class pulse2percept.implants.alpha.AlphaIMS(x=0, y=0, z=-100, rot=0, eye='RE', stim=None, preprocess=True, safe_mode=False)[source]

Alpha-IMS

This class creates an Alpha-IMS array with 1500 photovoltaic pixels (each 50um in diameter) as described in [Stingl2013], and places it in the subretinal space, such that the center of the array is located at (x,y,z), given in microns, and the array is rotated by rotation angle rot, given in degrees.

The device consists of 1500 50um-wide square pixels, arranged on a 39x39 rectangular grid with 72um pixel pitch.

The array is oriented upright in the visual field, such that an array with center (0,0) has the top three rows lie in the lower retina (upper visual field).

An electrode can be addressed by name, row/column index, or integer index (into the flattened array).

Note

Column order is reversed in a left-eye implant.

Parameters:

  • x/y/z (double) – 3D location of the center of the electrode array. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance). z can either be a list with 1500 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.

  • eye ({'RE', 'LE'}, optional) – Eye in which array is implanted.

  • 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 Alpha-IMS array centered on the fovea, at 100um distance from the retina, rotated counter-clockwise by 5 degrees:

>>> from pulse2percept.implants import AlphaIMS
>>> AlphaIMS(x=0, y=0, z=100, rot=5)
AlphaIMS(earray=ElectrodeGrid, eye='RE', preprocess=True,
         safe_mode=False, shape=(39, 39), stim=None)

Get access to the third electrode in the top row (by name or by row/column index):

>>> alpha_ims = AlphaIMS(x=0, y=0, z=100, rot=0)
>>> alpha_ims['A3']
SquareElectrode(a=50.0, activated=True, name='A3',
                x=-1224.0, y=-1368.0, z=100.0)
>>> alpha_ims[0, 2]
SquareElectrode(a=50.0, activated=True, name='A3',
                x=-1224.0, y=-1368.0, z=100.0)
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 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})
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).

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 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)

class pulse2percept.implants.alpha.AlphaAMS(x=0, y=0, z=0, rot=0, eye='RE', stim=None, preprocess=True, safe_mode=False)[source]

Alpha-AMS

This class creates an Alpha-AMS array with 1600 photovoltaic pixels (each 30um in diameter) as described in [Stingl2017], and places it in the subretinal space, such that the center of the array is located at (x,y,z), given in microns, and the array is rotated by rotation angle rot, given in degrees.

The device consists of 1600 30um-wide round pixels, arranged on a 40x40 rectangular grid with 70um pixel pitch.

The array is oriented upright in the visual field, such that an array with center (0,0) has the top three rows lie in the lower retina (upper visual field), as shown below:

An electrode can be addressed by name, row/column index, or integer index (into the flattened array).

Note

Column order is reversed in a left-eye implant.

Parameters:

  • x/y/z (double) – 3D location of the center of the electrode array. The coordinate system is centered over the fovea. Positive x values move the electrode into the nasal retina. Positive y values move the electrode into the superior retina. Positive z values move the electrode away from the retina into the vitreous humor (sometimes called electrode-retina distance). z can either be a list with 1600 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.

  • eye ({'RE', 'LE'}, optional) – Eye in which array is implanted.

  • 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 AlphaAMS array centered on the fovea, at 100um distance from the retina, rotated counter-clockwise by 5 degrees:

>>> from pulse2percept.implants import AlphaAMS
>>> AlphaAMS(x=0, y=0, z=100, rot=5)
AlphaAMS(earray=ElectrodeGrid, eye='RE', preprocess=True,
         safe_mode=False, shape=(40, 40), stim=None)

Get access to the third electrode in the top row (by name or by row/column index):

>>> alpha_ims = AlphaAMS(x=0, y=0, z=100, rot=0)
>>> alpha_ims['A3']
DiskElectrode(activated=True, name='A3', r=15.0, x=-1225.0,
              y=-1365.0, z=100.0)
>>> alpha_ims[0, 2]
DiskElectrode(activated=True, name='A3', r=15.0, x=-1225.0,
              y=-1365.0, z=100.0)
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 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})
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).

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 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)