{ "cells": [ { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n# Creating your own electrode array\n\nThis example shows how to create a new\n:py:class:`~pulse2percept.implants.ElectrodeArray` object.\n\nAs the base class for all electrode arrays in pulse2percept, the\n:py:class:`~pulse2percept.implants.ElectrodeArray` class provides a blue print\nfor the functionality that every electrode array should have.\n\nFirst and foremost, an :py:class:`~pulse2percept.implants.ElectrodeArray`\ncontains a collection of :py:class:`~pulse2percept.implants.Electrode` objects,\nand new electrodes can be added via the\n:py:func:`~pulse2percept.implants.ElectrodeArray.add_electrodes` method.\n\nIn addition, individual electrodes in the array can be accessed by indexing\nusing either their pre-assigned names (a string) or their place in the array\n(integer).\n\n## Arranging electrodes in a circle\n\nIn this example, we want to build a new type of electrode array that arranges\nall of its electrodes in a circle.\n\nTo do this, we need to create a new class ``CircleElectrodeArray`` that is\na child of :py:class:`~pulse2percept.implants.ElectrodeArray`:\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "```python\nclass CircleElectrodeArray(ElectrodeArray):\n \"\"\"Electrodes arranged in a circle\"\"\"\n ...\n```\nThis way, the ``CircleElectrodeArray`` class can access all public methods\nof :py:class:`~pulse2percept.implants.ElectrodeArray`.\n\nThe constructor then has the job of creating all electrodes in the array\nand placing them at the appropriate location; for example, by using the\n:py:func:`~pulse2percept.implants.ElectrodeArray.add_electrodes` method.\n\nThe constructor of the class should accept a number of arguments:\n\n- ``n_electrodes``: how many electrodes to arrange in a circle\n- ``radius``: the radius of the circle\n- ``x_center``: the x-coordinate of the center of the circle\n- ``y_center``: the y-coordinate of the center of the circle\n\nFor simplicity, we will use :py:class:`~pulse2percept.implants.DiskElectrode`\nobjects of a given radius (100um), although it would be relatively straightforward\nto allow the user to choose the electrode type.\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "from pulse2percept.implants import ElectrodeArray, DiskElectrode\nimport collections as coll\nimport numpy as np\n\n\nclass CircleElectrodeArray(ElectrodeArray):\n\n def __init__(self, n_electrodes, radius, x_center, y_center):\n \"\"\"Electrodes arranged in a circle\n\n Electrodes will be named 'A0', 'A1', ...\n\n Parameters\n ----------\n n_electrodes : int\n how many electrodes to arrange in a circle\n radius : float\n the radius of the circle (microns)\n x_center, y_center : float\n the x,y coordinates of the center of the circle (microns),\n where (0,0) is the center of the fovea\n \"\"\"\n # The job of the constructor is to create the electrodes. We start\n # with an empty collection:\n self._electrodes = coll.OrderedDict()\n # We then generate a number `n_electrodes` of electrodes, arranged on\n # the circumference of a circle:\n for n in range(n_electrodes):\n # Angular position of the electrode:\n ang = 2.0 * np.pi / n_electrodes * n\n # Create the disk electrode:\n electrode = DiskElectrode(x_center + np.cos(ang) * radius,\n y_center + np.sin(ang) * radius, 0, 100)\n # Add the electrode to the collection:\n self.add_electrode('A' + str(n), electrode)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Using the CircleElectrodeArray class\n\nTo use the new class, we need to specify all input arguments and pass them\nto the constructor:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "n_electrodes = 10\nradius = 1000 # radius in microns\nx_center = 0 # x-coordinate of circle center (microns)\ny_center = 0 # y-coordinate of circle center (microns)\n\n# Create a new instance of type CircleElectrodeArray:\nearray = CircleElectrodeArray(n_electrodes, radius, x_center, y_center)\nprint(earray)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Individual electrodes can be accessed by their name or integer index:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "earray[0]\n\nearray['A0']\n\nearray[0] == earray['A0']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Visualizing the electrode array\n\nElectrode arrays come with their own plotting method:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "earray.plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "By default, the method will use the current Axes object or create a new one\nif none exists. Alternatively, you can specify ``ax=`` yourself.\n\n## Extending the CircleElectrodeArray class\n\nSimilar to extending :py:class:`~pulse2percept.implants.ElectrodeArray` for\nour purposes, we can extend ``CircleElectrodeArray``.\n\nTo add new functionality, we could simply edit the above constructor.\nHowever, nobody stops us from creating our own hierarchy of classes.\n\nFor example, we could build a ``FlexibleCircleElectrodeArray`` that allows us\nto remove individual electrodes from the array:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "class FlexibleCircleElectrodeArray(CircleElectrodeArray):\n\n def remove(self, name):\n \"\"\"Deletean electrode from the array\n\n Parameters\n ----------\n name : int, string\n the name of the electrode to be removed\n \"\"\"\n del self.electrodes[name]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note how we didn't even specify a constructor.\nBy default, the class inherits all (public) functionality from its parent,\nincluding its constructor. So the following line will create the same\nelectrode array as above:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "flex_earray = FlexibleCircleElectrodeArray(\n n_electrodes, radius, x_center, y_center)\nprint(flex_earray)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "A single electrode can be removed by passing its name to the ``remove``\nmethod:\n\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "# Remove electrode 'A1'\nflex_earray.remove('A1')\n\n# Replot the implant:\nflex_earray.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 }