pulse2percept.implants.electrodes

Electrode, PointSource, DiskElectrode, SquareElectrode, HexElectrode

Classes

`DiskElectrode`(x, y, z, r[, name, activated])	Circular disk electrode
`Electrode`(x, y, z[, name, activated])	Abstract base class for all electrodes.
`HexElectrode`(x, y, z, a[, name, activated])	Hexagonal electrode
`PointSource`(x, y, z[, name, activated])	Idealized current point source
`SquareElectrode`(x, y, z, a[, name, activated])	Square electrode

class pulse2percept.implants.electrodes.Electrode(x, y, z, name=None, activated=True)[source]

Abstract base class for all electrodes.

Parameters:

x/y/z (double) – 3D location of the electrode (um). The coordinate system is centered over the fovea. Positive x values move the electrode into the right visual field. Positive y values move the electrode into the left visual field. Positive z values move the electrode either into the cortex or into the vitreos humor.
name (str, optional) – Electrode name
activated (bool) – To deactivate, set to False. Deactivated electrodes cannot receive stimuli.

Notes

Coordinates may be given as plain numbers of microns or as unitful quantities (e.g. 1.2 * mm), which are converted to microns. See pulse2percept.units. Electrodes always store plain numbers in microns: x, y and z are ordinary floats, and so is everything downstream of them.

coordinate_unit = um[source]: The unit electrode coordinates are stored in. Electrodes hold plain numbers, which is what every kernel downstream of them expects; this says what those numbers mean.

coordinates(unit=None)[source]

3D position of the electrode

Added in version 0.10.0.

Parameters:: unit (Unit, optional) – Length unit to express the position in. If None, the position is returned as it is stored (microns).
Returns:: coords – An ordinary NumPy array [x, y, z], never a Quantity.
Return type:: (3,) np.ndarray

Examples

>>> from pulse2percept.implants import DiskElectrode
>>> from pulse2percept.units import mm
>>> DiskElectrode(1000, 0, 100, 200).coordinates(mm)
array([1. , 0. , 0.1])

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 – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes

class pulse2percept.implants.electrodes.PointSource(x, y, z, name=None, activated=True)[source]

Idealized current point source

Parameters:

x/y/z (double) – 3D location of the electrode. 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).
name (str, optional) – Electrode name
activated (bool) – To deactivate, set to False. Deactivated electrodes cannot receive stimuli.

electric_potential(x, y, z, amp, sigma)[source]

Calculate electric potential at (x, y, z)

Parameters:

x/y/z (double) – 3D location (um) at which to evaluate the electric potential. May be given as a unitful quantity, e.g. 0.2 * mm.
amp (double) – amplitude of the constant current pulse
sigma (double) – resistivity of the extracellular solution

Returns:

pot (double) – The electric potential at (x, y, z)
The electric potential \(V(r)\) of a point source is given by
.. math:: – V(r) = frac{sigma I}{4 pi r},
where \(\sigma\) is the resistivity of the extracellular solution
(typically Ames medium, \(\sigma = 110 \Ohm cm\)),
\(I\) is the amplitude of the constant current pulse,
and \(r\) is the distance from the stimulating electrode to the
point at which the voltage is being computed.

coordinate_unit = um[source]: The unit electrode coordinates are stored in. Electrodes hold plain numbers, which is what every kernel downstream of them expects; this says what those numbers mean.

coordinates(unit=None)[source]

3D position of the electrode

Added in version 0.10.0.

Parameters:: unit (Unit, optional) – Length unit to express the position in. If None, the position is returned as it is stored (microns).
Returns:: coords – An ordinary NumPy array [x, y, z], never a Quantity.
Return type:: (3,) np.ndarray

Examples

>>> from pulse2percept.implants import DiskElectrode
>>> from pulse2percept.units import mm
>>> DiskElectrode(1000, 0, 100, 200).coordinates(mm)
array([1. , 0. , 0.1])

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 – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes

class pulse2percept.implants.electrodes.DiskElectrode(x, y, z, r, name=None, activated=True)[source]

Circular disk electrode

Parameters:

x/y/z (double) – 3D location of the electrode. 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).
r (double) – Disk radius (um) in the x,y plane
name (str, optional) – Electrode name
activated (bool) – To deactivate, set to False. Deactivated electrodes cannot receive stimuli.

Notes

Lengths may be given as plain numbers of microns or as unitful quantities (e.g. DiskElectrode(1 * mm, 0, 0.1 * mm, 200 * um)). See pulse2percept.units.

electric_potential(x, y, z, v0)[source]

Calculate electric potential at (x, y, z)

Parameters:

x/y/z (double) – 3D location (um) at which to evaluate the electric potential. May be given as a unitful quantity, e.g. 0.2 * mm.
v0 (double) – The quasi-static disk potential relative to a ground electrode at infinity

Returns:

pot – The electric potential at (x, y, z).

Return type:

double

The electric potential \(V(r,z)\) of a disk electrode is given by [WileyWebster1982]:

\[V(r,z) = \sin^{-1} \bigg\{ \frac{2a}{\sqrt{(r-a)^2 + z^2} + \sqrt{(r+a)^2 + z^2}} \bigg\} \times \frac{2 V_0}{\pi},\]

for \(z \neq 0\), where \(r\) and \(z\) are the radial and axial distances from the center of the disk, \(V_0\) is the disk potential, \(\sigma\) is the medium conductivity, and \(a\) is the disk radius.

coordinate_unit = um[source]: The unit electrode coordinates are stored in. Electrodes hold plain numbers, which is what every kernel downstream of them expects; this says what those numbers mean.

coordinates(unit=None)[source]

3D position of the electrode

Added in version 0.10.0.

Parameters:: unit (Unit, optional) – Length unit to express the position in. If None, the position is returned as it is stored (microns).
Returns:: coords – An ordinary NumPy array [x, y, z], never a Quantity.
Return type:: (3,) np.ndarray

Examples

>>> from pulse2percept.implants import DiskElectrode
>>> from pulse2percept.units import mm
>>> DiskElectrode(1000, 0, 100, 200).coordinates(mm)
array([1. , 0. , 0.1])

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 – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes

class pulse2percept.implants.electrodes.SquareElectrode(x, y, z, a, name=None, activated=True)[source]

Square electrode

Added in version 0.7.

Parameters:

x/y/z (double) – 3D location of the electrode. 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).
a (double) – Side length (um) of the square
name (str, optional) – Electrode name
activated (bool) – To deactivate, set to False. Deactivated electrodes cannot receive stimuli.

Notes

Lengths may be given as plain numbers of microns or as unitful quantities (e.g. 50 * um). See pulse2percept.units.

coordinate_unit = um[source]: The unit electrode coordinates are stored in. Electrodes hold plain numbers, which is what every kernel downstream of them expects; this says what those numbers mean.

coordinates(unit=None)[source]

3D position of the electrode

Added in version 0.10.0.

Parameters:: unit (Unit, optional) – Length unit to express the position in. If None, the position is returned as it is stored (microns).
Returns:: coords – An ordinary NumPy array [x, y, z], never a Quantity.
Return type:: (3,) np.ndarray

Examples

>>> from pulse2percept.implants import DiskElectrode
>>> from pulse2percept.units import mm
>>> DiskElectrode(1000, 0, 100, 200).coordinates(mm)
array([1. , 0. , 0.1])

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 – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes

class pulse2percept.implants.electrodes.HexElectrode(x, y, z, a, name=None, activated=True)[source]

Hexagonal electrode

Added in version 0.7.

Parameters:

x/y/z (double) – 3D location of the electrode. 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).
a (double) – Length (um) of line drawn from the center of the hexagon to the midpoint of one of its sides.
name (str, optional) – Electrode name
activated (bool) – To deactivate, set to False. Deactivated electrodes cannot receive stimuli.

Notes

Lengths may be given as plain numbers of microns or as unitful quantities (e.g. 50 * um). See pulse2percept.units.

coordinate_unit = um[source]: The unit electrode coordinates are stored in. Electrodes hold plain numbers, which is what every kernel downstream of them expects; this says what those numbers mean.

coordinates(unit=None)[source]

3D position of the electrode

Added in version 0.10.0.

Parameters:: unit (Unit, optional) – Length unit to express the position in. If None, the position is returned as it is stored (microns).
Returns:: coords – An ordinary NumPy array [x, y, z], never a Quantity.
Return type:: (3,) np.ndarray

Examples

>>> from pulse2percept.implants import DiskElectrode
>>> from pulse2percept.units import mm
>>> DiskElectrode(1000, 0, 100, 200).coordinates(mm)
array([1. , 0. , 0.1])

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 – Returns the axis object of the plot

Return type:

matplotlib.axes.Axes