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

Catalog/C6_Catalog.py

+98 −35

Original line number	Original line	Diff line number	Diff line
	@@ -5,6 +5,7 @@ import numpy as np
	import h5py as h5		import h5py as h5
	import healpy as hp		import healpy as hp
	import astropy.constants as cons		import astropy.constants as cons
			import traceback
	from astropy.coordinates import spherical_to_cartesian		from astropy.coordinates import spherical_to_cartesian
	from astropy.table import Table		from astropy.table import Table
	from scipy import interpolate		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.MockObject._util import tag_sed, getObservedSED, getABMAG, integrate_sed_bandpass, comoving_dist
	from ObservationSim.Astrometry.Astrometry_util import on_orbit_obs_position		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:		try:
	import importlib.resources as pkg_resources		import importlib.resources as pkg_resources
	except ImportError:		except ImportError:
	@@ -22,26 +28,40 @@ except ImportError:

	NSIDE = 128		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):		class C6_Catalog(CatalogBase):
	def __init__(self, config, chip, pointing, chip_output, filt, **kwargs):		def __init__(self, config, chip, pointing, chip_output, filt, **kwargs):
	super().__init__()		super().__init__()
	self.cat_dir = os.path.join(config["data_dir"], config["input_path"]["cat_dir"])		self.cat_dir = os.path.join(config["data_dir"], config["input_path"]["cat_dir"])
	self.seed_Av = config["random_seeds"]["seed_Av"]		self.seed_Av = config["random_seeds"]["seed_Av"]

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

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

	with pkg_resources.path('Catalog.data', 'SLOAN_SDSS.g.fits') as filter_path:		with pkg_resources.path('Catalog.data', 'SLOAN_SDSS.g.fits') as filter_path:
	self.normF_star = Table.read(str(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.config = config
	self.chip = chip		self.chip = chip
	self.pointing = pointing		self.pointing = pointing

	# (DEBUG)
	self.max_size = 0.		self.max_size = 0.

	if "star_cat" in config["input_path"] and config["input_path"]["star_cat"] and not config["run_option"]["galaxy_only"]:		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_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]))		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]))		dec = np.deg2rad(np.array([dec_max, dec_max, dec_min, dec_min]))
	vertices = spherical_to_cartesian(1., dec, ra)		# vertices = spherical_to_cartesian(1., dec, ra)
	self.pix_list = hp.query_polygon(NSIDE, np.array(vertices).T, inclusive=True)		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:		if self.logger is not None:
	msg = str(("HEALPix List: ", self.pix_list))		msg = str(("HEALPix List: ", self.pix_list))
	self.logger.info(msg)		self.logger.info(msg)
	@@ -144,16 +169,21 @@ class C6_Catalog(CatalogBase):
	)		)

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

	param = self.initialize_param()		param = self.initialize_param()
	param['ra'] = ra_arr[igals]		param['ra'] = ra_arr[igals]
	param['dec'] = dec_arr[igals]		param['dec'] = dec_arr[igals]
	param['ra_orig'] = gals['ra'][igals]		param['ra_orig'] = gals['ra'][igals]
	param['dec_orig'] = gals['dec'][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:		# if param['mag_use_normal'] >= 26.5:
	# continue		# continue
	param['z'] = gals['redshift'][igals]		param['z'] = gals['redshift'][igals]
	@@ -165,11 +195,16 @@ class C6_Catalog(CatalogBase):
	param['e2'] = gals['ellipticity_true'][igals][1]		param['e2'] = gals['ellipticity_true'][igals][1]

	# For shape calculation		# 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['e1_disk'] = param['e1']
	param['e2_disk'] = param['e2']		param['e2_disk'] = param['e2']
	param['e1_bulge'] = param['e1']		param['e1_bulge'] = param['e1']
	param['e2_bulge'] = param['e2']		param['e2_bulge'] = param['e2']


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

	@@ -211,7 +246,7 @@ class C6_Catalog(CatalogBase):
	# TEMP		# TEMP
	self.ids += 1		self.ids += 1
	# param['id'] = self.ids		# 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:		if param['star'] == 0:
	obj = Galaxy(param, self.rotation, logger=self.logger)		obj = Galaxy(param, self.rotation, logger=self.logger)
	@@ -264,8 +299,8 @@ class C6_Catalog(CatalogBase):
	input_time_str=time_str		input_time_str=time_str
	)		)
	for istars in range(nstars):		for istars in range(nstars):
	# (TEST)		# # (TEST)
	# if istars > 10:		# if istars > 100:
	# break		# break

	param = self.initialize_param()		param = self.initialize_param()
	@@ -283,7 +318,6 @@ class C6_Catalog(CatalogBase):
	# if param['mag_use_normal'] >= 26.5:		# if param['mag_use_normal'] >= 26.5:
	# continue		# continue
	self.ids += 1		self.ids += 1
	# param['id'] = self.ids
	param['id'] = stars['sourceID'][istars]		param['id'] = stars['sourceID'][istars]
	param['sed_type'] = stars['sourceID'][istars]		param['sed_type'] = stars['sourceID'][istars]
	param['model_tag'] = stars['model_tag'][istars]		param['model_tag'] = stars['model_tag'][istars]
	@@ -316,15 +350,28 @@ class C6_Catalog(CatalogBase):
	print(e)		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"]:		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):		# for i in range(76):
	file_path = os.path.join(self.galaxy_path, "galaxies%04d_C6.h5"%(i))		# file_path = os.path.join(self.galaxy_path, "galaxies%04d_C6.h5"%(i))
	gals_cat = h5.File(file_path, 'r')['galaxies']		# 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:		for pix in self.pix_list:
	try:		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)]		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		del gals
	except Exception as e:		except Exception as e:
			traceback.print_exc()
	self.logger.error(str(e))		self.logger.error(str(e))
	print(e)		print(e)
	if self.logger is not None:		if self.logger is not None:
	@@ -333,6 +380,19 @@ class C6_Catalog(CatalogBase):
	else:		else:
	print("number of objects in catalog: ", len(self.objs))		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):		def load_sed(self, obj, **kwargs):
	if obj.type == 'star':		if obj.type == 'star':
	@@ -344,11 +404,13 @@ class C6_Catalog(CatalogBase):
	feh=obj.param['feh']		feh=obj.param['feh']
	)		)
	elif obj.type == 'galaxy' or obj.type == 'quasar':		elif obj.type == 'galaxy' or obj.type == 'quasar':
	dist_L_pc = (1 + obj.z) * comoving_dist(z=obj.z)[0]		# dist_L_pc = (1 + obj.z) * comoving_dist(z=obj.z)[0]
	factor = (10 / dist_L_pc)**2		# factor = (10 / dist_L_pc)**2
			factor = 10*(-.4 self.cosmo.distmod(obj.z).value)
	flux = np.matmul(self.pcs, obj.coeff) * factor		flux = np.matmul(self.pcs, obj.coeff) * factor
	if np.any(flux < 0):		# if np.any(flux < 0):
	raise ValueError("Glaxy %s: negative SED fluxes"%obj.id)		# raise ValueError("Glaxy %s: negative SED fluxes"%obj.id)
			flux[flux < 0] = 0.
	sedcat = np.vstack((self.lamb_gal, flux)).T		sedcat = np.vstack((self.lamb_gal, flux)).T
	sed_data = getObservedSED(		sed_data = getObservedSED(
	sedCat=sedcat,		sedCat=sedcat,
	@@ -368,15 +430,16 @@ class C6_Catalog(CatalogBase):
	all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13		all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13
	sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))		sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))

	if obj.type == 'galaxy' or obj.type == 'quasar':		# if obj.type == 'galaxy' or obj.type == 'quasar':
	# integrate to get the magnitudes		# # integrate to get the magnitudes
	sed_photon = np.array([sed['WAVELENGTH'], sed['FLUX']]).T		# 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.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)
	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)
	interFlux = integrate_sed_bandpass(sed=sed_photon, bandpass=self.filt.bandpass_full)		# obj.param['mag_use_normal'] = getABMAG(interFlux, 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'])
	# 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 wave
	del flux		del flux

ObservationSim/Instrument/Chip/Chip.py

+1 −0

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


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

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

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

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

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

			if bounds.area() > 0:
	chip.img.setOrigin(0, 0)		chip.img.setOrigin(0, 0)
	stamp[bounds] = chip.img[bounds]		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,		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):		exptime=150., normFilter=None, grating_split_pos=3685):
			if normFilter is not None:
	norm_thr_rang_ids = normFilter['SENSITIVITY'] > 0.001		norm_thr_rang_ids = normFilter['SENSITIVITY'] > 0.001
	sedNormFactor = getNormFactorForSpecWithABMAG(ABMag=self.param['mag_use_normal'], spectrum=self.sed,		sedNormFactor = getNormFactorForSpecWithABMAG(ABMag=self.param['mag_use_normal'], spectrum=self.sed,
	norm_thr=normFilter,		norm_thr=normFilter,
	@@ -245,6 +250,8 @@ class Galaxy(MockObject):
	eWave=np.ceil(normFilter[norm_thr_rang_ids][-1][0]))		eWave=np.ceil(normFilter[norm_thr_rang_ids][-1][0]))
	if sedNormFactor == 0:		if sedNormFactor == 0:
	return False		return False
			else:
			sedNormFactor = 1.
	normalSED = Table(np.array([self.sed['WAVELENGTH'], self.sed['FLUX'] * sedNormFactor]).T,		normalSED = Table(np.array([self.sed['WAVELENGTH'], self.sed['FLUX'] * sedNormFactor]).T,
	names=('WAVELENGTH', 'FLUX'))		names=('WAVELENGTH', 'FLUX'))

ObservationSim/MockObject/MockObject.py

+15 −11

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

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

	from astropy import wcs

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

ObservationSim/MockObject/_util.py

+4 −1

Original line number	Original line	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]		sw, sf = sedCat[:,0], sedCat[:,1]
	# reddening		# reddening
	sf = reddening(sw, sf, av=av, model=redden)		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		# lyman forest correction
	sf = lyman_forest(sw, sf, redshift)		sf = lyman_forest(sw, sf, redshift)
	isedObs = (sw.copy(), sf.copy())		isedObs = (sw.copy(), sf.copy())