{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Demonstration of using an association function available in ``nmcog``\n", "\n", "The demonstration will be for a three-way function. For a overview of this function refer to the [guidebook](https://nmcog.readthedocs.io/en/latest/_static/Applying_Association.html)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Import `NEAL3Way` as a cognitive function" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Detected PyNN version 0.9.4 and Neo version 0.8.0\n" ] } ], "source": [ "from nmcog.spinnaker.associate import NEAL3Way" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setup the association\n", "One may think of a three-way association in terms of subject-predicate-object. Therefore, the set-up must first define the list of subjects, **a minumum of two subjects**. Below are some example,\n", "```\n", "bases[\"units\"] = [\"animal\", \"mammal\"]\n", "bases[\"units\"] = [\"animal\", \"mammal\", \"bird\", \"canary\"]\n", "bases[\"units\"] = [\"animal\", \"mammal\", \"bird\", \"rock\"]\n", "```\n", "However for for subjects in addition to defining them in a list one must also define how one of the subjects *is related* related to any of the remaining subjects in the defined list of subjects. A **minimum of one is-a** relation is required. For example,\n", "```\n", "bases[\"is-a\"] = [ [\"mammal\", \"animal\"] ]\n", "bases[\"is-a\"] = [ [\"canary\", \"bird\"], [\"bird\", \"animal\"], [\"mammal\", \"animal\"] ]\n", "bases[\"is-a\"] = [ [\"mammal\", \"animal\"], [\"bird\", \"animal\"] ]\n", "```\n", "Think of these as set of subjects and the set of relationships between the subjects.\n", "\n", "The *object* i.e. the property of the subject is also defined as list.\n", "```\n", "associate[\"properties\"] = [\"food\", \"fur\"]\n", "associate[\"properties\"] = [\"food\", \"fur\", \"flying\", \"yellow\"]\n", "associate[\"properties\"] = [\"food\", \"fur\", \"yellow\", \"feather\", \"hard\"]\n", "```\n", "Notice that these are the properties to be associated between base units and its predicate.\n", "\n", "Similarly, the *predicate* i.e. the relation is represented as a list, the set of possible relations between the above defined set of possible subjects and the set of possible objects.\n", "```\n", "associate[\"relations\"] = [\"eats\", \"has\", \"likes\"]\n", "associate[\"relations\"] = [\"eats\", \"likes\", \"travels\", \"has\", \"colored\"]\n", "associate[\"relations\"] = [\"eats\", \"has\", \"likes\", \"colored\", \"with\"]\n", "```\n", "\n", "Finally the set of possible associations, i.e. the connections between a subject and an object via a predicate is defined.\n", "```\n", "associate[\"connections\"] = [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"] ]\n", "associate[\"connections\"] = [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"], [\"bird\", \"travels\", \"flying\"], [\"canary\", \"colored\", \"yellow\"] ]\n", "associate[\"connections\"] = [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"], [\"bird\", \"with\", \"feather\"] ]\n", "```\n", "\n", "Although above shows the set-up in steps they are defined in two parameters as shown for each example below,\n", "\n", "**Example 1**\n", "```\n", "bases = {\"units\": [\"animal\", \"mammal\"],\n", " \"is-a\": [ [\"mammal\", \"animal\"] ]}\n", "associate = {\"properties\": [\"food\", \"fur\"],\n", " \"relations\": [\"eats\", \"has\", \"likes\"],\n", " \"connections\": [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"] ] }\n", "```\n", "\n", "**Example 2**\n", "```\n", "bases = {\"units\": [\"animal\", \"mammal\", \"bird\", \"canary\"],\n", " \"is-a\": [ [\"canary\", \"bird\"], [\"bird\", \"animal\"], [\"mammal\", \"animal\"] ]}\n", "associate = {\"properties\": [\"food\", \"fur\", \"flying\", \"yellow\"],\n", " \"relations\": [\"eats\", \"likes\", \"travels\", \"has\", \"colored\"],\n", " \"connections\": [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"],\n", " [\"bird\", \"travels\", \"flying\"], [\"canary\", \"colored\", \"yellow\"]] }\n", "```\n", "\n", "**Example 3**\n", "```\n", "bases = {\"units\": [\"animal\", \"mammal\", \"bird\", \"rock\"],\n", " \"is-a\": [ [\"mammal\", \"animal\"], [\"bird\", \"animal\"] ]}\n", "associate = {\"properties\": [\"food\", \"fur\", \"yellow\", \"feather\", \"hard\"],\n", " \"relations\": [\"eats\", \"has\", \"likes\", \"colored\", \"with\"],\n", " \"connections\": [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"], [\"bird\", \"with\", \"feather\"]\n", " ] }\n", "```\n", "\n", "**Example 4**\n", "```\n", "bases = {\"units\": [\"animal\", \"mammal\", \"bird\", \"rock\"],\n", " \"is-a\": [ [\"mammal\", \"animal\"], [\"bird\", \"animal\"] ]}\n", "associate = {\"properties\": [\"food\", \"fur\", \"yellow\", \"feather\", \"hard\"],\n", " \"relations\": [\"eats\", \"has\", \"likes\", \"colored\", \"gives\"],\n", " \"connections\": [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"], [\"bird\", \"has\", \"feather\"]\n", " ] }\n", "```" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "# Example 4\n", "bases = {\"units\": [\"animal\", \"mammal\", \"bird\", \"rock\"],\n", " \"is-a\": [ [\"mammal\", \"animal\"], [\"bird\", \"animal\"] ]}\n", "associate = {\"properties\": [\"food\", \"fur\", \"yellow\", \"feather\", \"hard\"],\n", " \"relations\": [\"eats\", \"has\", \"likes\", \"colored\", \"gives\"],\n", " \"connections\": [ [\"animal\", \"eats\", \"food\"], [\"mammal\", \"has\", \"fur\"], [\"bird\", \"has\", \"feather\"]\n", " ] }" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Choose `turnon` options\n", "That is, choose if you want to turn on all the associations in the set of possible connections or just some desired association defined in the set of possible connections" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "x = \"all\"\n", "#x = [\"animal\", \"food\", \"eats\"]\n", "#x = [\"animal\", \"food\"]\n", "#x = [\"mammal\", \"fur\", \"has\"]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Run it" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Created spalloc job 5336709\n", "Waiting for board power commands to complete.\n" ] } ], "source": [ "%%capture\n", "assos = NEAL3Way(bases, associate, turnon=x)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Visualize it\n", "\n", "### View all in one time series plot\n", "By default the figure is a plot of spike trains for the subjects, objects, and predicates." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
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');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
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');\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "assos.plot_all(form=\"2\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### View for a specific combination of subject-object-predicate\n", "\n", "For subject-object-predicate of animal-food-eats" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
');\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "assos.plot_specific(basename=\"animal\", relname=\"colored\", propname=\"food\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Get simulation results.\n", "\n", "Also, the user can get the results ([Neo SpikeTrains](https://neo.readthedocs.io/en/stable/api_reference.html#neo.core.SpikeTrain)) for further analysis." ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "sim_result = assos.get_results()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The result is a dictionary whose keys correspond to subject, object, and predicates defined prior to running the function." ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "dict_keys(['base', 'property', 'relation'])\n" ] } ], "source": [ "print(sim_result.keys())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Furthermore, the values for the keys are also dictionaries as shown below." ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "dict_keys(['all', 'animal', 'mammal', 'bird', 'rock'])\n" ] } ], "source": [ "print(sim_result[\"base\"].keys())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note apart from the \"all\" key others are self explanatory. The \"all\" key contains spike trains for all the subjects in one container." ] } ], "metadata": { "kernelspec": { "display_name": "sPyNNaker", "language": "python", "name": "spynnaker" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.8" } }, "nbformat": 4, "nbformat_minor": 2 }