diff --git a/.ipynb_checkpoints/inline viewer demo 2-checkpoint.ipynb b/.ipynb_checkpoints/inline viewer demo 2-checkpoint.ipynb
new file mode 100644
index 0000000..e5c98e3
--- /dev/null
+++ b/.ipynb_checkpoints/inline viewer demo 2-checkpoint.ipynb
@@ -0,0 +1,879 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/javascript": [
+ "/* Put everything inside the global mpl namespace */\n",
+ "window.mpl = {};\n",
+ "\n",
+ "\n",
+ "mpl.get_websocket_type = function() {\n",
+ " if (typeof(WebSocket) !== 'undefined') {\n",
+ " return WebSocket;\n",
+ " } else if (typeof(MozWebSocket) !== 'undefined') {\n",
+ " return MozWebSocket;\n",
+ " } else {\n",
+ " alert('Your browser does not have WebSocket support.' +\n",
+ " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n",
+ " 'Firefox 4 and 5 are also supported but you ' +\n",
+ " 'have to enable WebSockets in about:config.');\n",
+ " };\n",
+ "}\n",
+ "\n",
+ "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n",
+ " this.id = figure_id;\n",
+ "\n",
+ " this.ws = websocket;\n",
+ "\n",
+ " this.supports_binary = (this.ws.binaryType != undefined);\n",
+ "\n",
+ " if (!this.supports_binary) {\n",
+ " var warnings = document.getElementById(\"mpl-warnings\");\n",
+ " if (warnings) {\n",
+ " warnings.style.display = 'block';\n",
+ " warnings.textContent = (\n",
+ " \"This browser does not support binary websocket messages. \" +\n",
+ " \"Performance may be slow.\");\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " this.imageObj = new Image();\n",
+ "\n",
+ " this.context = undefined;\n",
+ " this.message = undefined;\n",
+ " this.canvas = undefined;\n",
+ " this.rubberband_canvas = undefined;\n",
+ " this.rubberband_context = undefined;\n",
+ " this.format_dropdown = undefined;\n",
+ "\n",
+ " this.image_mode = 'full';\n",
+ "\n",
+ " this.root = $('
');\n",
+ " this._root_extra_style(this.root)\n",
+ " this.root.attr('style', 'display: inline-block');\n",
+ "\n",
+ " $(parent_element).append(this.root);\n",
+ "\n",
+ " this._init_header(this);\n",
+ " this._init_canvas(this);\n",
+ " this._init_toolbar(this);\n",
+ "\n",
+ " var fig = this;\n",
+ "\n",
+ " this.waiting = false;\n",
+ "\n",
+ " this.ws.onopen = function () {\n",
+ " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n",
+ " fig.send_message(\"send_image_mode\", {});\n",
+ " if (mpl.ratio != 1) {\n",
+ " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n",
+ " }\n",
+ " fig.send_message(\"refresh\", {});\n",
+ " }\n",
+ "\n",
+ " this.imageObj.onload = function() {\n",
+ " if (fig.image_mode == 'full') {\n",
+ " // Full images could contain transparency (where diff images\n",
+ " // almost always do), so we need to clear the canvas so that\n",
+ " // there is no ghosting.\n",
+ " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n",
+ " }\n",
+ " fig.context.drawImage(fig.imageObj, 0, 0);\n",
+ " };\n",
+ "\n",
+ " this.imageObj.onunload = function() {\n",
+ " this.ws.close();\n",
+ " }\n",
+ "\n",
+ " this.ws.onmessage = this._make_on_message_function(this);\n",
+ "\n",
+ " this.ondownload = ondownload;\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype._init_header = function() {\n",
+ " var titlebar = $(\n",
+ " '');\n",
+ " var titletext = $(\n",
+ " '');\n",
+ " titlebar.append(titletext)\n",
+ " this.root.append(titlebar);\n",
+ " this.header = titletext[0];\n",
+ "}\n",
+ "\n",
+ "\n",
+ "\n",
+ "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n",
+ "\n",
+ "}\n",
+ "\n",
+ "\n",
+ "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n",
+ "\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype._init_canvas = function() {\n",
+ " var fig = this;\n",
+ "\n",
+ " var canvas_div = $('');\n",
+ "\n",
+ " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n",
+ "\n",
+ " function canvas_keyboard_event(event) {\n",
+ " return fig.key_event(event, event['data']);\n",
+ " }\n",
+ "\n",
+ " canvas_div.keydown('key_press', canvas_keyboard_event);\n",
+ " canvas_div.keyup('key_release', canvas_keyboard_event);\n",
+ " this.canvas_div = canvas_div\n",
+ " this._canvas_extra_style(canvas_div)\n",
+ " this.root.append(canvas_div);\n",
+ "\n",
+ " var canvas = $('');\n",
+ " canvas.addClass('mpl-canvas');\n",
+ " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n",
+ "\n",
+ " this.canvas = canvas[0];\n",
+ " this.context = canvas[0].getContext(\"2d\");\n",
+ "\n",
+ " var backingStore = this.context.backingStorePixelRatio ||\n",
+ "\tthis.context.webkitBackingStorePixelRatio ||\n",
+ "\tthis.context.mozBackingStorePixelRatio ||\n",
+ "\tthis.context.msBackingStorePixelRatio ||\n",
+ "\tthis.context.oBackingStorePixelRatio ||\n",
+ "\tthis.context.backingStorePixelRatio || 1;\n",
+ "\n",
+ " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n",
+ "\n",
+ " var rubberband = $('');\n",
+ " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n",
+ "\n",
+ " var pass_mouse_events = true;\n",
+ "\n",
+ " canvas_div.resizable({\n",
+ " start: function(event, ui) {\n",
+ " pass_mouse_events = false;\n",
+ " },\n",
+ " resize: function(event, ui) {\n",
+ " fig.request_resize(ui.size.width, ui.size.height);\n",
+ " },\n",
+ " stop: function(event, ui) {\n",
+ " pass_mouse_events = true;\n",
+ " fig.request_resize(ui.size.width, ui.size.height);\n",
+ " },\n",
+ " });\n",
+ "\n",
+ " function mouse_event_fn(event) {\n",
+ " if (pass_mouse_events)\n",
+ " return fig.mouse_event(event, event['data']);\n",
+ " }\n",
+ "\n",
+ " rubberband.mousedown('button_press', mouse_event_fn);\n",
+ " rubberband.mouseup('button_release', mouse_event_fn);\n",
+ " // Throttle sequential mouse events to 1 every 20ms.\n",
+ " rubberband.mousemove('motion_notify', mouse_event_fn);\n",
+ "\n",
+ " rubberband.mouseenter('figure_enter', mouse_event_fn);\n",
+ " rubberband.mouseleave('figure_leave', mouse_event_fn);\n",
+ "\n",
+ " canvas_div.on(\"wheel\", function (event) {\n",
+ " event = event.originalEvent;\n",
+ " event['data'] = 'scroll'\n",
+ " if (event.deltaY < 0) {\n",
+ " event.step = 1;\n",
+ " } else {\n",
+ " event.step = -1;\n",
+ " }\n",
+ " mouse_event_fn(event);\n",
+ " });\n",
+ "\n",
+ " canvas_div.append(canvas);\n",
+ " canvas_div.append(rubberband);\n",
+ "\n",
+ " this.rubberband = rubberband;\n",
+ " this.rubberband_canvas = rubberband[0];\n",
+ " this.rubberband_context = rubberband[0].getContext(\"2d\");\n",
+ " this.rubberband_context.strokeStyle = \"#000000\";\n",
+ "\n",
+ " this._resize_canvas = function(width, height) {\n",
+ " // Keep the size of the canvas, canvas container, and rubber band\n",
+ " // canvas in synch.\n",
+ " canvas_div.css('width', width)\n",
+ " canvas_div.css('height', height)\n",
+ "\n",
+ " canvas.attr('width', width * mpl.ratio);\n",
+ " canvas.attr('height', height * mpl.ratio);\n",
+ " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n",
+ "\n",
+ " rubberband.attr('width', width);\n",
+ " rubberband.attr('height', height);\n",
+ " }\n",
+ "\n",
+ " // Set the figure to an initial 600x600px, this will subsequently be updated\n",
+ " // upon first draw.\n",
+ " this._resize_canvas(600, 600);\n",
+ "\n",
+ " // Disable right mouse context menu.\n",
+ " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n",
+ " return false;\n",
+ " });\n",
+ "\n",
+ " function set_focus () {\n",
+ " canvas.focus();\n",
+ " canvas_div.focus();\n",
+ " }\n",
+ "\n",
+ " window.setTimeout(set_focus, 100);\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype._init_toolbar = function() {\n",
+ " var fig = this;\n",
+ "\n",
+ " var nav_element = $('')\n",
+ " nav_element.attr('style', 'width: 100%');\n",
+ " this.root.append(nav_element);\n",
+ "\n",
+ " // Define a callback function for later on.\n",
+ " function toolbar_event(event) {\n",
+ " return fig.toolbar_button_onclick(event['data']);\n",
+ " }\n",
+ " function toolbar_mouse_event(event) {\n",
+ " return fig.toolbar_button_onmouseover(event['data']);\n",
+ " }\n",
+ "\n",
+ " for(var toolbar_ind in mpl.toolbar_items) {\n",
+ " var name = mpl.toolbar_items[toolbar_ind][0];\n",
+ " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n",
+ " var image = mpl.toolbar_items[toolbar_ind][2];\n",
+ " var method_name = mpl.toolbar_items[toolbar_ind][3];\n",
+ "\n",
+ " if (!name) {\n",
+ " // put a spacer in here.\n",
+ " continue;\n",
+ " }\n",
+ " var button = $('');\n",
+ " button.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 = $('');\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 = $('');\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 = $('');\n",
+ "\n",
+ " var fmt_picker = $('');\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",
+ " '', {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 = $('');\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, fig.canvas.height);\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 overriden (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(\"\");\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('
');\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'] = '
';\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 = $('')\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 = $('');\n",
+ " button.click(method_name, toolbar_event);\n",
+ " button.mouseover(tooltip, toolbar_mouse_event);\n",
+ " nav_element.append(button);\n",
+ " }\n",
+ "\n",
+ " // Add the status bar.\n",
+ " var status_bar = $('');\n",
+ " nav_element.append(status_bar);\n",
+ " this.message = status_bar[0];\n",
+ "\n",
+ " // Add the close button to the window.\n",
+ " var buttongrp = $('');\n",
+ " var button = $('');\n",
+ " button.click(function (evt) { fig.handle_close(fig, {}); } );\n",
+ " button.mouseover('Stop Interaction', toolbar_mouse_event);\n",
+ " buttongrp.append(button);\n",
+ " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n",
+ " titlebar.prepend(buttongrp);\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype._root_extra_style = function(el){\n",
+ " var fig = this\n",
+ " el.on(\"remove\", function(){\n",
+ "\tfig.close_ws(fig, {});\n",
+ " });\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype._canvas_extra_style = function(el){\n",
+ " // this is important to make the div 'focusable\n",
+ " el.attr('tabindex', 0)\n",
+ " // reach out to IPython and tell the keyboard manager to turn it's self\n",
+ " // off when our div gets focus\n",
+ "\n",
+ " // location in version 3\n",
+ " if (IPython.notebook.keyboard_manager) {\n",
+ " IPython.notebook.keyboard_manager.register_events(el);\n",
+ " }\n",
+ " else {\n",
+ " // location in version 2\n",
+ " IPython.keyboard_manager.register_events(el);\n",
+ " }\n",
+ "\n",
+ "}\n",
+ "\n",
+ "mpl.figure.prototype._key_event_extra = function(event, name) {\n",
+ " var manager = IPython.notebook.keyboard_manager;\n",
+ " if (!manager)\n",
+ " manager = IPython.keyboard_manager;\n",
+ "\n",
+ " // Check for shift+enter\n",
+ " if (event.shiftKey && event.which == 13) {\n",
+ " this.canvas_div.blur();\n",
+ " // 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= 3 moved mimebundle to data attribute of output\n",
+ " data = data.data;\n",
+ " }\n",
+ " if (data['text/html'] == html_output) {\n",
+ " return [cell, data, j];\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ "}\n",
+ "\n",
+ "// Register the function which deals with the matplotlib target/channel.\n",
+ "// The kernel may be null if the page has been refreshed.\n",
+ "if (IPython.notebook.kernel != null) {\n",
+ " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n",
+ "}\n"
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "
"
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "import SpectrumViewer.InlineViewer as inline\n",
+ "%matplotlib notebook\n",
+ "fileName = 'SpectrumViewer/example_lite.fits'\n",
+ "fileSource = 'SDSS'\n",
+ "inline.view(fileName, fileSource)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "import SpectrumViewer.InlineViewer as inline\n",
+ "%matplotlib notebook\n",
+ "fileName = 'SpectrumViewer/example_lite.fits'\n",
+ "fileSource = 'SDSS'\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "NameError",
+ "evalue": "name 'filename' is not defined",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 2\u001b[0m \u001b[0mcoaddData\u001b[0m \u001b[1;33m=\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[0mzData\u001b[0m \u001b[1;33m=\u001b[0m\u001b[1;36m3\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 4\u001b[1;33m \u001b[0mhdulist\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mfits\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 5\u001b[0m \u001b[0mc\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mhdulist\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mcoaddData\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 6\u001b[0m \u001b[0mz\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mhdulist\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mzData\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;31mNameError\u001b[0m: name 'filename' is not defined"
+ ]
+ }
+ ],
+ "source": [
+ "from astropy.io import fits\n",
+ "coaddData =1\n",
+ "zData =3\n",
+ "hdulist = fits.open(fileName)\n",
+ "c=hdulist[coaddData].data\n",
+ "z=hdulist[zData].data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.1"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/SpectrumViewer - Copy/.ipynb_checkpoints/demo 1-checkpoint.ipynb b/SpectrumViewer - Copy/.ipynb_checkpoints/demo 1-checkpoint.ipynb
new file mode 100644
index 0000000..2fd6442
--- /dev/null
+++ b/SpectrumViewer - Copy/.ipynb_checkpoints/demo 1-checkpoint.ipynb
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/SpectrumViewer - Copy/.ipynb_checkpoints/demo 2-checkpoint.ipynb b/SpectrumViewer - Copy/.ipynb_checkpoints/demo 2-checkpoint.ipynb
new file mode 100644
index 0000000..3e3479f
--- /dev/null
+++ b/SpectrumViewer - Copy/.ipynb_checkpoints/demo 2-checkpoint.ipynb
@@ -0,0 +1,62 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "ename": "ModuleNotFoundError",
+ "evalue": "No module named 'SpectrumViewer'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[1;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mimport\u001b[0m \u001b[0mInlineViewer\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2\u001b[0m \u001b[0mget_ipython\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'matplotlib notebook'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[0mfileName\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'example_lite.fits'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[0mfileSource\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'SDSS'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 5\u001b[0m \u001b[0mInlineViewer\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mview\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfileName\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfileSource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;32mC:\\Users\\wzuo\\Developer\\Spectrum Viewer\\SpectrumViewer\\InlineViewer.py\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mimport\u001b[0m \u001b[0mSpectrumViewer\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSpecUtil_inline\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0minline\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mSpectrumViewer\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSDSSDriver\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mdriver\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mview\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfilesource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[0mcoaddObj\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mzObj\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mdriver\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloadFITS\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfilesource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 5\u001b[0m \u001b[0mspec\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0minline\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSpecUtil\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mcoaddObj\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mzObj\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;31mModuleNotFoundError\u001b[0m: No module named 'SpectrumViewer'"
+ ]
+ }
+ ],
+ "source": [
+ "import InlineViewer\n",
+ "%matplotlib notebook\n",
+ "fileName = 'example_lite.fits'\n",
+ "fileSource = 'SDSS'\n",
+ "InlineViewer.view(fileName, fileSource)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.1"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/SpectrumViewer - Copy/CoaddObj.py b/SpectrumViewer - Copy/CoaddObj.py
new file mode 100644
index 0000000..fdb2987
--- /dev/null
+++ b/SpectrumViewer - Copy/CoaddObj.py
@@ -0,0 +1,17 @@
+# This class init with a fits file in the directory and store all the data in the RAM
+import numpy as np
+class CoaddObj:
+ def __init__(self,flux,loglam=None,ivar=None,andMask=None,orMask=None
+ ,wdisp=None,sky=None,model=None):#type can be pfs
+ self.flux = flux
+ self.loglam = loglam
+ self.ivar =ivar
+ self.andMask =andMask
+ self.orMask = orMask
+ self.wdisp = wdisp
+ self.sky =sky
+ self.model = model
+ self.lam = np.power(10,self.loglam)
+
+
+
diff --git a/SpectrumViewer - Copy/InlineViewer.py b/SpectrumViewer - Copy/InlineViewer.py
new file mode 100644
index 0000000..8822b92
--- /dev/null
+++ b/SpectrumViewer - Copy/InlineViewer.py
@@ -0,0 +1,6 @@
+import SpectrumViewer.SpecUtil_inline as inline
+import SpectrumViewer.SDSSDriver as driver
+def view(filename, filesource):
+ coaddObj,zObj=driver.loadFITS(filename, filesource)
+ spec = inline.SpecUtil(filename, coaddObj, zObj)
+ spec.showfig()
diff --git a/SpectrumViewer - Copy/SDSSDriver.py b/SpectrumViewer - Copy/SDSSDriver.py
new file mode 100644
index 0000000..fb36ef1
--- /dev/null
+++ b/SpectrumViewer - Copy/SDSSDriver.py
@@ -0,0 +1,52 @@
+#load SDSS into workable object
+from astropy.io import fits
+#from py3.SciServer import Authentication, Config
+#from py3.SciServer import CasJobs
+from urllib.parse import urlparse
+import SpectrumViewer.CoaddObj as Coadd
+import SpectrumViewer.ZObj as Z
+# def getSpecObjID(ra, dec, width, height, context=None, URL=True):
+# leftBoundry = ra - width / 2
+# rightBoundry = ra + width / 2
+# upperBoundry = dec + height / 2
+# lowerBoundry = dec - height / 2
+# sqlQuery = 'select specObjID from dr7.specobjall Where (ra >' + str(leftBoundry) + ' and ra<' + str(
+# rightBoundry) + ') and (dec>' + str(lowerBoundry) + ' and dec<' + str(upperBoundry) + ')'
+# return CasJobs.executeQuery(sqlQuery, context='dr7', format='pandas')
+# def getRawFITSPathInDAS(SpecObjID):
+# sqlQuery = 'select dr7.fGetUrlFitsSpectrum('+SpecObjID+')'
+# response = CasJobs.executeQuery(sqlQuery, context='dr7', format='pandas')
+# url= response['Column1'][0]
+# parseResult = urlparse(url)
+# prefix = '/home/idies/workspace/sdss_das/das2'
+# path = prefix+parseResult.path
+# return path
+
+def loadFITS(filename,fileSource):
+
+ if fileSource=='SDSS':
+ coaddData =1
+ zData =3
+ hdulist = fits.open(filename)
+ c=hdulist[coaddData].data
+ z=hdulist[zData].data
+ coaddObj = Coadd.CoaddObj(
+ flux=c['flux'],
+ loglam=c['loglam'],
+ ivar=c['ivar'],
+ andMask=c['and_Mask'],
+ orMask=c['or_Mask'],
+ wdisp=c['wdisp'],
+ sky = c['sky'],
+ model=c['model'])
+ zObj = Z.ZObj(
+ LINENAME=z['LINENAME'],
+ LINEWAVE=z['LINEWAVE'],
+ LINEZ=z['LINEZ'],
+ LINEEW=z['LINEEW'],
+ LINEZ_ERR=z['LINEZ_ERR'],
+ LINEEW_ERR=z['LINEEW_ERR'])
+ return coaddObj,zObj
+
+ else:
+ print('Sorry, we are loyal to SDSS ONLY, for the time being. ')
\ No newline at end of file
diff --git a/SpectrumViewer - Copy/SpecUtil.py b/SpectrumViewer - Copy/SpecUtil.py
new file mode 100644
index 0000000..0309f4e
--- /dev/null
+++ b/SpectrumViewer - Copy/SpecUtil.py
@@ -0,0 +1,131 @@
+# this file hold utility functions that generate the plot and actual data
+import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
+import numpy as np
+class SpecUtil:
+ def __init__(self,coaddObj,zObj):
+ self.coaddObj = coaddObj
+ self.zObj=zObj
+ # self.totalFig = plt.figure()
+ # self.shownFig = plt.figure()
+ #self.totalFig = Figure(figsize=(5, 4), dpi=100)
+ self.shownFig = Figure(figsize=(5, 4), dpi=100)
+ self.shownFig = plt.figure()
+ self.plotDict = {0: True,
+ 1: True,
+ 2: True,
+ 3: True,
+ 4: True}
+ #0 flux 1 skyline 2 emission 3 absorb 4 model
+ #self.totalAx = self.totalFig.add_subplot(111)
+ #fluxLine,=self.totalAx.plot(self.coaddObj.lam,self.coaddObj.flux)
+ #skyLine, = self.totalAx.plot(self.coaddObj.lam,self.coaddObj.sky)
+
+ self.shownAx = self.shownFig.add_subplot(111)
+ self.shownAx.set_xlabel('lambda/Å')
+ self.shownAx.set_ylabel('10-17 ergs/s/cm2/Å')
+
+ for key in self.plotDict.keys():
+ if self.plotDict[key]:
+ try:
+ self.plotLines(self.shownAx, key)
+ except IndexError: # dict is longer than plot numbers in totalax
+ pass
+ self.shownAx.legend()
+ #self.shownAx = self.totalAx
+ def updateFig(self):
+ #self.shownAx.lines=[]
+ self.shownAx.clear()
+ self.shownAx.set_xlabel('lambda/Å')
+ self.shownAx.set_ylabel('10-17 ergs/s/cm2/Å')
+ for key in self.plotDict.keys():
+ if self.plotDict[key]:
+ try:
+ self.plotLines(self.shownAx,key)
+ except IndexError:
+ pass
+ #line1, = ax.plot(x, y, 'b-')
+ self.shownAx.legend()
+ #for phase in np.linspace(0, 10 * np.pi, 100):
+ # line1.set_ydata(np.sin(0.5 * x + phase))
+ # fig.canvas.draw()
+ def addFlux(self):
+ self.plotDict[0]=True
+ self.updateFig()
+ def removeFlux(self):
+ self.plotDict[0] = False
+ self.updateFig()
+
+ def addSkyline(self):
+ self.plotDict[1] = True
+ self.updateFig()
+ def removeSkyline(self):
+ self.plotDict[1] = False
+ self.updateFig()
+ def addEmissionLine(self):
+ self.plotDict[2] = True
+ self.updateFig()
+ def removeEmissionLine(self):
+ self.plotDict[2] = False
+ self.updateFig()
+ def addAbsorbLine(self):
+ self.plotDict[3] = True
+ self.updateFig()
+ def removeAbsorbLine(self):
+ self.plotDict[3] = False
+ self.updateFig()
+ def addModel(self):
+ self.plotDict[4] = True
+ self.updateFig()
+ def removeModel(self):
+ self.plotDict[4] = False
+ self.updateFig()
+ def plotLines(self,axes,actionIndex):
+ if actionIndex==0:
+ axes.plot(self.coaddObj.lam, self.coaddObj.flux,'C0',label='flux')
+ elif actionIndex==1:
+ axes.plot(self.coaddObj.lam, self.coaddObj.sky,'C1',label='skyline')
+ elif actionIndex==2:
+ #plot emission line
+ self.plotSegment(axes,actionIndex)
+
+ elif actionIndex ==3:
+ #plot absorption line
+ self.plotSegment(axes,actionIndex)
+
+
+ elif actionIndex ==4:
+
+ #plot best fit model
+ axes.plot(self.coaddObj.lam, self.coaddObj.model, 'C3', label='best fit model')
+ else:
+
+ pass
+ def plotSegment(self,axes,actionIndex):
+
+ # read e/a line from zobj and plot it on axes with function from axhspan
+ if actionIndex==2:#emissiaon line
+ for lineIndex in range(0,len(self.zObj.LINENAME)):
+
+ width = self.zObj.LINEEW[lineIndex]
+ if width >0:
+ #print(width)
+ position = self.zObj.LINEWAVE[lineIndex]
+ startPostition = position-width/2
+ endPostition = position + width / 2
+ name= self.zObj.LINENAME[lineIndex]
+ #print(name)
+ axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+ axes.text(position,0,name , rotation=90)
+ elif actionIndex==3:#absorption line
+ for lineIndex in range(0,len(self.zObj.LINENAME)):
+ width = self.zObj.LINEEW[lineIndex]
+ if width >0:
+ #print(width)
+ position = self.zObj.LINEWAVE[lineIndex]
+ startPostition = position-width/2
+ endPostition = position + width / 2
+ name= self.zObj.LINENAME[lineIndex]
+ #print(name)
+ axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+ axes.text(position,0,name , rotation=90)
diff --git a/SpectrumViewer - Copy/SpecUtil_inline.py b/SpectrumViewer - Copy/SpecUtil_inline.py
new file mode 100644
index 0000000..eff5af8
--- /dev/null
+++ b/SpectrumViewer - Copy/SpecUtil_inline.py
@@ -0,0 +1,170 @@
+# this file hold utility functions that generate the plot and actual data
+import matplotlib.pyplot as plt
+from matplotlib.widgets import Button
+from astropy.io import fits
+class SpecUtil(object):
+ def __init__(self,filename,coaddObj,zObj):
+ self.coaddObj = coaddObj
+ self.zObj=zObj
+ self.plotDict = {0: True,
+ 1: True,
+ 2: True,
+ 3: True,
+ 4: True}
+ #0 flux 1 skyline 2 emission 3 absorb 4 model
+ #self.updateFig()
+ self.figure = plt.figure(filename,figsize=(10, 8), dpi=100)
+ self.shownAx = self.figure.add_subplot(111)
+ plt.subplots_adjust(bottom=0.2)
+
+ self.axfluxbutton = plt.axes([0.1, 0.05, 0.1, 0.075])
+ self.fluxbutton = Button(self.axfluxbutton, 'flux')
+ self.fluxbutton.on_clicked(self.fluxClicked)
+
+ self.axskylinebutton = plt.axes([0.2, 0.05, 0.1, 0.075])
+ self.skylinebutton = Button(self.axskylinebutton, 'skyline')
+ self.skylinebutton.on_clicked(self.skylineClicked)
+
+ self.axabsorbbutton = plt.axes([0.3, 0.05, 0.1, 0.075])
+ self.absorbbutton = Button(self.axabsorbbutton, 'absorption')
+ self.absorbbutton.on_clicked(self.absorbClicked)
+
+ self.axemission = plt.axes([0.4, 0.05, 0.1, 0.075])
+ self.emissionbutton = Button(self.axemission, 'emission')
+ self.emissionbutton.on_clicked(self.emissionClicked)
+
+ self.axmodelbutton = plt.axes([0.5, 0.05, 0.1, 0.075])
+ self.modelbutton = Button(self.axmodelbutton, 'model')
+ self.modelbutton.on_clicked(self.modelClicked)
+
+ def showfig(self):
+ self.updateFig()
+ def updateFig(self):
+
+ # figure = plt.figure(figsize=(8, 4), dpi=100)
+ # shownAx=figure.add_subplot(111)
+ # plt.subplots_adjust(bottom=0.2)
+
+ self.shownAx.clear()
+ self.shownAx.set_xlabel('lambda/Å')
+ self.shownAx.set_ylabel('10-17 ergs/s/cm2/Å')
+ for key in self.plotDict.keys():
+ if self.plotDict[key]:
+ try:
+ self.plotLines(self.shownAx,key)
+ except IndexError:
+ pass
+
+ self.shownAx.legend()
+ plt.show()
+ def fluxClicked(self,event):
+ if self.plotDict[0]:
+ self.plotDict[0]=False
+ else:
+ self.plotDict[0] = True
+
+ self.updateFig()
+ def skylineClicked(self,event):
+ if self.plotDict[1]:
+ self.plotDict[1]=False
+ else:
+ self.plotDict[1] = True
+ self.updateFig()
+ def emissionClicked(self, event):
+ if self.plotDict[2]:
+ self.plotDict[2] = False
+ else:
+ self.plotDict[2] = True
+ self.updateFig()
+ def absorbClicked(self, event):
+ if self.plotDict[3]:
+ self.plotDict[3] = False
+ else:
+ self.plotDict[3] = True
+ self.updateFig()
+ def modelClicked(self, event):
+ if self.plotDict[4]:
+ self.plotDict[4] = False
+ else:
+ self.plotDict[4] = True
+ self.updateFig()
+ def addFlux(self):
+ self.plotDict[0]=True
+ self.updateFig()
+ def removeFlux(self):
+ self.plotDict[0] = False
+ self.updateFig()
+
+ def addSkyline(self):
+ self.plotDict[1] = True
+ self.updateFig()
+ def removeSkyline(self):
+ self.plotDict[1] = False
+ self.updateFig()
+ def addEmissionLine(self):
+ self.plotDict[2] = True
+ self.updateFig()
+ def removeEmissionLine(self):
+ self.plotDict[2] = False
+ self.updateFig()
+ def addAbsorbLine(self):
+ self.plotDict[3] = True
+ self.updateFig()
+ def removeAbsorbLine(self):
+ self.plotDict[3] = False
+ self.updateFig()
+ def addModel(self):
+ self.plotDict[4] = True
+ self.updateFig()
+ def removeModel(self):
+ self.plotDict[4] = False
+ self.updateFig()
+ def plotLines(self,axes,actionIndex):
+ if actionIndex==0:
+ axes.plot(self.coaddObj.lam, self.coaddObj.flux,'C0',label='flux')
+ elif actionIndex==1:
+ axes.plot(self.coaddObj.lam, self.coaddObj.sky,'C1',label='skyline')
+ elif actionIndex==2:
+ #plot emission line
+ self.plotSegment(axes,actionIndex)
+
+ elif actionIndex ==3:
+ #plot absorption line
+ self.plotSegment(axes,actionIndex)
+
+
+ elif actionIndex ==4:
+
+ #plot best fit model
+ axes.plot(self.coaddObj.lam, self.coaddObj.model, 'C3', label='best fit model')
+ else:
+
+ pass
+ def plotSegment(self,axes,actionIndex):
+
+ # read e/a line from zobj and plot it on axes with function from axhspan
+ if actionIndex==2:#emissiaon line
+ for lineIndex in range(0,len(self.zObj.LINENAME)):
+
+ width = self.zObj.LINEEW[lineIndex]
+ if width >0:
+ #print(width)
+ position = self.zObj.LINEWAVE[lineIndex]
+ startPostition = position-width/2
+ endPostition = position + width / 2
+ name= self.zObj.LINENAME[lineIndex]
+ #print(name)
+ axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+ axes.text(position,0,name , rotation=90)
+ elif actionIndex==3:#absorption line
+ for lineIndex in range(0,len(self.zObj.LINENAME)):
+ width = self.zObj.LINEEW[lineIndex]
+ if width >0:
+ #print(width)
+ position = self.zObj.LINEWAVE[lineIndex]
+ startPostition = position-width/2
+ endPostition = position + width / 2
+ name= self.zObj.LINENAME[lineIndex]
+ #print(name)
+ axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+ axes.text(position,0,name , rotation=90)
diff --git a/SpectrumViewer - Copy/SpecUtil_interactive.py b/SpectrumViewer - Copy/SpecUtil_interactive.py
new file mode 100644
index 0000000..fc610c6
--- /dev/null
+++ b/SpectrumViewer - Copy/SpecUtil_interactive.py
@@ -0,0 +1,142 @@
+# this file hold utility functions that generate the plot and actual data
+import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
+import numpy as np
+from ipywidgets import interactive
+class SpecUtil:
+ def __init__(self,coaddObj,zObj):
+ self.coaddObj = coaddObj
+ self.zObj=zObj
+ # self.totalFig = plt.figure()
+ # self.shownFig = plt.figure()
+ #self.totalFig = Figure(figsize=(5, 4), dpi=100)
+ #self.shownFig = Figure(figsize=(5, 4), dpi=100)
+ #self.shownFig = plt.figure()
+ self.plotDict = {0: True,
+ 1: True,
+ 2: True,
+ 3: True,
+ 4: True}
+ #0 flux 1 skyline 2 emission 3 absorb 4 model
+ #self.totalAx = self.totalFig.add_subplot(111)
+ #fluxLine,=self.totalAx.plot(self.coaddObj.lam,self.coaddObj.flux)
+ #skyLine, = self.totalAx.plot(self.coaddObj.lam,self.coaddObj.sky)
+
+ #self.shownAx = self.shownFig.add_subplot(111)
+ #self.updateFig()
+ #self.shownAx = self.totalAx
+ self.interactive_plot = interactive(self.showfig, flux=True,skyline=True,emission=True,absorb=True,model=True)
+ self.interactive_plot.children[0].layout.display = 'flex'
+ output = self.interactive_plot.children[-1]
+ output.layout.height = '550px'
+
+ def showfig(self,flux,skyline,emission,absorb,model):
+ self.plotDict[0] = flux
+ self.plotDict[1] =skyline
+ self.plotDict[2] =emission
+ self.plotDict[3] =absorb
+ self.plotDict[4] =model
+ self.updateFig()
+ def updateFig(self):
+ #self.shownAx.lines=[]
+ figure = plt.figure(figsize=(8, 4), dpi=100)
+ shownAx=figure.add_subplot(111)
+
+ #self.shownAx.clear()
+ shownAx.set_xlabel('lambda/Å')
+ shownAx.set_ylabel('10-17 ergs/s/cm2/Å')
+ for key in self.plotDict.keys():
+ if self.plotDict[key]:
+ try:
+ self.plotLines(shownAx,key)
+ except IndexError:
+ pass
+ #line1, = ax.plot(x, y, 'b-')
+ shownAx.legend()
+ #for phase in np.linspace(0, 10 * np.pi, 100):
+ # line1.set_ydata(np.sin(0.5 * x + phase))
+ # fig.canvas.draw()
+
+ plt.show()
+ def format_coord(self,x,y):
+ return 'x=%1.4f, y=%1.4f'%(x, y)
+ def addFlux(self):
+ self.plotDict[0]=True
+ self.updateFig()
+ def removeFlux(self):
+ self.plotDict[0] = False
+ self.updateFig()
+
+ def addSkyline(self):
+ self.plotDict[1] = True
+ self.updateFig()
+ def removeSkyline(self):
+ self.plotDict[1] = False
+ self.updateFig()
+ def addEmissionLine(self):
+ self.plotDict[2] = True
+ self.updateFig()
+ def removeEmissionLine(self):
+ self.plotDict[2] = False
+ self.updateFig()
+ def addAbsorbLine(self):
+ self.plotDict[3] = True
+ self.updateFig()
+ def removeAbsorbLine(self):
+ self.plotDict[3] = False
+ self.updateFig()
+ def addModel(self):
+ self.plotDict[4] = True
+ self.updateFig()
+ def removeModel(self):
+ self.plotDict[4] = False
+ self.updateFig()
+ def plotLines(self,axes,actionIndex):
+ if actionIndex==0:
+ axes.plot(self.coaddObj.lam, self.coaddObj.flux,'C0',label='flux')
+ elif actionIndex==1:
+ axes.plot(self.coaddObj.lam, self.coaddObj.sky,'C1',label='skyline')
+ elif actionIndex==2:
+ #plot emission line
+ self.plotSegment(axes,actionIndex)
+
+ elif actionIndex ==3:
+ #plot absorption line
+ self.plotSegment(axes,actionIndex)
+
+
+ elif actionIndex ==4:
+
+ #plot best fit model
+ axes.plot(self.coaddObj.lam, self.coaddObj.model, 'C3', label='best fit model')
+ else:
+
+ pass
+ def plotSegment(self,axes,actionIndex):
+
+ # read e/a line from zobj and plot it on axes with function from axhspan
+ if actionIndex==2:#emissiaon line
+ for lineIndex in range(0,len(self.zObj.LINENAME)):
+
+ width = self.zObj.LINEEW[lineIndex]
+ if width >0:
+ #print(width)
+ position = self.zObj.LINEWAVE[lineIndex]
+ startPostition = position-width/2
+ endPostition = position + width / 2
+ name= self.zObj.LINENAME[lineIndex]
+ #print(name)
+ axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+ axes.text(position,0,name , rotation=90)
+ elif actionIndex==3:#absorption line
+ for lineIndex in range(0,len(self.zObj.LINENAME)):
+ width = self.zObj.LINEEW[lineIndex]
+ if width >0:
+ #print(width)
+ position = self.zObj.LINEWAVE[lineIndex]
+ startPostition = position-width/2
+ endPostition = position + width / 2
+ name= self.zObj.LINENAME[lineIndex]
+ #print(name)
+ axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+ axes.text(position,0,name , rotation=90)
diff --git a/SpectrumViewer - Copy/WindowViewer.py b/SpectrumViewer - Copy/WindowViewer.py
new file mode 100644
index 0000000..93ffcd0
--- /dev/null
+++ b/SpectrumViewer - Copy/WindowViewer.py
@@ -0,0 +1,132 @@
+# show plotting result in a new window interactively
+# this is actual user interface all the object are hide away from user
+import matplotlib
+matplotlib.use("TkAgg")
+from SpectrumViewer import SDSSDriver as driver
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
+# implement the default mpl key bindings
+from matplotlib.backend_bases import key_press_handler
+import tkinter as Tk
+
+from SpectrumViewer import SpecUtil as SpecUtil
+def view(fileName,fileSource):
+ coaddObj, zObj = driver.loadFITS(fileName, fileSource)
+ #construn tk window and all components
+
+
+ root = Tk.Tk()
+ root.wm_title("Embedding in TK")
+ app = SpecController(root,coaddObj,zObj)
+ root.mainloop()
+
+class SpecController:
+ #take objs to construct specmodel and specview
+ def __init__(self,root,coaddObj,zObj):
+ self.model = SpecModel(coaddObj,zObj)
+ self.view = SpecView(root,self.model.specUtilObj.shownFig)
+ self.view.sidepanel.fluxTogg.bind("