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  {
   "cell_type": "markdown",
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   "source": [
    "# Interactively fit Brown Dwarf Spectra with the `gollum` dashboard\n",
    "\n",
    "In this tutorial we will see how the spectra of brown dwarfs vary as a function of their intrinsic properties.  We will fit observed spectra of a particular brown dwarf with the gollum dashboard, a dashboard which fits models based on properties including [effective temperature](https://en.wikipedia.org/wiki/Effective_temperature), [surface gravity](https://en.wikipedia.org/wiki/Surface_gravity), [metallicity](https://en.wikipedia.org/wiki/Metallicity), [rotational broadening](https://phys.libretexts.org/Bookshelves/Astronomy__Cosmology/Stellar_Atmospheres_(Tatum)/10%3A_Line_Profiles/10.06%3A_Rotational_Broadening), and [radial velocity](https://en.wikipedia.org/wiki/Radial_velocity#:~:text=The%20radial%20velocity%20of%20an,the%20point%20and%20the%20object.). The fitting for this tutorial will be based on the Sonora-Bobcat 2021 models, which takes into account effective temperature, surface gravity, and metallicity as intrinsic values."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9e54e2c6",
   "metadata": {},
   "outputs": [],
   "source": [
    "from gollum.sonora import SonoraGrid\n",
    "from specutils import Spectrum1D\n",
    "import pandas as pd\n",
    "import astropy.units as u"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ff4fbe7a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import HTML\n",
    "from IPython.display import Image"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7276493f",
   "metadata": {},
   "source": [
    "First, we will read in an example spectrum of this [ultracool dwarf](https://en.wikipedia.org/wiki/Ultra-cool_dwarf):  \n",
    "\n",
    "[2MASS J05591914-1404488](http://simbad.u-strasbg.fr/simbad/sim-id?Ident=2MASS+J05591914-1404488&NbIdent=1&Radius=2&Radius.unit=arcmin&submit=submit+id)\n",
    "\n",
    "We got its data from the Keck Telescope's [NIRSPEC spectrograph](https://www2.keck.hawaii.edu/inst/nirspec/). A specific section of this data is displayed below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "aaa230b5",
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('../../data/2mass0559_59.dat', \n",
    "                 delim_whitespace=True, \n",
    "                 comment='#', \n",
    "                 names=['wave', 'flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c0af6965",
   "metadata": {},
   "outputs": [],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7689e1b6",
   "metadata": {},
   "source": [
    "The unit for wavelength here is [microns](https://en.wikipedia.org/wiki/Micrometre) and the unit for flux is \"counts\"."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b0385025",
   "metadata": {},
   "outputs": [],
   "source": [
    "bdss_spectrum = Spectrum1D(spectral_axis=df.wave.values*u.micron, \n",
    "                           flux=df.flux.values*u.ct)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "761b08e9",
   "metadata": {},
   "outputs": [],
   "source": [
    "wl_lo, wl_hi = (bdss_spectrum.wavelength.value.min(), \n",
    "                bdss_spectrum.wavelength.value.max())"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "af70bb92",
   "metadata": {},
   "source": [
    "Next, we can read in the Sonora-Bobcat grid and show an interactive dashboard.  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2d297a2a",
   "metadata": {},
   "outputs": [],
   "source": [
    "grid = SonoraGrid(wl_lo=wl_lo, wl_hi=wl_hi)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fb6d9cf1",
   "metadata": {},
   "source": [
    "Awesome!  Now you can hand-in a data spectrum to overlay it onto the grid and begin fitting using the interactive sliders."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d25f222c",
   "metadata": {},
   "outputs": [],
   "source": [
    "grid.show_dashboard(data=bdss_spectrum, show_telluric=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dc73cf85",
   "metadata": {},
   "source": [
    "![dashboard demo](https://user-images.githubusercontent.com/98151293/167173097-31427d83-f7fc-4146-a520-34e6b97b3b1b.gif)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a1f1bf1e",
   "metadata": {},
   "source": [
    "The dashboard looks great!"
   ]
  }
 ],
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