{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# First Steps\n", "\n", "Now that you have installed Marvin, it's time to take your first steps. If you want to learn more about how Marvin works, then go see [General Info](https://api.sdss.org/doc/manga/marvin/general.html) to learn about Marvin Modes, Versions, or Downloading. If you just want to play, then read on.\n", "\n", "First let's run some boilerplate code for Python 2/3 compatibility and plotting in the notebook:" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "from __future__ import print_function, division, absolute_import\n", "import matplotlib.pyplot as plt\n", "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now, let’s import Marvin:" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "INFO: No release version set. Setting default to MPL-6\n" ] } ], "source": [ "import marvin" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's see what release we're using. Releases can be either MPLs (e.g. MPL-5) or DRs (e.g. DR13), however DRs are currently disabled in Marvin." ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "data": { "text/plain": [ "'MPL-6'" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "marvin.config.release" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "On intial import, Marvin will set the default data release to use the latest MPL available, currently MPL-6. You can change the version of MaNGA data using the Marvin [Config](https://api.sdss.org/doc/manga/marvin/api/general.html#marvin-config-class).\n", "\n" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "('MPL:', 'MPL-5')\n" ] } ], "source": [ "from marvin import config\n", "config.setRelease('MPL-5')\n", "\n", "print('MPL:', config.release)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "But let's work with MPL-6:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "'MPL-6'" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "config.setRelease('MPL-6')\n", "\n", "# check designated version\n", "config.release" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# My First Cube\n", "Now let’s play with a Marvin Cube!\n", "\n", "Import the Marvin-Tools Cube class:" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [], "source": [ "from marvin.tools.cube import Cube" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's load a cube from a local file. Start by specifying the full path and name of the file, such as:\n", "\n", "`/Users/Brian/Work/Manga/redux/v2_3_1/8485/stack/manga-8485-1901-LOGCUBE.fits.gz`\n", "\n", "**EDIT Next Cell**" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#----- EDIT THIS CELL -----#\n", "\n", "# filename = '/Users/Brian/Work/Manga/redux/v1_5_1/8485/stack/manga-8485-1901-LOGCUBE.fits.gz'\n", "filename = 'path/to/manga/cube/manga-8485-1901-LOGCUBE.fits.gz'\n", "\n", "filename = '/Users/andrews/manga/spectro/redux/v2_3_1/8485/stack/manga-8485-1901-LOGCUBE.fits.gz'\n", "filename = '/Users/Brian/Work/Manga/redux/v2_3_1/8485/stack/manga-8485-1901-LOGCUBE.fits.gz'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Create a Cube object:" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [], "source": [ "cc = Cube(filename=filename)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we have a Cube object:" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "print(cc)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "How about we look at some meta-data" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "(232.544703894, 48.6902009334, 'MaNGA dither')" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cc.ra, cc.dec, cc.header['SRVYMODE']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "...and the quality and target bits" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "[,\n", " ,\n", " ]" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cc.target_flags" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 16, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cc.quality_flag" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Get a Spaxel\n", "Cubes have several functions currently available: getSpaxel, getMaps, getAperture. Let's look at spaxels. We can retrieve spaxels from a cube easily via indexing. In this manner, spaxels are 0-indexed from the lower left corner. Let's get spaxel (x=10, y=10):" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "spax = cc[10,10]" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# print the spaxel to see the x,y coord from the lower left, and the coords relative to the cube center, x_cen/y_cen\n", "spax" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Spaxels have a spectrum associated with it. It has the wavelengths and fluxes of each spectral channel:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Alternatively grab a spaxel with getSpaxel. Use the xyorig keyword to set the coordinate origin point: 'lower' or 'center'. The default is \"center\"" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# let's grab the central spaxel\n", "spax = cc.getSpaxel(x=0, y=0)\n", "spax" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/latex": [ "$[3621.596,~3622.43,~3623.2642,~\\dots, 10349.038,~10351.422,~10353.805] \\; \\mathrm{\\mathring{A}}$" ], "text/plain": [ "" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "spax.flux.wavelength" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/latex": [ "$[0.54676276,~0.46566465,~0.4622981,~\\dots, 0,~0,~0] \\; \\mathrm{1 \\times 10^{-17}\\,\\frac{erg}{\\mathring{A}\\,s\\,spaxel\\,cm^{2}}}$" ], "text/plain": [ "" ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "spax.flux" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "### Plot the spectrum!" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# turn on interactive plotting\n", "%matplotlib notebook" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false, "scrolled": false }, "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 = $('
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