def __init__(self):
from speclite import filters
from scipy.spatial import cKDTree as KDTree
from desisim.io import read_basis_templates
self.bgs_meta = read_basis_templates(objtype='BGS', onlymeta=True)
self.bgs_tree = KDTree(self._bgs())
def test_HBETA(self):
'''Confirm that BGS H-beta flux matches meta table description'''
print('In function test_HBETA, seed = {}'.format(self.seed))
wave = np.arange(5000, 7000.1, 0.2)
# Need to choose just the star-forming galaxies.
from desisim.io import read_basis_templates
baseflux, basewave, basemeta = read_basis_templates(objtype='BGS')
keep = np.where(basemeta['HBETA_LIMIT'] == 0)[0]
bgs = BGS(wave=wave,
basewave=basewave,
baseflux=baseflux[keep, :],
basemeta=basemeta[keep])
flux, ww, meta = bgs.make_templates(
seed=self.seed,
nmodel=10,
zrange=(0.05, 0.4),
logvdisp_meansig=[np.log10(75), 0.0],
nocolorcuts=True,
nocontinuum=True)
for i in range(len(meta)):
z = meta['REDSHIFT'][i]
ii = (4854 * (1 + z) < wave) & (wave < 4868 * (1 + z))
hbetaflux = 1e-17 * np.sum(flux[i, ii] * np.gradient(wave[ii]))
self.assertAlmostEqual(hbetaflux, meta['HBETAFLUX'][i], 2)
def main():
seed = 123
ngal = 100
npergal = 50
# Read the mock catalog.
cat = h5py.File('galaxy_catalogue_0.hdf5')
gr = cat['Data']['g_r'][:ngal]
mag = cat['Data']['app_mag'][:ngal]
z = cat['Data']['z_obs'][:ngal]
zmin, zmax = np.min(z), np.max(z)
# Read the basis templates and initialize the output metadata table.
baseflux, basewave, basemeta = read_basis_templates('BGS')
meta = empty_metatable(objtype='BGS', nmodel=ngal)
bgs = BGS(minwave=3000, maxwave=11000.0)
for igal in range(ngal):
flux, wave, meta = bgs.make_templates(npergal, zrange=(zmin, zmax),
nocolorcuts=True)
pdb.set_trace()
def test_read_templates(self):
wave = np.arange(7000, 7020)
nspec = 3
for objtype in ['ELG', 'LRG', 'QSO', 'STAR', 'WD']:
flux, wave1, meta = io.read_basis_templates(objtype, outwave=wave, nspec=3)
ntemplates, nwave = flux.shape
self.assertEqual(nwave, len(wave))
self.assertEqual(ntemplates, nspec)
self.assertEqual(len(meta), nspec)
def test_read_templates(self):
wave = np.arange(7000, 7020)
nspec = 3
for objtype in ['ELG', 'LRG', 'QSO', 'STAR', 'WD']:
flux, wave1, meta = io.read_basis_templates(objtype,
outwave=wave,
nspec=3)
ntemplates, nwave = flux.shape
self.assertEqual(nwave, len(wave))
self.assertEqual(ntemplates, nspec)
self.assertEqual(len(meta), nspec)
def __init__(self, nproc=1):
from speclite import filters
from scipy.spatial import KDTree
self.nproc = nproc
self.bgs_meta = read_basis_templates(objtype='BGS', onlymeta=True)
self.elg_meta = read_basis_templates(objtype='ELG', onlymeta=True)
self.lrg_meta = read_basis_templates(objtype='LRG', onlymeta=True)
self.qso_meta = read_basis_templates(objtype='QSO', onlymeta=True)
self.wd_da_meta = read_basis_templates(objtype='WD', subtype='DA', onlymeta=True)
self.wd_db_meta = read_basis_templates(objtype='WD', subtype='DB', onlymeta=True)
self.decamwise = filters.load_filters('decam2014-g', 'decam2014-r', 'decam2014-z',
'wise2010-W1', 'wise2010-W2')
# Read all the stellar spectra and synthesize DECaLS/WISE fluxes.
self.star_phot()
#self.elg_phot()
#self.elg_kcorr = read_basis_templates(objtype='ELG', onlykcorr=True)
self.bgs_tree = KDTree(self._bgs())
self.elg_tree = KDTree(self._elg())
#self.lrg_tree = KDTree(self._lrg())
#self.qso_tree = KDTree(self._qso())
self.star_tree = KDTree(self._star())
self.wd_da_tree = KDTree(self._wd_da())
self.wd_db_tree = KDTree(self._wd_db())
def elg_kcorr(self):
"""Compute K-corrections for the ELG templates on a grid of redshift."""
flux, wave, meta = read_basis_templates(objtype='ELG')
nt = len(meta)
zmin, zmax, dz = 0.0, 2.0, 0.1
nz = np.round( (zmax - zmin) / dz ).astype('i2')
colors = dict(
redshift = np.linspace(0.0, 2.0, nz),
gr = np.zeros( (nt, nz) ),
rz = np.zeros( (nt, nz) )
)
#from time import time
#t0 = time()
#for iz, red in enumerate(colors['redshift']):
# print(iz)
# zwave = wave.astype('float') * (1 + red)
# phot = self.grz.get_ab_maggies(flux, zwave, mask_invalid=False)
# colors['gr'][:, iz] = -2.5 * np.log10( phot['decam2014-g'] / phot['decam2014-r'] )
# colors['rz'][:, iz] = -2.5 * np.log10( phot['decam2014-r'] / phot['decam2014-z'] )
#print( (time() - t0) / 60 )
from time import time
t0 = time()
zargs = list()
for red in colors['redshift']:
zargs.append( (red, flux, wave, self.grz) )
if self.nproc > 1:
pool = multiprocessing.Pool(self.nproc)
result = pool.map( _get_colors_onez, zargs )
pool.close()
else:
result = list()
for onearg in zargs:
result.append( _get_colors_onez(onearg) )
print( (time() - t0) / 60 )
import matplotlib.pyplot as plt
for tt in range(10):
plt.scatter(colors['rz'][tt, :], colors['gr'][tt, :])
plt.xlim(-0.5, 2.0) ; plt.ylim(-0.5, 2.0)
plt.show()
import pdb ; pdb.set_trace()
def star_phot(self):
"""Synthesize photometry for the full set of stellar templates."""
star_normfilter = 'decam2014-r'
star_flux, star_wave, star_meta = read_basis_templates(objtype='STAR')
star_maggies_table = self.decamwise.get_ab_maggies(star_flux, star_wave, mask_invalid=True)
star_maggies = np.zeros( (len(star_meta), len(self.decamwise)) )
for ff, key in enumerate(star_maggies_table.columns):
star_maggies[:, ff] = star_maggies_table[key] / star_maggies_table[star_normfilter] # maggies
self.star_flux_g = star_maggies[:, 0]
self.star_flux_r = star_maggies[:, 1]
self.star_flux_z = star_maggies[:, 2]
self.star_flux_w1 = star_maggies[:, 3]
self.star_flux_w2 = star_maggies[:, 4]
self.star_meta = star_meta
def __init__(self):
"""Read and cache the BAL template set.
Attributes:
balflux (numpy.ndarray): Array [nbase,npix] of the rest-frame BAL
templates.
balwave (numpy.ndarray): Array [npix] of rest-frame wavelengths
corresponding to BASEFLUX (Angstrom).
balmeta (astropy.Table): Table of metadata [nbase] for each template.
"""
from desisim.io import read_basis_templates
balflux, balwave, balmeta = read_basis_templates(objtype='BAL')
self.balflux = balflux
self.balwave = balwave
self.balmeta = balmeta
def __init__(self):
"""Read and cache the BAL template set.
Attributes:
balflux (numpy.ndarray): Array [nbase,npix] of the rest-frame BAL
templates.
balwave (numpy.ndarray): Array [npix] of rest-frame wavelengths
corresponding to BASEFLUX (Angstrom).
balmeta (astropy.Table): Table of metadata [nbase] for each template.
"""
from desisim.io import read_basis_templates
balflux, balwave, balmeta = read_basis_templates(objtype='BAL')
self.balflux = balflux
self.balwave = balwave
self.balmeta = balmeta
def main(args):
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='ELG archetypes')
parser.add_argument('-o', '--objtype', type=str, default='ELG', help='ELG', metavar='')
# Set up the logger.
if args.verbose:
log = get_logger(DEBUG)
else:
log = get_logger()
objtype = args.objtype.upper()
log.debug('Using OBJTYPE {}'.format(objtype))
baseflux, basewave, basemeta = read_basis_templates(objtype=objtype)
pdb.set_trace()
def sim_lenssource_spectra(BGSmags, fratios, seed=None, exptime=1000., nperchunk=500,
infofile='lenssource-truth.fits', debug=False):
"""Build the (noisy) lens+source spectra. No redshift-fitting.
"""
from astropy.io import fits
from desisim.templates import BGS, ELG
from desisim.scripts.quickspectra import sim_spectra
from desisim.io import read_basis_templates
from desispec.io import read_spectra
rand = np.random.RandomState(seed)
nsim = len(BGSmags)
assert(nsim == len(fratios))
if nperchunk > 500:
raise ValueError('nperchunk={} exceeds the maximum number allowed by redrock'.format(nperchunk))
nchunk = np.ceil(nsim / nperchunk).astype(int)
# [1] Build the noise-less lens (BGS) spectra.
# Read one healpix of the Buzzard mocks for redshift distribution.
mockfile = os.path.join(os.getenv('DESI_ROOT'), 'mocks', 'buzzard', 'buzzard_v1.6_desicut',
'8', '0', '0', 'Buzzard_v1.6_lensed-8-0.fits')
print('Reading {}'.format(mockfile))
mock_BGS = Table(fitsio.read(mockfile)) #columns='lmag z'.split()
# From the BGS template library, select a reddish galaxy
tflux, twave, tmeta_BGS = read_basis_templates('BGS')
i = np.argmin(np.abs(2.0 - tmeta_BGS['D4000']))
iredBGS = i
redspecBGS = tflux[i, :]
Itempl_BGS = np.array([iredBGS])
# LMAG: observed mag, DECam grizY
mock_mag_r = mock_BGS['LMAG'][:, 1] # r-band
dm = 0.01
zz_BGS = np.zeros_like(BGSmags)
for ii, mag in enumerate(BGSmags):
I = np.flatnonzero(np.abs(mock_mag_r - mag) <= dm)
zz_BGS[ii] = mock_BGS['Z'][rand.choice(I, size=1, replace=False)]
input_meta_BGS = Table()
input_meta_BGS['TEMPLATEID'] = [Itempl_BGS]*nsim
input_meta_BGS['SEED'] = np.arange(nsim) # [seed]*nsim #
input_meta_BGS['REDSHIFT'] = zz_BGS
input_meta_BGS['MAG'] = BGSmags
input_meta_BGS['MAGFILTER'] = ['decam2014-r']*nsim
BGSflux, BGSwave, BGSmeta, BGSobjmeta = BGS().make_templates(
input_meta=input_meta_BGS, nocolorcuts=True, seed=seed)
# [2] Build the noise-less source (ELG) spectra.
#ELGmags = maggen(BGSmags[:, np.newaxis], fratios[np.newaxis, :])
ELGmags = maggen(BGSmags, fratios)
# Select a single ELG template.
tflux, twave, tmeta_ELG = read_basis_templates('ELG')
i = np.argmin(np.abs(1.0 - tmeta_ELG['D4000'])) # MIGHT NEED TO ADJUST THIS LINE
iblueELG = i
bluespecELG = tflux[i, :]
Itempl_ELG = np.array([iblueELG])
# uncorrelated redshifts
zmin_ELG, zmax_ELG = 0.8, 1.4
zz_ELG = rand.uniform(zmin_ELG, zmax_ELG, nsim)
input_meta_ELG = Table()
input_meta_ELG['TEMPLATEID'] = [Itempl_ELG]*nsim
input_meta_ELG['SEED'] = [3]*nsim # [seed]*nsim # np.arange(nsim) hack!
input_meta_ELG['REDSHIFT'] = zz_ELG
input_meta_ELG['MAG'] = ELGmags
input_meta_ELG['MAGFILTER'] = ['decam2014-r']*nsim
ELGflux, ELGwave, ELGmeta, ELGobjmeta = ELG().make_templates(
input_meta=input_meta_ELG, nocolorcuts=True, seed=seed)
assert(np.all(BGSwave == ELGwave))
# Pack the simulation info into a table, for convenience.
siminfo = Table()
siminfo['TARGETID'] = np.arange(nsim, dtype=np.int64)
siminfo['LENS_Z'] = input_meta_BGS['REDSHIFT'].astype('f4')
siminfo['LENS_MAG'] = input_meta_BGS['MAG'].astype('f4')
siminfo['SOURCE_Z'] = input_meta_ELG['REDSHIFT'].astype('f4')
siminfo['SOURCE_MAG'] = input_meta_ELG['MAG'].astype('f4')
siminfo['FRATIO'] = fratios.astype('f4')
siminfo['CHUNK'] = np.zeros(nsim, dtype=np.int32)
# Generate simulated DESI spectra given real spectra and observing
# conditions. Divide the sample into chunks with a fixed number of
# spectra per chunk (but no more than 500).
obscond = {'AIRMASS': 1.3, 'EXPTIME': exptime, 'SEEING': 1.1,
'MOONALT': -60, 'MOONFRAC': 0.0, 'MOONSEP': 180}
simflux = BGSflux + ELGflux
simwave = BGSwave
for ichunk in np.arange(nchunk):
specfile = 'lenssource-spectra-chunk{:03d}.fits'.format(ichunk)
print('Writing chunk {}/{} to {}'.format(ichunk, nchunk-1, specfile))
i1 = ichunk * nperchunk
i2 = (ichunk+1) * nperchunk
siminfo['CHUNK'][i1:i2] = ichunk
sim_spectra(simwave, simflux[i1:i2, :], 'dark', specfile, obsconditions=obscond,
sourcetype='bgs', seed=seed, targetid=siminfo['TARGETID'][i1:i2],
redshift=siminfo['LENS_Z'][i1:i2])
if debug:
spectra = read_spectra(specfile)
for igal in np.arange(spectra.num_targets()):
qafile = 'lenssource-spectra-chunk{:03d}-{}.png'.format(ichunk, igal)
fig, ax = plt.subplots()
for band in spectra.bands:
ax.plot(spectra.wave[band], spectra.flux[band][igal, :])
ax.plot(simwave, simflux[i1:i2, :][igal, :], color='k', lw=2)
ax.set_ylim(np.median(simflux[i1:i2, :][igal, :]) + np.std(spectra.flux['r'][igal, :]) * np.array([-1.5, 3]))
fig.savefig(qafile)
plt.close()
# write out and return
hduflux = fits.PrimaryHDU(simflux)
hduflux.header['EXTNAME'] = 'FLUX'
hduflux.header['BUNIT'] = '10^(-17) erg/(s cm2 Angstrom)'
hdubgs = fits.ImageHDU(BGSflux)
hdubgs.header['EXTNAME'] = 'BGSFLUX'
hduelg = fits.ImageHDU(ELGflux)
hduelg.header['EXTNAME'] = 'ELGFLUX'
hduwave = fits.ImageHDU(simwave)
hduwave.header['EXTNAME'] = 'WAVE'
hduwave.header['BUNIT'] = 'Angstrom'
hduwave.header['AIRORVAC'] = ('vac', 'vacuum wavelengths')
hdutable = fits.convenience.table_to_hdu(siminfo)
hdutable.header['EXTNAME'] = 'METADATA'
hx = fits.HDUList([hduflux, hdubgs, hduelg, hduwave, hdutable])
print('Writing {}'.format(infofile))
hx.writeto(infofile, overwrite=True)
return siminfo
def __init__(self, nmodel=50, minwave=3600.0, maxwave=10000.0,
cdelt=2.0, wave=None, seed=None):
"""Read the QSO basis continuum templates, grzW1W2 filter profiles and initialize
the output wavelength array.
Note:
* Only a linearly-spaced output wavelength array is currently supported.
* The basis templates are only defined in the range 3500-10000 A (observed).
Args:
objtype (str): object type
nmodel (int, optional): Number of models to generate (default 50).
minwave (float, optional): minimum value of the output wavelength
array [default 3600 Angstrom].
maxwave (float, optional): minimum value of the output wavelength
array [default 10000 Angstrom].
cdelt (float, optional): spacing of the output wavelength array
[default 2 Angstrom/pixel].
wave (numpy.ndarray): Input/output observed-frame wavelength array,
overriding the minwave, maxwave, and cdelt arguments [Angstrom].
seed (long, optional): input seed for the random numbers
Attributes:
objtype (str): See Args.
nmodel (int): See Args.
seed (long): See Args.
rand (numpy.RandomState): instance of numpy.random.RandomState(seed)
wave (numpy.ndarray): Output wavelength array [Angstrom].
baseflux (numpy.ndarray): Array [nbase,npix] of the base rest-frame
QSO continuum spectra [erg/s/cm2/A].
basewave (numpy.ndarray): Array [npix] of rest-frame wavelengths
corresponding to BASEFLUX [Angstrom].
basemeta (astropy.Table): Table of meta-data for each base template [nbase].
gfilt (FILTERFUNC instance): DECam g-band filter profile class.
rfilt (FILTERFUNC instance): DECam r-band filter profile class.
zfilt (FILTERFUNC instance): DECam z-band filter profile class.
w1filt (FILTERFUNC instance): WISE W1-band filter profile class.
w2filt (FILTERFUNC instance): WISE W2-band filter profile class.
"""
from desisim.filterfunc import filterfunc as filt
from desisim.io import read_basis_templates
self.objtype = 'QSO'
self.nmodel = nmodel
self.seed = seed
self.rand = np.random.RandomState(seed=self.seed)
# Initialize the output wavelength array (linear spacing) unless it is
# already provided.
if wave is None:
npix = (maxwave-minwave)/cdelt+1
wave = np.linspace(minwave,maxwave,npix)
self.wave = wave
# Read the basis spectra.
baseflux, basewave, basemeta = read_basis_templates(objtype=self.objtype)
self.baseflux = baseflux
self.basewave = basewave
self.basemeta = basemeta
# Initialize the filter profiles.
self.gfilt = filt(filtername='decam_g.txt')
self.rfilt = filt(filtername='decam_r.txt')
self.zfilt = filt(filtername='decam_z.txt')
self.w1filt = filt(filtername='wise_w1.txt')
self.w2filt = filt(filtername='wise_w2.txt')