Note

Click here to download the full example code

Creating a grid of electrodes¶

This example shows how to use ElectrodeGrid.

Most current electrode arrays arrange their electrodes in a 2D grid.

Creating a rectangular grid¶

To create a rectangular grid, we need to specify:

The shape of the grid, passed as a tuple containing the desired number of rows and columns
The electrode-to-electrode spacing in microns
The (x, y) location of the center of the array
The rotation angle rot of the grid in degrees, where positive angles rotate all electrodes in the array in a counter-clockwise fashion on the retinal surface.

We can also specify:

A naming convention names for the rows and columns in the grid. For example, to label rows alphabetically and columns numerically, we would pass a tuple ('A', '1'). To label both alphabetically, we would pass ('A', 'A').
An electrode type etype, which must be a subclass of Electrode. By default, PointSource is chosen.
Any additional parameters that should be passed to the Electrode constructor, such as a radius r for DiskElectrode.

Let’s say we want to create a 2x3 rectangular grid of PointSource objects, each electrode spaced 500 microns apart, and the whole grid should be centered over the fovea:

from pulse2percept.models import AxonMapModel
from numpy import pi
from pulse2percept.implants import DiskElectrode
from pulse2percept.implants import ElectrodeGrid

grid = ElectrodeGrid((2, 3), 500)

We can access individual electrodes by indexing into grid:

The first electrode:

grid[0]

Out:

PointSource(activated=True, name='A1', x=-500.0, y=-250.0,
            z=0.0)

The first electrode by name:

grid['A1']

Out:

PointSource(activated=True, name='A1', x=-500.0, y=-250.0,
            z=0.0)

Accessing the x-coordinate of the first electrode:

grid[0].x

Out:

-500.0

Showing all electrodes:

grid[:]

Out:

[PointSource(activated=True, name='A1', x=-500.0, y=-250.0,
            z=0.0), PointSource(activated=True, name='A2', x=0.0, y=-250.0,
            z=0.0), PointSource(activated=True, name='A3', x=500.0, y=-250.0,
            z=0.0), PointSource(activated=True, name='B1', x=-500.0, y=250.0,
            z=0.0), PointSource(activated=True, name='B2', x=0.0, y=250.0,
            z=0.0), PointSource(activated=True, name='B3', x=500.0, y=250.0,
            z=0.0)]

We can iterate over all electrodes as if we were dealing with a dictionary:

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

Out:

A1 PointSource(activated=True, name='A1', x=-500.0, y=-250.0,
            z=0.0)
A2 PointSource(activated=True, name='A2', x=0.0, y=-250.0,
            z=0.0)
A3 PointSource(activated=True, name='A3', x=500.0, y=-250.0,
            z=0.0)
B1 PointSource(activated=True, name='B1', x=-500.0, y=250.0,
            z=0.0)
B2 PointSource(activated=True, name='B2', x=0.0, y=250.0,
            z=0.0)
B3 PointSource(activated=True, name='B3', x=500.0, y=250.0,
            z=0.0)

To make a grid of DiskElectrode objects, we need to explicitly specify the electrode type (etype) and the radius to use (r):

# 11x13 grid, 100-um disk electrodes spaced 500um apart:
disk_grid = ElectrodeGrid((11, 13), 500, etype=DiskElectrode, r=100)

disk_grid[:]

Out:

[DiskElectrode(activated=True, name='A1', r=100.0,
              x=-3000.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A2', r=100.0,
              x=-2500.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A3', r=100.0,
              x=-2000.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A4', r=100.0,
              x=-1500.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A5', r=100.0,
              x=-1000.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A6', r=100.0, x=-500.0,
              y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A7', r=100.0, x=0.0,
              y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A8', r=100.0, x=500.0,
              y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A9', r=100.0, x=1000.0,
              y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A10', r=100.0,
              x=1500.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A11', r=100.0,
              x=2000.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A12', r=100.0,
              x=2500.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='A13', r=100.0,
              x=3000.0, y=-2500.0, z=0.0), DiskElectrode(activated=True, name='B1', r=100.0,
              x=-3000.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B2', r=100.0,
              x=-2500.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B3', r=100.0,
              x=-2000.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B4', r=100.0,
              x=-1500.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B5', r=100.0,
              x=-1000.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B6', r=100.0, x=-500.0,
              y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B7', r=100.0, x=0.0,
              y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B8', r=100.0, x=500.0,
              y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B9', r=100.0, x=1000.0,
              y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B10', r=100.0,
              x=1500.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B11', r=100.0,
              x=2000.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B12', r=100.0,
              x=2500.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='B13', r=100.0,
              x=3000.0, y=-2000.0, z=0.0), DiskElectrode(activated=True, name='C1', r=100.0,
              x=-3000.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C2', r=100.0,
              x=-2500.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C3', r=100.0,
              x=-2000.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C4', r=100.0,
              x=-1500.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C5', r=100.0,
              x=-1000.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C6', r=100.0, x=-500.0,
              y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C7', r=100.0, x=0.0,
              y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C8', r=100.0, x=500.0,
              y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C9', r=100.0, x=1000.0,
              y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C10', r=100.0,
              x=1500.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C11', r=100.0,
              x=2000.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C12', r=100.0,
              x=2500.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='C13', r=100.0,
              x=3000.0, y=-1500.0, z=0.0), DiskElectrode(activated=True, name='D1', r=100.0,
              x=-3000.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D2', r=100.0,
              x=-2500.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D3', r=100.0,
              x=-2000.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D4', r=100.0,
              x=-1500.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D5', r=100.0,
              x=-1000.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D6', r=100.0, x=-500.0,
              y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D7', r=100.0, x=0.0,
              y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D8', r=100.0, x=500.0,
              y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D9', r=100.0, x=1000.0,
              y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D10', r=100.0,
              x=1500.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D11', r=100.0,
              x=2000.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D12', r=100.0,
              x=2500.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='D13', r=100.0,
              x=3000.0, y=-1000.0, z=0.0), DiskElectrode(activated=True, name='E1', r=100.0,
              x=-3000.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E2', r=100.0,
              x=-2500.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E3', r=100.0,
              x=-2000.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E4', r=100.0,
              x=-1500.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E5', r=100.0,
              x=-1000.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E6', r=100.0, x=-500.0,
              y=-500.0, z=0.0), DiskElectrode(activated=True, name='E7', r=100.0, x=0.0,
              y=-500.0, z=0.0), DiskElectrode(activated=True, name='E8', r=100.0, x=500.0,
              y=-500.0, z=0.0), DiskElectrode(activated=True, name='E9', r=100.0, x=1000.0,
              y=-500.0, z=0.0), DiskElectrode(activated=True, name='E10', r=100.0,
              x=1500.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E11', r=100.0,
              x=2000.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E12', r=100.0,
              x=2500.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='E13', r=100.0,
              x=3000.0, y=-500.0, z=0.0), DiskElectrode(activated=True, name='F1', r=100.0,
              x=-3000.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F2', r=100.0,
              x=-2500.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F3', r=100.0,
              x=-2000.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F4', r=100.0,
              x=-1500.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F5', r=100.0,
              x=-1000.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F6', r=100.0, x=-500.0,
              y=0.0, z=0.0), DiskElectrode(activated=True, name='F7', r=100.0, x=0.0,
              y=0.0, z=0.0), DiskElectrode(activated=True, name='F8', r=100.0, x=500.0,
              y=0.0, z=0.0), DiskElectrode(activated=True, name='F9', r=100.0, x=1000.0,
              y=0.0, z=0.0), DiskElectrode(activated=True, name='F10', r=100.0,
              x=1500.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F11', r=100.0,
              x=2000.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F12', r=100.0,
              x=2500.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='F13', r=100.0,
              x=3000.0, y=0.0, z=0.0), DiskElectrode(activated=True, name='G1', r=100.0,
              x=-3000.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G2', r=100.0,
              x=-2500.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G3', r=100.0,
              x=-2000.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G4', r=100.0,
              x=-1500.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G5', r=100.0,
              x=-1000.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G6', r=100.0, x=-500.0,
              y=500.0, z=0.0), DiskElectrode(activated=True, name='G7', r=100.0, x=0.0,
              y=500.0, z=0.0), DiskElectrode(activated=True, name='G8', r=100.0, x=500.0,
              y=500.0, z=0.0), DiskElectrode(activated=True, name='G9', r=100.0, x=1000.0,
              y=500.0, z=0.0), DiskElectrode(activated=True, name='G10', r=100.0,
              x=1500.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G11', r=100.0,
              x=2000.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G12', r=100.0,
              x=2500.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='G13', r=100.0,
              x=3000.0, y=500.0, z=0.0), DiskElectrode(activated=True, name='H1', r=100.0,
              x=-3000.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H2', r=100.0,
              x=-2500.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H3', r=100.0,
              x=-2000.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H4', r=100.0,
              x=-1500.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H5', r=100.0,
              x=-1000.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H6', r=100.0, x=-500.0,
              y=1000.0, z=0.0), DiskElectrode(activated=True, name='H7', r=100.0, x=0.0,
              y=1000.0, z=0.0), DiskElectrode(activated=True, name='H8', r=100.0, x=500.0,
              y=1000.0, z=0.0), DiskElectrode(activated=True, name='H9', r=100.0, x=1000.0,
              y=1000.0, z=0.0), DiskElectrode(activated=True, name='H10', r=100.0,
              x=1500.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H11', r=100.0,
              x=2000.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H12', r=100.0,
              x=2500.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='H13', r=100.0,
              x=3000.0, y=1000.0, z=0.0), DiskElectrode(activated=True, name='I1', r=100.0,
              x=-3000.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I2', r=100.0,
              x=-2500.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I3', r=100.0,
              x=-2000.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I4', r=100.0,
              x=-1500.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I5', r=100.0,
              x=-1000.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I6', r=100.0, x=-500.0,
              y=1500.0, z=0.0), DiskElectrode(activated=True, name='I7', r=100.0, x=0.0,
              y=1500.0, z=0.0), DiskElectrode(activated=True, name='I8', r=100.0, x=500.0,
              y=1500.0, z=0.0), DiskElectrode(activated=True, name='I9', r=100.0, x=1000.0,
              y=1500.0, z=0.0), DiskElectrode(activated=True, name='I10', r=100.0,
              x=1500.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I11', r=100.0,
              x=2000.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I12', r=100.0,
              x=2500.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='I13', r=100.0,
              x=3000.0, y=1500.0, z=0.0), DiskElectrode(activated=True, name='J1', r=100.0,
              x=-3000.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J2', r=100.0,
              x=-2500.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J3', r=100.0,
              x=-2000.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J4', r=100.0,
              x=-1500.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J5', r=100.0,
              x=-1000.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J6', r=100.0, x=-500.0,
              y=2000.0, z=0.0), DiskElectrode(activated=True, name='J7', r=100.0, x=0.0,
              y=2000.0, z=0.0), DiskElectrode(activated=True, name='J8', r=100.0, x=500.0,
              y=2000.0, z=0.0), DiskElectrode(activated=True, name='J9', r=100.0, x=1000.0,
              y=2000.0, z=0.0), DiskElectrode(activated=True, name='J10', r=100.0,
              x=1500.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J11', r=100.0,
              x=2000.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J12', r=100.0,
              x=2500.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='J13', r=100.0,
              x=3000.0, y=2000.0, z=0.0), DiskElectrode(activated=True, name='K1', r=100.0,
              x=-3000.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K2', r=100.0,
              x=-2500.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K3', r=100.0,
              x=-2000.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K4', r=100.0,
              x=-1500.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K5', r=100.0,
              x=-1000.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K6', r=100.0, x=-500.0,
              y=2500.0, z=0.0), DiskElectrode(activated=True, name='K7', r=100.0, x=0.0,
              y=2500.0, z=0.0), DiskElectrode(activated=True, name='K8', r=100.0, x=500.0,
              y=2500.0, z=0.0), DiskElectrode(activated=True, name='K9', r=100.0, x=1000.0,
              y=2500.0, z=0.0), DiskElectrode(activated=True, name='K10', r=100.0,
              x=1500.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K11', r=100.0,
              x=2000.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K12', r=100.0,
              x=2500.0, y=2500.0, z=0.0), DiskElectrode(activated=True, name='K13', r=100.0,
              x=3000.0, y=2500.0, z=0.0)]

Note

You can also specify a list of radii, one value for each electrode in the grid.

We can visualize the grid by using its plot method:

disk_grid.plot()

Out:

<AxesSubplot:xlabel='x (microns)', ylabel='y (microns)'>

Creating a hexagonal grid¶

To create a hexagonal grid instead, all we need to do is change the grid type from ‘rect’ (default) to ‘hex’:

hex_grid = ElectrodeGrid((11, 13), 500, type='hex', etype=DiskElectrode, r=100)

hex_grid.plot()

Out:

<AxesSubplot:xlabel='x (microns)', ylabel='y (microns)'>

The following example centers the grid on (x,y) = (-600um, 200 um), z=150um away from the retinal surface, and rotates it clockwise by 45 degrees (note the minus sign):

offset_grid = ElectrodeGrid((11, 13), 500, type='hex', x=-600, y=200, z=150,
                            rot=-45, etype=DiskElectrode, r=100)

Note

Clockwise/counter-clockwise rotations refer to rotations on the retinal surface (that is, as if seen on a fundus photograph).

We can also plot the grid on top of a map of retinal nerve fiber bundles:

AxonMapModel().plot()
offset_grid.plot()

Out:

<AxesSubplot:xlabel='x (microns)', ylabel='y (microns)'>

Total running time of the script: ( 0 minutes 0.690 seconds)

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