{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "This notebook prepare the catalogues that will be analysed by CIGALE for SED fitting and physical parameter estimation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import os\n",
    "os.environ['LOG_LEVEL'] = 'INFO'\n",
    "\n",
    "from astropy.table import Table\n",
    "\n",
    "from herschelhelp.filters import correct_galactic_extinction\n",
    "from herschelhelp.external import convert_table_for_cigale"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "SUFFIX = '20180218'\n",
    "master_catalogue = Table.read(\"../../dmu32/dmu32_GAMA-12/data/GAMA-12_{}_cigale.fits\".format(SUFFIX))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "12369415"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(master_catalogue)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# Best sources\n",
    "\n",
    "Define a good far-IR measurement as:\n",
    "- an existing flux in the band;\n",
    "- the flag from XID+ must not be set;\n",
    "- the signal to noise ratio must be over 2."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "good = {}\n",
    "for band in [ 'spire_250', 'spire_350', 'spire_500']:\n",
    "    good[band] = (~np.isnan(master_catalogue['f_{}'.format(band)]) & \n",
    "                                   ~master_catalogue['flag_{}'.format(band)])\n",
    "    good[band][good[band]] &= (master_catalogue[good[band]]['f_{}'.format(band)] /\n",
    "                              master_catalogue[good[band]]['ferr_{}'.format(band)] >= 2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "We will keep only sources with at leat 2 good far-IR measurements (we may actually use less sources are not all may have a redshift)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "combined_good = np.sum(list(good.values()), axis=0) >= 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of good sources: 108139\n"
     ]
    }
   ],
   "source": [
    "print(\"Number of good sources: {}\".format(np.sum(combined_good)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "# Only sources with at least two optical and at least two near infrared detections\n",
    "optnir = ((master_catalogue['flag_optnir_det'] == 3) \n",
    "          | (master_catalogue['flag_optnir_det'] == 7))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# Ldust catalogue for CIGALE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "#best_catalogue = master_catalogue[combined_good].copy()\n",
    "best_catalogue = master_catalogue[optnir].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "# Correction for galactic extinction\n",
    "best_catalogue = correct_galactic_extinction(best_catalogue, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true,
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:herschelhelp.external:For 7118 sources, the band omegacam_u should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 6145 sources, the band omegacam_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 6131 sources, the band suprime_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 6140 sources, the band decam_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 6139 sources, the band gpc1_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 5728 sources, the band suprime_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 5697 sources, the band gpc1_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 5661 sources, the band omegacam_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 5570 sources, the band decam_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 54 sources, the band gpc1_i should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 145 sources, the band omegacam_i should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 52 sources, the band suprime_i should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n"
     ]
    }
   ],
   "source": [
    "# Convertion to CIGALE format\n",
    "best_catalogue = convert_table_for_cigale(best_catalogue, inplace=True, remove_zerofluxes=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "## Band selection\n",
    "\n",
    "We want to use only one filter for similar bands. We define an order of preference and set to NaN the flux in the lower prefered bands when a prefered band is available. Some band may have a 0 flux, we set there values to NaN."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "u_bands = [             \"omegacam_u\"]\n",
    "g_bands = [\"suprime_g\", \"omegacam_g\", \"decam_g\", \"gpc1_g\"]\n",
    "r_bands = [\"suprime_r\", \"omegacam_r\", \"decam_r\", \"gpc1_r\"]\n",
    "i_bands = [\"suprime_i\", \"omegacam_i\",            \"gpc1_i\"]\n",
    "z_bands = [\"suprime_z\",               \"decam_z\", \"gpc1_z\"]\n",
    "y_bands = [\"suprime_y\",                          \"gpc1_y\"]\n",
    "\n",
    "def remove_unneeded_fluxes(list_of_bands):\n",
    "    for band_idx, band in enumerate(list_of_bands[:-1]):\n",
    "        mask = ~np.isnan(best_catalogue[band])\n",
    "        for lower_band in list_of_bands[band_idx+1:]:\n",
    "            best_catalogue[lower_band][mask] = np.nan\n",
    "            best_catalogue[\"{}_err\".format(lower_band)][mask] = np.nan"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "remove_unneeded_fluxes(g_bands)\n",
    "remove_unneeded_fluxes(u_bands)\n",
    "remove_unneeded_fluxes(r_bands)\n",
    "remove_unneeded_fluxes(i_bands)\n",
    "remove_unneeded_fluxes(z_bands)\n",
    "remove_unneeded_fluxes(y_bands)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "best_catalogue.write(\"data_tmp/GAMA-12_cigale_optnir_extcor_{}.fits\".format(SUFFIX), overwrite=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Main catalogue for CIGALE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#best_catalogue = master_catalogue[combined_good].copy()\n",
    "best_catalogue = master_catalogue[combined_good].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Correction for galactic extinction\n",
    "best_catalogue = correct_galactic_extinction(best_catalogue, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:herschelhelp.external:For 448 sources, the band omegacam_u should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 349 sources, the band omegacam_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 344 sources, the band suprime_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 347 sources, the band decam_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 347 sources, the band gpc1_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 311 sources, the band suprime_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 308 sources, the band gpc1_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 308 sources, the band omegacam_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 302 sources, the band decam_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n"
     ]
    }
   ],
   "source": [
    "# Convertion to CIGALE format\n",
    "best_catalogue = convert_table_for_cigale(best_catalogue, inplace=True, remove_zerofluxes=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "remove_unneeded_fluxes(g_bands)\n",
    "remove_unneeded_fluxes(u_bands)\n",
    "remove_unneeded_fluxes(r_bands)\n",
    "remove_unneeded_fluxes(i_bands)\n",
    "remove_unneeded_fluxes(z_bands)\n",
    "remove_unneeded_fluxes(y_bands)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "best_catalogue.write(\"data_tmp/GAMA-12_cigale_best_extcor_{}.fits\".format(SUFFIX), overwrite=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# Catalogue using spectroscopic redshift"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "best_catalogue = master_catalogue[optnir].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "best_catalogue.remove_column(\"redshift\")\n",
    "best_catalogue[\"zspec\"].name = \"redshift\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "best_catalogue = best_catalogue[~np.isnan(best_catalogue[\"redshift\"])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of sources with z-spec: 69941\n"
     ]
    }
   ],
   "source": [
    "print(\"Number of sources with z-spec: {}\".format(len(best_catalogue)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "# Correction for galactic extinction\n",
    "best_catalogue = correct_galactic_extinction(best_catalogue, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:herschelhelp.external:For 488 sources, the band omegacam_u should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 150 sources, the band omegacam_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 147 sources, the band suprime_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 149 sources, the band decam_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 149 sources, the band gpc1_g should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 66 sources, the band suprime_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 66 sources, the band gpc1_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 65 sources, the band omegacam_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 65 sources, the band decam_r should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 19 sources, the band gpc1_i should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 26 sources, the band omegacam_i should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n",
      "INFO:herschelhelp.external:For 19 sources, the band suprime_i should not be used because it overlaps or is below the Lyman limit at the redshift of these sources. These fluxes were set to NaN.\n"
     ]
    }
   ],
   "source": [
    "# Convertion to CIGALE format\n",
    "os.environ['LOG_LEVEL'] = 'INFO'\n",
    "best_catalogue = convert_table_for_cigale(best_catalogue, inplace=True, remove_zerofluxes=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "remove_unneeded_fluxes(g_bands)\n",
    "remove_unneeded_fluxes(u_bands)\n",
    "remove_unneeded_fluxes(r_bands)\n",
    "remove_unneeded_fluxes(i_bands)\n",
    "remove_unneeded_fluxes(z_bands)\n",
    "remove_unneeded_fluxes(y_bands)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "best_catalogue.write(\"data_tmp/GAMA-12_cigale_optnir_extcor_zspec_{}.fits\".format(SUFFIX), overwrite=True)"
   ]
  }
 ],
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