From 459577a48576d90b04c91f8181fdd6d1346548c5 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Wed, 12 Feb 2014 10:34:10 -0500
Subject: [PATCH 01/27] Convert UVES tutorial to ipython notebook format

---
 tutorials/UVES/UVES.ipynb | 1478 +++++++++++++++++++++++++++++++++++++
 1 file changed, 1478 insertions(+)
 create mode 100644 tutorials/UVES/UVES.ipynb

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
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--- /dev/null
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@@ -0,0 +1,1478 @@
+{
+ "metadata": {
+  "name": ""
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "heading",
+     "level": 1,
+     "metadata": {},
+     "source": [
+      "Analyzing UVES Spectroscopy with Astropy"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "This tutorial follows my real live data analysis of MN Lup and the code developed\n",
+      "below is taken (with only minor modifications) from the code that I used to\n",
+      "actually prepare the publication. The plots that will be developed below\n",
+      "appear in very similar form in the article published in ApJ.\n",
+      "\n",
+      "The examples below depend on each other and the plots in the last section make\n",
+      "use of things calculated in the earlier sections. Thus, if you need to restart\n",
+      "your python session in the course of this tutorial, please execute all the code\n",
+      "again.\n",
+      "\n",
+      "Also, this tutorial works best if you follow along and execute the code shown\n",
+      "on your own computer. The page is already quite long and I do not include the\n",
+      "output you would see on your screen in this document."
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Before you proceed"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Please download this tar file <../downloads/astropy_UVES.tar.gz> and extract\n",
+      "the content, either by clicking on the link or by executing this\n",
+      "python code"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "import urllib2, tarfile\n",
+      "url = 'http://python4astronomers.github.io/_downloads/astropy_UVES.tar.gz'\n",
+      "tarfile.open(fileobj=urllib2.urlopen(url), mode='r|*').extractall()\n",
+      "cd UVES\n",
+      "ls"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Then start up IPython with the ``--pylab`` option to enable easy plotting"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Acknowledgments"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      ":Authors: Moritz Guenther\n",
+      ":Copyright: 2013 Moritz Guenther\n",
+      "\n",
+      "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",
+      "under program ID 087.V0991(A)."
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Scientific background"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "In this tutorial we analyze data from MN Lup, a T Tauri star in the\n",
+      "Taurus-Auriga star forming region located at a distance of about 140 pc. MN Lup\n",
+      "has been observed simultaneously with XMM-Newton and the UVES spectrograph on the\n",
+      "VLT. MN Lup is suspected to be a classical T Tauri star, that is accreting mass\n",
+      "from a circumstellar disk. MN Lup has been Doppler imaged by `Strassmeier et al.\n",
+      "(2005, A&A, 440, 1105) <http://adsabs.harvard.edu/abs/2005A%26A...440.1105S>`_\n",
+      "with a very similar UVES setup and those authors claim an rotationally modulated\n",
+      "accretion spot.\n",
+      "\n",
+      "In the X-ray data we find moderate indications for accretion. In this\n",
+      "tutorial we analyze (some of) the UVES data to search for rotationally modulated\n",
+      "features in the emission line profiles, which could be due to an accretion spot\n",
+      "on the stellar surface."
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Reading the data"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The previous astropy tutorial already covered\n",
+      ":ref:`handling-fits-files` and :ref:`wcs-transformations`, so the explanation here\n",
+      "is only very brief. Check the `astropy documentation <http://docs.astropy.org>`_\n",
+      "or the other two tutorials for more details::"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "from glob import glob\n",
+      "\n",
+      "import numpy as np\n",
+      "\n",
+      "from astropy.wcs import WCS\n",
+      "from astropy.io import fits\n",
+      "\n",
+      "# glob searches through directories similar to the Unix shell\n",
+      "filelist = glob('*.fits')\n",
+      "# sort alphabetically - given the way the filenames are\n",
+      "# this also sorts in time\n",
+      "filelist.sort()\n",
+      "\n",
+      "Read the first fits file in the list and check what is in there::\n",
+      "    \n",
+      "sp = fits.open(filelist[0])\n",
+      "sp.info()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Read the first fits file in the list and check what is in there::"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "sp = fits.open(filelist[0])\n",
+      "sp.info()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "raw",
+     "metadata": {},
+     "source": [
+      "We see that the data is given as the primary image and all other info is\n",
+      "part of the primary header. So, we can extract the WCS from that header\n",
+      "to get the wavelength coordinate"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "header = sp[0].header\n",
+      "\n",
+      "wcs = WCS(header)\n",
+      "#make index array\n",
+      "index = np.arange(header['NAXIS1'])\n",
+      "\n",
+      "wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)\n",
+      "wavelength.shape\n",
+      "#Ahh, this has the wrong dimension. So we flatten it.\n",
+      "wavelength = wavelength.flatten("
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The flux is contained in the primary image"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "flux = sp[0].data"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Making code reusable as a function"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Now, we do not want to repeat this process for every single file by hand,\n",
+      "so let us define a function that takes the filename as input and returns\n",
+      "the wavelength and flux arrays and the time of the observation.\n",
+      "In python, functions are created with the ``def`` statements.\n",
+      "All lines that have an indentation level below the `def` statement are part\n",
+      "of the function. Functions can (but do not have to) return values using\n",
+      "the ``return`` statement.\n",
+      "\n",
+      "If a function ``func`` is contained in a file called ``spectra_utils.py`` in\n",
+      "the current directory, then this file can be imported into a python session in\n",
+      "order to use the function `func` with the following command"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "import spectra_utils\n",
+      "a = spectra_utils.func(param1, param2, ...)\n",
+      "\n",
+      "Alternatively, you can import just one (or a few) of many different functions\n",
+      "that are defined in your file ``spectra_utils.py``::\n",
+      "\n",
+      "from spectra_utils import func\n",
+      "a = func(param1, param2, ...)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "You will recognize that python does not make a difference between modules that come\n",
+      "with python (e.g. `glob`), external modules (e.g. `numpy` or `astropy`) and modules\n",
+      "that you write yourself. The syntax to import those modules or functions\n",
+      "is the same in all cases, provided that the directory where your module is\n",
+      "defined is in the search path (`more about python modules and the search path\n",
+      "<http://docs.python.org/2/tutorial/modules.html>`_)."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "You can also define a function on the interactive interpreter by just\n",
+      "typing it line by line. However, \n",
+      "if you work in an interactive session, then the function ends as soon as there\n",
+      "is a blank line. This makes it a little inconvenient to copy and paste more\n",
+      "than the simplest functions into an interpreter.\n",
+      "Fortunately, ipython offers two magic functions that take care of this\n",
+      "\n",
+      "1) You can mark code in some editor, copy it to the clipboard and then\n",
+      "type ``%paste`` in ipython.\n",
+      "2) You type ``%cpaste`` in ipython you can paste code (e.g. with the\n",
+      "mouse) and ipython will correct the leading number of white spaces and\n",
+      "ignore empty lines.\n",
+      "          \n",
+      "These two tricks can be used with any type of code, but are particularly useful\n",
+      "to define functions."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Once you used ``import spectra_utils`` python will not monitor the source file.\n",
+      "If you change the source code of ``func`` in the file, you need to\n",
+      "``reload(spectra_utils)`` to load the new version of ``func``.\n",
+      "\n",
+      "So, after all this discussion, we can now define a function that automates the\n",
+      "loading of a single spectrum using the commands we developed above. Even if\n",
+      "this function is fairly short, we still add some documentation to the header,\n",
+      "so that we can look up what parameters it needs when we come back to this\n",
+      "project a while later. Personally, I comment every function that is longer\n",
+      "than two lines"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def read_spec(filename):\n",
+      "    '''Read a UVES spectrum from the ESO pipeline\n",
+      "\n",
+      "    Parameters\n",
+      "    ----------\n",
+      "    filename : string\n",
+      "    name of the fits file with the data\n",
+      "\n",
+      "    Returns\n",
+      "    -------\n",
+      "    wavelength : np.ndarray\n",
+      "    wavelength (in Ang)\n",
+      "    flux : np.ndarray\n",
+      "    flux (in erg/s/cm**2)\n",
+      "    date_obs : string\n",
+      "    time of observation\n",
+      "    '''\n",
+      "    sp = fits.open(filename)\n",
+      "    header = sp[0].header\n",
+      "\n",
+      "    wcs = WCS(header)\n",
+      "#make index array\n",
+      "    index = np.arange(header['NAXIS1'])\n",
+      "\n",
+      "    wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)\n",
+      "    wavelength = wavelength.flatten()\n",
+      "    flux = sp[0].data\n",
+      "\n",
+      "    date_obs = header['Date-OBS']\n",
+      "    return wavelength, flux, date_obs"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "Try to find out how you can read the help for this function from the\n",
+      "command line"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "help(read_spec)\n",
+      "#or\n",
+      "read_spec?"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The dataset of UVES spectra should have been taken using all the same setup.\n",
+      "Write a function that returns the exposure time (``EXPTIME``),\n",
+      "the wavelength zero point\n",
+      "(``CRVAL1``), and the arm used (UVES has a red and a blue arm - see keyword\n",
+      "``HIERARCH ESO INS PATH``). Then check that all exposures have the same\n",
+      "setup."
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def read_setup(filename):\n",
+      "    '''Get setup for UVES spectrum from the ESO pipeline\n",
+      "\n",
+      "    Parameters\n",
+      "    ----------\n",
+      "    filename : string\n",
+      "    name of the fits file with the data\n",
+      "\n",
+      "    Returns\n",
+      "    -------\n",
+      "    exposure_time : float\n",
+      "    wavelength_zero_point : float\n",
+      "    optical_arm : string\n",
+      "    '''\n",
+      "    sp = fits.open(filelist[0])\n",
+      "    header = sp[0].header\n",
+      "\n",
+      "    return header['EXPTIME'], header['CRVAL1'], header['HIERARCH ESO INS PATH']\n",
+      "\n",
+      "# Let's just print the setup on the screen\n",
+      "# We'll see if it's all the same.\n",
+      "    for f in filelist:\n",
+      "    print read_setup(f)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The UVES pipeline that was used to reduce the data that we use in the this example\n",
+      "employs a fixed wavelength grid (see exercise above),\n",
+      "thus the ``wavelength`` is the same for all spectra.\n",
+      "This makes it easy to define an array that can hold the fluxes of all\n",
+      "observations. Then, we loop over the list of all filenames and fill this array\n",
+      "with data"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "flux = np.zeros((len(filelist), len(wavelength)))\n",
+      "# date comes as string with 23 characters (dtype = 'S23')\n",
+      "date = np.zeros((len(filelist)), dtype = 'S23')\n",
+      "\n",
+      "for i, fname in enumerate(filelist):\n",
+      "w, f, date_obs = read_spec(fname)\n",
+      "flux[i,:] = f\n",
+      "date[i] = date_obs"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 1,
+     "metadata": {},
+     "source": [
+      "Units and constants in astropy"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Often, one has to keep track of the units for certain values. Was the wavelength\n",
+      "given in Angstrom or in nm? In X-ray observations, a common unit of wavelength is\n",
+      "keV. How many nm is 0.65 keV?\n",
+      "`astropy.units <http://docs.astropy.org/en/v0.2.1/units/index.html>`_\n",
+      "offers a framework that can take\n",
+      "care of this book-keeping and propagate the units through many (but not all)\n",
+      "mathematical operations (e.g. addition, division, multiplication).\n",
+      "Furthermore,\n",
+      "`astropy.constants <http://docs.astropy.org/en/v0.2.1/constants/index.html>`_  supplies the values of\n",
+      "many physical and astronomical constants.\n",
+      "The easiest way to attach a unit to a number is by multiplication"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "import astropy.units as u\n",
+      "from astropy.constants.si import c, G, M_sun, R_sun\n",
+      "\n",
+      "wavelength = wavelength * u.AA\n",
+      "\n",
+      "# Let's define some constants we need for the exercises further down\n",
+      "# Again, we multiply the value with a unit here\n",
+      "heliocentric = -23. * u.km/u.s\n",
+      "v_rad = -4.77 * u.km / u.s  # Strassmeier et al. (2005)\n",
+      "R_MN_Lup = 0.9 * R_sun      # Strassmeier et al. (2005)\n",
+      "M_MN_Lup = 0.6 * M_sun      # Strassmeier et al. (2005)\n",
+      "vsini = 74.6 * u.km / u.s   # Strassmeier et al. (2005)\n",
+      "period = 0.439 * u.day      # Strassmeier et al. (2005)\n",
+      "\n",
+      "inclination = 45. * u.degree # Strassmeier et al. (2005)\n",
+      "# All numpy trigonometric functions expect the input in radian.\n",
+      "# So far, astropy does not know this, so we need to convert the\n",
+      "# angle manually\n",
+      "incl = inclination.to(u.radian)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Now, we can use those variables in our calculations. MN Lup is a T Tauri\n",
+      "star (TTS), which is possibly surrounded by an accretion disk. In the spectra\n",
+      "we will be looking for signatures of accretion. We expect those accretion\n",
+      "signatures to appear close to the free-fall velocity v that a mass m reaches, when\n",
+      "it hits the stellar surface. We can calculate the infall speed using simple\n",
+      "energy conservation"
+     ]
+    },
+    {
+     "cell_type": "raw",
+     "metadata": {},
+     "source": [
+      "E_{kin}  =  E_{grav}\n",
+      "\n",
+      "\\frac{1}{2} m v^2  =  G \\frac{m M_*}{R_*}"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "So, let us calculate the free-fall velocity for MN Lup"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "v_accr = (2.* G * M_MN_Lup/R_MN_Lup)**0.5 \n",
+      "print v_accr\n",
+      "# Maybe astronomers prefer it in the traditional cgs system?\n",
+      "print v_accr.cgs\n",
+      "# Or in some really obscure unit?\n",
+      "print v_accr.to(u.mile / u.hour)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "How does the accretion velocity relate to the rotational velocity?"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "v_rot = vsini / np.sin(incl)\n",
+      "v_accr / v_rot"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Oh, what is that? The seconds are gone, but ``astropy.quantity`` objects keep\n",
+      "their different length units unless told otherwise"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "(v_accr / v_rot).decompose()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The reason for this is that it is not uncommon to use different length units in\n",
+      "a single constant, e.g. the Hubble constant is commonly given in \"km/ (s * Mpc)\".\n",
+      "\"km\" and \"Mpc\" are both units of length, but generally you do *not* want to\n",
+      "shorten this to \"1/s\".\n",
+      "\n",
+      "We can now use the ``astropy.units`` mechanism to correct the wavelength\n",
+      "scale to the heliocentric velocity scale"
+     ]
+    },
+    {
+     "cell_type": "raw",
+     "metadata": {},
+     "source": [
+      "\\lambda_{heliocentric} = \\lambda_{bariocentric} * (1 + \\frac{v_{helio}}{c})"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Naively, we could try"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "wavelength = wavelength * (1. + heliocentric/c)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "However, this fails, because ``heliocentric/c`` is in units of \"km/m\" and ``1.``\n",
+      "is just a number. From the notation above, it is not clear what we actually want.\n",
+      "Do we ask for the value of ``heliocentric/c + 1.`` or do we want to simplify the\n",
+      "units of  ``heliocentric/c`` and after that add ``1.``?\n",
+      "There are several ways to make the instruction precise,\n",
+      "but one is to explicitly add ``u.dimensionless_unscaled`` to ``1.``\n",
+      "to tell astropy that this number is dimensionless and does not carry any scaling"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "wavelength = wavelength * (1. * u.dimensionless_unscaled+ heliocentric/c)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "I want to mention one more feature here (check out\n",
+      "`astropy.units <http://docs.astropy.org/en/v0.2.1/units/index.html>`_ for\n",
+      "more): The ability to convert the spectral axis to frequencies or energies.\n",
+      "Normally, a unit of length is not equivalent to a unit of energy or to a\n",
+      "frequency, but this conversion makes sense for the wavelength of a spectrum.\n",
+      "This is how it can be done"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "wavelength.to(u.keV, equivalencies=u.spectral())\n",
+      "wavelength.to(u.Hz, equivalencies=u.spectral())"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Spectroscopically, MN Lup is classified as spectral type M0 V, thus\n",
+      "the gravitational acceleration on the surface :math:`\\log(g)`\n",
+      "should be comparable to the sun.\n",
+      "(For non-stellar astronomers: Conventionally, all values are given\n",
+      "in the cgs system. The value for the sun is :math:`\\log(g) = 4.4`.)\n",
+      "\n",
+      "Calculate :math:`\\log(g)` for MN Lup with the values for the mass\n",
+      "and radius given above. Those values were determined from\n",
+      "evolutionary tracks. Check if the :math:`\\log(g)` is consistent\n",
+      "with the value expected from spectroscopy"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The values from evolutionary tracks are indeed consistent with the\n",
+      "spectroscopically estimated surface gravity"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "print np.log10((G*M_MN_Lup/R_MN_Lup**2).cgs)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Write a function that turns a wavelength scale into a velocity scale.\n",
+      "We want to input a wavelengths array and the rest wavelength of a spectral\n",
+      "line. We need this function later to show the red- and blueshift of the\n",
+      "spectrum relative to the the Ca II H line. Use the following definition\n",
+      "to make sure the that code below can use it later"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def wave2doppler(wavelength_array, wavelength_line):\n",
+      "    .. do something ..\n",
+      "    return array_of_dopplershifts"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "You can test if you function works by calculating the a Dopplershift\n",
+      "of the following wavelengths relative to :math:`H_\\alpha`"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "waveclosetoHa = np.array([6562.,6563,6565.]) * u.AA\n",
+      "print wave2doppler(waveclosetoHa, 656.489 * u.nm)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "I get -132, -86 and +5 km/s"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def wave2doppler(w, w0):\n",
+      "    doppler = ((w-w0)/w0 * c)\n",
+      "    return doppler\n",
+      "\n",
+      "print wave2doppler(waveclosetoHa, 656.489 * u.nm).decompose().to(u.km/u.s)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Write a function that takes a wavelength array and the rest wavelength of\n",
+      "a spectral line as input, turns it into a Doppler shift (you can use\n",
+      "the function from the last exercise),\n",
+      "subtracts the radial velocity of MN Lup (4.77 km/s) and expresses\n",
+      "the resulting velocity in units of vsini.\n",
+      "We need this function later to show the red- and blueshift of the\n",
+      "spectrum relative to the Ca II H line. Use the following definition\n",
+      "to make sure the that code below can use it later"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def w2vsini(wavelength_array, wavelength_line):\n",
+      "    .. do something ..\n",
+      "    return array_of_shifts_in_vsini"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def w2vsini(w, w0):\n",
+      "    v = wave2doppler(w, w0) - 4.77 * u.km/u.s\n",
+      "    return v / vsini"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Converting times"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "`astropy.time <http://docs.astropy.org/en/v0.2.1/time/index.html>`_\n",
+      "provides methods to convert times and dates between different\n",
+      "systems and formats. Since the ESO fits headers already contain the time of the\n",
+      "observation in different systems, we could just read the keyword in the time\n",
+      "system we like, but we will use ``astropy.time`` to make this conversion here.\n",
+      "``astropy.time.Time`` will parse many common input formats (strings, floats), but\n",
+      "unless the format is unambiguous the format needs to be specified (e.g. a number\n",
+      "could mean JD or MJD or year). Also, the time system needs to be given (e.g. UTC).\n",
+      "Below are several examples, initialized from different header keywords"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "from astropy.time import Time\n",
+      "t1 = Time(header['MJD-Obs'], format = 'mjd', scale = 'utc')\n",
+      "t2 = Time(header['Date-Obs'], scale = 'utc')"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Times can be expressed in different formats"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "t1\n",
+      "t1.isot\n",
+      "t2"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "or be converted to a different time system"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "t1.tt"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Times can also be initialized from arrays and we can calculate time differences"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "obs_times = Time(date, scale = 'utc')\n",
+      "delta_t = obs_times - Time(date[0], scale = 'utc')"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Now, we want to express the time difference between the individual spectra of\n",
+      "MN Lup in rotational periods. While the unit of ``delta_t`` is days, unfortunately\n",
+      "``astropy.time.Time`` and ``astropy.units.Quantity`` objects do not work together\n",
+      "yet, so we will have to convert from one to the other explicitly"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "delta_p = delta_t.val * u.day / period"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Normalize the flux to the local continuum"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "In this example we want to look at the time evolution of a single specific\n",
+      "emission line in the spectrum. In order to estimate the equivalent width\n",
+      "or make reasonable plots we need to normalize the flux to the local continuum.\n",
+      "In this specific case the emission line is bright and the continuum can be\n",
+      "described reasonably by a second-order polynomial."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "So, we define two regions left and right of the emission line, where we fit the\n",
+      "polynomial. Looking at the figure, ``[3925*u.AA, 3930*u.AA]`` and\n",
+      "``[3938*u.AA, 3945*u.AA]`` seem right for that. Then, we normalize the flux by\n",
+      "this polynomial.\n",
+      "\n",
+      "The following function will do that"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "def region_around_line(w, flux, cont):\n",
+      "    '''cut out and normalize flux around a line\n",
+      "\n",
+      "    Parameters\n",
+      "    ----------\n",
+      "    w : 1 dim np.ndarray\n",
+      "    array of wavelengths\n",
+      "    flux : np.ndarray of shape (N, len(w))\n",
+      "    array of flux values for different spectra in the series\n",
+      "    cont : list of lists\n",
+      "    wavelengths for continuum normalization [[low1,up1],[low2, up2]]\n",
+      "    that described two areas on both sides of the line\n",
+      "    '''\n",
+      "#index is true in the region where we fit the polynomial\n",
+      "    indcont = ((w > cont[0][0]) & (w < cont[0][1])) |((w > cont[1][0]) & (w < cont[1][1]))\n",
+      "#index of the region we want to return\n",
+      "    indrange = (w > cont[0][0]) & (w < cont[1][1])\n",
+      "# make a flux array of shape\n",
+      "# (number of spectra, number of points in indrange)\n",
+      "    f = np.zeros((flux.shape[0], indrange.sum()))\n",
+      "    for i in range(flux.shape[0]):\n",
+      "# fit polynomial of second order to the continuum region\n",
+      "    linecoeff = np.polyfit(w[indcont], flux[i, indcont],2)\n",
+      "# divide the flux by the polynomial and put the result in our\n",
+      "# new flux array\n",
+      "    f[i,:] = flux[i,indrange]/np.polyval(linecoeff, w[indrange])\n",
+      "    return w[indrange], f\n",
+      "\n",
+      "    wcaII, fcaII = region_around_line(wavelength, flux,\n",
+      "    [[3925*u.AA, 3930*u.AA],[3938*u.AA, 3945*u.AA]])"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Publication ready output"
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Tables"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "We will calculate the equivalent width in Angstroms of the emission line\n",
+      "for the first spectrum"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "ew = fcaII[0,:] - 1.\n",
+      "ew = ew[:-1] * np.diff(wcaII.to(u.AA).value)\n",
+      "print ew.sum()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Using ``numpy`` array notation we can actually process all spectra at once"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "delta_lam = np.diff(wcaII.to(u.AA).value)\n",
+      "ew = np.sum((fcaII - 1.)[:,:-1] * delta_lam[np.newaxis, :], axis=1)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Now, we want to generate a LaTeX table of the observation times, period\n",
+      "and equivalent width that we can directly paste into our manuscript. To do so,\n",
+      "we first collect all the columns and make an ``astropy.table.Table`` object. (Please\n",
+      "check `astropy.table <http://docs.astropy.org/en/v0.2.1/table/index.html>`_\n",
+      "or :ref:`tabular-data` for more\n",
+      "details on ``Table``). So, here is the code"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "from astropy.table import Column, Table\n",
+      "import astropy.io.ascii as ascii\n",
+      "\n",
+      "datecol = Column(name = 'Obs Date', data = date)\n",
+      "pcol = Column(name = 'phase', data = delta_p, format = '{:.1f}')\n",
+      "ewcol = Column(name = 'EW', data = ew, format = '{:.1f}', units = '\\\\AA')\n",
+      "tab = Table((datecol, pcol, ewcol))\n",
+      "# latexdicts['AA'] contains the style specifics for A&A (\\hline etc.)\n",
+      "tab.write('EWtab.tex', latexdict = ascii.latexdicts['AA'])"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Plots"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "We will make two plots. The plotting is done with\n",
+      "`matplotlib <http://matplotlib.org>`_, and does not involve Astropy itself.\n",
+      "Plotting is introduced in :ref:`plotting-and-images` and more details on\n",
+      "plotting can be found there. When in doubt, use the search engine of your choice\n",
+      "and ask the internet. Here, I mainly want to illustrate that Astropy can be\n",
+      "used in real-live data analysis.\n",
+      "Thus, I do not explain every step in the plotting in detail.\n",
+      "The plots we produce below appear in very\n",
+      "similar form in Guenther et al. 2013 (ApJ, 771, 70)."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "In both cases we want the x-axis to show the Doppler shift expressed in units\n",
+      "of the rotational velocity. In this way, features that are rotationally\n",
+      "modulated will stick out between -1 and +1"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "x = w2vsini(wcaII, 393.366 * u.nm).decompose()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "First, we will show the line profile"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "import matplotlib.pyplot as plt\n",
+      "# set reasonable figsize for 1-column figures\n",
+      "fig = plt.figure(figsize = (4,3))\n",
+      "ax = fig.add_subplot(1,1,1)\n",
+      "ax.plot(x, fcaII[0,:])\n",
+      "ax.set_xlim([-3,+3])\n",
+      "ax.set_xlabel('line shift [v sin(i)]')\n",
+      "ax.set_ylabel('flux')\n",
+      "ax.set_title('Ca II H line in MN Lup')\n",
+      "# when using this interface, we need to explicitly call the draw routine\n",
+      "plt.draw()\n",
+      "\n",
+      ".. image:: CaII-lines-one.png\n",
+      ":scale: 100%\n",
+      ":align: center"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "The plot above shows only a single spectrum. Plot all spectra into a single\n",
+      "plot and introduce a sensible offset between them, so that we can follow\n",
+      "the time evolution of the line."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "There are clearly several ways to produce a well looking plot. Here is one\n",
+      "way"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "yshift = np.arange((fcaII.shape[0])) * 0.5\n",
+      "#shift the second night up by a little more\n",
+      "yshift[:] += 1.5\n",
+      "yshift[13:] += 1\n",
+      "\n",
+      "fig = plt.figure(figsize = (4,3))\n",
+      "ax = fig.add_subplot(1,1,1)\n",
+      "\n",
+      "for i in range(25):\n",
+      "ax.plot(x, fcaII[i,:]+yshift[i], 'k')\n",
+      "\n",
+      "#separately show the mean line profile in a different color\n",
+      "ax.plot(x, np.mean(fcaII, axis =0), 'b')\n",
+      "ax.set_xlim([-2.5,+2.5])\n",
+      "ax.set_xlabel('line shift [$v \\\\sin i$]')\n",
+      "ax.set_ylabel('flux')\n",
+      "ax.set_title('Ca II H line in MN Lup')\n",
+      "fig.subplots_adjust(bottom = 0.15)\n",
+      "plt.draw()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Next, we will make a more advanced plot. For each spectrum we calculate\n",
+      "the difference to the mean flux"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "fmean = np.mean(fcaII, axis=0)\n",
+      "fdiff = fcaII - fmean[np.newaxis,:]"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "In the following simple plot, we can already see features moving through the line.\n",
+      "However, the axis scales are not right, the gap between both nights is not visible\n",
+      "and there is no proper labeling"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "fig = plt.figure(figsize = (4,3))\n",
+      "ax = fig.add_subplot(1,1,1)\n",
+      "im = ax.imshow(fdiff, aspect = \"auto\", origin = 'lower')"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "In the following, we will plot the spectra from both nights separately.\n",
+      "Also, we will pass the ``extent`` keyword to ``ax.imshow`` which takes care\n",
+      "of the axis"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "ind1 = delta_p < 1 * u.dimensionless_unscaled\n",
+      "ind2 = delta_p > 1 * u.dimensionless_unscaled\n",
+      "\n",
+      "fig = plt.figure(figsize = (4,3))\n",
+      "ax = fig.add_subplot(1,1,1)\n",
+      "\n",
+      "for ind in [ind1, ind2]:\n",
+      "im = ax.imshow(fdiff[ind,:], extent = (np.min(x), np.max(x), np.min(delta_p[ind]), np.max(delta_p[ind])), aspect = \"auto\", origin = 'lower')\n",
+      "\n",
+      "ax.set_ylim([np.min(delta_p), np.max(delta_p)])\n",
+      "ax.set_xlim([-1.9,1.9])\n",
+      "plt.draw()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Now, this plot is already much better, but there are still some things that can be\n",
+      "improved:\n",
+      "\n",
+      "* Introduce an offset on the y-axis to reduce the amount of white space.\n",
+      "* Strictly speaking, the image shown is not quite the right scale because the\n",
+      "``extent`` keyword gives the edges of the image shown, while ``x`` and\n",
+      "``delta_p`` contain the bin mid-points.\n",
+      "* Use a gray scale instead of color to save publication charges.\n",
+      "* Add labels to the axis.\n",
+      "\n",
+      "The following code addresses these points"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "# shift a little for plotting purposes\n",
+      "pplot = delta_p.copy().value\n",
+      "pplot[ind2] -= 1.5\n",
+      "# image goes from x1 to x2, but really x1 should be middle of first pixel\n",
+      "delta_t = np.median(np.diff(delta_p))/2.\n",
+      "delta_x = np.median(np.diff(x))/2.\n",
+      "# imshow does the normalization for plotting really well, but here I do it\n",
+      "# by hand to ensure it goes -1,+1 (that makes color bar look good)\n",
+      "fdiff = fdiff / np.max(np.abs(fdiff))\n",
+      "\n",
+      "fig = plt.figure(figsize = (4,3))\n",
+      "ax = fig.add_subplot(1,1,1)\n",
+      "\n",
+      "for ind in [ind1, ind2]:\n",
+      "im = ax.imshow(fdiff[ind,:],\n",
+      "extent = (np.min(x)-delta_x, np.max(x)+delta_x,\n",
+      "np.min(pplot[ind])-delta_t, np.max(pplot[ind])+delta_t),\n",
+      "aspect = \"auto\", origin = 'lower', cmap = plt.cm.Greys_r)\n",
+      "\n",
+      "ax.set_ylim([np.min(pplot)-delta_t, np.max(pplot)+delta_t])\n",
+      "ax.set_xlim([-1.9,1.9])\n",
+      "ax.set_xlabel('vel in $v\\\\sin i$')\n",
+      "ax.xaxis.set_major_locator(plt.MaxNLocator(4))\n",
+      "\n",
+      "def pplot(y, pos):\n",
+      "'The two args are the value and tick position'\n",
+      "'Function to make tick labels look good.'\n",
+      "if y < 0.5:\n",
+      "yreal = y\n",
+      "else:\n",
+      "yreal = y + 1.5\n",
+      "return yreal\n",
+      "\n",
+      "formatter = plt.FuncFormatter(pplot)\n",
+      "ax.yaxis.set_major_formatter(formatter)\n",
+      "ax.set_ylabel('period')\n",
+      "fig.subplots_adjust(left = 0.15, bottom = 0.15, right = 0.99, top = 0.99)\n",
+      "plt.draw()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "heading",
+     "level": 3,
+     "metadata": {},
+     "source": [
+      "Exercise"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Understand the code for the last plot. Some of the commands used are\n",
+      "already pretty advanced stuff. Remember, any internet search engine can be\n",
+      "your friend."
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Clearly, I did not develop this code for scratch.\n",
+      "The `matplotlib gallery <http://matplotlib.org/gallery.html>`_ is my\n",
+      "preferred place to look for plotting solutions."
+     ]
+    },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Contributing to Astropy"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "`Astropy <http://astropy.org>`_ is an open-source and community-developed\n",
+      "Python package, which means that is only as good as the contribution of the\n",
+      "astronomical community. Clearly, there will always people who have more fun writing\n",
+      "code and others who have more fun using it. However, if you find a bug and do not\n",
+      "report it, then it is unlikely to be fixed. If you wish for a specific feature,\n",
+      "then you can either implement it and contribute it or at least fill in a feature\n",
+      "request.\n",
+      "\n",
+      "If you want to get help or discuss issues with other Astropy users, you can\n",
+      "sign up for the `astropy mailing list\n",
+      "<http://mail.scipy.org/mailman/listinfo/astropy>`_.\n",
+      "Alternatively, the `astropy-dev\n",
+      "<http://groups.google.com/group/astropy-dev>`_ list is where you should go to\n",
+      "discuss more technical aspects of Astropy with the developers.\n",
+      "\n",
+      "If you have come across something that you believe is a bug, please open a\n",
+      "ticket in the Astropy `issue tracker\n",
+      "<http://github.com/astropy/astropy/issues>`_, and we will look into it\n",
+      "promptly.\n",
+      "\n",
+      "Please try to include an example that demonstrates the issue and will allow the\n",
+      "developers to reproduce and fix the problem.  If you are seeing a crash\n",
+      "then frequently it will help to include the full Python stack trace as well as\n",
+      "information about your operating system (e.g. MacOSX version or Linux version).\n",
+      "\n",
+      "Here is a practical example.\n",
+      ":ref:`Above <formula-vaccr>` we calculated the free-fall\n",
+      "velocity onto MN Lup like this"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "v_accr = (2.*G *M_MN_Lup / R_MN_Lup)**0.5"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Mathematically, the following statement is equivalent"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "v_accr2 = np.sqrt((2.*G * M_MN_Lup/R_MN_Lup))"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": []
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "However, this raises a warning and automatically converts the quantity object\n",
+      "to an numpy array and the unit is lost. If you believe that is a bug that should\n",
+      "be fixed, you might chose to report it in the `issue tracker\n",
+      "<http://github.com/astropy/astropy/issues>`_.\n",
+      "(But please check if somebody else has reported the same thing before, so we do\n",
+      "not clutter the issue tracker needlessly.)"
+     ]
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}
\ No newline at end of file

From c06a16e8c89ebf97f127219bca2b83772c147145 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Fri, 14 Feb 2014 11:58:36 -0500
Subject: [PATCH 02/27] Use download_file function to downlaod tar file  with
 UVES data

---
 tutorials/UVES/UVES.ipynb | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 84f325c7e..16fc78fb6 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -55,11 +55,12 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "import urllib2, tarfile\n",
+      "import tarfile\n",
+      "from astropy.utils.data import download_file\n",
       "url = 'http://python4astronomers.github.io/_downloads/astropy_UVES.tar.gz'\n",
-      "tarfile.open(fileobj=urllib2.urlopen(url), mode='r|*').extractall()\n",
-      "cd UVES\n",
-      "ls"
+      "f = tarfile.open(download_file(url, cache=True), mode='r|*')\n",
+      "location_for_data_file = '.'  # CHANGE TO WHEREVER YOU WANT THE DATA TO BE EXTRACTED\n",
+      "f.extractall(path=location_for_data_file)"
      ],
      "language": "python",
      "metadata": {},
@@ -148,7 +149,7 @@
       "from astropy.io import fits\n",
       "\n",
       "# glob searches through directories similar to the Unix shell\n",
-      "filelist = glob('*.fits')\n",
+      "filelist = glob('UVES/*.fits')\n",
       "# sort alphabetically - given the way the filenames are\n",
       "# this also sorts in time\n",
       "filelist.sort()\n",
@@ -1475,4 +1476,4 @@
    "metadata": {}
   }
  ]
-}
\ No newline at end of file
+}

From bb31a2953c9692245c0945f7996036dff4bb7a49 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Tue, 18 Feb 2014 21:35:34 -0500
Subject: [PATCH 03/27] Replace :ref: and :math: markup syntax

---
 tutorials/UVES/UVES.ipynb | 57 +++++++++++++++++----------------------
 1 file changed, 25 insertions(+), 32 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 16fc78fb6..1f1aa3746 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -46,9 +46,8 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Please download this tar file <../downloads/astropy_UVES.tar.gz> and extract\n",
-      "the content, either by clicking on the link or by executing this\n",
-      "python code"
+      "Please download the tar file and extract\n",
+      "the content by executing this python code"
      ]
     },
     {
@@ -132,8 +131,8 @@
      "metadata": {},
      "source": [
       "The previous astropy tutorial already covered\n",
-      ":ref:`handling-fits-files` and :ref:`wcs-transformations`, so the explanation here\n",
-      "is only very brief. Check the `astropy documentation <http://docs.astropy.org>`_\n",
+      "[handling FITS files](../FITS-header.html) and WCS transformations, so the explanation here\n",
+      "is only very brief. Check the [astropy documentation](http://docs.astropy.org)\n",
       "or the other two tutorials for more details::"
      ]
     },
@@ -276,8 +275,7 @@
       "with python (e.g. `glob`), external modules (e.g. `numpy` or `astropy`) and modules\n",
       "that you write yourself. The syntax to import those modules or functions\n",
       "is the same in all cases, provided that the directory where your module is\n",
-      "defined is in the search path (`more about python modules and the search path\n",
-      "<http://docs.python.org/2/tutorial/modules.html>`_)."
+      "defined is in the search path [more about python modules and the search path](http://docs.python.org/2/tutorial/modules.html)."
      ]
     },
     {
@@ -483,12 +481,12 @@
       "Often, one has to keep track of the units for certain values. Was the wavelength\n",
       "given in Angstrom or in nm? In X-ray observations, a common unit of wavelength is\n",
       "keV. How many nm is 0.65 keV?\n",
-      "`astropy.units <http://docs.astropy.org/en/v0.2.1/units/index.html>`_\n",
+      "[`astropy.units`](http://docs.astropy.org/en/v0.2.1/units/index.html)\n",
       "offers a framework that can take\n",
       "care of this book-keeping and propagate the units through many (but not all)\n",
       "mathematical operations (e.g. addition, division, multiplication).\n",
       "Furthermore,\n",
-      "`astropy.constants <http://docs.astropy.org/en/v0.2.1/constants/index.html>`_  supplies the values of\n",
+      "[`astropy.constants`](http://docs.astropy.org/en/v0.2.1/constants/index.html)  supplies the values of\n",
       "many physical and astronomical constants.\n",
       "The easiest way to attach a unit to a number is by multiplication"
      ]
@@ -534,12 +532,11 @@
      ]
     },
     {
-     "cell_type": "raw",
+     "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "E_{kin}  =  E_{grav}\n",
-      "\n",
-      "\\frac{1}{2} m v^2  =  G \\frac{m M_*}{R_*}"
+      "$$E_{kin}  =  E_{grav}$$\n",
+      "$$\\frac{1}{2} m v^2  =  G \\frac{m M_*}{R_*}$$"
      ]
     },
     {
@@ -614,10 +611,10 @@
      ]
     },
     {
-     "cell_type": "raw",
+     "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "\\lambda_{heliocentric} = \\lambda_{bariocentric} * (1 + \\frac{v_{helio}}{c})"
+      "$\\lambda_{heliocentric} = \\lambda_{bariocentric} * (1 + \\frac{v_{helio}}{c})$"
      ]
     },
     {
@@ -665,7 +662,7 @@
      "metadata": {},
      "source": [
       "I want to mention one more feature here (check out\n",
-      "`astropy.units <http://docs.astropy.org/en/v0.2.1/units/index.html>`_ for\n",
+      "[`astropy.units`](http://docs.astropy.org/en/v0.2.1/units/index.html) for\n",
       "more): The ability to convert the spectral axis to frequencies or energies.\n",
       "Normally, a unit of length is not equivalent to a unit of energy or to a\n",
       "frequency, but this conversion makes sense for the wavelength of a spectrum.\n",
@@ -854,7 +851,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "`astropy.time <http://docs.astropy.org/en/v0.2.1/time/index.html>`_\n",
+      "[`astropy.time`](http://docs.astropy.org/en/v0.2.1/time/index.html\n",
       "provides methods to convert times and dates between different\n",
       "systems and formats. Since the ESO fits headers already contain the time of the\n",
       "observation in different systems, we could just read the keyword in the time\n",
@@ -1082,8 +1079,8 @@
       "Now, we want to generate a LaTeX table of the observation times, period\n",
       "and equivalent width that we can directly paste into our manuscript. To do so,\n",
       "we first collect all the columns and make an ``astropy.table.Table`` object. (Please\n",
-      "check `astropy.table <http://docs.astropy.org/en/v0.2.1/table/index.html>`_\n",
-      "or :ref:`tabular-data` for more\n",
+      "check [`astropy.table`](http://docs.astropy.org/en/v0.2.1/table/index.html)\n",
+      "or `tabular-data` for more\n",
       "details on ``Table``). So, here is the code"
      ]
     },
@@ -1118,8 +1115,8 @@
      "metadata": {},
      "source": [
       "We will make two plots. The plotting is done with\n",
-      "`matplotlib <http://matplotlib.org>`_, and does not involve Astropy itself.\n",
-      "Plotting is introduced in :ref:`plotting-and-images` and more details on\n",
+      "[`matplotlib`](http://matplotlib.org), and does not involve Astropy itself.\n",
+      "Plotting is introduced in `plotting-and-images` and more details on\n",
       "plotting can be found there. When in doubt, use the search engine of your choice\n",
       "and ask the internet. Here, I mainly want to illustrate that Astropy can be\n",
       "used in real-live data analysis.\n",
@@ -1387,7 +1384,7 @@
      "metadata": {},
      "source": [
       "Clearly, I did not develop this code for scratch.\n",
-      "The `matplotlib gallery <http://matplotlib.org/gallery.html>`_ is my\n",
+      "The [matplotlib gallery](http://matplotlib.org/gallery.html) is my\n",
       "preferred place to look for plotting solutions."
      ]
     },
@@ -1403,7 +1400,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "`Astropy <http://astropy.org>`_ is an open-source and community-developed\n",
+      "[Astropy](http://astropy.org) is an open-source and community-developed\n",
       "Python package, which means that is only as good as the contribution of the\n",
       "astronomical community. Clearly, there will always people who have more fun writing\n",
       "code and others who have more fun using it. However, if you find a bug and do not\n",
@@ -1412,15 +1409,12 @@
       "request.\n",
       "\n",
       "If you want to get help or discuss issues with other Astropy users, you can\n",
-      "sign up for the `astropy mailing list\n",
-      "<http://mail.scipy.org/mailman/listinfo/astropy>`_.\n",
-      "Alternatively, the `astropy-dev\n",
-      "<http://groups.google.com/group/astropy-dev>`_ list is where you should go to\n",
+      "sign up for the [astropy mailing list](http://mail.scipy.org/mailman/listinfo/astropy).\n",
+      "Alternatively, the [astropy-dev](http://groups.google.com/group/astropy-dev) list is where you should go to\n",
       "discuss more technical aspects of Astropy with the developers.\n",
       "\n",
       "If you have come across something that you believe is a bug, please open a\n",
-      "ticket in the Astropy `issue tracker\n",
-      "<http://github.com/astropy/astropy/issues>`_, and we will look into it\n",
+      "ticket in the Astropy [issue tracker](http://github.com/astropy/astropy/issues), and we will look into it\n",
       "promptly.\n",
       "\n",
       "Please try to include an example that demonstrates the issue and will allow the\n",
@@ -1429,7 +1423,7 @@
       "information about your operating system (e.g. MacOSX version or Linux version).\n",
       "\n",
       "Here is a practical example.\n",
-      ":ref:`Above <formula-vaccr>` we calculated the free-fall\n",
+      "Above we calculated the free-fall\n",
       "velocity onto MN Lup like this"
      ]
     },
@@ -1466,8 +1460,7 @@
      "source": [
       "However, this raises a warning and automatically converts the quantity object\n",
       "to an numpy array and the unit is lost. If you believe that is a bug that should\n",
-      "be fixed, you might chose to report it in the `issue tracker\n",
-      "<http://github.com/astropy/astropy/issues>`_.\n",
+      "be fixed, you might chose to report it in the [issue tracker](http://github.com/astropy/astropy/issues).\n",
       "(But please check if somebody else has reported the same thing before, so we do\n",
       "not clutter the issue tracker needlessly.)"
      ]

From 31da50dfc49ac67ebc1660c760e3cf9e29680d96 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sat, 19 Apr 2014 22:59:06 -0400
Subject: [PATCH 04/27] Replace sphinx math markup

---
 tutorials/UVES/UVES.ipynb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 1f1aa3746..dfb5380b7 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -693,14 +693,14 @@
      "metadata": {},
      "source": [
       "Spectroscopically, MN Lup is classified as spectral type M0 V, thus\n",
-      "the gravitational acceleration on the surface :math:`\\log(g)`\n",
+      "the gravitational acceleration on the surface $\\log(g)$\n",
       "should be comparable to the sun.\n",
       "(For non-stellar astronomers: Conventionally, all values are given\n",
-      "in the cgs system. The value for the sun is :math:`\\log(g) = 4.4`.)\n",
+      "in the cgs system. The value for the sun is $\\log(g) = 4.4$.)\n",
       "\n",
-      "Calculate :math:`\\log(g)` for MN Lup with the values for the mass\n",
+      "Calculate $\\log(g)$ for MN Lup with the values for the mass\n",
       "and radius given above. Those values were determined from\n",
-      "evolutionary tracks. Check if the :math:`\\log(g)` is consistent\n",
+      "evolutionary tracks. Check if the $\\log(g)$ is consistent\n",
       "with the value expected from spectroscopy"
      ]
     },
@@ -758,7 +758,7 @@
      "metadata": {},
      "source": [
       "You can test if you function works by calculating the a Dopplershift\n",
-      "of the following wavelengths relative to :math:`H_\\alpha`"
+      "of the following wavelengths relative to $H_\\alpha$"
      ]
     },
     {

From 380b7b66234dd0046469023c4f05b5f98758ef91 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sat, 19 Apr 2014 23:11:47 -0400
Subject: [PATCH 05/27] Fix link to Strassmeier et al. 2005 reference

---
 tutorials/UVES/UVES.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index dfb5380b7..12fe12319 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -107,8 +107,8 @@
       "Taurus-Auriga star forming region located at a distance of about 140 pc. MN Lup\n",
       "has been observed simultaneously with XMM-Newton and the UVES spectrograph on the\n",
       "VLT. MN Lup is suspected to be a classical T Tauri star, that is accreting mass\n",
-      "from a circumstellar disk. MN Lup has been Doppler imaged by `Strassmeier et al.\n",
-      "(2005, A&A, 440, 1105) <http://adsabs.harvard.edu/abs/2005A%26A...440.1105S>`_\n",
+      "from a circumstellar disk. MN Lup has been Doppler imaged by\n",
+      "[Strassmeier et al. 2005](http://adsabs.harvard.edu/abs/2005A%26A...440.1105S)\n",
       "with a very similar UVES setup and those authors claim an rotationally modulated\n",
       "accretion spot.\n",
       "\n",

From 0fbf96522bdf9cbbddcf9dcd765a7cac63c3466f Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sun, 18 May 2014 13:47:14 -0400
Subject: [PATCH 06/27] Replace double colon at end of line by single colon

---
 tutorials/UVES/UVES.ipynb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 12fe12319..f4e02b514 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -133,7 +133,7 @@
       "The previous astropy tutorial already covered\n",
       "[handling FITS files](../FITS-header.html) and WCS transformations, so the explanation here\n",
       "is only very brief. Check the [astropy documentation](http://docs.astropy.org)\n",
-      "or the other two tutorials for more details::"
+      "or the other two tutorials for more details:"
      ]
     },
     {
@@ -153,7 +153,7 @@
       "# this also sorts in time\n",
       "filelist.sort()\n",
       "\n",
-      "Read the first fits file in the list and check what is in there::\n",
+      "Read the first fits file in the list and check what is in there:\n",
       "    \n",
       "sp = fits.open(filelist[0])\n",
       "sp.info()"
@@ -166,7 +166,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Read the first fits file in the list and check what is in there::"
+      "Read the first fits file in the list and check what is in there:"
      ]
     },
     {
@@ -258,7 +258,7 @@
       "a = spectra_utils.func(param1, param2, ...)\n",
       "\n",
       "Alternatively, you can import just one (or a few) of many different functions\n",
-      "that are defined in your file ``spectra_utils.py``::\n",
+      "that are defined in your file ``spectra_utils.py``:\n",
       "\n",
       "from spectra_utils import func\n",
       "a = func(param1, param2, ...)"

From bd0afff84d74b74bc69f7b61816818936bd7e4be Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sun, 18 May 2014 13:52:44 -0400
Subject: [PATCH 07/27] Fix sphinx mark-up in acknowledgements section

---
 tutorials/UVES/UVES.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index f4e02b514..769019b22 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -84,8 +84,8 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      ":Authors: Moritz Guenther\n",
-      ":Copyright: 2013 Moritz Guenther\n",
+      "Authors: Moritz Guenther\n",
+      "Copyright: 2013 Moritz Guenther\n",
       "\n",
       "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",
       "under program ID 087.V0991(A)."

From c854f2f8f36509d54f9c2a2a5eeaaa8fffe76a06 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sun, 18 May 2014 14:28:58 -0400
Subject: [PATCH 08/27] Fix formatting issues in text cells

---
 tutorials/UVES/UVES.ipynb | 22 +++++++---------------
 1 file changed, 7 insertions(+), 15 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 769019b22..2378bb507 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -151,12 +151,7 @@
       "filelist = glob('UVES/*.fits')\n",
       "# sort alphabetically - given the way the filenames are\n",
       "# this also sorts in time\n",
-      "filelist.sort()\n",
-      "\n",
-      "Read the first fits file in the list and check what is in there:\n",
-      "    \n",
-      "sp = fits.open(filelist[0])\n",
-      "sp.info()"
+      "filelist.sort()"
      ],
      "language": "python",
      "metadata": {},
@@ -181,7 +176,7 @@
      "outputs": []
     },
     {
-     "cell_type": "raw",
+     "cell_type": "markdown",
      "metadata": {},
      "source": [
       "We see that the data is given as the primary image and all other info is\n",
@@ -202,7 +197,7 @@
       "wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)\n",
       "wavelength.shape\n",
       "#Ahh, this has the wrong dimension. So we flatten it.\n",
-      "wavelength = wavelength.flatten("
+      "wavelength = wavelength.flatten()"
      ],
      "language": "python",
      "metadata": {},
@@ -363,15 +358,12 @@
      ]
     },
     {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
       "Try to find out how you can read the help for this function from the\n",
       "command line"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": []
+     ]
     },
     {
      "cell_type": "code",

From c1b61ee2f895dac1b7b3fb9eae5b292fbdaea2f9 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 15:39:37 -0400
Subject: [PATCH 09/27] Add CC license information to UVES tutorial

---
 tutorials/UVES/UVES.ipynb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 2378bb507..b847266f2 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -84,7 +84,11 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
+      "License: This tutorial is made available under the terms of the\n",
+	"[Creative Commons Attribution 3.0 License](http://creativecommons.org/licenses/by/3.0/)\n",
+      "\n",
       "Authors: Moritz Guenther\n",
+      "\n",
       "Copyright: 2013 Moritz Guenther\n",
       "\n",
       "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",

From 4276997fc1865e98f9e4f3b6c519fe249b5f476e Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 15:48:57 -0400
Subject: [PATCH 10/27] Delete UVES.rst and UVES.py files

---
 tutorials/UVES/UVES.py  | 242 ------------
 tutorials/UVES/UVES.rst | 841 ----------------------------------------
 2 files changed, 1083 deletions(-)
 delete mode 100644 tutorials/UVES/UVES.py
 delete mode 100644 tutorials/UVES/UVES.rst

diff --git a/tutorials/UVES/UVES.py b/tutorials/UVES/UVES.py
deleted file mode 100644
index d1ef88f17..000000000
--- a/tutorials/UVES/UVES.py
+++ /dev/null
@@ -1,242 +0,0 @@
-from glob import glob
-
-import numpy as np
-import matplotlib.pyplot as plt
-
-from astropy.wcs import WCS
-from astropy.io import fits
-
-filelist = glob('data/*.fits')
-filelist.sort()
-sp = fits.open(filelist[0])
-header = sp[0].header
-
-wcs = WCS(header)
-index = np.arange(header['NAXIS1'])
-wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)
-wavelength = wavelength.flatten()
-
-    
-flux = sp[0].data
-
-
-
-def read_spec(filename):
-        '''Read a UVES spectrum from the ESO pipeline
-
-        Parameters
-        ----------
-        filename : string
-           name of the fits file with the data
-
-        Returns
-        -------
-        wavelength : np.ndarray
-            wavelength (in Ang)
-        flux : np.ndarray
-            flux (in erg/s/cm**2)
-        date_obs : string
-            time of observation
-        '''
-        sp = fits.open(filename)
-        header = sp[0].header
-
-        wcs = WCS(header)
-        #make index array
-        index = np.arange(header['NAXIS1'])
-
-        wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)
-        wavelength = wavelength.flatten()
-        flux = sp[0].data
-
-        date_obs = header['Date-OBS']
-        return wavelength, flux, date_obs
-
-flux = np.zeros((len(filelist), len(wavelength)))
-date = np.zeros((len(filelist)), dtype = 'S23')
-
-for i, fname in enumerate(filelist):
-        w, f, date_obs = read_spec(fname)
-        flux[i,:] = f
-        date[i] = date_obs
-
-
-import astropy.units as u
-from astropy.constants.si import c, G, M_sun, R_sun
-
-wavelength = wavelength * u.AA
-
-# Let's define some constants we need for the excersices further down
-# Again, we multiply the value with a unit here
-heliocentric = -23. * u.km/u.s
-v_rad = -4.77 * u.km / u.s  # Strassmeier et al. (2005)
-R_MN_Lup = 0.9 * R_sun      # Strassmeier et al. (2005)
-M_MN_Lup = 0.6 * M_sun      # Strassmeier et al. (2005)
-vsini = 74.6 * u.km / u.s   # Strassmeier et al. (2005)
-period = 0.439 * u.day      # Strassmeier et al. (2005)
-    
-inclination = 45. * u.degree # Strassmeier et al. (2005)
-incl = inclination.to(u.radian)
-
-wavelength = wavelength * (1. * u.dimensionless_unscaled+ heliocentric/c)
-
-
-def wave2doppler(w, w0):
-        doppler = ((w-w0)/w0 * c)
-        return doppler
-
-
-
-def w2vsini(w, w0):
-        v = wave2doppler(w, w0) - 4.77 * u.km/u.s
-        return v / vsini
-
-from astropy.time import Time
-obs_times = Time(date, scale = 'utc')
-delta_t = obs_times - Time(date[0], scale = 'utc')
-delta_p = delta_t.val * u.day / period
-
-
-
-fig = plt.figure()
-ax = fig.add_subplot(1,1,1)
-ax.plot(wavelength, flux[0,:])
-ax.set_xlim([3900, 4000])
-ax.set_ylim([0,2000])
-ax.set_xlabel('wavelength [$\AA$]')
-ax.set_ylabel('flux')
-fig.savefig('CaII.png')
-
-def region_around_line(w, flux, cont):
-        '''cut out and normalize flux around a line
-
-        Parameters
-        ----------
-        w : 1 dim np.ndarray
-            array of wanvelenghts
-        flux : np.ndarray of shape (N, len(w))
-            array of flux values for different spectra in the series
-        cont : list of lists
-            wavelengths for continuum normalization [[low1,up1],[low2, up2]]
-            that described two areas on both sides of the line
-        '''
-        #index is true in the region where we fit the polynomial
-        indcont = ((w > cont[0][0]) & (w < cont[0][1])) | ((w > cont[1][0]) & (w < cont[1][1]))
-        #index of the region we want to return
-        indrange = (w > cont[0][0]) & (w < cont[1][1])
-        # make a flux array of shape
-        # (nuber of spectra, number of pointsin indrange)
-        f = np.zeros((flux.shape[0], indrange.sum()))
-        for i in range(flux.shape[0]):
-            # fit polynom of second order to the continuum region
-            linecoeff = np.polyfit(w[indcont], flux[i, indcont],2)
-            # devide the flux by the polynom and put the result in our
-            # new flux array
-            f[i,:] = flux[i,indrange]/np.polyval(linecoeff, w[indrange])
-        return w[indrange], f
-
-wcaII, fcaII = region_around_line(wavelength, flux, 
-                   [[3925*u.AA, 3930*u.AA],[3938*u.AA, 3945*u.AA]])
-
-
-x = w2vsini(wcaII, 393.366 * u.nm).decompose()
-
-
-import matplotlib.pyplot as plt
-# set reasonable figsize for 1-column figures
-fig = plt.figure(figsize = (4,3))
-ax = fig.add_subplot(1,1,1)
-ax.plot(x, fcaII[0,:])
-ax.set_xlim([-3,+3])
-ax.set_xlabel('line shift [v sin(i)]')
-ax.set_ylabel('flux')
-ax.set_title('Ca II H line in MN Lup')
-# when using this interface, we need to explicitly call the draw routine
-plt.draw()
-fig.savefig('CaII-lines-one.png')
-
-
-yshift = np.arange((fcaII.shape[0])) * 0.5
-yshift[:] += 1.5
-yshift[13:] += 1
-
-fig = plt.figure(figsize = (4,3))
-ax = fig.add_subplot(1,1,1)
-        
-for i in range(25):
-     ax.plot(x, fcaII[i,:]+yshift[i], 'k')
-
-ax.plot(x, np.mean(fcaII, axis =0), 'b')
-ax.set_xlim([-2.5,+2.5])
-ax.set_xlabel('line shift [$v \\sin i$]')
-ax.set_ylabel('flux')
-ax.set_title('Ca II H line in MN Lup')
-fig.subplots_adjust(bottom = 0.15)
-plt.draw()
-fig.savefig('CaII-lines-all.png')
-
-
-fmean = np.mean(fcaII, axis=0)
-fdiff = fcaII - fmean[np.newaxis,:]
-
-
-fig = plt.figure(figsize = (4,3))
-ax = fig.add_subplot(1,1,1)
-im = ax.imshow(fdiff, aspect = "auto", origin = 'lower')
-fig.savefig('CaII-1.png')
-
-ind1 = delta_p < 1 * u.dimensionless_unscaled
-ind2 = ~ind1
-
-fig = plt.figure(figsize = (4,3))
-ax = fig.add_subplot(1,1,1)
-
-for ind in [ind1, ind2]:
-    im = ax.imshow(fdiff[ind,:], extent = (np.min(x), np.max(x), np.min(delta_p[ind]), np.max(delta_p[ind])), aspect = "auto", origin = 'lower')
-        
-ax.set_ylim([np.min(delta_p), np.max(delta_p)])
-ax.set_xlim([-1.9,1.9])
-plt.draw()
-fig.savefig('CaII-2.png')
-    
-
-# shift a little for plotting purposes
-pplot = delta_p.copy().value
-pplot[ind2] -= 1.5
-# image goes from x1 to x2, but really x1 should be middle of first pixel
-delta_t = np.median(np.diff(delta_p))/2.
-delta_x = np.median(np.diff(x))/2.
-# imshow does the normalization for plotting really well, but here I do it
-# by hand to ensure it goes -1,+1 (that makes color bar look good)
-fdiff = fdiff / np.max(np.abs(fdiff))
-fig = plt.figure(figsize = (4,3))
-ax = fig.add_subplot(1,1,1)
-
-for ind in [ind1, ind2]:
-        im = ax.imshow(fdiff[ind,:], 
-             extent = (np.min(x)-delta_x, np.max(x)+delta_x, 
-                       np.min(pplot[ind])-delta_t, np.max(pplot[ind])+delta_t),
-             aspect = "auto", origin = 'lower', cmap = plt.cm.Greys_r)
-        
-ax.set_ylim([np.min(pplot)-delta_t, np.max(pplot)+delta_t])
-ax.set_xlim([-1.9,1.9])
-ax.set_xlabel('vel in $v\\sin i$')
-ax.xaxis.set_major_locator(plt.MaxNLocator(4))
- 
-def pplot(y, pos):
-        'The two args are the value and tick position'
-        'Function to make tick labels look good.'
-        if y < 0.5:
-            yreal = y
-        else:
-            yreal = y + 1.5
-        return yreal
-
-
-formatter = plt.FuncFormatter(pplot)
-ax.yaxis.set_major_formatter(formatter)
-ax.set_ylabel('period')
-fig.subplots_adjust(left = 0.15, bottom = 0.15, right = 0.99, top = 0.99)
-plt.draw()
-fig.savefig('CaII-3.png')
-
diff --git a/tutorials/UVES/UVES.rst b/tutorials/UVES/UVES.rst
deleted file mode 100644
index f8b6af499..000000000
--- a/tutorials/UVES/UVES.rst
+++ /dev/null
@@ -1,841 +0,0 @@
-Analyzing UVES Spectroscopy with Astropy
-=======================================
-
-This tutorial follows my real live data analysis of MN Lup and the code developed
-below is taken (with only minor modifications) from the code that I used to
-actually prepare the publication. The plots that will be developed below
-appear in very similar form in the article published in ApJ.
-
-The examples below depend on each other and the plots in the last section make
-use of things calculated in the earlier sections. Thus, if you need to restart
-your python session in the course of this tutorial, please execute all the code
-again.
-
-Also, this tutorial works best if you follow along and execute the code shown
-on your own computer. The page is already quite long and I do not include the
-output you would see on your screen in this document.
-
-.. toctree::
-
-
-Before you proceed
-------------------
-Please download this
-:download:`this tar file <../downloads/astropy_UVES.tar.gz>` and extract
-the content, either by clicking on the link or by executing this
-python code::
-
-    import urllib2, tarfile
-    url = 'http://python4astronomers.github.io/_downloads/astropy_UVES.tar.gz'
-    tarfile.open(fileobj=urllib2.urlopen(url), mode='r|*').extractall()
-    cd UVES
-    ls
-
-Then start up IPython with the ``--pylab`` option to enable easy plotting::
-
-    ipython --pylab
-
-Acknowledgments
----------------
-
-:Authors: Moritz Guenther
-:Copyright: 2013 Moritz Guenther
-
-Based on observations made with ESO Telescopes at the La Silla Paranal Observatory
-under program ID 087.V0991(A).
-
-
-Scientific background
----------------------
-In this tutorial we analyze data from MN Lup, a T Tauri star in the
-Taurus-Auriga star forming region located at a distance of about 140 pc. MN Lup
-has been observed simultaneously with XMM-Newton and the UVES spectrograph on the
-VLT. MN Lup is suspected to be a classical T Tauri star, that is accreting mass
-from a circumstellar disk. MN Lup has been Doppler imaged by `Strassmeier et al.
-(2005, A&A, 440, 1105) <http://adsabs.harvard.edu/abs/2005A%26A...440.1105S>`_
-with a very similar UVES setup and those authors claim an rotationally modulated
-accretion spot.
-
-In the X-ray data we find moderate indications for accretion. In this
-tutorial we analyze (some of) the UVES data to search for rotationally modulated
-features in the emission line profiles, which could be due to an accretion spot
-on the stellar surface.
-
-Reading the data
-----------------
-The previous astropy tutorial already covered
-:ref:`handling-fits-files` and :ref:`wcs-transformations`, so the explanation here
-is only very brief. Check the `astropy documentation <http://docs.astropy.org>`_
-or the other two tutorials for more details::
-
-    from glob import glob
-
-    import numpy as np
-
-    from astropy.wcs import WCS
-    from astropy.io import fits
-
-    # glob searches through directories similar to the Unix shell
-    filelist = glob('*.fits')
-    # sort alphabetically - given the way the filenames are
-    # this also sorts in time
-    filelist.sort()
-
-Read the first fits file in the list and check what is in there::
-    
-    sp = fits.open(filelist[0])
-    sp.info()
-
-We see that the data is given as the primary image and all other info is
-part of the primary header. So, we can extract the WCS from that header
-to get the wavelength coordinate::
-    
-    header = sp[0].header
-
-    wcs = WCS(header)
-    #make index array
-    index = np.arange(header['NAXIS1'])
-
-    wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)
-    wavelength.shape
-    #Ahh, this has the wrong dimension. So we flatten it.
-    wavelength = wavelength.flatten()
-
-The flux is contained in the primary image::
-    
-    flux = sp[0].data
-
-    
-Making code reusable as a function
-----------------------------------
-
-Now, we do not want to repeat this process for every single file by hand,
-so let us define a function that takes the filename as input and returns
-the wavelength and flux arrays and the time of the observation.
-In python, functions are created with the ``def`` statements.
-All lines that have an indentation level below the `def` statement are part
-of the function. Functions can (but do not have to) return values using
-the ``return`` statement.
-
-If a function ``func`` is contained in a file called ``spectra_utils.py`` in
-the current directory, then this file can be imported into a python session in
-order to use the function `func` with the following command::
-
-    import spectra_utils
-    a = spectra_utils.func(param1, param2, ...)
-
-Alternatively, you can import just one (or a few) of many different functions
-that are defined in your file ``spectra_utils.py``::
-
-    from spectra_utils import func
-    a = func(param1, param2, ...)
-
-You will recognize that python does not make a difference between modules that come
-with python (e.g. `glob`), external modules (e.g. `numpy` or `astropy`) and modules
-that you write yourself. The syntax to import those modules or functions
-is the same in all cases, provided that the directory where your module is
-defined is in the search path (`more about python modules and the search path
-<http://docs.python.org/2/tutorial/modules.html>`_).
-
-.. note::
-    You can also define a function on the interactive interpreter by just
-    typing it line by line. However, 
-    if you work in an interactive session, then the function ends as soon as there
-    is a blank line. This makes it a little inconvenient to copy and paste more
-    than the simplest functions into an interpreter.
-    Fortunately, ipython offers two magic functions that take care of this:
-
-    #) You can mark code in some editor, copy it to the clipboard and then
-       type ``%paste`` in ipython.
-    #) You type ``%cpaste`` in ipython you can paste code (e.g. with the
-       mouse) and ipython will correct the leading number of white spaces and
-       ignore empty lines.
-          
-    These two tricks can be used with any type of code, but are particularly useful
-    to define functions.
-
-.. note::
-    Once you used ``import spectra_utils`` python will not monitor the source file.
-    If you change the source code of ``func`` in the file, you need to
-    ``reload(spectra_utils)`` to load the new version of ``func``.
-
-So, after all this discussion, we can now define a function that automates the
-loading of a single spectrum using the commands we developed above. Even if
-this function is fairly short, we still add some documentation to the header,
-so that we can look up what parameters it needs when we come back to this
-project a while later. Personally, I comment every function that is longer
-than two lines::
-
-    def read_spec(filename):
-        '''Read a UVES spectrum from the ESO pipeline
-
-        Parameters
-        ----------
-        filename : string
-           name of the fits file with the data
-
-        Returns
-        -------
-        wavelength : np.ndarray
-            wavelength (in Ang)
-        flux : np.ndarray
-            flux (in erg/s/cm**2)
-        date_obs : string
-            time of observation
-        '''
-        sp = fits.open(filename)
-        header = sp[0].header
-
-        wcs = WCS(header)
-        #make index array
-        index = np.arange(header['NAXIS1'])
-
-        wavelength = wcs.wcs_pix2world(index[:,np.newaxis], 0)
-        wavelength = wavelength.flatten()
-        flux = sp[0].data
-
-        date_obs = header['Date-OBS']
-        return wavelength, flux, date_obs
-
-.. admonition::  Exercise
-
-    Try to find out how you can read the help for this function from the
-    command line.
-.. raw:: html
-
-   <p class="flip1">Click to Show/Hide Solution</p> <div class="panel1">
-
-::
-
-    help(read_spec)
-    #or
-    read_spec?
-
-.. raw:: html
-
-   </div>
-
-.. admonition::  Exercise
-
-    The dataset of UVES spectra should have been taken using all the same setup.
-    Write a function that returns the exposure time (``EXPTIME``),
-    the wavelength zero point
-    (``CRVAL1``), and the arm used (UVES has a red and a blue arm - see keyword
-    ``HIERARCH ESO INS PATH``). Then check that all exposures have the same
-    setup.
-    
-    
-.. raw:: html
-
-   <p class="flip2">Click to Show/Hide Solution</p> <div class="panel2">
-
-::
-
-    def read_setup(filename):
-        '''Get setup for UVES spectrum from the ESO pipeline
-
-        Parameters
-        ----------
-        filename : string
-           name of the fits file with the data
-
-        Returns
-        -------
-        exposure_time : float
-        wavelength_zero_point : float
-        optical_arm : string
-        '''
-        sp = fits.open(filelist[0])
-        header = sp[0].header
-
-        return header['EXPTIME'], header['CRVAL1'], header['HIERARCH ESO INS PATH']
-
-    # Let's just print the setup on the screen
-    # We'll see if it's all the same.
-    for f in filelist:
-        print read_setup(f)
-
-.. raw:: html
-
-   </div>
-
-The UVES pipeline that was used to reduce the data that we use in the this example
-employs a fixed wavelength grid (see exercise above),
-thus the ``wavelength`` is the same for all spectra.
-This makes it easy to define an array that can hold the fluxes of all
-observations. Then, we loop over the list of all filenames and fill this array
-with data::
-
-    flux = np.zeros((len(filelist), len(wavelength)))
-    # date comes as string with 23 characters (dtype = 'S23')
-    date = np.zeros((len(filelist)), dtype = 'S23')
-
-    for i, fname in enumerate(filelist):
-        w, f, date_obs = read_spec(fname)
-        flux[i,:] = f
-        date[i] = date_obs
-
-Units and constants in astropy
-------------------------------
-Often, one has to keep track of the units for certain values. Was the wavelength
-given in Angstrom or in nm? In X-ray observations, a common unit of wavelength is
-keV. How many nm is 0.65 keV?
-`astropy.units <http://docs.astropy.org/en/v0.2.1/units/index.html>`_
-offers a framework that can take
-care of this book-keeping and propagate the units through many (but not all)
-mathematical operations (e.g. addition, division, multiplication). 
-Furthermore, 
-`astropy.constants <http://docs.astropy.org/en/v0.2.1/constants/index.html>`_  supplies the values of
-many physical and astronomical constants.
-The easiest way to attach a unit to a number is by multiplication::
-
-    import astropy.units as u
-    from astropy.constants.si import c, G, M_sun, R_sun
-
-    wavelength = wavelength * u.AA
-
-    # Let's define some constants we need for the exercises further down
-    # Again, we multiply the value with a unit here
-    heliocentric = -23. * u.km/u.s
-    v_rad = -4.77 * u.km / u.s  # Strassmeier et al. (2005)
-    R_MN_Lup = 0.9 * R_sun      # Strassmeier et al. (2005)
-    M_MN_Lup = 0.6 * M_sun      # Strassmeier et al. (2005)
-    vsini = 74.6 * u.km / u.s   # Strassmeier et al. (2005)
-    period = 0.439 * u.day      # Strassmeier et al. (2005)
-    
-    inclination = 45. * u.degree # Strassmeier et al. (2005)
-    # All numpy trigonometric functions expect the input in radian.
-    # So far, astropy does not know this, so we need to convert the
-    # angle manually
-    incl = inclination.to(u.radian)
-
-Now, we can use those variables in our calculations. MN Lup is a T Tauri
-star (TTS), which is possibly surrounded by an accretion disk. In the spectra
-we will be looking for signatures of accretion. We expect those accretion
-signatures to appear close to the free-fall velocity v that a mass m reaches, when
-it hits the stellar surface. We can calculate the infall speed using simple
-energy conservation:
-
-.. _formula-vaccr:
-
-.. math::
-    E_{kin}  =  E_{grav}
-
-    \frac{1}{2} m v^2  =  G \frac{m M_*}{R_*}
-
-So, let us calculate the free-fall velocity for MN Lup::
-
-    >>> v_accr = (2.* G * M_MN_Lup/R_MN_Lup)**0.5 
-    >>> print v_accr
-    504469.027564 m / (s)
-    >>> # Maybe astronomers prefer it in the traditional cgs system?
-    >>> print v_accr.cgs
-    50446902.7564 cm / (s)
-    >>> # Or in some really obscure unit?
-    >>> print v_accr.to(u.mile / u.hour)
-    1128465.07598 mi / (h)
-
-How does the accretion velocity relate to the rotational velocity?
-::
-  
-    v_rot = vsini / np.sin(incl)
-    v_accr / v_rot
-
-Oh, what is that? The seconds are gone, but ``astropy.quantity`` objects keep
-their different length units unless told otherwise::
-
-    (v_accr / v_rot).decompose()
-
-The reason for this is that it is not uncommon to use different length units in
-a single constant, e.g. the Hubble constant is commonly given in "km/ (s * Mpc)".
-"km" and "Mpc" are both units of length, but generally you do *not* want to
-shorten this to "1/s".
-
-We can now use the ``astropy.units`` mechanism to correct the wavelength
-scale to the heliocentric velocity scale:
-
-.. math::
-
-    \lambda_{heliocentric} = \lambda_{bariocentric} * (1 + \frac{v_{helio}}{c})
-    
-Naively, we could try::
-
-    wavelength = wavelength * (1. + heliocentric/c)
-    TypeError: unsupported operand type(s) for +: 'float' and 'Quantity'
-
-However, this fails, because ``heliocentric/c`` is in units of "km/m" and ``1.``
-is just a number. From the notation above, it is not clear what we actually want.
-Do we ask for the value of ``heliocentric/c + 1.`` or do we want to simplify the
-units of  ``heliocentric/c`` and after that add ``1.``?
-There are several ways to make the instruction precise, 
-but one is to explicitly add ``u.dimensionless_unscaled`` to ``1.``
-to tell astropy that this number is dimensionless and does not carry any scaling::
-
-    wavelength = wavelength * (1. * u.dimensionless_unscaled+ heliocentric/c)
-
-I want to mention one more feature here (check out 
-`astropy.units <http://docs.astropy.org/en/v0.2.1/units/index.html>`_ for
-more): The ability to convert the spectral axis to frequencies or energies.
-Normally, a unit of length is not equivalent to a unit of energy or to a
-frequency, but this conversion makes sense for the wavelength of a spectrum.
-This is how it can be done::
-
-    wavelength.to(u.keV, equivalencies=u.spectral())
-    wavelength.to(u.Hz, equivalencies=u.spectral())
-
-.. admonition::  Exercise
-
-    Spectroscopically, MN Lup is classified as spectral type M0 V, thus
-    the gravitational acceleration on the surface :math:`\log(g)` 
-    should be comparable to the sun.
-    (For non-stellar astronomers: Conventionally, all values are given
-    in the cgs system. The value for the sun is :math:`\log(g) = 4.4`.)
-   
-    Calculate :math:`\log(g)` for MN Lup with the values for the mass
-    and radius given above. Those values were determined from 
-    evolutionary tracks. Check if the :math:`\log(g)` is consistent
-    with the value expected from spectroscopy.
-    
-.. raw:: html
-
-   <p class="flip7">Click to Show/Hide Solution</p> <div class="panel7">
-
-The values from evolutionary tracks are indeed consistent with the 
-spectroscopically estimated surface gravity::
-   
-    >>> print np.log10((G*M_MN_Lup/R_MN_Lup**2).cgs)
-    4.3080943799180433
-
-.. raw:: html
-
-   </div>
-
-
-.. admonition::  Exercise
-
-    Write a function that turns a wavelength scale into a velocity scale.
-    We want to input a wavelengths array and the rest wavelength of a spectral
-    line. We need this function later to show the red- and blueshift of the
-    spectrum relative to the the Ca II H line. Use the following definition
-    to make sure the that code below can use it later::
-
-        def wave2doppler(wavelength_array, wavelength_line):
-            .. do something ..
-            return array_of_dopplershifts
-
-    You can test if you function works by calculating the a Dopplershift
-    of the following wavelengths relative to :math:`H_\alpha`::
-
-        waveclosetoHa = np.array([6562.,6563,6565.]) * u.AA
-        print wave2doppler(waveclosetoHa, 656.489 * u.nm)
-
-    I get -132, -86 and +5 km/s.
-    
-.. raw:: html
-
-   <p class="flip3">Click to Show/Hide Solution</p> <div class="panel3">
-
-::
-
-    def wave2doppler(w, w0):
-        doppler = ((w-w0)/w0 * c)
-        return doppler
-
-    print wave2doppler(waveclosetoHa, 656.489 * u.nm).decompose().to(u.km/u.s)
-
-.. raw:: html
-
-   </div>
-
-.. admonition::  Exercise
-
-    Write a function that takes a wavelength array and the rest wavelength of
-    a spectral line as input, turns it into a Doppler shift (you can use
-    the function from the last exercise),
-    subtracts the radial velocity of MN Lup (4.77 km/s) and expresses
-    the resulting velocity in units of vsini.
-    We need this function later to show the red- and blueshift of the
-    spectrum relative to the Ca II H line. Use the following definition
-    to make sure the that code below can use it later::
-
-        def w2vsini(wavelength_array, wavelength_line):
-            .. do something ..
-            return array_of_shifts_in_vsini
-
-.. raw:: html
-
-   <p class="flip4">Click to Show/Hide Solution</p> <div class="panel4">
-
-::
-
-    def w2vsini(w, w0):
-        v = wave2doppler(w, w0) - 4.77 * u.km/u.s
-        return v / vsini
-
-.. raw:: html
-
-   </div>
-
-Converting times
-----------------
-`astropy.time <http://docs.astropy.org/en/v0.2.1/time/index.html>`_ 
-provides methods to convert times and dates between different
-systems and formats. Since the ESO fits headers already contain the time of the
-observation in different systems, we could just read the keyword in the time
-system we like, but we will use ``astropy.time`` to make this conversion here.
-``astropy.time.Time`` will parse many common input formats (strings, floats), but
-unless the format is unambiguous the format needs to be specified (e.g. a number
-could mean JD or MJD or year). Also, the time system needs to be given (e.g. UTC).
-Below are several examples, initialized from different header keywords::
-
-    from astropy.time import Time
-    t1 = Time(header['MJD-Obs'], format = 'mjd', scale = 'utc')
-    t2 = Time(header['Date-Obs'], scale = 'utc')
-
-Times can be expressed in different formats::
-
-    >>> t1
-    <Time object: scale='utc' format='mjd' vals=55784.9749105>
-    >>> t1.isot
-    '2011-08-11T23:23:52.266'
-    >>> t2
-    <Time object: scale='utc' format='isot' vals=2011-08-11T23:23:52.266>
-
-or be converted to a different time system::
-
-    >>> t1.tt
-    <Time object: scale='tt' format='mjd' vals=55784.9756765>
-    
-Times can also be initialized from arrays and we can calculate time differences::
-
-    obs_times = Time(date, scale = 'utc')
-    delta_t = obs_times - Time(date[0], scale = 'utc')
-
-Now, we want to express the time difference between the individual spectra of
-MN Lup in rotational periods. While the unit of ``delta_t`` is days, unfortunately
-``astropy.time.Time`` and ``astropy.units.Quantity`` objects do not work together
-yet, so we will have to convert from one to the other explicitly::
-
-    delta_p = delta_t.val * u.day / period
-
-
-Normalize the flux to the local continuum
------------------------------------------
-In this example we want to look at the time evolution of a single specific
-emission line in the spectrum. In order to estimate the equivalent width
-or make reasonable plots we need to normalize the flux to the local continuum.
-In this specific case the emission line is bright and the continuum can be
-described reasonably by a second-order polynomial.
-
-.. image:: CaII.png
-   :scale: 50%
-   :align: center
-
-So, we define two regions left and right of the emission line, where we fit the
-polynomial. Looking at the figure, ``[3925*u.AA, 3930*u.AA]`` and
-``[3938*u.AA, 3945*u.AA]`` seem right for that. Then, we normalize the flux by
-this polynomial.
-
-The following function will do that::
-
-    def region_around_line(w, flux, cont):
-        '''cut out and normalize flux around a line
-
-        Parameters
-        ----------
-        w : 1 dim np.ndarray
-            array of wavelengths
-        flux : np.ndarray of shape (N, len(w))
-            array of flux values for different spectra in the series
-        cont : list of lists
-            wavelengths for continuum normalization [[low1,up1],[low2, up2]]
-            that described two areas on both sides of the line
-        '''
-        #index is true in the region where we fit the polynomial
-        indcont = ((w > cont[0][0]) & (w < cont[0][1])) |((w > cont[1][0]) & (w < cont[1][1]))
-        #index of the region we want to return
-        indrange = (w > cont[0][0]) & (w < cont[1][1])
-        # make a flux array of shape
-        # (number of spectra, number of points in indrange)
-        f = np.zeros((flux.shape[0], indrange.sum()))
-        for i in range(flux.shape[0]):
-            # fit polynomial of second order to the continuum region
-            linecoeff = np.polyfit(w[indcont], flux[i, indcont],2)
-            # divide the flux by the polynomial and put the result in our
-            # new flux array
-            f[i,:] = flux[i,indrange]/np.polyval(linecoeff, w[indrange])
-        return w[indrange], f
-
-    wcaII, fcaII = region_around_line(wavelength, flux, 
-                   [[3925*u.AA, 3930*u.AA],[3938*u.AA, 3945*u.AA]])
-
-Publication ready output
-------------------------
-
-Tables
-^^^^^^
-We will calculate the equivalent width in Angstroms of the emission line
-for the first spectrum::
-
-    ew = fcaII[0,:] - 1.
-    ew = ew[:-1] * np.diff(wcaII.to(u.AA).value)
-    print ew.sum()
-
-Using ``numpy`` array notation we can actually process all spectra at once::
-
-    delta_lam = np.diff(wcaII.to(u.AA).value)
-    ew = np.sum((fcaII - 1.)[:,:-1] * delta_lam[np.newaxis, :], axis=1)
-    
-Now, we want to generate a LaTeX table of the observation times, period
-and equivalent width that we can directly paste into our manuscript. To do so,
-we first collect all the columns and make an ``astropy.table.Table`` object. (Please
-check `astropy.table <http://docs.astropy.org/en/v0.2.1/table/index.html>`_
-or :ref:`tabular-data` for more
-details on ``Table``). So, here is the code::
-
-    from astropy.table import Column, Table
-    import astropy.io.ascii as ascii
-
-    datecol = Column(name = 'Obs Date', data = date)
-    pcol = Column(name = 'phase', data = delta_p, format = '{:.1f}')
-    ewcol = Column(name = 'EW', data = ew, format = '{:.1f}', units = '\\AA')
-    tab = Table((datecol, pcol, ewcol))
-    # latexdicts['AA'] contains the style specifics for A&A (\hline etc.)
-    tab.write('EWtab.tex', latexdict = ascii.latexdicts['AA'])
-    
-Plots
-^^^^^
-We will make two plots. The plotting is done with
-`matplotlib <http://matplotlib.org>`_, and does not involve Astropy itself.
-Plotting is introduced in :ref:`plotting-and-images` and more details on
-plotting can be found there. When in doubt, use the search engine of your choice
-and ask the internet. Here, I mainly want to illustrate that Astropy can be
-used in real-live data analysis.
-Thus, I do not explain every step in the plotting in detail.
-The plots we produce below appear in very
-similar form in Guenther et al. 2013 (ApJ, 771, 70).
-
-In both cases we want the x-axis to show the Doppler shift expressed in units
-of the rotational velocity. In this way, features that are rotationally
-modulated will stick out between -1 and +1::
-
-    x = w2vsini(wcaII, 393.366 * u.nm).decompose()
-
-First, we will show the line profile::
-
-    import matplotlib.pyplot as plt
-    # set reasonable figsize for 1-column figures
-    fig = plt.figure(figsize = (4,3))
-    ax = fig.add_subplot(1,1,1)
-    ax.plot(x, fcaII[0,:])
-    ax.set_xlim([-3,+3])
-    ax.set_xlabel('line shift [v sin(i)]')
-    ax.set_ylabel('flux')
-    ax.set_title('Ca II H line in MN Lup')
-    # when using this interface, we need to explicitly call the draw routine
-    plt.draw()
-
-.. image:: CaII-lines-one.png
-   :scale: 100%
-   :align: center
-
-
-.. admonition::  Exercise
-
-    The plot above shows only a single spectrum. Plot all spectra into a single
-    plot and introduce a sensible offset between them, so that we can follow
-    the time evolution of the line.
-
-.. raw:: html
-
-   <p class="flip5">Click to Show/Hide Solution</p> <div class="panel5">
-
-There are clearly several ways to produce a well looking plot. Here is one
-way::
-
-    yshift = np.arange((fcaII.shape[0])) * 0.5
-    #shift the second night up by a little more
-    yshift[:] += 1.5
-    yshift[13:] += 1
-
-    fig = plt.figure(figsize = (4,3))
-    ax = fig.add_subplot(1,1,1)
-        
-    for i in range(25):
-        ax.plot(x, fcaII[i,:]+yshift[i], 'k')
-
-    #separately show the mean line profile in a different color
-    ax.plot(x, np.mean(fcaII, axis =0), 'b')
-    ax.set_xlim([-2.5,+2.5])
-    ax.set_xlabel('line shift [$v \\sin i$]')
-    ax.set_ylabel('flux')
-    ax.set_title('Ca II H line in MN Lup')
-    fig.subplots_adjust(bottom = 0.15)
-    plt.draw()
-
-.. image:: CaII-lines-all.png
-   :scale: 100%
-   :align: center
-
-.. raw:: html
-
-   </div>
-
-Next, we will make a more advanced plot. For each spectrum we calculate
-the difference to the mean flux::
-
-    fmean = np.mean(fcaII, axis=0)
-    fdiff = fcaII - fmean[np.newaxis,:]
-
-
-In the following simple plot, we can already see features moving through the line.
-However, the axis scales are not right, the gap between both nights is not visible
-and there is no proper labeling::
-
-    fig = plt.figure(figsize = (4,3))
-    ax = fig.add_subplot(1,1,1)
-    im = ax.imshow(fdiff, aspect = "auto", origin = 'lower')
-
-.. image:: CaII-1.png
-   :scale: 100%
-   :align: center
-
-
-In the following, we will plot the spectra from both nights separately.
-Also, we will pass the ``extent`` keyword to ``ax.imshow`` which takes care
-of the axis::
-
-    ind1 = delta_p < 1 * u.dimensionless_unscaled
-    ind2 = delta_p > 1 * u.dimensionless_unscaled
-
-    fig = plt.figure(figsize = (4,3))
-    ax = fig.add_subplot(1,1,1)
-
-    for ind in [ind1, ind2]:
-        im = ax.imshow(fdiff[ind,:], extent = (np.min(x), np.max(x), np.min(delta_p[ind]), np.max(delta_p[ind])), aspect = "auto", origin = 'lower')
-        
-    ax.set_ylim([np.min(delta_p), np.max(delta_p)])
-    ax.set_xlim([-1.9,1.9])
-    plt.draw()
-
-.. image:: CaII-2.png
-   :scale: 100%
-   :align: center
-
-
-Now, this plot is already much better, but there are still some things that can be
-improved:
-
-* Introduce an offset on the y-axis to reduce the amount of white space.
-* Strictly speaking, the image shown is not quite the right scale because the
-   ``extent`` keyword gives the edges of the image shown, while ``x`` and
-   ``delta_p`` contain the bin mid-points.
-* Use a gray scale instead of color to save publication charges.
-* Add labels to the axis.
-
-The following code addresses these points::
-
-    # shift a little for plotting purposes
-    pplot = delta_p.copy().value
-    pplot[ind2] -= 1.5
-    # image goes from x1 to x2, but really x1 should be middle of first pixel
-    delta_t = np.median(np.diff(delta_p))/2.
-    delta_x = np.median(np.diff(x))/2.
-    # imshow does the normalization for plotting really well, but here I do it
-    # by hand to ensure it goes -1,+1 (that makes color bar look good)
-    fdiff = fdiff / np.max(np.abs(fdiff))
-
-    fig = plt.figure(figsize = (4,3))
-    ax = fig.add_subplot(1,1,1)
-
-    for ind in [ind1, ind2]:
-        im = ax.imshow(fdiff[ind,:], 
-             extent = (np.min(x)-delta_x, np.max(x)+delta_x, 
-                       np.min(pplot[ind])-delta_t, np.max(pplot[ind])+delta_t),
-             aspect = "auto", origin = 'lower', cmap = plt.cm.Greys_r)
-        
-    ax.set_ylim([np.min(pplot)-delta_t, np.max(pplot)+delta_t])
-    ax.set_xlim([-1.9,1.9])
-    ax.set_xlabel('vel in $v\\sin i$')
-    ax.xaxis.set_major_locator(plt.MaxNLocator(4))
- 
-    def pplot(y, pos):
-        'The two args are the value and tick position'
-        'Function to make tick labels look good.'
-        if y < 0.5:
-            yreal = y
-        else:
-            yreal = y + 1.5
-        return yreal
-
-    formatter = plt.FuncFormatter(pplot)
-    ax.yaxis.set_major_formatter(formatter)
-    ax.set_ylabel('period')
-    fig.subplots_adjust(left = 0.15, bottom = 0.15, right = 0.99, top = 0.99)
-    plt.draw()
-
-.. image:: CaII-3.png
-   :scale: 100%
-   :align: center
-
-.. admonition::  Exercise
-
-    Understand the code for the last plot. Some of the commands used are
-    already pretty advanced stuff. Remember, any internet search engine can be
-    your friend.
-    
-.. raw:: html
-
-   <p class="flip6">Click to Show/Hide Solution</p> <div class="panel6">
-
-Clearly, I did not develop this code for scratch.
-The `matplotlib gallery <http://matplotlib.org/gallery.html>`_ is my
-preferred place to look for plotting solutions.
-
-.. raw:: html
-
-   </div>
-
-Contributing to Astropy
------------------------
-`Astropy <http://astropy.org>`_ is an open-source and community-developed
-Python package, which means that is only as good as the contribution of the
-astronomical community. Clearly, there will always people who have more fun writing
-code and others who have more fun using it. However, if you find a bug and do not
-report it, then it is unlikely to be fixed. If you wish for a specific feature,
-then you can either implement it and contribute it or at least fill in a feature
-request.
-
-If you want to get help or discuss issues with other Astropy users, you can
-sign up for the `astropy mailing list
-<http://mail.scipy.org/mailman/listinfo/astropy>`_.
-Alternatively, the `astropy-dev
-<http://groups.google.com/group/astropy-dev>`_ list is where you should go to
-discuss more technical aspects of Astropy with the developers.
-
-If you have come across something that you believe is a bug, please open a
-ticket in the Astropy `issue tracker
-<http://github.com/astropy/astropy/issues>`_, and we will look into it
-promptly.
-
-Please try to include an example that demonstrates the issue and will allow the
-developers to reproduce and fix the problem.  If you are seeing a crash
-then frequently it will help to include the full Python stack trace as well as
-information about your operating system (e.g. MacOSX version or Linux version).
-
-Here is a practical example. 
-:ref:`Above <formula-vaccr>` we calculated the free-fall
-velocity onto MN Lup like this::
-
-    v_accr = (2.*G *M_MN_Lup / R_MN_Lup)**0.5
-
-Mathematically, the following statement is equivalent::
-
-    v_accr2 = np.sqrt((2.*G * M_MN_Lup/R_MN_Lup))
-
-However, this raises a warning and automatically converts the quantity object
-to an numpy array and the unit is lost. If you believe that is a bug that should
-be fixed, you might chose to report it in the `issue tracker
-<http://github.com/astropy/astropy/issues>`_.
-(But please check if somebody else has reported the same thing before, so we do
-not clutter the issue tracker needlessly.)

From feb988a50c7d2f8cc3806a3aa62c5ecce85f428c Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 16:10:49 -0400
Subject: [PATCH 11/27] Add metadata in UVES notebook file and remove
 metadata.cfg (thanks @eteq for indications)

---
 tutorials/UVES/UVES.ipynb   | 13 ++++++++++---
 tutorials/UVES/metadata.cfg | 10 ----------
 2 files changed, 10 insertions(+), 13 deletions(-)
 delete mode 100644 tutorials/UVES/metadata.cfg

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index b847266f2..31795177b 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -1,6 +1,13 @@
 {
  "metadata": {
-  "name": ""
+  "astropy-tutorials": {
+   "author": "Hans Moritz G\u00fcnther <hguenther@cfa.harvard.edu>, Miguel de Val-Borro <valborro@princeton.edu>",
+   "date": "May 2014",
+   "link_name": "Analyzing UVES Spectroscopy with Astropy",
+   "name": "",
+   "published": true
+  },
+  "signature": "sha256:40684e0019d49a16624ba52d009646de9f71e418b85bdb50e2e8835714186512"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -85,7 +92,7 @@
      "metadata": {},
      "source": [
       "License: This tutorial is made available under the terms of the\n",
-	"[Creative Commons Attribution 3.0 License](http://creativecommons.org/licenses/by/3.0/)\n",
+      "[Creative Commons Attribution 3.0 License](http://creativecommons.org/licenses/by/3.0/)\n",
       "\n",
       "Authors: Moritz Guenther\n",
       "\n",
@@ -1465,4 +1472,4 @@
    "metadata": {}
   }
  ]
-}
+}
\ No newline at end of file
diff --git a/tutorials/UVES/metadata.cfg b/tutorials/UVES/metadata.cfg
deleted file mode 100644
index a6b6063d8..000000000
--- a/tutorials/UVES/metadata.cfg
+++ /dev/null
@@ -1,10 +0,0 @@
-[config]
-
-# Name of the link to the tutorial
-link_name: Analyzing UVES Spectrocopy with Astropy
-
-# Information about the tutorial
-author: Hans Moritz Günther
-date: April 2013
-
-published: false
\ No newline at end of file

From 94f283740f0a7b91880bb32b16377b071ba358ab Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 16:24:40 -0400
Subject: [PATCH 12/27] Corrections from @eteq and @hamogu

---
 tutorials/UVES/UVES.ipynb | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 31795177b..48f3de3f8 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -29,7 +29,8 @@
       "This tutorial follows my real live data analysis of MN Lup and the code developed\n",
       "below is taken (with only minor modifications) from the code that I used to\n",
       "actually prepare the publication. The plots that will be developed below\n",
-      "appear in very similar form in the article published in ApJ.\n",
+      "appear in very similar form in the article published in\n",
+      "[ApJ, Volume 771, Issue 1, article id. 70, 12 pp](http://adsabs.harvard.edu/abs/2013ApJ...771...70G).\n",
       "\n",
       "The examples below depend on each other and the plots in the last section make\n",
       "use of things calculated in the earlier sections. Thus, if you need to restart\n",
@@ -141,7 +142,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "The previous astropy tutorial already covered\n",
+      "A previous astropy tutorial already covered\n",
       "[handling FITS files](../FITS-header.html) and WCS transformations, so the explanation here\n",
       "is only very brief. Check the [astropy documentation](http://docs.astropy.org)\n",
       "or the other two tutorials for more details:"
@@ -1472,4 +1473,4 @@
    "metadata": {}
   }
  ]
-}
\ No newline at end of file
+}

From 67f3c95633802d9ec130867ae370d08de3544d3c Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 16:37:51 -0400
Subject: [PATCH 13/27] Move acknowledgements section to the top

---
 tutorials/UVES/UVES.ipynb | 46 +++++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 48f3de3f8..902cd5646 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -22,6 +22,29 @@
       "Analyzing UVES Spectroscopy with Astropy"
      ]
     },
+    {
+     "cell_type": "heading",
+     "level": 2,
+     "metadata": {},
+     "source": [
+      "Acknowledgments"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "License: This tutorial is made available under the terms of the\n",
+      "[Creative Commons Attribution 3.0 License](http://creativecommons.org/licenses/by/3.0/)\n",
+      "\n",
+      "Authors: Moritz Guenther\n",
+      "\n",
+      "Copyright: 2013 Moritz Guenther\n",
+      "\n",
+      "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",
+      "under program ID 087.V0991(A)."
+     ]
+    },
     {
      "cell_type": "markdown",
      "metadata": {},
@@ -80,29 +103,6 @@
       "Then start up IPython with the ``--pylab`` option to enable easy plotting"
      ]
     },
-    {
-     "cell_type": "heading",
-     "level": 2,
-     "metadata": {},
-     "source": [
-      "Acknowledgments"
-     ]
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "License: This tutorial is made available under the terms of the\n",
-      "[Creative Commons Attribution 3.0 License](http://creativecommons.org/licenses/by/3.0/)\n",
-      "\n",
-      "Authors: Moritz Guenther\n",
-      "\n",
-      "Copyright: 2013 Moritz Guenther\n",
-      "\n",
-      "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",
-      "under program ID 087.V0991(A)."
-     ]
-    },
     {
      "cell_type": "heading",
      "level": 2,

From b948dd55f00bcc556e46a030ed9d3365c3601815 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 17:16:08 -0400
Subject: [PATCH 14/27] remove references to ipython start up and pasting

---
 tutorials/UVES/UVES.ipynb | 28 ----------------------------
 1 file changed, 28 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 902cd5646..03c1ddfa6 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -96,13 +96,6 @@
      "metadata": {},
      "outputs": []
     },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Then start up IPython with the ``--pylab`` option to enable easy plotting"
-     ]
-    },
     {
      "cell_type": "heading",
      "level": 2,
@@ -285,27 +278,6 @@
       "defined is in the search path [more about python modules and the search path](http://docs.python.org/2/tutorial/modules.html)."
      ]
     },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "You can also define a function on the interactive interpreter by just\n",
-      "typing it line by line. However, \n",
-      "if you work in an interactive session, then the function ends as soon as there\n",
-      "is a blank line. This makes it a little inconvenient to copy and paste more\n",
-      "than the simplest functions into an interpreter.\n",
-      "Fortunately, ipython offers two magic functions that take care of this\n",
-      "\n",
-      "1) You can mark code in some editor, copy it to the clipboard and then\n",
-      "type ``%paste`` in ipython.\n",
-      "2) You type ``%cpaste`` in ipython you can paste code (e.g. with the\n",
-      "mouse) and ipython will correct the leading number of white spaces and\n",
-      "ignore empty lines.\n",
-      "          \n",
-      "These two tricks can be used with any type of code, but are particularly useful\n",
-      "to define functions."
-     ]
-    },
     {
      "cell_type": "markdown",
      "metadata": {},

From ff794375e60509e9d640ce84b30c9ffe3d539e24 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 17:18:04 -0400
Subject: [PATCH 15/27] Add missing period

---
 tutorials/UVES/UVES.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 03c1ddfa6..45b2314e2 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -422,7 +422,7 @@
       "thus the ``wavelength`` is the same for all spectra.\n",
       "This makes it easy to define an array that can hold the fluxes of all\n",
       "observations. Then, we loop over the list of all filenames and fill this array\n",
-      "with data"
+      "with data."
      ]
     },
     {

From edf2dd34ec781296a7b98d2700204a8991a7fb1f Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 19 May 2014 17:26:56 -0400
Subject: [PATCH 16/27] Replace links to the documentation by the latest stable
 version

---
 tutorials/UVES/UVES.ipynb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 45b2314e2..262f7e5e0 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -457,12 +457,12 @@
       "Often, one has to keep track of the units for certain values. Was the wavelength\n",
       "given in Angstrom or in nm? In X-ray observations, a common unit of wavelength is\n",
       "keV. How many nm is 0.65 keV?\n",
-      "[`astropy.units`](http://docs.astropy.org/en/v0.2.1/units/index.html)\n",
+      "[`astropy.units`](http://docs.astropy.org/en/stable/units/index.html)\n",
       "offers a framework that can take\n",
       "care of this book-keeping and propagate the units through many (but not all)\n",
       "mathematical operations (e.g. addition, division, multiplication).\n",
       "Furthermore,\n",
-      "[`astropy.constants`](http://docs.astropy.org/en/v0.2.1/constants/index.html)  supplies the values of\n",
+      "[`astropy.constants`](http://docs.astropy.org/en/stable/constants/index.html)  supplies the values of\n",
       "many physical and astronomical constants.\n",
       "The easiest way to attach a unit to a number is by multiplication"
      ]
@@ -638,7 +638,7 @@
      "metadata": {},
      "source": [
       "I want to mention one more feature here (check out\n",
-      "[`astropy.units`](http://docs.astropy.org/en/v0.2.1/units/index.html) for\n",
+      "[`astropy.units`](http://docs.astropy.org/en/stable/units/index.html) for\n",
       "more): The ability to convert the spectral axis to frequencies or energies.\n",
       "Normally, a unit of length is not equivalent to a unit of energy or to a\n",
       "frequency, but this conversion makes sense for the wavelength of a spectrum.\n",
@@ -827,7 +827,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "[`astropy.time`](http://docs.astropy.org/en/v0.2.1/time/index.html\n",
+      "[`astropy.time`](http://docs.astropy.org/en/stable/time/index.html)\n",
       "provides methods to convert times and dates between different\n",
       "systems and formats. Since the ESO fits headers already contain the time of the\n",
       "observation in different systems, we could just read the keyword in the time\n",
@@ -1055,7 +1055,7 @@
       "Now, we want to generate a LaTeX table of the observation times, period\n",
       "and equivalent width that we can directly paste into our manuscript. To do so,\n",
       "we first collect all the columns and make an ``astropy.table.Table`` object. (Please\n",
-      "check [`astropy.table`](http://docs.astropy.org/en/v0.2.1/table/index.html)\n",
+      "check [`astropy.table`](http://docs.astropy.org/en/stable/table/index.html)\n",
       "or `tabular-data` for more\n",
       "details on ``Table``). So, here is the code"
      ]

From 655d8882afdd1f2e75e1a92252a4f8c8a89df639 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Wed, 21 May 2014 10:29:53 -0400
Subject: [PATCH 17/27] Add comment in the exercise about finding help for a
 function

---
 tutorials/UVES/UVES.ipynb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 262f7e5e0..f02267339 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -354,8 +354,9 @@
      "collapsed": false,
      "input": [
       "help(read_spec)\n",
-      "#or\n",
-      "read_spec?"
+      "# or\n",
+      "read_spec?\n",
+      "# In the IPython notebook, the easiest way to see the help for a function is to type read_spec<TAB>"
      ],
      "language": "python",
      "metadata": {},

From 6547ff378ee91099ad4c53c342d3dd25a6291df5 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Wed, 21 May 2014 10:47:42 -0400
Subject: [PATCH 18/27] Use the doppler_optical equivalency to convert
 wavelength to veloctiy

---
 tutorials/UVES/UVES.ipynb | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index f02267339..656dcb261 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -760,11 +760,14 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
+      "# This function uses the Doppler equivalency between wavelength and velocity\n",
+      "import astropy.units as u\n",
       "def wave2doppler(w, w0):\n",
-      "    doppler = ((w-w0)/w0 * c)\n",
-      "    return doppler\n",
+      "    w0_equiv = u.doppler_optical(w0)\n",
+      "    w_equiv = w.to(u.km/u.s, equivalencies=w0_equiv)\n",
+      "    return w_equiv\n",
       "\n",
-      "print wave2doppler(waveclosetoHa, 656.489 * u.nm).decompose().to(u.km/u.s)"
+      "print wave2doppler(waveclosetoHa, 656.489 * u.nm).decompose()"
      ],
      "language": "python",
      "metadata": {},

From 18dca9567cf97dca1a0a29146f8782a4ba1b1b62 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Thu, 22 May 2014 15:42:14 -0400
Subject: [PATCH 19/27] Include comments and corrections from @eteq

---
 tutorials/UVES/UVES.ipynb | 152 ++++++++++++++++----------------------
 1 file changed, 65 insertions(+), 87 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 656dcb261..13c8d7e74 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -7,7 +7,7 @@
    "name": "",
    "published": true
   },
-  "signature": "sha256:40684e0019d49a16624ba52d009646de9f71e418b85bdb50e2e8835714186512"
+  "signature": "sha256:1f74796dfdd5b13d06d2a9bd9913a15fe6aa475e7967f8bd969ddcf17fb1e825"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -78,7 +78,12 @@
      "metadata": {},
      "source": [
       "Please download the tar file and extract\n",
-      "the content by executing this python code"
+      "the content by executing the python code below.\n",
+      "Executing this block will download and extract a tar file with data\n",
+      "necessary for this tutorial. By default it will run in whatever\n",
+      "directory you have placed this notebook. If that's some place\n",
+      "you don't want to fill with data files, change the\n",
+      "location_for_data_file variable."
      ]
     },
     {
@@ -94,7 +99,8 @@
      ],
      "language": "python",
      "metadata": {},
-     "outputs": []
+     "outputs": [],
+     "prompt_number": 1
     },
     {
      "cell_type": "heading",
@@ -186,7 +192,10 @@
      "source": [
       "We see that the data is given as the primary image and all other info is\n",
       "part of the primary header. So, we can extract the WCS from that header\n",
-      "to get the wavelength coordinate"
+      "to get the wavelength coordinate.\n",
+      "If you see warnings about a non-standard RADECSYS, don't worry\n",
+      "about this - the WCS will still work, it just doesn't\n",
+      "fully conform to the WCS standard."
      ]
     },
     {
@@ -212,7 +221,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "The flux is contained in the primary image"
+      "The flux is contained in the primary image."
      ]
     },
     {
@@ -247,30 +256,17 @@
       "\n",
       "If a function ``func`` is contained in a file called ``spectra_utils.py`` in\n",
       "the current directory, then this file can be imported into a python session in\n",
-      "order to use the function `func` with the following command"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "import spectra_utils\n",
-      "a = spectra_utils.func(param1, param2, ...)\n",
+      "order to use the function `func` with the following command\n",
+      "\n",
+      "```import spectra_utils\n",
+      "a = spectra_utils.func(param1, param2, ...)```\n",
       "\n",
       "Alternatively, you can import just one (or a few) of many different functions\n",
       "that are defined in your file ``spectra_utils.py``:\n",
       "\n",
-      "from spectra_utils import func\n",
-      "a = func(param1, param2, ...)"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": []
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
+      "```from spectra_utils import func\n",
+      "a = func(param1, param2, ...)```\n",
+      "\n",
       "You will recognize that python does not make a difference between modules that come\n",
       "with python (e.g. `glob`), external modules (e.g. `numpy` or `astropy`) and modules\n",
       "that you write yourself. The syntax to import those modules or functions\n",
@@ -291,7 +287,7 @@
       "this function is fairly short, we still add some documentation to the header,\n",
       "so that we can look up what parameters it needs when we come back to this\n",
       "project a while later. Personally, I comment every function that is longer\n",
-      "than two lines"
+      "than two lines."
      ]
     },
     {
@@ -346,7 +342,7 @@
      "metadata": {},
      "source": [
       "Try to find out how you can read the help for this function from the\n",
-      "command line"
+      "command line."
      ]
     },
     {
@@ -407,7 +403,7 @@
       "\n",
       "# Let's just print the setup on the screen\n",
       "# We'll see if it's all the same.\n",
-      "    for f in filelist:\n",
+      "for f in filelist:\n",
       "    print read_setup(f)"
      ],
      "language": "python",
@@ -435,9 +431,9 @@
       "date = np.zeros((len(filelist)), dtype = 'S23')\n",
       "\n",
       "for i, fname in enumerate(filelist):\n",
-      "w, f, date_obs = read_spec(fname)\n",
-      "flux[i,:] = f\n",
-      "date[i] = date_obs"
+      "    w, f, date_obs = read_spec(fname)\n",
+      "    flux[i,:] = f\n",
+      "    date[i] = date_obs"
      ],
      "language": "python",
      "metadata": {},
@@ -465,7 +461,7 @@
       "Furthermore,\n",
       "[`astropy.constants`](http://docs.astropy.org/en/stable/constants/index.html)  supplies the values of\n",
       "many physical and astronomical constants.\n",
-      "The easiest way to attach a unit to a number is by multiplication"
+      "The easiest way to attach a unit to a number is by multiplication."
      ]
     },
     {
@@ -505,7 +501,7 @@
       "we will be looking for signatures of accretion. We expect those accretion\n",
       "signatures to appear close to the free-fall velocity v that a mass m reaches, when\n",
       "it hits the stellar surface. We can calculate the infall speed using simple\n",
-      "energy conservation"
+      "energy conservation."
      ]
     },
     {
@@ -520,7 +516,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "So, let us calculate the free-fall velocity for MN Lup"
+      "So, let us calculate the free-fall velocity for MN Lup."
      ]
     },
     {
@@ -532,7 +528,8 @@
       "# Maybe astronomers prefer it in the traditional cgs system?\n",
       "print v_accr.cgs\n",
       "# Or in some really obscure unit?\n",
-      "print v_accr.to(u.mile / u.hour)"
+      "from astropy.units import imperial\n",
+      "print v_accr.to(imperial / u.hour)"
      ],
      "language": "python",
      "metadata": {},
@@ -561,7 +558,7 @@
      "metadata": {},
      "source": [
       "Oh, what is that? The seconds are gone, but ``astropy.quantity`` objects keep\n",
-      "their different length units unless told otherwise"
+      "their different length units unless told otherwise."
      ]
     },
     {
@@ -584,7 +581,7 @@
       "shorten this to \"1/s\".\n",
       "\n",
       "We can now use the ``astropy.units`` mechanism to correct the wavelength\n",
-      "scale to the heliocentric velocity scale"
+      "scale to the heliocentric velocity scale."
      ]
     },
     {
@@ -598,7 +595,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Naively, we could try"
+      "Naively, we could try:"
      ]
     },
     {
@@ -621,7 +618,7 @@
       "units of  ``heliocentric/c`` and after that add ``1.``?\n",
       "There are several ways to make the instruction precise,\n",
       "but one is to explicitly add ``u.dimensionless_unscaled`` to ``1.``\n",
-      "to tell astropy that this number is dimensionless and does not carry any scaling"
+      "to tell astropy that this number is dimensionless and does not carry any scaling."
      ]
     },
     {
@@ -643,7 +640,7 @@
       "more): The ability to convert the spectral axis to frequencies or energies.\n",
       "Normally, a unit of length is not equivalent to a unit of energy or to a\n",
       "frequency, but this conversion makes sense for the wavelength of a spectrum.\n",
-      "This is how it can be done"
+      "This is how it can be done:"
      ]
     },
     {
@@ -678,7 +675,7 @@
       "Calculate $\\log(g)$ for MN Lup with the values for the mass\n",
       "and radius given above. Those values were determined from\n",
       "evolutionary tracks. Check if the $\\log(g)$ is consistent\n",
-      "with the value expected from spectroscopy"
+      "with the value expected from spectroscopy."
      ]
     },
     {
@@ -686,14 +683,14 @@
      "metadata": {},
      "source": [
       "The values from evolutionary tracks are indeed consistent with the\n",
-      "spectroscopically estimated surface gravity"
+      "spectroscopically estimated surface gravity."
      ]
     },
     {
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "print np.log10((G*M_MN_Lup/R_MN_Lup**2).cgs)"
+      "print np.log10((G*M_MN_Lup/R_MN_Lup**2)/u.grams)"
      ],
      "language": "python",
      "metadata": {},
@@ -715,35 +712,16 @@
       "We want to input a wavelengths array and the rest wavelength of a spectral\n",
       "line. We need this function later to show the red- and blueshift of the\n",
       "spectrum relative to the the Ca II H line. Use the following definition\n",
-      "to make sure the that code below can use it later"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "def wave2doppler(wavelength_array, wavelength_line):\n",
-      "    .. do something ..\n",
-      "    return array_of_dopplershifts"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": []
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
+      "to make sure the that code below can use it later.\n",
       "You can test if you function works by calculating the a Dopplershift\n",
-      "of the following wavelengths relative to $H_\\alpha$"
+      "of the following wavelengths relative to $H_\\alpha$."
      ]
     },
     {
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "waveclosetoHa = np.array([6562.,6563,6565.]) * u.AA\n",
-      "print wave2doppler(waveclosetoHa, 656.489 * u.nm)"
+      "waveclosetoHa = np.array([6562.,6563,6565.]) * u.AA"
      ],
      "language": "python",
      "metadata": {},
@@ -753,7 +731,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "I get -132, -86 and +5 km/s"
+      "I get -132, -86 and +5 km/s."
      ]
     },
     {
@@ -767,7 +745,7 @@
       "    w_equiv = w.to(u.km/u.s, equivalencies=w0_equiv)\n",
       "    return w_equiv\n",
       "\n",
-      "print wave2doppler(waveclosetoHa, 656.489 * u.nm).decompose()"
+      "print wave2doppler(waveclosetoHa, 656.489 * u.nm).to(u.km/u.s)"
      ],
      "language": "python",
      "metadata": {},
@@ -792,7 +770,7 @@
       "the resulting velocity in units of vsini.\n",
       "We need this function later to show the red- and blueshift of the\n",
       "spectrum relative to the Ca II H line. Use the following definition\n",
-      "to make sure the that code below can use it later"
+      "to make sure the that code below can use it later."
      ]
     },
     {
@@ -800,7 +778,7 @@
      "collapsed": false,
      "input": [
       "def w2vsini(wavelength_array, wavelength_line):\n",
-      "    .. do something ..\n",
+      "    # .. replace this with your implementation ..\n",
       "    return array_of_shifts_in_vsini"
      ],
      "language": "python",
@@ -839,7 +817,7 @@
       "``astropy.time.Time`` will parse many common input formats (strings, floats), but\n",
       "unless the format is unambiguous the format needs to be specified (e.g. a number\n",
       "could mean JD or MJD or year). Also, the time system needs to be given (e.g. UTC).\n",
-      "Below are several examples, initialized from different header keywords"
+      "Below are several examples, initialized from different header keywords."
      ]
     },
     {
@@ -858,7 +836,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Times can be expressed in different formats"
+      "Times can be expressed in different formats."
      ]
     },
     {
@@ -877,7 +855,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "or be converted to a different time system"
+      "or be converted to a different time system."
      ]
     },
     {
@@ -894,7 +872,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Times can also be initialized from arrays and we can calculate time differences"
+      "Times can also be initialized from arrays and we can calculate time differences."
      ]
     },
     {
@@ -915,7 +893,7 @@
       "Now, we want to express the time difference between the individual spectra of\n",
       "MN Lup in rotational periods. While the unit of ``delta_t`` is days, unfortunately\n",
       "``astropy.time.Time`` and ``astropy.units.Quantity`` objects do not work together\n",
-      "yet, so we will have to convert from one to the other explicitly"
+      "yet, so we will have to convert from one to the other explicitly."
      ]
     },
     {
@@ -956,7 +934,7 @@
       "``[3938*u.AA, 3945*u.AA]`` seem right for that. Then, we normalize the flux by\n",
       "this polynomial.\n",
       "\n",
-      "The following function will do that"
+      "The following function will do that:"
      ]
     },
     {
@@ -1019,7 +997,7 @@
      "metadata": {},
      "source": [
       "We will calculate the equivalent width in Angstroms of the emission line\n",
-      "for the first spectrum"
+      "for the first spectrum."
      ]
     },
     {
@@ -1038,7 +1016,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Using ``numpy`` array notation we can actually process all spectra at once"
+      "Using ``numpy`` array notation we can actually process all spectra at once."
      ]
     },
     {
@@ -1061,7 +1039,7 @@
       "we first collect all the columns and make an ``astropy.table.Table`` object. (Please\n",
       "check [`astropy.table`](http://docs.astropy.org/en/stable/table/index.html)\n",
       "or `tabular-data` for more\n",
-      "details on ``Table``). So, here is the code"
+      "details on ``Table``). So, here is the code:"
      ]
     },
     {
@@ -1111,7 +1089,7 @@
      "source": [
       "In both cases we want the x-axis to show the Doppler shift expressed in units\n",
       "of the rotational velocity. In this way, features that are rotationally\n",
-      "modulated will stick out between -1 and +1"
+      "modulated will stick out between -1 and +1."
      ]
     },
     {
@@ -1128,7 +1106,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "First, we will show the line profile"
+      "First, we will show the line profile."
      ]
     },
     {
@@ -1177,7 +1155,7 @@
      "metadata": {},
      "source": [
       "There are clearly several ways to produce a well looking plot. Here is one\n",
-      "way"
+      "way."
      ]
     },
     {
@@ -1213,7 +1191,7 @@
      "metadata": {},
      "source": [
       "Next, we will make a more advanced plot. For each spectrum we calculate\n",
-      "the difference to the mean flux"
+      "the difference to the mean flux."
      ]
     },
     {
@@ -1233,7 +1211,7 @@
      "source": [
       "In the following simple plot, we can already see features moving through the line.\n",
       "However, the axis scales are not right, the gap between both nights is not visible\n",
-      "and there is no proper labeling"
+      "and there is no proper labeling."
      ]
     },
     {
@@ -1254,7 +1232,7 @@
      "source": [
       "In the following, we will plot the spectra from both nights separately.\n",
       "Also, we will pass the ``extent`` keyword to ``ax.imshow`` which takes care\n",
-      "of the axis"
+      "of the axis."
      ]
     },
     {
@@ -1292,7 +1270,7 @@
       "* Use a gray scale instead of color to save publication charges.\n",
       "* Add labels to the axis.\n",
       "\n",
-      "The following code addresses these points"
+      "The following code addresses these points."
      ]
     },
     {
@@ -1404,7 +1382,7 @@
       "\n",
       "Here is a practical example.\n",
       "Above we calculated the free-fall\n",
-      "velocity onto MN Lup like this"
+      "velocity onto MN Lup like this."
      ]
     },
     {
@@ -1421,7 +1399,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Mathematically, the following statement is equivalent"
+      "Mathematically, the following statement is equivalent:"
      ]
     },
     {

From 094b1b1afb6dc6f0d312c3dfd1130a786ecadea2 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 25 Aug 2014 11:08:19 -0400
Subject: [PATCH 20/27] Add short description to metadata dictionary

---
 tutorials/UVES/UVES.ipynb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 13c8d7e74..f2dc4ca5e 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -5,7 +5,8 @@
    "date": "May 2014",
    "link_name": "Analyzing UVES Spectroscopy with Astropy",
    "name": "",
-   "published": true
+   "published": true,
+   "description" : "This tutorial demonstrates the data analysis of MN Lup obtained with the UVES spectrograph on the VLT."
   },
   "signature": "sha256:1f74796dfdd5b13d06d2a9bd9913a15fe6aa475e7967f8bd969ddcf17fb1e825"
  },

From 25765a828a367f6cf6268b235f2043f98e6cb0e8 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 25 Aug 2014 11:27:40 -0400
Subject: [PATCH 21/27] Update date and copyright notice

---
 tutorials/UVES/UVES.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index f2dc4ca5e..d75492ec5 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -2,7 +2,7 @@
  "metadata": {
   "astropy-tutorials": {
    "author": "Hans Moritz G\u00fcnther <hguenther@cfa.harvard.edu>, Miguel de Val-Borro <valborro@princeton.edu>",
-   "date": "May 2014",
+   "date": "August 2014",
    "link_name": "Analyzing UVES Spectroscopy with Astropy",
    "name": "",
    "published": true,
@@ -40,7 +40,7 @@
       "\n",
       "Authors: Moritz Guenther\n",
       "\n",
-      "Copyright: 2013 Moritz Guenther\n",
+      "Copyright: 2013, 2014 Moritz Guenther\n",
       "\n",
       "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",
       "under program ID 087.V0991(A)."

From 5977e5ab439809fba17adaeeccbbc44e2789a6f7 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 25 Aug 2014 11:35:17 -0400
Subject: [PATCH 22/27] Replace print statement by function

---
 tutorials/UVES/UVES.ipynb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index d75492ec5..b4701d3d8 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -405,7 +405,7 @@
       "# Let's just print the setup on the screen\n",
       "# We'll see if it's all the same.\n",
       "for f in filelist:\n",
-      "    print read_setup(f)"
+      "    print(read_setup(f))"
      ],
      "language": "python",
      "metadata": {},
@@ -525,12 +525,12 @@
      "collapsed": false,
      "input": [
       "v_accr = (2.* G * M_MN_Lup/R_MN_Lup)**0.5 \n",
-      "print v_accr\n",
+      "print(v_accr)\n",
       "# Maybe astronomers prefer it in the traditional cgs system?\n",
-      "print v_accr.cgs\n",
+      "print(v_accr.cgs)\n",
       "# Or in some really obscure unit?\n",
       "from astropy.units import imperial\n",
-      "print v_accr.to(imperial / u.hour)"
+      "print(v_accr.to(imperial / u.hour))"
      ],
      "language": "python",
      "metadata": {},
@@ -691,7 +691,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "print np.log10((G*M_MN_Lup/R_MN_Lup**2)/u.grams)"
+      "print(np.log10((G*M_MN_Lup/R_MN_Lup**2)/u.grams))"
      ],
      "language": "python",
      "metadata": {},
@@ -746,7 +746,7 @@
       "    w_equiv = w.to(u.km/u.s, equivalencies=w0_equiv)\n",
       "    return w_equiv\n",
       "\n",
-      "print wave2doppler(waveclosetoHa, 656.489 * u.nm).to(u.km/u.s)"
+      "print(wave2doppler(waveclosetoHa, 656.489 * u.nm).to(u.km/u.s))"
      ],
      "language": "python",
      "metadata": {},
@@ -1007,7 +1007,7 @@
      "input": [
       "ew = fcaII[0,:] - 1.\n",
       "ew = ew[:-1] * np.diff(wcaII.to(u.AA).value)\n",
-      "print ew.sum()"
+      "print(ew.sum())"
      ],
      "language": "python",
      "metadata": {},

From 0a3443f2a1a0abc43a27f65b25ee8ea531211857 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 25 Aug 2014 11:37:48 -0400
Subject: [PATCH 23/27] Remove remaining rst syntax

---
 tutorials/UVES/UVES.ipynb | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index b4701d3d8..5ed22b246 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -1124,11 +1124,7 @@
       "ax.set_ylabel('flux')\n",
       "ax.set_title('Ca II H line in MN Lup')\n",
       "# when using this interface, we need to explicitly call the draw routine\n",
-      "plt.draw()\n",
-      "\n",
-      ".. image:: CaII-lines-one.png\n",
-      ":scale: 100%\n",
-      ":align: center"
+      "plt.draw()"
      ],
      "language": "python",
      "metadata": {},

From 8c065af517e983f70906de179a9bb6f0c5fd09db Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Mon, 25 Aug 2014 12:21:01 -0400
Subject: [PATCH 24/27] Correct errors uncovered by `python prepare_deploy.py
 run convert`

---
 tutorials/UVES/UVES.ipynb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 5ed22b246..307a54387 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -530,7 +530,7 @@
       "print(v_accr.cgs)\n",
       "# Or in some really obscure unit?\n",
       "from astropy.units import imperial\n",
-      "print(v_accr.to(imperial / u.hour))"
+      "print(v_accr.to(imperial.yd / u.hour))"
      ],
      "language": "python",
      "metadata": {},
@@ -691,7 +691,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "print(np.log10((G*M_MN_Lup/R_MN_Lup**2)/u.grams))"
+      "print(np.log10((G*M_MN_Lup/R_MN_Lup**2)/u.cm*u.second**2))"
      ],
      "language": "python",
      "metadata": {},
@@ -901,7 +901,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "delta_p = delta_t.val * u.day / period"
+      "delta_p = delta_t.value * u.day / period"
      ],
      "language": "python",
      "metadata": {},
@@ -964,13 +964,13 @@
       "    f = np.zeros((flux.shape[0], indrange.sum()))\n",
       "    for i in range(flux.shape[0]):\n",
       "# fit polynomial of second order to the continuum region\n",
-      "    linecoeff = np.polyfit(w[indcont], flux[i, indcont],2)\n",
+      "        linecoeff = np.polyfit(w[indcont], flux[i, indcont],2)\n",
       "# divide the flux by the polynomial and put the result in our\n",
       "# new flux array\n",
-      "    f[i,:] = flux[i,indrange]/np.polyval(linecoeff, w[indrange])\n",
+      "        f[i,:] = flux[i,indrange]/np.polyval(linecoeff, w[indrange])\n",
       "    return w[indrange], f\n",
       "\n",
-      "    wcaII, fcaII = region_around_line(wavelength, flux,\n",
+      "wcaII, fcaII = region_around_line(wavelength, flux,\n",
       "    [[3925*u.AA, 3930*u.AA],[3938*u.AA, 3945*u.AA]])"
      ],
      "language": "python",
@@ -1052,7 +1052,7 @@
       "\n",
       "datecol = Column(name = 'Obs Date', data = date)\n",
       "pcol = Column(name = 'phase', data = delta_p, format = '{:.1f}')\n",
-      "ewcol = Column(name = 'EW', data = ew, format = '{:.1f}', units = '\\\\AA')\n",
+      "ewcol = Column(name = 'EW', data = ew, format = '{:.1f}', unit = '\\\\AA')\n",
       "tab = Table((datecol, pcol, ewcol))\n",
       "# latexdicts['AA'] contains the style specifics for A&A (\\hline etc.)\n",
       "tab.write('EWtab.tex', latexdict = ascii.latexdicts['AA'])"

From 8c7785c81a81e7ad01b03e7d81b524697145e55b Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sat, 6 Sep 2014 16:31:25 -0400
Subject: [PATCH 25/27] Update ApJ paper reference

---
 tutorials/UVES/UVES.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 307a54387..ecfd6e913 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -54,7 +54,7 @@
       "below is taken (with only minor modifications) from the code that I used to\n",
       "actually prepare the publication. The plots that will be developed below\n",
       "appear in very similar form in the article published in\n",
-      "[ApJ, Volume 771, Issue 1, article id. 70, 12 pp](http://adsabs.harvard.edu/abs/2013ApJ...771...70G).\n",
+      "[ApJ, 771, 1, 70](http://adsabs.harvard.edu/abs/2013ApJ...771...70G).\n",
       "\n",
       "The examples below depend on each other and the plots in the last section make\n",
       "use of things calculated in the earlier sections. Thus, if you need to restart\n",

From c474abcbf3ac023f6ba58bd31cb2bcb63011ba5e Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sun, 7 Sep 2014 18:14:03 -0400
Subject: [PATCH 26/27] Updated author list

---
 tutorials/UVES/UVES.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index ecfd6e913..10beb7fff 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -38,9 +38,9 @@
       "License: This tutorial is made available under the terms of the\n",
       "[Creative Commons Attribution 3.0 License](http://creativecommons.org/licenses/by/3.0/)\n",
       "\n",
-      "Authors: Moritz Guenther\n",
+      "Authors: Moritz Guenther, Miguel de Val-Borro\n",
       "\n",
-      "Copyright: 2013, 2014 Moritz Guenther\n",
+      "Copyright: 2013, 2014 Moritz Guenther, Miguel de Val-Borro\n",
       "\n",
       "Based on observations made with ESO Telescopes at the La Silla Paranal Observatory\n",
       "under program ID 087.V0991(A)."

From eab6067d50dbb53501544f3353676150cfaff785 Mon Sep 17 00:00:00 2001
From: Miguel de Val-Borro <miguel.deval@gmail.com>
Date: Sat, 13 Sep 2014 15:48:07 -0400
Subject: [PATCH 27/27] Change url variable to the updated UVES data

* Switching to data.astropy.org
---
 tutorials/UVES/UVES.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/UVES/UVES.ipynb b/tutorials/UVES/UVES.ipynb
index 10beb7fff..745b66821 100644
--- a/tutorials/UVES/UVES.ipynb
+++ b/tutorials/UVES/UVES.ipynb
@@ -93,7 +93,7 @@
      "input": [
       "import tarfile\n",
       "from astropy.utils.data import download_file\n",
-      "url = 'http://python4astronomers.github.io/_downloads/astropy_UVES.tar.gz'\n",
+      "url = 'http://data.astropy.org/tutorials/UVES/data_UVES.tar.gz'\n",
       "f = tarfile.open(download_file(url, cache=True), mode='r|*')\n",
       "location_for_data_file = '.'  # CHANGE TO WHEREVER YOU WANT THE DATA TO BE EXTRACTED\n",
       "f.extractall(path=location_for_data_file)"