molecularDisc.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "/* Put everything inside the global mpl namespace */\n",
       "window.mpl = {};\n",
       "\n",
       "\n",
       "mpl.get_websocket_type = function() {\n",
       "    if (typeof(WebSocket) !== 'undefined') {\n",
       "        return WebSocket;\n",
       "    } else if (typeof(MozWebSocket) !== 'undefined') {\n",
       "        return MozWebSocket;\n",
       "    } else {\n",
       "        alert('Your browser does not have WebSocket support. ' +\n",
       "              'Please try Chrome, Safari or Firefox ≥ 6. ' +\n",
       "              'Firefox 4 and 5 are also supported but you ' +\n",
       "              'have to enable WebSockets in about:config.');\n",
       "    };\n",
       "}\n",
       "\n",
       "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n",
       "    this.id = figure_id;\n",
       "\n",
       "    this.ws = websocket;\n",
       "\n",
       "    this.supports_binary = (this.ws.binaryType != undefined);\n",
       "\n",
       "    if (!this.supports_binary) {\n",
       "        var warnings = document.getElementById(\"mpl-warnings\");\n",
       "        if (warnings) {\n",
       "            warnings.style.display = 'block';\n",
       "            warnings.textContent = (\n",
       "                \"This browser does not support binary websocket messages. \" +\n",
       "                    \"Performance may be slow.\");\n",
       "        }\n",
       "    }\n",
       "\n",
       "    this.imageObj = new Image();\n",
       "\n",
       "    this.context = undefined;\n",
       "    this.message = undefined;\n",
       "    this.canvas = undefined;\n",
       "    this.rubberband_canvas = undefined;\n",
       "    this.rubberband_context = undefined;\n",
       "    this.format_dropdown = undefined;\n",
       "\n",
       "    this.image_mode = 'full';\n",
       "\n",
       "    this.root = $('<div/>');\n",
       "    this._root_extra_style(this.root)\n",
       "    this.root.attr('style', 'display: inline-block');\n",
       "\n",
       "    $(parent_element).append(this.root);\n",
       "\n",
       "    this._init_header(this);\n",
       "    this._init_canvas(this);\n",
       "    this._init_toolbar(this);\n",
       "\n",
       "    var fig = this;\n",
       "\n",
       "    this.waiting = false;\n",
       "\n",
       "    this.ws.onopen =  function () {\n",
       "            fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n",
       "            fig.send_message(\"send_image_mode\", {});\n",
       "            if (mpl.ratio != 1) {\n",
       "                fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n",
       "            }\n",
       "            fig.send_message(\"refresh\", {});\n",
       "        }\n",
       "\n",
       "    this.imageObj.onload = function() {\n",
       "            if (fig.image_mode == 'full') {\n",
       "                // Full images could contain transparency (where diff images\n",
       "                // almost always do), so we need to clear the canvas so that\n",
       "                // there is no ghosting.\n",
       "                fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n",
       "            }\n",
       "            fig.context.drawImage(fig.imageObj, 0, 0);\n",
       "        };\n",
       "\n",
       "    this.imageObj.onunload = function() {\n",
       "        fig.ws.close();\n",
       "    }\n",
       "\n",
       "    this.ws.onmessage = this._make_on_message_function(this);\n",
       "\n",
       "    this.ondownload = ondownload;\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._init_header = function() {\n",
       "    var titlebar = $(\n",
       "        '<div class=\"ui-dialog-titlebar ui-widget-header ui-corner-all ' +\n",
       "        'ui-helper-clearfix\"/>');\n",
       "    var titletext = $(\n",
       "        '<div class=\"ui-dialog-title\" style=\"width: 100%; ' +\n",
       "        'text-align: center; padding: 3px;\"/>');\n",
       "    titlebar.append(titletext)\n",
       "    this.root.append(titlebar);\n",
       "    this.header = titletext[0];\n",
       "}\n",
       "\n",
       "\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n",
       "\n",
       "}\n",
       "\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n",
       "\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._init_canvas = function() {\n",
       "    var fig = this;\n",
       "\n",
       "    var canvas_div = $('<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 = $('<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 = $('<canvas/>');\n",
       "    rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n",
       "\n",
       "    var pass_mouse_events = true;\n",
       "\n",
       "    canvas_div.resizable({\n",
       "        start: function(event, ui) {\n",
       "            pass_mouse_events = false;\n",
       "        },\n",
       "        resize: function(event, ui) {\n",
       "            fig.request_resize(ui.size.width, ui.size.height);\n",
       "        },\n",
       "        stop: function(event, ui) {\n",
       "            pass_mouse_events = true;\n",
       "            fig.request_resize(ui.size.width, ui.size.height);\n",
       "        },\n",
       "    });\n",
       "\n",
       "    function mouse_event_fn(event) {\n",
       "        if (pass_mouse_events)\n",
       "            return fig.mouse_event(event, event['data']);\n",
       "    }\n",
       "\n",
       "    rubberband.mousedown('button_press', mouse_event_fn);\n",
       "    rubberband.mouseup('button_release', mouse_event_fn);\n",
       "    // Throttle sequential mouse events to 1 every 20ms.\n",
       "    rubberband.mousemove('motion_notify', mouse_event_fn);\n",
       "\n",
       "    rubberband.mouseenter('figure_enter', mouse_event_fn);\n",
       "    rubberband.mouseleave('figure_leave', mouse_event_fn);\n",
       "\n",
       "    canvas_div.on(\"wheel\", function (event) {\n",
       "        event = event.originalEvent;\n",
       "        event['data'] = 'scroll'\n",
       "        if (event.deltaY < 0) {\n",
       "            event.step = 1;\n",
       "        } else {\n",
       "            event.step = -1;\n",
       "        }\n",
       "        mouse_event_fn(event);\n",
       "    });\n",
       "\n",
       "    canvas_div.append(canvas);\n",
       "    canvas_div.append(rubberband);\n",
       "\n",
       "    this.rubberband = rubberband;\n",
       "    this.rubberband_canvas = rubberband[0];\n",
       "    this.rubberband_context = rubberband[0].getContext(\"2d\");\n",
       "    this.rubberband_context.strokeStyle = \"#000000\";\n",
       "\n",
       "    this._resize_canvas = function(width, height) {\n",
       "        // Keep the size of the canvas, canvas container, and rubber band\n",
       "        // canvas in synch.\n",
       "        canvas_div.css('width', width)\n",
       "        canvas_div.css('height', height)\n",
       "\n",
       "        canvas.attr('width', width * mpl.ratio);\n",
       "        canvas.attr('height', height * mpl.ratio);\n",
       "        canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n",
       "\n",
       "        rubberband.attr('width', width);\n",
       "        rubberband.attr('height', height);\n",
       "    }\n",
       "\n",
       "    // Set the figure to an initial 600x600px, this will subsequently be updated\n",
       "    // upon first draw.\n",
       "    this._resize_canvas(600, 600);\n",
       "\n",
       "    // Disable right mouse context menu.\n",
       "    $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n",
       "        return false;\n",
       "    });\n",
       "\n",
       "    function set_focus () {\n",
       "        canvas.focus();\n",
       "        canvas_div.focus();\n",
       "    }\n",
       "\n",
       "    window.setTimeout(set_focus, 100);\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._init_toolbar = function() {\n",
       "    var fig = this;\n",
       "\n",
       "    var nav_element = $('<div/>');\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 = $('<button/>');\n",
       "        button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +\n",
       "                        'ui-button-icon-only');\n",
       "        button.attr('role', 'button');\n",
       "        button.attr('aria-disabled', 'false');\n",
       "        button.click(method_name, toolbar_event);\n",
       "        button.mouseover(tooltip, toolbar_mouse_event);\n",
       "\n",
       "        var icon_img = $('<span/>');\n",
       "        icon_img.addClass('ui-button-icon-primary ui-icon');\n",
       "        icon_img.addClass(image);\n",
       "        icon_img.addClass('ui-corner-all');\n",
       "\n",
       "        var tooltip_span = $('<span/>');\n",
       "        tooltip_span.addClass('ui-button-text');\n",
       "        tooltip_span.html(tooltip);\n",
       "\n",
       "        button.append(icon_img);\n",
       "        button.append(tooltip_span);\n",
       "\n",
       "        nav_element.append(button);\n",
       "    }\n",
       "\n",
       "    var fmt_picker_span = $('<span/>');\n",
       "\n",
       "    var fmt_picker = $('<select/>');\n",
       "    fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');\n",
       "    fmt_picker_span.append(fmt_picker);\n",
       "    nav_element.append(fmt_picker_span);\n",
       "    this.format_dropdown = fmt_picker[0];\n",
       "\n",
       "    for (var ind in mpl.extensions) {\n",
       "        var fmt = mpl.extensions[ind];\n",
       "        var option = $(\n",
       "            '<option/>', {selected: fmt === mpl.default_extension}).html(fmt);\n",
       "        fmt_picker.append(option);\n",
       "    }\n",
       "\n",
       "    // Add hover states to the ui-buttons\n",
       "    $( \".ui-button\" ).hover(\n",
       "        function() { $(this).addClass(\"ui-state-hover\");},\n",
       "        function() { $(this).removeClass(\"ui-state-hover\");}\n",
       "    );\n",
       "\n",
       "    var status_bar = $('<span class=\"mpl-message\"/>');\n",
       "    nav_element.append(status_bar);\n",
       "    this.message = status_bar[0];\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {\n",
       "    // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n",
       "    // which will in turn request a refresh of the image.\n",
       "    this.send_message('resize', {'width': x_pixels, 'height': y_pixels});\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.send_message = function(type, properties) {\n",
       "    properties['type'] = type;\n",
       "    properties['figure_id'] = this.id;\n",
       "    this.ws.send(JSON.stringify(properties));\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.send_draw_message = function() {\n",
       "    if (!this.waiting) {\n",
       "        this.waiting = true;\n",
       "        this.ws.send(JSON.stringify({type: \"draw\", figure_id: this.id}));\n",
       "    }\n",
       "}\n",
       "\n",
       "\n",
       "mpl.figure.prototype.handle_save = function(fig, msg) {\n",
       "    var format_dropdown = fig.format_dropdown;\n",
       "    var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n",
       "    fig.ondownload(fig, format);\n",
       "}\n",
       "\n",
       "\n",
       "mpl.figure.prototype.handle_resize = function(fig, msg) {\n",
       "    var size = msg['size'];\n",
       "    if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {\n",
       "        fig._resize_canvas(size[0], size[1]);\n",
       "        fig.send_message(\"refresh\", {});\n",
       "    };\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.handle_rubberband = function(fig, msg) {\n",
       "    var x0 = msg['x0'] / mpl.ratio;\n",
       "    var y0 = (fig.canvas.height - msg['y0']) / mpl.ratio;\n",
       "    var x1 = msg['x1'] / mpl.ratio;\n",
       "    var y1 = (fig.canvas.height - msg['y1']) / mpl.ratio;\n",
       "    x0 = Math.floor(x0) + 0.5;\n",
       "    y0 = Math.floor(y0) + 0.5;\n",
       "    x1 = Math.floor(x1) + 0.5;\n",
       "    y1 = Math.floor(y1) + 0.5;\n",
       "    var min_x = Math.min(x0, x1);\n",
       "    var min_y = Math.min(y0, y1);\n",
       "    var width = Math.abs(x1 - x0);\n",
       "    var height = Math.abs(y1 - y0);\n",
       "\n",
       "    fig.rubberband_context.clearRect(\n",
       "        0, 0, fig.canvas.width / mpl.ratio, fig.canvas.height / mpl.ratio);\n",
       "\n",
       "    fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.handle_figure_label = function(fig, msg) {\n",
       "    // Updates the figure title.\n",
       "    fig.header.textContent = msg['label'];\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.handle_cursor = function(fig, msg) {\n",
       "    var cursor = msg['cursor'];\n",
       "    switch(cursor)\n",
       "    {\n",
       "    case 0:\n",
       "        cursor = 'pointer';\n",
       "        break;\n",
       "    case 1:\n",
       "        cursor = 'default';\n",
       "        break;\n",
       "    case 2:\n",
       "        cursor = 'crosshair';\n",
       "        break;\n",
       "    case 3:\n",
       "        cursor = 'move';\n",
       "        break;\n",
       "    }\n",
       "    fig.rubberband_canvas.style.cursor = cursor;\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.handle_message = function(fig, msg) {\n",
       "    fig.message.textContent = msg['message'];\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.handle_draw = function(fig, msg) {\n",
       "    // Request the server to send over a new figure.\n",
       "    fig.send_draw_message();\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.handle_image_mode = function(fig, msg) {\n",
       "    fig.image_mode = msg['mode'];\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.updated_canvas_event = function() {\n",
       "    // Called whenever the canvas gets updated.\n",
       "    this.send_message(\"ack\", {});\n",
       "}\n",
       "\n",
       "// A function to construct a web socket function for onmessage handling.\n",
       "// Called in the figure constructor.\n",
       "mpl.figure.prototype._make_on_message_function = function(fig) {\n",
       "    return function socket_on_message(evt) {\n",
       "        if (evt.data instanceof Blob) {\n",
       "            /* FIXME: We get \"Resource interpreted as Image but\n",
       "             * transferred with MIME type text/plain:\" errors on\n",
       "             * Chrome.  But how to set the MIME type?  It doesn't seem\n",
       "             * to be part of the websocket stream */\n",
       "            evt.data.type = \"image/png\";\n",
       "\n",
       "            /* Free the memory for the previous frames */\n",
       "            if (fig.imageObj.src) {\n",
       "                (window.URL || window.webkitURL).revokeObjectURL(\n",
       "                    fig.imageObj.src);\n",
       "            }\n",
       "\n",
       "            fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n",
       "                evt.data);\n",
       "            fig.updated_canvas_event();\n",
       "            fig.waiting = false;\n",
       "            return;\n",
       "        }\n",
       "        else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == \"data:image/png;base64\") {\n",
       "            fig.imageObj.src = evt.data;\n",
       "            fig.updated_canvas_event();\n",
       "            fig.waiting = false;\n",
       "            return;\n",
       "        }\n",
       "\n",
       "        var msg = JSON.parse(evt.data);\n",
       "        var msg_type = msg['type'];\n",
       "\n",
       "        // Call the  \"handle_{type}\" callback, which takes\n",
       "        // the figure and JSON message as its only arguments.\n",
       "        try {\n",
       "            var callback = fig[\"handle_\" + msg_type];\n",
       "        } catch (e) {\n",
       "            console.log(\"No handler for the '\" + msg_type + \"' message type: \", msg);\n",
       "            return;\n",
       "        }\n",
       "\n",
       "        if (callback) {\n",
       "            try {\n",
       "                // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n",
       "                callback(fig, msg);\n",
       "            } catch (e) {\n",
       "                console.log(\"Exception inside the 'handler_\" + msg_type + \"' callback:\", e, e.stack, msg);\n",
       "            }\n",
       "        }\n",
       "    };\n",
       "}\n",
       "\n",
       "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n",
       "mpl.findpos = function(e) {\n",
       "    //this section is from http://www.quirksmode.org/js/events_properties.html\n",
       "    var targ;\n",
       "    if (!e)\n",
       "        e = window.event;\n",
       "    if (e.target)\n",
       "        targ = e.target;\n",
       "    else if (e.srcElement)\n",
       "        targ = e.srcElement;\n",
       "    if (targ.nodeType == 3) // defeat Safari bug\n",
       "        targ = targ.parentNode;\n",
       "\n",
       "    // jQuery normalizes the pageX and pageY\n",
       "    // pageX,Y are the mouse positions relative to the document\n",
       "    // offset() returns the position of the element relative to the document\n",
       "    var x = e.pageX - $(targ).offset().left;\n",
       "    var y = e.pageY - $(targ).offset().top;\n",
       "\n",
       "    return {\"x\": x, \"y\": y};\n",
       "};\n",
       "\n",
       "/*\n",
       " * return a copy of an object with only non-object keys\n",
       " * we need this to avoid circular references\n",
       " * http://stackoverflow.com/a/24161582/3208463\n",
       " */\n",
       "function simpleKeys (original) {\n",
       "  return Object.keys(original).reduce(function (obj, key) {\n",
       "    if (typeof original[key] !== 'object')\n",
       "        obj[key] = original[key]\n",
       "    return obj;\n",
       "  }, {});\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.mouse_event = function(event, name) {\n",
       "    var canvas_pos = mpl.findpos(event)\n",
       "\n",
       "    if (name === 'button_press')\n",
       "    {\n",
       "        this.canvas.focus();\n",
       "        this.canvas_div.focus();\n",
       "    }\n",
       "\n",
       "    var x = canvas_pos.x * mpl.ratio;\n",
       "    var y = canvas_pos.y * mpl.ratio;\n",
       "\n",
       "    this.send_message(name, {x: x, y: y, button: event.button,\n",
       "                             step: event.step,\n",
       "                             guiEvent: simpleKeys(event)});\n",
       "\n",
       "    /* This prevents the web browser from automatically changing to\n",
       "     * the text insertion cursor when the button is pressed.  We want\n",
       "     * to control all of the cursor setting manually through the\n",
       "     * 'cursor' event from matplotlib */\n",
       "    event.preventDefault();\n",
       "    return false;\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._key_event_extra = function(event, name) {\n",
       "    // Handle any extra behaviour associated with a key event\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.key_event = function(event, name) {\n",
       "\n",
       "    // Prevent repeat events\n",
       "    if (name == 'key_press')\n",
       "    {\n",
       "        if (event.which === this._key)\n",
       "            return;\n",
       "        else\n",
       "            this._key = event.which;\n",
       "    }\n",
       "    if (name == 'key_release')\n",
       "        this._key = null;\n",
       "\n",
       "    var value = '';\n",
       "    if (event.ctrlKey && event.which != 17)\n",
       "        value += \"ctrl+\";\n",
       "    if (event.altKey && event.which != 18)\n",
       "        value += \"alt+\";\n",
       "    if (event.shiftKey && event.which != 16)\n",
       "        value += \"shift+\";\n",
       "\n",
       "    value += 'k';\n",
       "    value += event.which.toString();\n",
       "\n",
       "    this._key_event_extra(event, name);\n",
       "\n",
       "    this.send_message(name, {key: value,\n",
       "                             guiEvent: simpleKeys(event)});\n",
       "    return false;\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.toolbar_button_onclick = function(name) {\n",
       "    if (name == 'download') {\n",
       "        this.handle_save(this, null);\n",
       "    } else {\n",
       "        this.send_message(\"toolbar_button\", {name: name});\n",
       "    }\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {\n",
       "    this.message.textContent = tooltip;\n",
       "};\n",
       "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Pan axes with left mouse, zoom with right\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n",
       "\n",
       "mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n",
       "\n",
       "mpl.default_extension = \"png\";var comm_websocket_adapter = function(comm) {\n",
       "    // Create a \"websocket\"-like object which calls the given IPython comm\n",
       "    // object with the appropriate methods. Currently this is a non binary\n",
       "    // socket, so there is still some room for performance tuning.\n",
       "    var ws = {};\n",
       "\n",
       "    ws.close = function() {\n",
       "        comm.close()\n",
       "    };\n",
       "    ws.send = function(m) {\n",
       "        //console.log('sending', m);\n",
       "        comm.send(m);\n",
       "    };\n",
       "    // Register the callback with on_msg.\n",
       "    comm.on_msg(function(msg) {\n",
       "        //console.log('receiving', msg['content']['data'], msg);\n",
       "        // Pass the mpl event to the overridden (by mpl) onmessage function.\n",
       "        ws.onmessage(msg['content']['data'])\n",
       "    });\n",
       "    return ws;\n",
       "}\n",
       "\n",
       "mpl.mpl_figure_comm = function(comm, msg) {\n",
       "    // This is the function which gets called when the mpl process\n",
       "    // starts-up an IPython Comm through the \"matplotlib\" channel.\n",
       "\n",
       "    var id = msg.content.data.id;\n",
       "    // Get hold of the div created by the display call when the Comm\n",
       "    // socket was opened in Python.\n",
       "    var element = $(\"#\" + id);\n",
       "    var ws_proxy = comm_websocket_adapter(comm)\n",
       "\n",
       "    function ondownload(figure, format) {\n",
       "        window.open(figure.imageObj.src);\n",
       "    }\n",
       "\n",
       "    var fig = new mpl.figure(id, ws_proxy,\n",
       "                           ondownload,\n",
       "                           element.get(0));\n",
       "\n",
       "    // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n",
       "    // web socket which is closed, not our websocket->open comm proxy.\n",
       "    ws_proxy.onopen();\n",
       "\n",
       "    fig.parent_element = element.get(0);\n",
       "    fig.cell_info = mpl.find_output_cell(\"<div id='\" + id + \"'></div>\");\n",
       "    if (!fig.cell_info) {\n",
       "        console.error(\"Failed to find cell for figure\", id, fig);\n",
       "        return;\n",
       "    }\n",
       "\n",
       "    var output_index = fig.cell_info[2]\n",
       "    var cell = fig.cell_info[0];\n",
       "\n",
       "};\n",
       "\n",
       "mpl.figure.prototype.handle_close = function(fig, msg) {\n",
       "    var width = fig.canvas.width/mpl.ratio\n",
       "    fig.root.unbind('remove')\n",
       "\n",
       "    // Update the output cell to use the data from the current canvas.\n",
       "    fig.push_to_output();\n",
       "    var dataURL = fig.canvas.toDataURL();\n",
       "    // Re-enable the keyboard manager in IPython - without this line, in FF,\n",
       "    // the notebook keyboard shortcuts fail.\n",
       "    IPython.keyboard_manager.enable()\n",
       "    $(fig.parent_element).html('<img src=\"' + dataURL + '\" width=\"' + width + '\">');\n",
       "    fig.close_ws(fig, msg);\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.close_ws = function(fig, msg){\n",
       "    fig.send_message('closing', msg);\n",
       "    // fig.ws.close()\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.push_to_output = function(remove_interactive) {\n",
       "    // Turn the data on the canvas into data in the output cell.\n",
       "    var width = this.canvas.width/mpl.ratio\n",
       "    var dataURL = this.canvas.toDataURL();\n",
       "    this.cell_info[1]['text/html'] = '<img src=\"' + dataURL + '\" width=\"' + width + '\">';\n",
       "}\n",
       "\n",
       "mpl.figure.prototype.updated_canvas_event = function() {\n",
       "    // Tell IPython that the notebook contents must change.\n",
       "    IPython.notebook.set_dirty(true);\n",
       "    this.send_message(\"ack\", {});\n",
       "    var fig = this;\n",
       "    // Wait a second, then push the new image to the DOM so\n",
       "    // that it is saved nicely (might be nice to debounce this).\n",
       "    setTimeout(function () { fig.push_to_output() }, 1000);\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._init_toolbar = function() {\n",
       "    var fig = this;\n",
       "\n",
       "    var nav_element = $('<div/>');\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) { continue; };\n",
       "\n",
       "        var button = $('<button class=\"btn btn-default\" href=\"#\" title=\"' + name + '\"><i class=\"fa ' + image + ' fa-lg\"></i></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 = $('<span class=\"mpl-message\" style=\"text-align:right; float: right;\"/>');\n",
       "    nav_element.append(status_bar);\n",
       "    this.message = status_bar[0];\n",
       "\n",
       "    // Add the close button to the window.\n",
       "    var buttongrp = $('<div class=\"btn-group inline pull-right\"></div>');\n",
       "    var button = $('<button class=\"btn btn-mini btn-primary\" href=\"#\" title=\"Stop Interaction\"><i class=\"fa fa-power-off icon-remove icon-large\"></i></button>');\n",
       "    button.click(function (evt) { fig.handle_close(fig, {}); } );\n",
       "    button.mouseover('Stop Interaction', toolbar_mouse_event);\n",
       "    buttongrp.append(button);\n",
       "    var titlebar = this.root.find($('.ui-dialog-titlebar'));\n",
       "    titlebar.prepend(buttongrp);\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function(el){\n",
       "    var fig = this\n",
       "    el.on(\"remove\", function(){\n",
       "\tfig.close_ws(fig, {});\n",
       "    });\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function(el){\n",
       "    // this is important to make the div 'focusable\n",
       "    el.attr('tabindex', 0)\n",
       "    // reach out to IPython and tell the keyboard manager to turn it's self\n",
       "    // off when our div gets focus\n",
       "\n",
       "    // location in version 3\n",
       "    if (IPython.notebook.keyboard_manager) {\n",
       "        IPython.notebook.keyboard_manager.register_events(el);\n",
       "    }\n",
       "    else {\n",
       "        // location in version 2\n",
       "        IPython.keyboard_manager.register_events(el);\n",
       "    }\n",
       "\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._key_event_extra = function(event, name) {\n",
       "    var manager = IPython.notebook.keyboard_manager;\n",
       "    if (!manager)\n",
       "        manager = IPython.keyboard_manager;\n",
       "\n",
       "    // Check for shift+enter\n",
       "    if (event.shiftKey && event.which == 13) {\n",
       "        this.canvas_div.blur();\n",
       "        // 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",
       "\n",
       "mpl.figure.prototype.handle_save = function(fig, msg) {\n",
       "    fig.ondownload(fig, null);\n",
       "}\n",
       "\n",
       "\n",
       "mpl.find_output_cell = function(html_output) {\n",
       "    // Return the cell and output element which can be found *uniquely* in the notebook.\n",
       "    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n",
       "    // IPython event is triggered only after the cells have been serialised, which for\n",
       "    // our purposes (turning an active figure into a static one), is too late.\n",
       "    var cells = IPython.notebook.get_cells();\n",
       "    var ncells = cells.length;\n",
       "    for (var i=0; i<ncells; i++) {\n",
       "        var cell = cells[i];\n",
       "        if (cell.cell_type === 'code'){\n",
       "            for (var j=0; j<cell.output_area.outputs.length; j++) {\n",
       "                var data = cell.output_area.outputs[j];\n",
       "                if (data.data) {\n",
       "                    // IPython >= 3 moved mimebundle to data attribute of output\n",
       "                    data = data.data;\n",
       "                }\n",
       "                if (data['text/html'] == html_output) {\n",
       "                    return [cell, data, j];\n",
       "                }\n",
       "            }\n",
       "        }\n",
       "    }\n",
       "}\n",
       "\n",
       "// Register the function which deals with the matplotlib target/channel.\n",
       "// The kernel may be null if the page has been refreshed.\n",
       "if (IPython.notebook.kernel != null) {\n",
       "    IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n",
       "}\n"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div id='df2929ad-b226-48df-8f27-62ec1fcffd31'></div>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "\n",
    "%matplotlib notebook\n",
    "\n",
    "\n",
    "#\n",
    "# EMRA L4/L5 CO synthetic observations of a protoplanetary disc. \n",
    "#\n",
    "# Started by T. J. Haworth October 2020\n",
    "#\n",
    "#\n",
    "#\n",
    "\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from matplotlib.widgets import Slider\n",
    "from astropy.io import fits\n",
    "import matplotlib.colors as colors\n",
    "\n",
    "#cube45=\"intensity_test_45.fits\"\n",
    "cube45=\"intensity_dusttest.fits\"\n",
    "\n",
    "cube45_hdu_list = fits.open(cube45)\n",
    "cube45_image_data = cube45_hdu_list[0].data\n",
    "\n",
    "fig, (ax1,ax2) = plt.subplots(1,2,figsize=(8,7))\n",
    "plt.subplots_adjust(left=0.25, bottom=0.35)\n",
    "\n",
    "axcolor = 'lightgoldenrodyellow'\n",
    "\n",
    "axvel = plt.axes([0.25, 0.1, 0.65, 0.03], facecolor=axcolor)\n",
    "axinc = plt.axes([0.25, 0.15, 0.65, 0.03], facecolor=axcolor)\n",
    "\n",
    "velMin=-5.0\n",
    "velMax=5.0\n",
    "nV=80.\n",
    "delta_vel=(velMax-velMin)/nV\n",
    "vel0 = 0.0\n",
    "\n",
    "incMin=0.0\n",
    "incMax=90.0\n",
    "delta_inc=5.0\n",
    "inc0=45.0\n",
    "\n",
    "svel=Slider(axvel, 'Velocity, km/s', velMin, velMax, valinit=vel0, valstep=delta_vel)\n",
    "sinc=Slider(axinc, 'Inclination, degrees', incMin, incMax, valinit=inc0, valstep=delta_inc)\n",
    "\n",
    "ax1.imshow(cube45_image_data[40,:,:], norm=colors.LogNorm())\n",
    "ax1.set_ylabel(\"\")\n",
    "ax1.set_xlabel(\"\")\n",
    "#plt.colorbar()\n",
    "\n",
    "\n",
    "lineProf=np.zeros(80)\n",
    "vel=np.zeros(80)\n",
    "for i in range(0,80):\n",
    "    lineProf[i]=np.sum(cube45_image_data[i,:,:])-np.sum(cube45_image_data[2,:,:])\n",
    "    vel[i]=-5.0+delta_vel*i\n",
    "lineProf[:]=lineProf[:]/max(lineProf[:])\n",
    "ax2.set_ylim(0.25, 1.1)    \n",
    "ax2.set_xlim(-4.9, 4.9)    \n",
    "ax2.set_xlabel(\"velocity\")\n",
    "ax2.set_ylabel(\"I\")\n",
    "ax2.plot(vel, lineProf)\n",
    "\n",
    "def update(val):\n",
    "    ax1.cla()\n",
    "    ax2.cla()\n",
    "    incInt=int(sinc.val)\n",
    "    fileString=\"intensity_dusttest_\"+str(incInt)+\".fits\"\n",
    "    cube_hdu_list = fits.open(fileString)\n",
    "    cube_image_data = cube_hdu_list[0].data\n",
    "    index = int( (velMin + svel.val)/delta_vel)\n",
    "    ax1.imshow(cube_image_data[index,:,:], norm=colors.LogNorm())\n",
    "    ax1.set_ylabel(\"\")\n",
    "    ax1.set_xlabel(\"\")\n",
    "    lineProf=np.zeros(80)\n",
    "    vel=np.zeros(80)    \n",
    "    for i in range(0,80):\n",
    "        lineProf[i]=np.sum(cube_image_data[i,:,:])-np.sum(cube_image_data[2,:,:])\n",
    "        vel[i]=-5.0+delta_vel*i\n",
    "    lineProf[:]=lineProf[:]/max(lineProf[:])\n",
    "    ax2.set_ylim(0.25, 1.1)\n",
    "    ax2.set_xlim(-4.9, 4.9)    \n",
    "    ax2.set_xlabel(\"velocity\")\n",
    "    ax2.set_ylabel(\"I\")\n",
    "    ax2.plot(vel, lineProf)\n",
    "\n",
    "svel.on_changed(update)\n",
    "sinc.on_changed(update)\n",
    "\n",
    "plt.show()\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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