{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Dimensionality reduction and blind source separation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Requires **HyperSpy v1.3** or above." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This tutorial shows how to perform matrix factorization and blind source separation on spectra using HyperSpy. The same procedure can be used to analyse objects of higher dimensionality." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Credits and changes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* 23/8/2016 Michael Walls. Extra explanations.\n", "* 27/7/2016 Francisco de la Peña. Updated for HyperSpy v1.0.1.\n", "* 6/3/2016 Francisco de la Peña. Adapted from previous tutorials for the SCANDEM workshop." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Table of contents" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "1. [Singular value decomposition](#1.-Singular-value-decomposition)\n", "2. [Blind source separation](#2.-Blind-source-separation)\n", "3. [Pre-processing](#3.-Pre-processing)\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 1. Singular value decomposition" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is a powerful method for reducing noise in hyperspectral datasets. Here we begin with a few lines of matrix algebra outlining the principles of the technique, but the demo can be followed easily without a full understanding of the mathematics. As with the \"getting started\" demo you can run this one interactively by downloading it and saving it as a .ipynb file.\n", "\n", "Lets start by supposing a line-spectrum $D$ that can be described by a\n", "linear model.\n", "\n", "$D=\\left[d_{i,j}\\right]_{m\\times n}={\\displaystyle \\left[{\\color{green}p_{i,j}}\\right]_{m\\times{\\color{red}l}}\\times}\\left[{\\color{red}{\\color{blue}s_{i,j}}}\\right]_{{\\color{red}l}\\times n}$\n", "where $m$ is the *number of pixels* in the line scan, $n$ the *number of channels* in the spectrum and $l$ the *number of components* e.g. spectra of individual compounds.\n", "\n", "Normally, what we actually measure is a noisy version of $D$, $D'$,\n", "\n", "$D'={\\displaystyle \\left[d'_{i,j}\\right]_{m\\times n}=\\left[{\\color{green}p_{i,j}}\\right]_{m\\times{\\color{red}l}}\\times}\\left[{\\color{red}{\\color{blue}s_{i,j}}}\\right]_{{\\color{red}l}\\times n}+\\mathrm{Noise}$\n", "\n", "\n", "$D'$ could be factorized as follows:\n", "\n", "$D'={\\displaystyle \\left[{\\tilde{\\color{green}p}}_{{i,j}}\\right]_{m\\times{\\color{red}k}}\\times}\\left[\\tilde{s}_{i,j}\\right]_{{\\color{red}k}\\times n}\n", "$ where $k\\leq\\min\\left(m,n\\right)$.\n", "\n", "Extra constraints are needed to fully determine the matrix factorization. When we add the orthogonality constraint we refer to this decomposition as singular value decomposition (SVD).\n", "\n", "In our assumption of a linear model:\n", "\n", "$D'={\\displaystyle \\left[{\\tilde{\\color{green}p}}_{{i,j}}\\right]_{m\\times{\\color{red}l}}\\times}\\left[\\tilde{s}_{i,j}\\right]_{{\\color{red}l}\\times n}+\n", "{\\displaystyle \\left[{\\tilde{\\color{green}p}}_{{i,j}}\\right]_{m\\times{\\color{red}{k-l}}}\\times}\\left[\\tilde{s}_{i,j}\\right]_{{\\color{red}{k-l}}\\times n}$\n", "\n", "With \n", "\n", "$D\\approx{\\displaystyle \\left[{\\tilde{\\color{green}p}}_{{i,j}}\\right]_{m\\times{\\color{red}l}}\\times}\\left[\\tilde{s}_{i,j}\\right]_{{\\color{red}l}\\times n}$\n", "\n", "$\\mathrm{Noise}\\approx{\\displaystyle \\left[{\\tilde{\\color{green}p}}_{{i,j}}\\right]_{m\\times{\\color{red}{k-l}}}\\times}\\left[\\tilde{s}_{i,j}\\right]_{{\\color{red}{k-l}}\\times n}$\n", "\n", "\n", " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We start by downloading the data for this demo, activating the matplotlib backend, importing HyperSpy and loading a dataset. " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Download and unpack the machine learning example data" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "from urllib.request import urlretrieve, urlopen\n", "from zipfile import ZipFile\n", "files = urlretrieve(\"https://www.dropbox.com/s/dt6bc3dtg373ahw/machine_learning.zip?raw=1\", \"./machine_learning.zip\")\n", "\n", "with ZipFile(\"machine_learning.zip\") as z:\n", " z.extractall()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Set up matplotlib and import Hyperspy\n", "\n", "**NOTE**: In the online version of this document we use the `inline` backend that displays interactive figures inside the Jupyter Notebook. However, for interactive data analysis purposes most would prefer to use the `qt` or `widget` backends." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "WARNING:hyperspy_gui_traitsui:The nbAgg matplotlib backend is not supported by the installed traitsui version and the ETS toolkit has been set to null. To set the ETS toolkit independently from the matplotlib backend, set it before importing matplotlib.\n", "WARNING:hyperspy_gui_traitsui:The traitsui GUI elements are not available.\n" ] } ], "source": [ "%matplotlib widget \n", "import hyperspy.api as hs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Load a dataset" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s = hs.load(\"machine_learning/CL1.hdf5\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is a synthetic electron energy-loss spectroscopy dataset. The procedure, although not fully general, can easily be used as is or with minor adaptation to analyse other kinds of data including images and higher dimensional signals." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "s.plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To perform SVD in HyperSpy we use the `decomposition` method that, by default, performs SVD." ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s.decomposition()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The result of the decomposition is stored in the `learning_results` attribute." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Decomposition parameters:\n", "-------------------------\n", "\n", "Decomposition algorithm : \tsvd\n", "Poissonian noise normalization : False\n", "Output dimension : None\n", "Centre : None\n" ] } ], "source": [ "s.learning_results.summary()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "SVD decomposes the data in so-called \"components\" and sorts them in order of decreasing relevance. It is often useful to estimate the dimensionality of the data by plotting the explained variance against the component index on a logarithmic y-scale. This plot is sometimes called a scree-plot and it should drop quickly, eventually becoming a slowly descending line. The point at which it becomes linear is often a good estimation of the dimensionality of the data (or equivalently, the number of components that should be retained).\n", "\n", "To plot the scree plot, run the `plot_explained_variance_ratio` method e.g.:\n" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "ax = hs.plot.plot_spectra([scree_plot.isig[:20],\n", " s.get_explained_variance_ratio().isig[:20]],\n", " legend=(\"Std\", \"Normalized\"))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's improve the plot using some [matplotlib](http://matplotlib.org/) commands:" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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" }, { "name": "stderr", "output_type": "stream", "text": [ "/home/fjd29/Python/hyperspy3/hyperspy/signal.py:1511: VisibleDeprecationWarning: The 'comp_label' argument will be deprecated in 2.0, please use 'title' instead\n", " VisibleDeprecationWarning)\n" ] }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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" }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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" }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "(s - sc).inav[30,30].plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 2. Blind source separation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Independent component analysis" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As we have seen in the previous section, the principal components are a linear mixture of EELS elemental maps and spectra, but the mixing matrix is unknown. We can use blind source separation (BSS) to estimate the mixing matrix. In this case we will use independent component analysis. BSS is performed in HyperSpy using the `blind_source_separation` method that by default uses \"FastICA\" which is a well-tested ICA routine." ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s.blind_source_separation(4, diff_order=1)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The results are also stored in the `learning_results` attribute:" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Decomposition parameters:\n", "-------------------------\n", "\n", "Decomposition algorithm : \tsvd\n", "Poissonian noise normalization : True\n", "Output dimension : None\n", "Centre : None\n", "\n", "Demixing parameters:\n", "------------------------\n", "BSS algorithm : sklearn_fasticaNumber of components : 4\n" ] } ], "source": [ "s.learning_results.summary()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And can be visualised with the following commands:" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "_ = s.plot_bss_loadings()\n", "_ = s.plot_bss_factors()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Or usually more conveniently:" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e16c35ee8c9241e38f3e2b7814b7b2e5" } }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "s.plot_bss_results()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Non-negative matrix factorization" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "By using a different matrix factorization method, non-negative matrix factorization (NMF) we can decompose the data into \"elemental\" components directly. NMF replaces the orthogonality constraint in SVD by a positivity constraint." ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s.decomposition(True, algorithm=\"nmf\", output_dimension=4)" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "_ = s.plot_decomposition_loadings()\n", "_ = s.plot_decomposition_factors()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "ICA and NMF both do a good job, NMF being slightly better in this case. However, some mixing remains in both cases. In the case of ICA the main cause is noise as we will show by analysing in the same way an identical dataset with less noise." ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "s2 = hs.load(\"machine_learning/CL2.hdf5\")\n", "s2.decomposition(True)\n", "s2.blind_source_separation(4, diff_order=2)\n", "_ = s2.plot_bss_loadings()\n", "_ = s2.plot_bss_factors()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note that the better SNR permits using a second numerical derivative which enhances the independence of the sources, improving the performance of ICA in this case." ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "s2.decomposition(True, algorithm=\"nmf\", output_dimension=4)\n", "_ = s2.plot_decomposition_loadings()\n", "_ = s2.plot_decomposition_factors()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "For this dataset with better SNR ICA outperforms NMF" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 3. Pre-processing" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "EELS datasets sometime suffer from energy instability. This introduces a non-linearity in the data, resulting in a higher number of components than there are genuine spectral signatures coming from the object. As an example let's have a look at the `CL3` dataset." ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s3 = hs.load(\"machine_learning/CL3.hdf5\")" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/fjd29/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py:524: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).\n", " max_open_warning, RuntimeWarning)\n" ] }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "s3.plot()" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s3.decomposition(True)" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/fjd29/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py:524: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).\n", " max_open_warning, RuntimeWarning)\n" ] }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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" }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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" }, { "data": { "text/plain": [ "" ] }, "execution_count": 36, "metadata": {}, "output_type": "execute_result" } ], "source": [ "s3.plot_explained_variance_ratio()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The scree plot is now more similar to the scree plot of the `CL1` dataset. However the alignment is not perfect and the scree plot still shows the effect of the remaining instability in the dataset. Nevertheless, performing BSS on the first four components results in very similar components to those of `CL1`" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/fjd29/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py:524: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).\n", " max_open_warning, RuntimeWarning)\n" ] }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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": [ "s3.blind_source_separation(4, diff_order=2)\n", "_ = s3.plot_bss_loadings()\n", "_ = s3.plot_bss_factors()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Another usual complication in real data are spikes. As an example, let's load the \"CL4\" dataset." ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s4 = hs.load(\"machine_learning/CL4.hdf5\")" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "s4.decomposition(True)" ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/fjd29/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py:524: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).\n", " max_open_warning, RuntimeWarning)\n" ] }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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\nmpl.figure.prototype._root_extra_style = function(el){\n var fig = this\n el.on(\"remove\", function(){\n\tfig.close_ws(fig, {});\n });\n}\n\nmpl.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\nmpl.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 // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n}\n\nmpl.figure.prototype.handle_save = function(fig, msg) {\n fig.ondownload(fig, null);\n}\n\n\nmpl.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.\nif (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" }, { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\nwindow.mpl = {};\n\n\nmpl.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\nmpl.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 this.ws.close();\n }\n\n this.ws.onmessage = this._make_on_message_function(this);\n\n this.ondownload = ondownload;\n}\n\nmpl.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\nmpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n\n}\n\n\nmpl.figure.prototype._root_extra_style = function(canvas_div) {\n\n}\n\nmpl.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\nmpl.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 = $('