LearningPython.astroquery.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# A quick look at `ASTROQUERY`\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "\n",
    "from astropy.table import Table\n",
    "\n",
    "import astropy.constants as c\n",
    "import astropy.units as u"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## `ASTROQUERY`\n",
    "\n",
    "We'll load in a Simbad search from `astroquery` and use it to extract K-band magnitudes for several stars from the Simbad database."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: AstropyDeprecationWarning: astropy.extern.six will be removed in 4.0, use the six module directly if it is still needed [astropy.extern.six]\n"
     ]
    }
   ],
   "source": [
    "from astroquery.simbad import Simbad"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The first step is to create a custom simbad search that allows us to add new VOTABLE codes to request."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create custom search\n",
    "customSimbad = Simbad()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--NOTES--\n",
      "\n",
      "1. The parameter filtername must correspond to an existing filter. Filters include: B,V,R,I,J,K.  They are checked by SIMBAD but not astroquery.simbad\n",
      "\n",
      "2. Fields beginning with rvz display the data as it is in the database. Fields beginning with rv force the display as a radial velocity. Fields beginning with z force the display as a redshift\n",
      "\n",
      "3. For each measurement catalog, the VOTable contains all fields of the first measurement. When applicable, the first measurement is the mean one. \n",
      "\n",
      "Available VOTABLE fields:\n",
      "\n",
      "bibcodelist(y1-y2)\n",
      "biblio\n",
      "cel\n",
      "cl.g\n",
      "coo(opt)\n",
      "coo_bibcode\n",
      "coo_err_angle\n",
      "coo_err_maja\n",
      "coo_err_mina\n",
      "coo_qual\n",
      "coo_wavelength\n",
      "coordinates\n",
      "dec(opt)\n",
      "dec_prec\n",
      "diameter\n",
      "dim\n",
      "dim_angle\n",
      "dim_bibcode\n",
      "dim_incl\n",
      "dim_majaxis\n",
      "dim_minaxis\n",
      "dim_qual\n",
      "dim_wavelength\n",
      "dimensions\n",
      "distance\n",
      "distance_result\n",
      "einstein\n",
      "fe_h\n",
      "flux(filtername)\n",
      "flux_bibcode(filtername)\n",
      "flux_error(filtername)\n",
      "flux_name(filtername)\n",
      "flux_qual(filtername)\n",
      "flux_system(filtername)\n",
      "flux_unit(filtername)\n",
      "fluxdata(filtername)\n",
      "gcrv\n",
      "gen\n",
      "gj\n",
      "hbet\n",
      "hbet1\n",
      "hgam\n",
      "id(opt)\n",
      "ids\n",
      "iras\n",
      "irc\n",
      "iso\n",
      "iue\n",
      "jp11\n",
      "link_bibcode\n",
      "main_id\n",
      "measurements\n",
      "membership\n",
      "mesplx\n",
      "mespm\n",
      "mk\n",
      "morphtype\n",
      "mt\n",
      "mt_bibcode\n",
      "mt_qual\n",
      "otype\n",
      "otype(opt)\n",
      "otypes\n",
      "parallax\n",
      "plx\n",
      "plx_bibcode\n",
      "plx_error\n",
      "plx_prec\n",
      "plx_qual\n",
      "pm\n",
      "pm_bibcode\n",
      "pm_err_angle\n",
      "pm_err_maja\n",
      "pm_err_mina\n",
      "pm_qual\n",
      "pmdec\n",
      "pmdec_prec\n",
      "pmra\n",
      "pmra_prec\n",
      "pos\n",
      "posa\n",
      "propermotions\n",
      "ra(opt)\n",
      "ra_prec\n",
      "rot\n",
      "rv_value\n",
      "rvz_bibcode\n",
      "rvz_error\n",
      "rvz_qual\n",
      "rvz_radvel\n",
      "rvz_type\n",
      "rvz_wavelength\n",
      "sao\n",
      "sp\n",
      "sp_bibcode\n",
      "sp_nature\n",
      "sp_qual\n",
      "sptype\n",
      "td1\n",
      "typed_id\n",
      "ubv\n",
      "uvby\n",
      "uvby1\n",
      "v*\n",
      "velocity\n",
      "xmm\n",
      "z_value\n",
      "For more information on a field:\n",
      "Simbad.get_field_description ('field_name') \n",
      "Currently active VOTABLE fields:\n",
      " ['main_id', 'flux(K)', 'flux_error(K)', 'flux_system(K)']\n"
     ]
    }
   ],
   "source": [
    "# List VOTABLE options\n",
    "customSimbad.list_votable_fields()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Now we activate the VOTABLE fields we want. We'll remove the coordinates column and enable K-band magnitudes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/howk/miniconda3/lib/python3.7/site-packages/astroquery/simbad/core.py:416: UserWarning: coordinates: this field is not set\n",
      "  warnings.warn(\"{field}: this field is not set\".format(field=field))\n"
     ]
    }
   ],
   "source": [
    "customSimbad.remove_votable_fields('coordinates')\n",
    "customSimbad.add_votable_fields('flux(K)','flux_error(K)','flux_system(K)')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Do a search\n",
    "\n",
    "We will search on object names. First define the names in which we're interested, then do the search:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "stars = ['HD233622','HD218915','HD14633']\n",
    "simbaddata = customSimbad.query_objects(stars)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<i>Table masked=True length=3</i>\n",
       "<table id=\"table4723304656-733737\" class=\"table-striped table-bordered table-condensed\">\n",
       "<thead><tr><th>idx</th><th>MAIN_ID</th><th>FLUX_K</th><th>FLUX_ERROR_K</th><th>FLUX_SYSTEM_K</th></tr></thead>\n",
       "<thead><tr><th></th><th></th><th>mag</th><th></th><th></th></tr></thead>\n",
       "<tr><td>0</td><td>HD 233622</td><td>10.429</td><td>0.019</td><td>Vega</td></tr>\n",
       "<tr><td>1</td><td>HD 218915</td><td>7.196</td><td>0.021</td><td>Vega</td></tr>\n",
       "<tr><td>2</td><td>HD  14633</td><td>8.121</td><td>0.021</td><td>Vega</td></tr>\n",
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       "jQuery.extend( jQuery.fn.dataTableExt.oSort, {\n",
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     "execution_count": 11,
     "metadata": {},
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   ],
   "source": [
    "simbaddata.show_in_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "From here we can extract the magnitudes for our own use! Take care, as the data are in a masked table column; if we want to transform them to an array, the approach is a bit wonky..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([10.429,  7.196,  8.121], dtype=float32)"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Kmags = (simbaddata['FLUX_K']).data.data\n",
    "Kmags"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Direct Gaia catalog search\n",
    "\n",
    "Now we'll try a direct catalog search. In this case we need the coordinates, so we'll do a 2-step process: \n",
    "\n",
    "1. Get coordinates from SIMBAD\n",
    "2. Get refined coordinates, magnitudes from Gaia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " MAIN_ID        RA           DEC      ... FLUX_K FLUX_ERROR_K FLUX_SYSTEM_K\n",
      "             \"h:m:s\"       \"d:m:s\"    ...  mag                             \n",
      "--------- ------------- ------------- ... ------ ------------ -------------\n",
      "HD 233622 09 21 33.6008 +50 05 56.366 ... 10.429        0.019          Vega\n",
      "HD 218915 23 11 06.9480 +53 03 29.651 ...  7.196        0.021          Vega\n",
      "HD  14633 02 22 54.2920 +41 28 47.723 ...  8.121        0.021          Vega\n"
     ]
    }
   ],
   "source": [
    "from astroquery.simbad import Simbad\n",
    "from astroquery.gaia import Gaia\n",
    "\n",
    "# Our objects\n",
    "stars = ['HD233622','HD218915','HD14633']\n",
    "\n",
    "# Create custom Simbad search\n",
    "customSimbad = Simbad()\n",
    "customSimbad.add_votable_fields('flux(K)','flux_error(K)','flux_system(K)')\n",
    "simbaddata = customSimbad.query_objects(stars)\n",
    "simbaddata.pprint()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<i>Table masked=True length=3</i>\n",
       "<table id=\"table4731095192-608120\" class=\"table-striped table-bordered table-condensed\">\n",
       "<thead><tr><th>idx</th><th>MAIN_ID</th><th>RA</th><th>DEC</th><th>RA_PREC</th><th>DEC_PREC</th><th>COO_ERR_MAJA</th><th>COO_ERR_MINA</th><th>COO_ERR_ANGLE</th><th>COO_QUAL</th><th>COO_WAVELENGTH</th><th>COO_BIBCODE</th><th>FLUX_K</th><th>FLUX_ERROR_K</th><th>FLUX_SYSTEM_K</th></tr></thead>\n",
       "<thead><tr><th></th><th></th><th>&quot;h:m:s&quot;</th><th>&quot;d:m:s&quot;</th><th></th><th></th><th>mas</th><th>mas</th><th>deg</th><th></th><th></th><th></th><th>mag</th><th></th><th></th></tr></thead>\n",
       "<tr><td>0</td><td>HD 233622</td><td>09 21 33.6008</td><td>+50 05 56.366</td><td>14</td><td>14</td><td>0.048</td><td>0.046</td><td>90</td><td>A</td><td>O</td><td>2018yCat.1345....0G</td><td>10.429</td><td>0.019</td><td>Vega</td></tr>\n",
       "<tr><td>1</td><td>HD 218915</td><td>23 11 06.9480</td><td>+53 03 29.651</td><td>14</td><td>14</td><td>0.035</td><td>0.034</td><td>90</td><td>A</td><td>O</td><td>2018yCat.1345....0G</td><td>7.196</td><td>0.021</td><td>Vega</td></tr>\n",
       "<tr><td>2</td><td>HD  14633</td><td>02 22 54.2920</td><td>+41 28 47.723</td><td>14</td><td>14</td><td>0.118</td><td>0.077</td><td>90</td><td>A</td><td>O</td><td>2018yCat.1345....0G</td><td>8.121</td><td>0.021</td><td>Vega</td></tr>\n",
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       "<script>\n",
       "\n",
       "var astropy_sort_num = function(a, b) {\n",
       "    var a_num = parseFloat(a);\n",
       "    var b_num = parseFloat(b);\n",
       "\n",
       "    if (isNaN(a_num) && isNaN(b_num))\n",
       "        return ((a < b) ? -1 : ((a > b) ? 1 : 0));\n",
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       "    else\n",
       "        return isNaN(a_num) ? -1 : 1;\n",
       "}\n",
       "\n",
       "require.config({paths: {\n",
       "    datatables: 'https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min'\n",
       "}});\n",
       "require([\"datatables\"], function(){\n",
       "    console.log(\"$('#table4731095192-608120').dataTable()\");\n",
       "    \n",
       "jQuery.extend( jQuery.fn.dataTableExt.oSort, {\n",
       "    \"optionalnum-asc\": astropy_sort_num,\n",
       "    \"optionalnum-desc\": function (a,b) { return -astropy_sort_num(a, b); }\n",
       "});\n",
       "\n",
       "    $('#table4731095192-608120').dataTable({\n",
       "        order: [],\n",
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     },
     "execution_count": 55,
     "metadata": {},
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    }
   ],
   "source": [
    "simbaddata.show_in_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Create the SkyCoord coordinates in order to do the Gaia search"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "from astropy.coordinates import SkyCoord\n",
    "\n",
    "coords = SkyCoord(simbaddata['RA'],simbaddata['DEC'], unit=(u.hourangle, u.degree), frame='icrs')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Perform the Gaia search\n",
    "\n",
    "It seems you need to search for one star at a time when using coordinates?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Query finished.\n"
     ]
    }
   ],
   "source": [
    "a=Gaia.cone_search_async(coords[2],radius=0.05*u.arcmin)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<i>Table masked=True length=1</i>\n",
       "<table id=\"table4785232192-375795\" class=\"table-striped table-bordered table-condensed\">\n",
       "<thead><tr><th>idx</th><th>dist</th><th>solution_id</th><th>designation</th><th>source_id</th><th>random_index</th><th>ref_epoch</th><th>ra</th><th>ra_error</th><th>dec</th><th>dec_error</th><th>parallax</th><th>parallax_error</th><th>parallax_over_error</th><th>pmra</th><th>pmra_error</th><th>pmdec</th><th>pmdec_error</th><th>ra_dec_corr</th><th>ra_parallax_corr</th><th>ra_pmra_corr</th><th>ra_pmdec_corr</th><th>dec_parallax_corr</th><th>dec_pmra_corr</th><th>dec_pmdec_corr</th><th>parallax_pmra_corr</th><th>parallax_pmdec_corr</th><th>pmra_pmdec_corr</th><th>astrometric_n_obs_al</th><th>astrometric_n_obs_ac</th><th>astrometric_n_good_obs_al</th><th>astrometric_n_bad_obs_al</th><th>astrometric_gof_al</th><th>astrometric_chi2_al</th><th>astrometric_excess_noise</th><th>astrometric_excess_noise_sig</th><th>astrometric_params_solved</th><th>astrometric_primary_flag</th><th>astrometric_weight_al</th><th>astrometric_pseudo_colour</th><th>astrometric_pseudo_colour_error</th><th>mean_varpi_factor_al</th><th>astrometric_matched_observations</th><th>visibility_periods_used</th><th>astrometric_sigma5d_max</th><th>frame_rotator_object_type</th><th>matched_observations</th><th>duplicated_source</th><th>phot_g_n_obs</th><th>phot_g_mean_flux</th><th>phot_g_mean_flux_error</th><th>phot_g_mean_flux_over_error</th><th>phot_g_mean_mag</th><th>phot_bp_n_obs</th><th>phot_bp_mean_flux</th><th>phot_bp_mean_flux_error</th><th>phot_bp_mean_flux_over_error</th><th>phot_bp_mean_mag</th><th>phot_rp_n_obs</th><th>phot_rp_mean_flux</th><th>phot_rp_mean_flux_error</th><th>phot_rp_mean_flux_over_error</th><th>phot_rp_mean_mag</th><th>phot_bp_rp_excess_factor</th><th>phot_proc_mode</th><th>bp_rp</th><th>bp_g</th><th>g_rp</th><th>radial_velocity</th><th>radial_velocity_error</th><th>rv_nb_transits</th><th>rv_template_teff</th><th>rv_template_logg</th><th>rv_template_fe_h</th><th>phot_variable_flag</th><th>l</th><th>b</th><th>ecl_lon</th><th>ecl_lat</th><th>priam_flags</th><th>teff_val</th><th>teff_percentile_lower</th><th>teff_percentile_upper</th><th>a_g_val</th><th>a_g_percentile_lower</th><th>a_g_percentile_upper</th><th>e_bp_min_rp_val</th><th>e_bp_min_rp_percentile_lower</th><th>e_bp_min_rp_percentile_upper</th><th>flame_flags</th><th>radius_val</th><th>radius_percentile_lower</th><th>radius_percentile_upper</th><th>lum_val</th><th>lum_percentile_lower</th><th>lum_percentile_upper</th><th>datalink_url</th><th>epoch_photometry_url</th></tr></thead>\n",
       "<thead><tr><th></th><th></th><th></th><th></th><th></th><th></th><th>yr</th><th>deg</th><th>mas</th><th>deg</th><th>mas</th><th>mas</th><th>mas</th><th></th><th>mas / yr</th><th>mas / yr</th><th>mas / yr</th><th>mas / yr</th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th>mas</th><th></th><th></th><th></th><th>1 / mas2</th><th>1 / um</th><th>1 / um</th><th></th><th></th><th></th><th>mas</th><th></th><th></th><th></th><th></th><th>electron / s</th><th>electron / s</th><th></th><th>mag</th><th></th><th>electron / s</th><th>electron / s</th><th></th><th>mag</th><th></th><th>electron / s</th><th>electron / s</th><th></th><th>mag</th><th></th><th></th><th>mag</th><th>mag</th><th>mag</th><th>km / s</th><th>km / s</th><th></th><th>K</th><th>log(cm.s**-2)</th><th>dex</th><th></th><th>deg</th><th>deg</th><th>deg</th><th>deg</th><th></th><th>K</th><th>K</th><th>K</th><th>mag</th><th>mag</th><th>mag</th><th>mag</th><th>mag</th><th>mag</th><th></th><th>Rsun</th><th>Rsun</th><th>Rsun</th><th>Lsun</th><th>Lsun</th><th>Lsun</th><th></th><th></th></tr></thead>\n",
       "<tr><td>0</td><td>3.068965180181487e-05</td><td>1635721458409799680</td><td>Gaia DR2 339061352757048576</td><td>339061352757048576</td><td>1420208327</td><td>2015.5</td><td>35.72621443474856</td><td>0.11835843642190819</td><td>41.47989300174014</td><td>0.07659247486657224</td><td>0.19805274950189342</td><td>0.12671823929313705</td><td>1.562938</td><td>-0.40277279244577624</td><td>0.18224723043314162</td><td>-6.996017967712323</td><td>0.16460217299960303</td><td>-0.19112848</td><td>0.67939997</td><td>-0.0055224868</td><td>0.13023035</td><td>-0.15630893</td><td>0.008108797</td><td>-0.021769358</td><td>0.033079922</td><td>0.18233244</td><td>-0.004052784</td><td>114</td><td>114</td><td>112</td><td>2</td><td>22.716328</td><td>899.28815</td><td>0.2715207578813032</td><td>19.699603977151476</td><td>31</td><td>True</td><td>10.916305</td><td>1.8623596040257107</td><td>0.026168900055632695</td><td>-0.13727054</td><td>13</td><td>9</td><td>0.09356257</td><td>0</td><td>18</td><td>False</td><td>139</td><td>20545585.35474411</td><td>24029.563207836596</td><td>855.0129</td><td>7.4065695</td><td>15</td><td>16617570.757283395</td><td>57031.84398929029</td><td>291.37354</td><td>7.299969</td><td>15</td><td>7131383.08083617</td><td>20522.195623912343</td><td>347.4961</td><td>7.6289854</td><td>1.1559151</td><td>1</td><td>-0.3290162</td><td>-0.106600285</td><td>-0.22241592</td><td>--</td><td>--</td><td>0</td><td>--</td><td>--</td><td>--</td><td>NOT_AVAILABLE</td><td>140.77786684484906</td><td>-18.20054148043417</td><td>47.54706018230171</td><td>25.701907417735143</td><td>100102</td><td>8868.667</td><td>7963.25</td><td>9593.0</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>--</td><td>http://geadata.esac.esa.int/data-server/datalink/links?ID=339061352757048576</td><td>--</td></tr>\n",
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   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
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       "<i>Table masked=True length=1</i>\n",
       "<table id=\"table4804331000\" class=\"table-striped table-bordered table-condensed\">\n",
       "<thead><tr><th>phot_g_mean_mag</th><th>phot_bp_mean_mag</th></tr></thead>\n",
       "<thead><tr><th>mag</th><th>mag</th></tr></thead>\n",
       "<thead><tr><th>float32</th><th>float32</th></tr></thead>\n",
       "<tr><td>7.4065695</td><td>7.299969</td></tr>\n",
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       "<Table masked=True length=1>\n",
       "phot_g_mean_mag phot_bp_mean_mag\n",
       "      mag             mag       \n",
       "    float32         float32     \n",
       "--------------- ----------------\n",
       "      7.4065695         7.299969"
      ]
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     "execution_count": 58,
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