{ "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\n", "\n", "SUFFIX = '20171206'" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true, "deletable": true, "editable": true }, "outputs": [], "source": [ "master_catalogue = Table.read(\"../../dmu32/dmu32_GAMA-09/data/GAMA-09_{}_cigale.fits\".format(SUFFIX))" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true, "deletable": true, "editable": true }, "outputs": [ { "data": { "text/plain": [ "12937982" ] }, "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: 130293\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 prediction 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 997 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 905 sources, the band megacam_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 444 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 436 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 443 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 431 sources, the band megacam_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 441 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 298 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 297 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 295 sources, the band megacam_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 295 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 291 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 1 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" ] } ], "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": [ "#Based on expecting number counts in checks and diagnostics\n", "u_bands = [\"megacam_u\", \"omegacam_u\"]\n", "g_bands = [\"megacam_g\", \"suprime_g\", \"omegacam_g\", \"decam_g\", \"gpc1_g\"]\n", "r_bands = [\"megacam_r\", \"suprime_r\", \"omegacam_r\", \"decam_r\", \"gpc1_r\"]\n", "i_bands = [\"megacam_i\", \"suprime_i\", \"omegacam_i\", \"gpc1_i\"]\n", "z_bands = [\"megacam_z\", \"suprime_z\", \"decam_z\", \"gpc1_z\"]\n", "y_bands = [ \"suprime_y\", \"vista_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-09_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 144 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 132 sources, the band megacam_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 46 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 44 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 46 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 44 sources, the band megacam_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 46 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 18 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 18 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 18 sources, the band megacam_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 18 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 18 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-09_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: 30803\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 402 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 348 sources, the band megacam_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 101 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 96 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 99 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 93 sources, the band megacam_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 97 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 18 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 18 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 17 sources, the band megacam_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 17 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 17 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 5 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 6 sources, the band megacam_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 7 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 5 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-09_cigale_optnir_extcor_zspec_{}.fits\".format(SUFFIX), overwrite=True)" ] } ], "metadata": { "kernelspec": { "display_name": "Python (herschelhelp_internal)", "language": "python", "name": "helpint" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.4" } }, "nbformat": 4, "nbformat_minor": 2 }