adjust to new C6 catalog (379dedfb) · Commits · Liu Dezi / csst_msc_sim

Catalog/C6_Catalog.py

+98 −35

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@ import numpy as np
		import h5py as h5
		import healpy as hp
		import astropy.constants as cons
		import traceback
		from astropy.coordinates import spherical_to_cartesian
		from astropy.table import Table
		from scipy import interpolate
		@@ -14,6 +15,11 @@ from ObservationSim.MockObject import CatalogBase, Star, Galaxy, Quasar
		from ObservationSim.MockObject._util import tag_sed, getObservedSED, getABMAG, integrate_sed_bandpass, comoving_dist
		from ObservationSim.Astrometry.Astrometry_util import on_orbit_obs_position

		# (TEST)
		from astropy.cosmology import FlatLambdaCDM
		from astropy import constants
		from astropy import units as U

		try:
		import importlib.resources as pkg_resources
		except ImportError:
		@@ -22,26 +28,40 @@ except ImportError:

		NSIDE = 128

		def get_bundleIndex(healpixID_ring, bundleOrder=4, healpixOrder=7):
		assert NSIDE == 2**healpixOrder
		shift = healpixOrder - bundleOrder
		shift = 2*shift

		nside_bundle = 2**bundleOrder
		nside_healpix= 2**healpixOrder

		healpixID_nest= hp.ring2nest(nside_healpix, healpixID_ring)
		bundleID_nest = (healpixID_nest >> shift)
		bundleID_ring = hp.nest2ring(nside_bundle, bundleID_nest)

		return bundleID_ring

		class C6_Catalog(CatalogBase):
		def __init__(self, config, chip, pointing, chip_output, filt, **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"]

		# (TEST)
		self.cosmo = FlatLambdaCDM(H0=67.66, Om0=0.3111)

		self.chip_output = chip_output
		self.filt = filt
		self.logger = chip_output.logger

		with pkg_resources.path('Catalog.data', 'SLOAN_SDSS.g.fits') as filter_path:
		self.normF_star = Table.read(str(filter_path))
		# with pkg_resources.path('Catalog.data', 'lsst_throuput_g.fits') as filter_path:
		# self.normF_galaxy = Table.read(str(filter_path))

		self.config = config
		self.chip = chip
		self.pointing = pointing

		# (DEBUG)
		self.max_size = 0.

		if "star_cat" in config["input_path"] and config["input_path"]["star_cat"] and not config["run_option"]["galaxy_only"]:
		@@ -80,8 +100,13 @@ class C6_Catalog(CatalogBase):
		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)
		# vertices = spherical_to_cartesian(1., dec, ra)
		self.pix_list = hp.query_polygon(
		NSIDE,
		hp.ang2vec(np.radians(90.) - dec, ra),
		inclusive=True
		)
		# self.pix_list = hp.query_polygon(NSIDE, np.array(vertices).T, inclusive=True)
		if self.logger is not None:
		msg = str(("HEALPix List: ", self.pix_list))
		self.logger.info(msg)
		@@ -144,16 +169,21 @@ class C6_Catalog(CatalogBase):
		)

		for igals in range(ngals):
		# (TEST)
		# # (TEST)
		# if igals > 100:
		# break
		# if igals != 1186:
		# continue

		param = self.initialize_param()
		param['ra'] = ra_arr[igals]
		param['dec'] = dec_arr[igals]
		param['ra_orig'] = gals['ra'][igals]
		param['dec_orig'] = gals['dec'][igals]
		# param['mag_use_normal'] = gals['mag_true_g_lsst'][igals]
		param['mag_use_normal'] = gals['mag_csst_%s'%(self.filt.filter_type)][igals]
		if self.filt.is_too_dim(mag=param['mag_use_normal'], margin=self.config["obs_setting"]["mag_lim_margin"]):
		continue

		# if param['mag_use_normal'] >= 26.5:
		# continue
		param['z'] = gals['redshift'][igals]
		@@ -165,11 +195,16 @@ class C6_Catalog(CatalogBase):
		param['e2'] = gals['ellipticity_true'][igals][1]

		# For shape calculation

		param['ell_total'] = np.sqrt(param['e1']2 + param['e2']2)
		if param['ell_total'] > 0.9:
		continue
		param['e1_disk'] = param['e1']
		param['e2_disk'] = param['e2']
		param['e1_bulge'] = param['e1']
		param['e2_bulge'] = param['e2']


		param['delta_ra'] = 0
		param['delta_dec'] = 0

		@@ -211,7 +246,7 @@ class C6_Catalog(CatalogBase):
		# TEMP
		self.ids += 1
		# param['id'] = self.ids
		param['id'] = str(pix_id) + '%02d'%(cat_id) + '%08d'%(igals)
		param['id'] = '%06d'%(int(pix_id)) + '%06d'%(cat_id) + '%08d'%(igals)

		if param['star'] == 0:
		obj = Galaxy(param, self.rotation, logger=self.logger)
		@@ -264,8 +299,8 @@ class C6_Catalog(CatalogBase):
		input_time_str=time_str
		)
		for istars in range(nstars):
		# (TEST)
		# if istars > 10:
		# # (TEST)
		# if istars > 100:
		# break

		param = self.initialize_param()
		@@ -283,7 +318,6 @@ class C6_Catalog(CatalogBase):
		# if param['mag_use_normal'] >= 26.5:
		# continue
		self.ids += 1
		# param['id'] = self.ids
		param['id'] = stars['sourceID'][istars]
		param['sed_type'] = stars['sourceID'][istars]
		param['model_tag'] = stars['model_tag'][istars]
		@@ -316,15 +350,28 @@ class C6_Catalog(CatalogBase):
		print(e)

		if "galaxy_cat" in self.config["input_path"] and self.config["input_path"]["galaxy_cat"] and not self.config["run_option"]["star_only"]:
		for i in range(76):
		file_path = os.path.join(self.galaxy_path, "galaxies%04d_C6.h5"%(i))
		gals_cat = h5.File(file_path, 'r')['galaxies']
		# for i in range(76):
		# file_path = os.path.join(self.galaxy_path, "galaxies%04d_C6.h5"%(i))
		# gals_cat = h5.File(file_path, 'r')['galaxies']
		# for pix in self.pix_list:
		# try:
		# gals = gals_cat[str(pix)]
		# self._load_gals(gals, pix_id=pix, cat_id=i)
		# del gals
		# except Exception as e:
		# traceback.print_exc()
		# self.logger.error(str(e))
		# print(e)
		for pix in self.pix_list:
		try:
		bundleID = get_bundleIndex(pix)
		file_path = os.path.join(self.galaxy_path, "galaxies_C6_bundle{:06}.h5".format(bundleID))
		gals_cat = h5.File(file_path, 'r')['galaxies']
		gals = gals_cat[str(pix)]
		self._load_gals(gals, pix_id=pix, cat_id=i)
		self._load_gals(gals, pix_id=pix, cat_id=bundleID)
		del gals
		except Exception as e:
		traceback.print_exc()
		self.logger.error(str(e))
		print(e)
		if self.logger is not None:
		@@ -333,6 +380,19 @@ class C6_Catalog(CatalogBase):
		else:
		print("number of objects in catalog: ", len(self.objs))

		# (TEST)
		# def convert_mags(self, obj):
		# spec = np.matmul(obj.coeff, self.pcs.T)
		# lamb = self.lamb_gal * U.angstrom
		# unit_sed = ((lamb * lamb)/constants.cU.erg/U.second/U.cm*2/U.angstrom).to(U.jansky)
		# unit_sed = unit_sed.value
		# lamb = lamb.value
		# lamb *= (1 + obj.z)
		# spec *= (1 + obj.z)
		# mags = -2.5 * np.log10(unit_sed*spec) + 8.9
		# mags += self.cosmo.distmod(obj.z).value
		# return lamb, mags


		def load_sed(self, obj, **kwargs):
		if obj.type == 'star':
		@@ -344,11 +404,13 @@ class C6_Catalog(CatalogBase):
		feh=obj.param['feh']
		)
		elif obj.type == 'galaxy' or obj.type == 'quasar':
		dist_L_pc = (1 + obj.z) * comoving_dist(z=obj.z)[0]
		factor = (10 / dist_L_pc)**2
		# dist_L_pc = (1 + obj.z) * comoving_dist(z=obj.z)[0]
		# factor = (10 / dist_L_pc)**2
		factor = 10*(-.4 self.cosmo.distmod(obj.z).value)
		flux = np.matmul(self.pcs, obj.coeff) * factor
		if np.any(flux < 0):
		raise ValueError("Glaxy %s: negative SED fluxes"%obj.id)
		# if np.any(flux < 0):
		# raise ValueError("Glaxy %s: negative SED fluxes"%obj.id)
		flux[flux < 0] = 0.
		sedcat = np.vstack((self.lamb_gal, flux)).T
		sed_data = getObservedSED(
		sedCat=sedcat,
		@@ -368,15 +430,16 @@ class C6_Catalog(CatalogBase):
		all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13
		sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))

		if obj.type == 'galaxy' or obj.type == 'quasar':
		# integrate to get the magnitudes
		sed_photon = np.array([sed['WAVELENGTH'], sed['FLUX']]).T
		# print("sed_photon = ", sed_photon)
		sed_photon = galsim.LookupTable(x=np.array(sed_photon[:, 0]), f=np.array(sed_photon[:, 1]), interpolant='nearest')
		sed_photon = galsim.SED(sed_photon, wave_type='A', flux_type='1', fast=False)
		interFlux = integrate_sed_bandpass(sed=sed_photon, bandpass=self.filt.bandpass_full)
		obj.param['mag_use_normal'] = getABMAG(interFlux, self.filt.bandpass_full)
		# print("mag_use_normal = %.3f"%obj.param['mag_use_normal'])
		# if obj.type == 'galaxy' or obj.type == 'quasar':
		# # integrate to get the magnitudes
		# sed_photon = np.array([sed['WAVELENGTH'], sed['FLUX']]).T
		# sed_photon = galsim.LookupTable(x=np.array(sed_photon[:, 0]), f=np.array(sed_photon[:, 1]), interpolant='nearest')
		# sed_photon = galsim.SED(sed_photon, wave_type='A', flux_type='1', fast=False)
		# interFlux = integrate_sed_bandpass(sed=sed_photon, bandpass=self.filt.bandpass_full)
		# obj.param['mag_use_normal'] = getABMAG(interFlux, self.filt.bandpass_full)
		# # print("mag_use_normal = %.3f"%obj.param['mag_use_normal'])
		# # mag = getABMAG(interFlux, self.filt.bandpass_full)
		# # print("mag diff = %.3f"%(mag - obj.param['mag_use_normal']))

		del wave
		del flux

ObservationSim/Instrument/Chip/Chip.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -229,6 +229,7 @@ class Chip(FocalPlane):


		def getSkyCoverage(self, wcs):
		# print("In getSkyCoverage: xmin = %.3f, xmax = %.3f, ymin = %.3f, ymax = %.3f"%(self.bound.xmin, self.bound.xmax, self.bound.ymin, self.bound.ymax))
		return super().getSkyCoverage(wcs, self.bound.xmin, self.bound.xmax, self.bound.ymin, self.bound.ymax)

ObservationSim/MockObject/Galaxy.py

+33 −26

Original line number	Diff line number	Diff line
		@@ -137,6 +137,7 @@ class Galaxy(MockObject):
		# return False
		continue
		nphotons_sum += nphotons

		# print("nphotons_sub-band_%d = %.2f"%(i, nphotons))

		psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold)
		@@ -171,8 +172,10 @@ class Galaxy(MockObject):
		# photons_list.append(photons)

		stamp = gal.drawImage(wcs=real_wcs_local, method='phot', offset=offset, save_photons=True)

		xmax = max(xmax, stamp.xmax)
		ymax = max(ymax, stamp.ymax)

		photons = stamp.photons
		photons.x += x_nominal
		photons.y += y_nominal
		@@ -184,6 +187,8 @@ class Galaxy(MockObject):
		stamp.wcs = real_wcs_local
		stamp.setCenter(x_nominal, y_nominal)
		bounds = stamp.bounds & galsim.BoundsI(0, chip.npix_x - 1, 0, chip.npix_y - 1)

		if bounds.area() > 0:
		chip.img.setOrigin(0, 0)
		stamp[bounds] = chip.img[bounds]

		@@ -237,7 +242,7 @@ class Galaxy(MockObject):

		def drawObj_slitless(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0,
		exptime=150., normFilter=None, grating_split_pos=3685):

		if normFilter is not None:
		norm_thr_rang_ids = normFilter['SENSITIVITY'] > 0.001
		sedNormFactor = getNormFactorForSpecWithABMAG(ABMag=self.param['mag_use_normal'], spectrum=self.sed,
		norm_thr=normFilter,
		@@ -245,6 +250,8 @@ class Galaxy(MockObject):
		eWave=np.ceil(normFilter[norm_thr_rang_ids][-1][0]))
		if sedNormFactor == 0:
		return False
		else:
		sedNormFactor = 1.
		normalSED = Table(np.array([self.sed['WAVELENGTH'], self.sed['FLUX'] * sedNormFactor]).T,
		names=('WAVELENGTH', 'FLUX'))

ObservationSim/MockObject/MockObject.py

+15 −11

Original line number	Diff line number	Diff line
		import galsim
		import numpy as np
		import astropy.constants as cons
		from astropy import wcs
		from astropy.table import Table

		from ObservationSim.MockObject._util import magToFlux, VC_A, convolveGaussXorders
		@@ -99,8 +100,6 @@ class MockObject(object):
		dy = y - self.y_nominal
		self.offset = galsim.PositionD(dx, dy)

		from astropy import wcs

		if img_header is not None:
		self.real_wcs = galsim.FitsWCS(header=img_header)
		else:
		@@ -224,6 +223,11 @@ class MockObject(object):
		stamp.wcs = real_wcs_local
		stamp.setCenter(x_nominal, y_nominal)
		bounds = stamp.bounds & galsim.BoundsI(0, chip.npix_x - 1, 0, chip.npix_y - 1)

		# # (DEBUG)
		# print("stamp bounds: ", stamp.bounds)
		# print(bounds)
		if bounds.area() > 0:
		chip.img.setOrigin(0, 0)
		stamp[bounds] = chip.img[bounds]
		for i in range(len(photons_list)):

ObservationSim/MockObject/_util.py

+4 −1

Original line number	Diff line number	Diff line
		@@ -455,7 +455,10 @@ def getObservedSED(sedCat, redshift=0.0, av=0.0, redden=0):
		sw, sf = sedCat[:,0], sedCat[:,1]
		# reddening
		sf = reddening(sw, sf, av=av, model=redden)
		sw, sf = swz, sf(z**3)
		# sw, sf = swz, sf(z**3)
		sw, sf = sw*z, sf/z
		# sw, sf = sw*z, sf

		# lyman forest correction
		sf = lyman_forest(sw, sf, redshift)
		isedObs = (sw.copy(), sf.copy())