{ "cells": [ { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n# Creating a grid of electrodes\n\nThis example shows how to use\n:py:class:`~pulse2percept.implants.ElectrodeGrid`.\n\nMost current electrode arrays arrange their electrodes in a 2D grid.\n\n## Creating a rectangular grid\n\nTo create a rectangular grid, we need to specify:\n\n- The ``shape`` of the grid, passed as a tuple containing the desired number\n of rows and columns\n- The electrode-to-electrode ``spacing`` in microns\n- The (``x``, ``y``) location of the center of the array\n- The rotation angle ``rot`` of the grid in degrees, where positive angles\n rotate all electrodes in the array in a counter-clockwise fashion on the\n retinal surface.\n\nWe can also specify:\n\n- A naming convention ``names`` for the rows and columns in the grid.\n For example, to label rows alphabetically and columns numerically, we would\n pass a tuple ``('A', '1')``. To label both alphabetically, we would pass\n ``('A', 'A')``.\n- An electrode type ``etype``, which must be a subclass of\n :py:class:`~pulse2percept.implants.Electrode`. By default,\n :py:class:`~pulse2percept.implants.PointSource` is chosen.\n- Any additional parameters that should be passed to the\n :py:class:`~pulse2percept.implants.Electrode` constructor, such as a radius\n ``r`` for :py:class:`~pulse2percept.implants.DiskElectrode`.\n\nLet's say we want to create a 2x3 rectangular grid of\n:py:class:`~pulse2percept.implants.PointSource` objects, each electrode spaced\n500 microns apart, and the whole grid should be centered over the fovea:\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "from pulse2percept.models import AxonMapModel\nfrom numpy import pi\nfrom pulse2percept.implants import DiskElectrode\nfrom pulse2percept.implants import ElectrodeGrid\n\ngrid = ElectrodeGrid((2, 3), 500)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can access individual electrodes by indexing into ``grid``:\n\nThe first electrode:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "grid[0]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The first electrode by name:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "grid['A1']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Accessing the x-coordinate of the first electrode:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "grid[0].x" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Showing all electrodes:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "grid[:]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can iterate over all electrodes as if we were dealing with a dictionary:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "for name, electrode in grid.electrodes.items():\n print(name, electrode)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To make a grid of :py:class:`~pulse2percept.implants.DiskElectrode` objects,\nwe need to explicitly specify the electrode type (``etype``) and the radius\nto use (``r``):\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "# 11x13 grid, 100-um disk electrodes spaced 500um apart:\ndisk_grid = ElectrodeGrid((11, 13), 500, etype=DiskElectrode, r=100)\n\ndisk_grid[:]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "

Note

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

\n\nWe can visualize the grid by using its ``plot`` method:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "disk_grid.plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Creating a hexagonal grid\n\nTo create a hexagonal grid instead, all we need to do is change the grid type\nfrom 'rect' (default) to 'hex':\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "hex_grid = ElectrodeGrid((11, 13), 500, type='hex', etype=DiskElectrode, r=100)\n\nhex_grid.plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The following example centers the grid on (x,y) = (-600um, 200 um),\nz=150um away from the retinal surface, and rotates it clockwise by 45 degrees\n(note the minus sign):\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "offset_grid = ElectrodeGrid((11, 13), 500, type='hex', x=-600, y=200, z=150,\n rot=-45, etype=DiskElectrode, r=100)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "

Note

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

\n\nWe can also plot the grid on top of a map of retinal nerve fiber bundles:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "AxonMapModel().plot()\noffset_grid.plot()" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }