C3Catalog.py

import os
import galsim
import random
import numpy as np
import h5py as h5
import healpy as hp
import astropy.constants as cons
from astropy.coordinates import spherical_to_cartesian
from astropy.table import Table
from scipy import interpolate

from ObservationSim.MockObject import CatalogBase, Star, Galaxy, Quasar
from ObservationSim.MockObject._util import seds, sed_assign, extAv, tag_sed, getObservedSED

NSIDE = 128

class C3Catalog(CatalogBase):
    def __init__(self, config, **kwargs):
        super().__init__()
        self.cat_dir = os.path.join(config["data_dir"], config["input_path"]["cat_dir"])
        self.seed_Av = config["random_seeds"]["seed_Av"]
        self.normalize_dir = os.path.join(config["data_dir"], config["SLS_path"]["SLS_norm"])

        self.normF_star = Table.read(os.path.join(self.normalize_dir, 'SLOAN_SDSS.g.fits'))
        self.normF_galaxy = Table.read(os.path.join(self.normalize_dir, 'lsst_throuput_g.fits'))
        
        try:
            self.chip = kwargs["chip"]
        except:
            raise ValueError('For Cycle-3 Catalog class, must give a "chip" object to initiate')

        if "star_cat" in config["input_path"] and config["input_path"]["star_cat"]:
            star_file = config["input_path"]["star_cat"]
            star_SED_file = config["SED_templates_path"]["star_SED"]
            self.star_path = os.path.join(self.cat_dir, star_file)
            self.star_SED_path = os.path.join(config["data_dir"], star_SED_file)
            self._load_SED_lib_star()
        if "galaxy_cat" in config["input_path"] and config["input_path"]["galaxy_cat"]:
            galaxy_file = config["input_path"]["galaxy_cat"]
            self.galaxy_path = os.path.join(self.cat_dir, galaxy_file)
            self.galaxy_SED_path = os.path.join(config["data_dir"], config["SED_templates_path"]["galaxy_SED"])
            self._load_SED_lib_gals()
        if "rotateEll" in config["shear_setting"]:
            self.rotation = float(int(config["shear_setting"]["rotateEll"]/45.))
        else:
            self.rotation = 0.

        self._get_healpix_list()
        self._load()

    def _get_healpix_list(self):
        self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)
        ra_min, ra_max, dec_min, dec_max = self.sky_coverage.xmin, self.sky_coverage.xmax, self.sky_coverage.ymin, self.sky_coverage.ymax
        ra = np.deg2rad(np.array([ra_min, ra_max, ra_max, ra_min]))
        dec = np.deg2rad(np.array([dec_max, dec_max, dec_min, dec_min]))
        vertices = spherical_to_cartesian(1., dec, ra)
        self.pix_list = hp.query_polygon(NSIDE, np.array(vertices).T, inclusive=True)
        print("HEALPix List: ", self.pix_list)

    def load_norm_filt(self, obj):
        if obj.type == "star":
            return self.normF_star
        elif obj.type == "galaxy" or obj.type == "quasar":
            return self.normF_galaxy
        else:
            return None

    def _load_SED_lib_star(self):
        self.tempSED_star = h5.File(self.star_SED_path,'r')

    def _load_SED_lib_gals(self):
        self.tempSed_gal, self.tempRed_gal = seds("galaxy.list", seddir=self.galaxy_SED_path)

    def _load_gals(self, gals, pix_id=None):
        ngals = len(gals['galaxyID'])
        self.rng_sedGal = random.Random()
        self.rng_sedGal.seed(pix_id) # Use healpix index as the random seed
        self.ud = galsim.UniformDeviate(pix_id)
        for igals in range(ngals):
            param = self.initialize_param()
            param['ra'] = gals['ra_true'][igals]
            param['dec'] = gals['dec_true'][igals]
            param['z'] = gals['redshift_true'][igals]
            param['model_tag'] = 'None'
            param['gamma1'] = 0
            param['gamma2'] = 0
            param['kappa'] = 0
            param['delta_ra'] = 0
            param['delta_dec'] = 0
            sersicB = gals['sersic_bulge'][igals]
            hlrMajB = gals['size_bulge_true'][igals]
            hlrMinB = gals['size_minor_bulge_true'][igals]
            sersicD = gals['sersic_disk'][igals]
            hlrMajD = gals['size_disk_true'][igals]
            hlrMinD = gals['size_minor_disk_true'][igals]
            aGal = gals['size_true'][igals]
            bGal = gals['size_minor_true'][igals]
            param['bfrac'] = gals['bulge_to_total_ratio_i'][igals]
            param['theta'] = gals['position_angle_true'][igals]
            param['hlr_bulge'] = np.sqrt(hlrMajB * hlrMinB)
            param['hlr_disk'] = np.sqrt(hlrMajD * hlrMinD)
            param['ell_bulge'] = (hlrMajB - hlrMinB)/(hlrMajB + hlrMinB)
            param['ell_disk'] = (hlrMajD - hlrMinD)/(hlrMajD + hlrMinD)
            param['ell_tot'] = (aGal - bGal) / (aGal + bGal)

            # Assign each galaxy a template SED
            param['sed_type'] = sed_assign(phz=param['z'], btt=param['bfrac'], rng=self.rng_sedGal)
            param['redden'] = self.tempRed_gal[param['sed_type']]
            param['av'] = self.avGal[int(self.ud()*self.nav)]
            if param['sed_type'] <= 5:
                param['av'] = 0.0
                param['redden'] = 0
            param['star'] = 0   # Galaxy
            if param['sed_type'] >= 29:
                param['av'] = 0.6 * param['av'] / 3.0 # for quasar, av=[0, 0.2], 3.0=av.max-av.im
                param['star'] = 2 # Quasar

            if not self.chip.isContainObj(ra_obj=param['ra'], dec_obj=param['dec'], margin=200):
                continue
            param['mag_use_normal'] = gals['mag_true_g_lsst'][igals]
            if param['mag_use_normal'] >= 26.5:
                continue
            self.ids += 1
            param['id'] = self.ids
            
            if param['star'] == 0:
                obj = Galaxy(param, self.rotation)
                self.objs.append(obj)
            if param['star'] == 2:
                obj = Quasar(param)
                self.objs.append(obj)

    def _load_stars(self, stars, pix_id=None):
        nstars = len(stars['sourceID'])
        for istars in range(nstars):
            param = self.initialize_param()
            param['ra'] = stars['RA'][istars]
            param['dec'] = stars['Dec'][istars]
            if not self.chip.isContainObj(ra_obj=param['ra'], dec_obj=param['dec'], margin=200):
                continue
            param['mag_use_normal'] = stars['app_sdss_g'][istars]
            if param['mag_use_normal'] >= 26.5:
                continue
            self.ids += 1
            param['id'] = self.ids
            param['sed_type'] = stars['sourceID'][istars]
            param['model_tag'] = stars['model_tag'][istars]
            param['teff'] = stars['teff'][istars]
            param['logg'] = stars['grav'][istars]
            param['feh'] = stars['feh'][istars]
            param['z'] = 0.0
            param['star'] = 1   # Star
            obj = Star(param)
            self.objs.append(obj)

    def _load(self, **kwargs):
        self.nav = 15005
        self.avGal = extAv(self.nav, seed=self.seed_Av)
        gals_cat = h5.File(self.galaxy_path, 'r')['galaxies']
        star_cat = h5.File(self.star_path, 'r')['catalog']
        self.objs = []
        self.ids = 0
        for pix in self.pix_list:
            gals = gals_cat[str(pix)]
            stars = star_cat[str(pix)]
            self._load_gals(gals, pix_id=pix)
            self._load_stars(stars, pix_id=pix)
        print("number of objects in catalog: ", len(self.objs))
        del self.avGal


    def load_sed(self, obj, **kwargs):
        if obj.type == 'star':
            _, wave, flux = tag_sed(
                h5file=self.tempSED_star,
                model_tag=obj.param['model_tag'],
                teff=obj.param['teff'],
                logg=obj.param['logg'],
                feh=obj.param['feh']
            )
        elif obj.type == 'galaxy' or obj.type == 'quasar':
            sed_data = getObservedSED(
                sedCat=self.tempSed_gal[obj.sed_type],
                redshift=obj.z,
                av=obj.param["av"],
                redden=obj.param["redden"]
            )
            wave, flux = sed_data[0], sed_data[1]
        else:
            raise ValueError("Object type not known")
        speci = interpolate.interp1d(wave, flux)
        # lamb = np.arange(2500, 10001 + 0.5, 0.5)
        lamb = np.arange(2400, 11001 + 0.5, 0.5)
        y = speci(lamb)
        # erg/s/cm2/A --> photo/s/m2/A
        all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13
        sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))
        return sed