SEDSIMPLE Tutorial.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Using SEDkit with SIMPLE\n",
    "\n",
    "This notebook will walk you through an example of how you can use the sedsimple.py package to use SEDkit with data loaded from the SIMPLE database.\n",
    "\n",
    "## Requirements\n",
    "\n",
    "You must have sedsimple.py in the current working directory (or in your python path) for imports to properly work. You will also need a copy of the SIMPLE database. This is most easily done with the binary file available at https://github.com/SIMPLE-AstroDB/SIMPLE-binary. You will also need to have SEDkit and AstrodbKit2 installed. See https://github.com/dr-rodriguez/SEDkitSIMPLE for more details."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from astropy.table import Table\n",
    "from sedsimple import SEDSIMPLE\n",
    "from astrodbkit.astrodb import Database"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Initialization\n",
    "\n",
    "The first step you need to do is to establish a connection to the SIMPLE database. If you have it in your current working directory it's as easy as:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "db = Database('sqlite:///SIMPLE.sqlite')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Refer to the AstrodbKit2 documentation at https://astrodbkit2.readthedocs.io/en/latest/ if you want more information on what you can do with the database. For now, we'll move into establishing an SED object that includes data from SIMPLE."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[sedkit] SED initialized\n",
      "[sedkit] Setting name to 'Trappist-1'\n",
      "[sedkit] 1 record for Trappist-1 found in Simbad.\n",
      "[sedkit] Setting sky_coords to <SkyCoord (ICRS): (ra, dec) in deg\n",
      "    (23.10815789, -5.04139917)>\n",
      "Response received from server:\n",
      "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2 Final//EN\">\n",
      "<title>500 Internal Server Error</title>\n",
      "<h1>Internal Server Error</h1>\n",
      "<p>The server encountered an internal error and was unable to complete your request.  Either the server is overloaded or there is an error in the application.</p>\n",
      "\n",
      "[sedkit] There was a problem determining the interstellar reddening. Setting to 0. You can manually set this with the 'reddening' attribute.\n",
      "[sedkit] Setting parallax to (<Quantity 80.2123 mas>, <Quantity 0.0716 mas>) with reference '2020yCat.1350....0G'\n",
      "[sedkit] Setting distance to (<Quantity 12.47 pc>, <Quantity 0.01 pc>, <Quantity 0.01 pc>) with reference '2020yCat.1350....0G'\n",
      "Response received from server:\n",
      "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2 Final//EN\">\n",
      "<title>500 Internal Server Error</title>\n",
      "<h1>Internal Server Error</h1>\n",
      "<p>The server encountered an internal error and was unable to complete your request.  Either the server is overloaded or there is an error in the application.</p>\n",
      "\n",
      "[sedkit] There was a problem determining the interstellar reddening. Setting to 0. You can manually set this with the 'reddening' attribute.\n",
      "[sedkit] Setting spectral_type to (67.5, 0.5, 'V', None, None) with reference '2000AJ....120.1085G'\n",
      "[SIMPLE] Trappist-1 matched to 2MASS J23062928-0502285 in the database\n",
      "[SIMPLE] Target name Trappist-1 resolved to 2MASS J23062928-0502285 in database.\n",
      "[SIMPLE] Autoloading information from database\n",
      "[sedkit] Setting sky_coords to <SkyCoord (ICRS): (ra, dec) in deg\n",
      "    (346.62201, -5.041274)>\n",
      "Response received from server:\n",
      "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2 Final//EN\">\n",
      "<title>500 Internal Server Error</title>\n",
      "<h1>Internal Server Error</h1>\n",
      "<p>The server encountered an internal error and was unable to complete your request.  Either the server is overloaded or there is an error in the application.</p>\n",
      "\n",
      "[sedkit] There was a problem determining the interstellar reddening. Setting to 0. You can manually set this with the 'reddening' attribute.\n",
      "[SIMPLE] 3 parallaxes found. Attempting to load adopted one...\n",
      "[sedkit] Setting parallax to (<Quantity 80.21231613 mas>, <Quantity 0.07160574 mas>) with reference '2021A&A...649A...1G'\n",
      "[sedkit] Setting distance to (<Quantity 12.47 pc>, <Quantity 0.01 pc>, <Quantity 0.01 pc>) with reference '2021A&A...649A...1G'\n",
      "Response received from server:\n",
      "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2 Final//EN\">\n",
      "<title>500 Internal Server Error</title>\n",
      "<h1>Internal Server Error</h1>\n",
      "<p>The server encountered an internal error and was unable to complete your request.  Either the server is overloaded or there is an error in the application.</p>\n",
      "\n",
      "[sedkit] There was a problem determining the interstellar reddening. Setting to 0. You can manually set this with the 'reddening' attribute.\n",
      "[SIMPLE] 18 photometry values found. Attempting to load...\n",
      "[sedkit] Setting 2MASS.H photometry to 10.718 (0.021) with reference '2003tmc..book.....C'\n",
      "[sedkit] Setting 2MASS.J photometry to 11.354 (0.022) with reference '2003tmc..book.....C'\n",
      "[sedkit] Setting 2MASS.Ks photometry to 10.296 (0.023) with reference '2003tmc..book.....C'\n",
      "[sedkit] Setting Cousins.I photometry to 14.024 (0.115) with reference '2006AJ....132.1234C'\n",
      "[sedkit] Setting Cousins.R photometry to 16.466 (0.065) with reference '2006AJ....132.1234C'\n",
      "[sedkit] Setting Gaia.G photometry to 15.645 (0.001) with reference '2018A&A...616A...1G'\n",
      "[sedkit] Setting Gaia.rp photometry to 14.097 (0.009) with reference '2018A&A...616A...1G'\n",
      "[sedkit] Setting Gaia.G photometry to 15.623 (0.001) with reference '2021A&A...649A...1G'\n",
      "[sedkit] Setting Gaia.rp photometry to 14.104 (0.002) with reference '2021A&A...649A...1G'\n",
      "[sedkit] Setting Johnson.V photometry to 18.798 (0.082) with reference '2006AJ....132.1234C'\n",
      "[sedkit] Setting WFCAM.H photometry to 10.775 (0.023) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WFCAM.J photometry to 11.319 (0.022) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WFCAM.K photometry to 10.269 (0.023) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WFCAM.Y photometry to 12.098 (0.055) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WISE.W1 photometry to 10.042 (0.023) with reference '2012yCat.2311....0C'\n",
      "[sedkit] Setting WISE.W2 photometry to 9.799 (0.020) with reference '2012yCat.2311....0C'\n",
      "[sedkit] Setting WISE.W3 photometry to 9.528 (0.041) with reference '2012yCat.2311....0C'\n",
      "[sedkit] Setting WISE.W4 photometry to 8.397 (nan) with reference '2012yCat.2311....0C'\n",
      "[SIMPLE] 2 spectral types found. Attempting to load adopted one...\n",
      "[SIMPLE] 2 spectra found. Attempting to load...\n",
      "[sedkit] Spectrum 'New Spectrum' added with reference '2018AJ....155...34C'\n",
      "[sedkit] Spectrum 'New Spectrum' added with reference '2007AJ....133..439C'\n"
     ]
    }
   ],
   "source": [
    "sed = SEDSIMPLE(db, 'Trappist-1', auto_db=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The SEDSIMPLE Class inherits from SEDkit's SED Class and as such can do everything already implemented. It adds a few extra methods for loading data, which are automatically called if `auto_db=True` is set. \n",
    "You may notice above some messages with `[sedkit]` and `[SIMPLE]`. The former come from the original code, while the later come from this implementation. Let's walk through what happened."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Walkthrough\n",
    "\n",
    "The first thing that SEDSIMPLE does, regardless of whether you have `auto_db` set, is to check the provided name against the database. In this case, Trappist-1 is known as 2MASS J23062928-0502285 in the database. For convenience, this name and the inventory of data is stored in the SEDSIMPLE object:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2MASS J23062928-0502285\n"
     ]
    }
   ],
   "source": [
    "print(sed.db_source)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "=========================\n",
      "Sources\n",
      "         source             ra       dec    ... other_references comments\n",
      "----------------------- --------- --------- ... ---------------- --------\n",
      "2MASS J23062928-0502285 346.62201 -5.041274 ...             None     None\n",
      "=========================\n",
      "ModeledParameters\n",
      "parameter value  value_error  unit comments reference\n",
      "--------- ------ ----------- ----- -------- ---------\n",
      "    T eff 2557.0        64.0     K     None    Fili15\n",
      "    log g   5.22        0.08   dex     None    Fili15\n",
      "     mass  86.07        9.28 M_jup     None    Fili15\n",
      "   radius   1.14        0.04 R_jup     None    Fili15\n",
      "=========================\n",
      "Names\n",
      "          other_name         \n",
      "-----------------------------\n",
      "      2MASS J23062928-0502285\n",
      " Gaia DR2 2635476908753563008\n",
      "Gaia EDR3 2635476908753563008\n",
      "                   Trappist-1\n",
      "=========================\n",
      "Parallaxes\n",
      "     parallax        parallax_error   adopted comments reference\n",
      "----------------- ------------------- ------- -------- ---------\n",
      "            78.76                1.04   False     None    Bart17\n",
      "80.45124261077767 0.12107673660785581   False     None   GaiaDR2\n",
      "80.21231612635748 0.07160574197769165    True     None  GaiaEDR3\n",
      "=========================\n",
      "Photometry\n",
      "   band       magnitude      ... reference\n",
      "--------- ------------------ ... ---------\n",
      "  2MASS.H             10.718 ...    Cutr03\n",
      "  2MASS.J             11.354 ...    Cutr03\n",
      " 2MASS.Ks             10.296 ...    Cutr03\n",
      "Cousins.I             14.024 ...    Cost06\n",
      "Cousins.R             16.466 ...    Cost06\n",
      "  GAIA2.G 15.645121574401855 ...   GaiaDR2\n",
      "GAIA2.Grp 14.096701622009277 ...   GaiaDR2\n",
      "  GAIA3.G 15.622553825378418 ...  GaiaEDR3\n",
      "GAIA3.Grp 14.103951454162598 ...  GaiaEDR3\n",
      "Johnson.V             18.798 ...    Cost06\n",
      "  WFCAM.H             10.775 ... Best20.42\n",
      "  WFCAM.J             11.319 ... Best20.42\n",
      "  WFCAM.K             10.269 ... Best20.42\n",
      "  WFCAM.Y             12.098 ... Best20.42\n",
      "  WISE.W1             10.042 ...    Cutr12\n",
      "  WISE.W2              9.799 ...    Cutr12\n",
      "  WISE.W3              9.528 ...    Cutr12\n",
      "  WISE.W4              8.397 ...    Cutr12\n",
      "=========================\n",
      "ProperMotions\n",
      "      mu_ra           mu_ra_error            mu_dec       ... comments reference\n",
      "----------------- ------------------- ------------------- ... -------- ---------\n",
      "930.8785357703113 0.24656444455477666 -479.40341833983086 ...     None   GaiaDR2\n",
      "930.7875225817781 0.08676905184984207  -479.0375409528857 ...     None  GaiaEDR3\n",
      "           922.02                0.61             -461.88 ...     None    Wein16\n",
      "=========================\n",
      "RadialVelocities\n",
      "radial_velocity_km_s radial_velocity_error_km_s adopted comments reference\n",
      "-------------------- -------------------------- ------- -------- ---------\n",
      "               -52.0                       0.13    None     None    Jons20\n",
      "=========================\n",
      "Spectra\n",
      "                      access_url                      ... other_references\n",
      "----------------------------------------------------- ... ----------------\n",
      "https://s3.amazonaws.com/bdnyc/SpeX/Prism/U12171.fits ...             None\n",
      "    https://s3.amazonaws.com/bdnyc/RCspec/U12171.fits ...             None\n",
      "=========================\n",
      "SpectralTypes\n",
      "spectral_type_string spectral_type_code ... comments reference\n",
      "-------------------- ------------------ ... -------- ---------\n",
      "                M7.5               67.5 ...     None    Gizi00\n",
      "                  M8               68.0 ...     None    Gill16\n"
     ]
    }
   ],
   "source": [
    "# Browse inventory; converting to Astropy Table for easier reading\n",
    "for key, tab in sed.inventory.items():\n",
    "    print('=========================')\n",
    "    print(key)\n",
    "    print(Table(tab))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "At any point, you can refer to the data by accessing the inventory and providing the table name. The default format is a list of dictionary entries."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[{'spectral_type_string': 'M7.5', 'spectral_type_code': 67.5, 'spectral_type_error': None, 'regime': 'optical', 'adopted': None, 'photometric': None, 'comments': None, 'reference': 'Gizi00'}, {'spectral_type_string': 'M8', 'spectral_type_code': 68.0, 'spectral_type_error': None, 'regime': 'nir', 'adopted': None, 'photometric': None, 'comments': None, 'reference': 'Gill16'}]\n"
     ]
    }
   ],
   "source": [
    "print(sed.inventory['SpectralTypes'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "When `auto_db` is set, SEDSIMPLE calls several methods that each load specific information. We'll call them again one by one here.\n",
    "\n",
    "First, we'll load coordinates, which uses information from the Sources table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[sedkit] Setting sky_coords to <SkyCoord (ICRS): (ra, dec) in deg\n",
      "    (346.62201, -5.041274)>\n",
      "Response received from server:\n",
      "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2 Final//EN\">\n",
      "<title>500 Internal Server Error</title>\n",
      "<h1>Internal Server Error</h1>\n",
      "<p>The server encountered an internal error and was unable to complete your request.  Either the server is overloaded or there is an error in the application.</p>\n",
      "\n",
      "[sedkit] There was a problem determining the interstellar reddening. Setting to 0. You can manually set this with the 'reddening' attribute.\n"
     ]
    }
   ],
   "source": [
    "sed.load_coords_db()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we'll load distance information from the Parallaxes table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[SIMPLE] 3 parallaxes found. Attempting to load adopted one...\n",
      "[sedkit] Setting parallax to (<Quantity 80.21231613 mas>, <Quantity 0.07160574 mas>) with reference '2021A&A...649A...1G'\n",
      "[sedkit] Setting distance to (<Quantity 12.47 pc>, <Quantity 0.01 pc>, <Quantity 0.01 pc>) with reference '2021A&A...649A...1G'\n",
      "Response received from server:\n",
      "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2 Final//EN\">\n",
      "<title>500 Internal Server Error</title>\n",
      "<h1>Internal Server Error</h1>\n",
      "<p>The server encountered an internal error and was unable to complete your request.  Either the server is overloaded or there is an error in the application.</p>\n",
      "\n",
      "[sedkit] There was a problem determining the interstellar reddening. Setting to 0. You can manually set this with the 'reddening' attribute.\n"
     ]
    }
   ],
   "source": [
    "sed.load_parallax_db()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we'll load any photometry from the Photometry table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[SIMPLE] 18 photometry values found. Attempting to load...\n",
      "[sedkit] Setting 2MASS.H photometry to 10.718 (0.021) with reference '2003tmc..book.....C'\n",
      "[sedkit] Setting 2MASS.J photometry to 11.354 (0.022) with reference '2003tmc..book.....C'\n",
      "[sedkit] Setting 2MASS.Ks photometry to 10.296 (0.023) with reference '2003tmc..book.....C'\n",
      "[sedkit] Setting Cousins.I photometry to 14.024 (0.115) with reference '2006AJ....132.1234C'\n",
      "[sedkit] Setting Cousins.R photometry to 16.466 (0.065) with reference '2006AJ....132.1234C'\n",
      "[sedkit] Setting Gaia.G photometry to 15.645 (0.001) with reference '2018A&A...616A...1G'\n",
      "[sedkit] Setting Gaia.rp photometry to 14.097 (0.009) with reference '2018A&A...616A...1G'\n",
      "[sedkit] Setting Gaia.G photometry to 15.623 (0.001) with reference '2021A&A...649A...1G'\n",
      "[sedkit] Setting Gaia.rp photometry to 14.104 (0.002) with reference '2021A&A...649A...1G'\n",
      "[sedkit] Setting Johnson.V photometry to 18.798 (0.082) with reference '2006AJ....132.1234C'\n",
      "[sedkit] Setting WFCAM.H photometry to 10.775 (0.023) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WFCAM.J photometry to 11.319 (0.022) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WFCAM.K photometry to 10.269 (0.023) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WFCAM.Y photometry to 12.098 (0.055) with reference '2021AJ....161...42B'\n",
      "[sedkit] Setting WISE.W1 photometry to 10.042 (0.023) with reference '2012yCat.2311....0C'\n",
      "[sedkit] Setting WISE.W2 photometry to 9.799 (0.020) with reference '2012yCat.2311....0C'\n",
      "[sedkit] Setting WISE.W3 photometry to 9.528 (0.041) with reference '2012yCat.2311....0C'\n",
      "[sedkit] Setting WISE.W4 photometry to 8.397 (nan) with reference '2012yCat.2311....0C'\n"
     ]
    }
   ],
   "source": [
    "sed.load_photometry_db()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we'll load the best (adopted) spectral type from the SpectralTypes table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[SIMPLE] 2 spectral types found. Attempting to load adopted one...\n"
     ]
    }
   ],
   "source": [
    "sed.load_spectral_type_db()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note that there was no output. This is because no spectral type is marked as adopted for this particular source in the database. You can manually edit the database if you feel this is incorrect.\n",
    "\n",
    "Finally, let's add all spectra from the Spectra table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[SIMPLE] 2 spectra found. Attempting to load...\n",
      "[sedkit] Spectrum 'New Spectrum' added with reference '2018AJ....155...34C'\n",
      "[sedkit] Spectrum 'New Spectrum' added with reference '2007AJ....133..439C'\n"
     ]
    }
   ],
   "source": [
    "sed.load_spectra_db(column='access_url')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There are two available spectra for this source, but only one of them can be easily imported. The other fails due to the formatting of the data and will need be manually transformed. This is beyond the scope of this tutorial. \n",
    "\n",
    "Note the use of `column='spectrum'`, this allows you to load data from different fields in the Spectra table. Most likely you will want spectrum, but original_spectrum and local_spectrum are other options. Refer to the [SIMPLE documentation](https://github.com/SIMPLE-AstroDB/SIMPLE-db/tree/main/documentation) for more information.\n",
    "\n",
    "If you want to fetch an individual spectrum from the database, perhaps to do your own modifications you can use:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "564 <class 'specutils.spectra.spectral_axis.SpectralAxis'> Angstrom\n",
      "564 <class 'astropy.units.quantity.Quantity'> W / (um m2)\n",
      "564 <class 'astropy.units.quantity.Quantity'> W / (um m2)\n",
      "2018AJ....155...34C\n"
     ]
    }
   ],
   "source": [
    "spec = sed.inventory['Spectra'][0]  # select first entry in the Spectra table\n",
    "wave, flux, flux_unc, ref = sed.fetch_single_spectrum_db(spec)\n",
    "print(len(wave), type(wave), wave.unit)\n",
    "print(len(flux), type(flux), flux.unit)\n",
    "print(len(flux_unc), type(flux_unc), flux_unc.unit)\n",
    "print(ref)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With these wavelength, flux, flux_unc arrays and the reference, you can add them to the SED object in the usual manner:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[sedkit] Spectrum 'New Spectrum' added with reference '2018AJ....155...34C'\n"
     ]
    }
   ],
   "source": [
    "sed.add_spectrum((wave, flux, flux_unc), ref=ref)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can pass along additional parameters to `fetch_single_spectrum_db` if you need to use a different specutils converter or want to ensure missing uncertainties have some approximate scaling, for example:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1479 <class 'specutils.spectra.spectral_axis.SpectralAxis'> Angstrom\n",
      "1479 <class 'astropy.units.quantity.Quantity'> erg / (Angstrom s cm2)\n",
      "2007AJ....133..439C\n"
     ]
    }
   ],
   "source": [
    "spec = sed.inventory['Spectra'][1]  # select first entry in the Spectra table\n",
    "wave, flux, flux_unc, ref = sed.fetch_single_spectrum_db(spec)\n",
    "print(len(wave), type(wave), wave.unit)\n",
    "print(len(flux), type(flux), flux.unit)\n",
    "# if flux_unc is not None: print(len(flux_unc), type(flux_unc), flux_unc.unit)\n",
    "print(ref)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In the above case, we see that the spectra is malformed and will need to be addressed before it can be added to the SED object. Attempting different loaders (see https://specutils.readthedocs.io/en/stable/spectrum1d.html#list-of-loaders) can help, but an understanding of how the data was produced may be needed."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### !! As a reminder: you do not need to call these individual methods if you are using `auto_db=True` !!\n",
    "\n",
    "## Generating the SED\n",
    "\n",
    "With these data in place, either loaded manually or by `auto_db` you can now proceed to the usual steps in SED generation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[sedkit] Setting fbol to (<Quantity 1.24153219e-10 erg / (cm2 s)>, <Quantity 3.79366668e-13 erg / (cm2 s)>) with reference 'This Work'\n",
      "[sedkit] Setting Lbol to (<Quantity 2.3099461e+30 erg / s>, <Quantity 7.97156513e+27 erg / s>) with reference 'This Work'\n",
      "[sedkit] Setting Lbol_sun to (-3.219, 0.001) with reference 'This Work'\n",
      "[sedkit] Setting mbol to (13.283, 0.003) with reference 'This Work'\n",
      "[sedkit] Setting Mbol to (12.804, 0.003) with reference 'This Work'\n",
      "[sedkit] Setting logg to 'None'\n",
      "[sedkit] Could not calculate logg without Lbol and age\n",
      "[sedkit] Setting mass to 'None'\n",
      "[sedkit] Setting mass to (<Quantity 0.07 solMass>, <Quantity 0. solMass>, <Quantity 0. solMass>) with reference '2013ApJS..208....9P'\n",
      "[sedkit] Setting Teff to (<Quantity 2335 K>, <Quantity 77 K>) with reference 'This Work'\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div style=\"display: table;\"><div style=\"display: table-row;\"><div style=\"display: table-cell;\"><b title=\"bokeh.plotting.figure.Figure\">Figure</b>(</div><div style=\"display: table-cell;\">id&nbsp;=&nbsp;'1033', <span id=\"1397\" style=\"cursor: pointer;\">&hellip;)</span></div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">above&nbsp;=&nbsp;[],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">align&nbsp;=&nbsp;'start',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">aspect_ratio&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">aspect_scale&nbsp;=&nbsp;1,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background_fill_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background_fill_color&nbsp;=&nbsp;'#ffffff',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">below&nbsp;=&nbsp;[LogAxis(id='1044', ...)],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">border_fill_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">border_fill_color&nbsp;=&nbsp;'#ffffff',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">center&nbsp;=&nbsp;[Grid(id='1047', ...), Grid(id='1051', ...), Legend(id='1080', ...)],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">css_classes&nbsp;=&nbsp;[],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">disabled&nbsp;=&nbsp;False,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_x_ranges&nbsp;=&nbsp;{},</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_x_scales&nbsp;=&nbsp;{},</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_y_ranges&nbsp;=&nbsp;{},</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_y_scales&nbsp;=&nbsp;{},</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">frame_height&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">frame_width&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">height&nbsp;=&nbsp;400,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">height_policy&nbsp;=&nbsp;'auto',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">hidpi&nbsp;=&nbsp;True,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">inner_height&nbsp;=&nbsp;0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">inner_width&nbsp;=&nbsp;0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">js_event_callbacks&nbsp;=&nbsp;{},</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">js_property_callbacks&nbsp;=&nbsp;{},</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">left&nbsp;=&nbsp;[LogAxis(id='1048', ...)],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_factor&nbsp;=&nbsp;10,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_interval&nbsp;=&nbsp;300,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_threshold&nbsp;=&nbsp;2000,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_timeout&nbsp;=&nbsp;500,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">margin&nbsp;=&nbsp;(0, 0, 0, 0),</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">match_aspect&nbsp;=&nbsp;False,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">max_height&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">max_width&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border&nbsp;=&nbsp;5,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_bottom&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_left&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_right&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_top&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_height&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_width&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">name&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outer_height&nbsp;=&nbsp;0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outer_width&nbsp;=&nbsp;0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_cap&nbsp;=&nbsp;'butt',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_color&nbsp;=&nbsp;'#e5e5e5',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_dash&nbsp;=&nbsp;[],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_dash_offset&nbsp;=&nbsp;0,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_join&nbsp;=&nbsp;'bevel',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_width&nbsp;=&nbsp;1,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">output_backend&nbsp;=&nbsp;'canvas',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">renderers&nbsp;=&nbsp;[GlyphRenderer(id='1068', ...), GlyphRenderer(id='1089', ...), GlyphRenderer(id='1108', ...), GlyphRenderer(id='1115', ...), GlyphRenderer(id='1138', ...)],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">reset_policy&nbsp;=&nbsp;'standard',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">right&nbsp;=&nbsp;[],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">sizing_mode&nbsp;=&nbsp;None,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">subscribed_events&nbsp;=&nbsp;[],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">syncable&nbsp;=&nbsp;True,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">tags&nbsp;=&nbsp;[],</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">title&nbsp;=&nbsp;Title(id='1034', ...),</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">title_location&nbsp;=&nbsp;'above',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar&nbsp;=&nbsp;Toolbar(id='1058', ...),</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar_location&nbsp;=&nbsp;'right',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar_sticky&nbsp;=&nbsp;True,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">visible&nbsp;=&nbsp;True,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">width&nbsp;=&nbsp;900,</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">width_policy&nbsp;=&nbsp;'auto',</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">x_range&nbsp;=&nbsp;Range1d(id='1159', ...),</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">x_scale&nbsp;=&nbsp;LogScale(id='1040', ...),</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">y_range&nbsp;=&nbsp;Range1d(id='1160', ...),</div></div><div class=\"1396\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">y_scale&nbsp;=&nbsp;LogScale(id='1042', ...))</div></div></div>\n",
       "<script>\n",
       "(function() {\n",
       "  let expanded = false;\n",
       "  const ellipsis = document.getElementById(\"1397\");\n",
       "  ellipsis.addEventListener(\"click\", function() {\n",
       "    const rows = document.getElementsByClassName(\"1396\");\n",
       "    for (let i = 0; i < rows.length; i++) {\n",
       "      const el = rows[i];\n",
       "      el.style.display = expanded ? \"none\" : \"table-row\";\n",
       "    }\n",
       "    ellipsis.innerHTML = expanded ? \"&hellip;)\" : \"&lsaquo;&lsaquo;&lsaquo;\";\n",
       "    expanded = !expanded;\n",
       "  });\n",
       "})();\n",
       "</script>\n"
      ],
      "text/plain": [
       "Figure(id='1033', ...)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sed.plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><i>Table length=18</i>\n",
       "<table id=\"table5400296512\" class=\"table-striped table-bordered table-condensed\">\n",
       "<thead><tr><th>param</th><th>value</th><th>unc</th><th>units</th></tr></thead>\n",
       "<thead><tr><th>object</th><th>object</th><th>object</th><th>object</th></tr></thead>\n",
       "<tr><td>name</td><td>Trappist-1</td><td>--</td><td>--</td></tr>\n",
       "<tr><td>ra</td><td>346.62201</td><td>--</td><td>deg</td></tr>\n",
       "<tr><td>...</td><td>...</td><td>...</td><td>...</td></tr>\n",
       "<tr><td>mass</td><td>0.07</td><td>0.0</td><td>solMass</td></tr>\n",
       "<tr><td>radius</td><td>0.15</td><td>0.01</td><td>solRad</td></tr>\n",
       "</table></div>"
      ],
      "text/plain": [
       "<Table length=18>\n",
       "param    value     unc    units \n",
       "object   object   object  object\n",
       "------ ---------- ------ -------\n",
       "  name Trappist-1     --      --\n",
       "    ra  346.62201     --     deg\n",
       "   ...        ...    ...     ...\n",
       "  mass       0.07    0.0 solMass\n",
       "radius       0.15   0.01  solRad"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sed.results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "sedkit-3.11",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}