def test_create_physicsmodel_no_subgrid(self):
"""
Test create_physicsmodel.py, assuming no subgrids
"""
# run create_physicsmodel
create_physicsmodel.create_physicsmodel(self.settings,
nsubs=self.settings.n_subgrid,
nprocs=1)
# check that files match
# - isochrones
table_cache = Table.read(
self.iso_fname_cache,
format="ascii.csv",
comment="#",
delimiter=",",
)
table_new = Table.read(
f"./{self.settings.project}/{self.settings.project}_iso.csv",
format="ascii.csv",
comment="#",
delimiter=",",
)
compare_tables(table_cache, table_new)
# - spectra with priors
compare_hdf5(
self.priors_fname_cache,
f"./{self.settings.project}/{self.settings.project}_spec_w_priors.grid.hd5",
)
# - SEDs grid
compare_hdf5(
self.seds_fname_cache,
f"./{self.settings.project}/{self.settings.project}_seds.grid.hd5",
)
def test_toothpick_noisemodel():
# download the needed files
asts_fname = download_rename('fake_stars_b15_27_all.hd5')
filter_fname = download_rename('filters.hd5')
vega_fname = download_rename('vega.hd5')
hst_fname = download_rename('hst_whitedwarf_frac_covar.fits')
seds_fname = download_rename('beast_example_phat_seds.grid.hd5')
# download cached version of noisemodel on the sed grid
noise_fname_cache = download_rename('beast_example_phat_noisemodel.hd5')
################
# get the modesedgrid on which to generate the noisemodel
modelsedgrid = FileSEDGrid(seds_fname)
# absflux calibration covariance matrix for HST specific filters (AC)
filters = [
'HST_WFC3_F275W', 'HST_WFC3_F336W', 'HST_ACS_WFC_F475W',
'HST_ACS_WFC_F814W', 'HST_WFC3_F110W', 'HST_WFC3_F160W'
]
absflux_a_matrix = hst_frac_matrix(filters,
hst_fname=hst_fname,
filterLib=filter_fname)
# generate the AST noise model
noise_fname = '/tmp/beast_example_phat_noisemodel.hd5'
noisemodel.make_toothpick_noise_model(noise_fname,
asts_fname,
modelsedgrid,
absflux_a_matrix=absflux_a_matrix,
vega_fname=vega_fname)
# compare the new to the cached version
compare_hdf5(noise_fname_cache, noise_fname)
def test_trim_grid(self):
"""
Generate trim the sed grid and noise model using cached versions of the
both and compare the result to a cached version.
"""
# read in the observed data
obsdata = Observations(self.obs_fname_cache, self.settings.filters,
self.settings.obs_colnames)
# get the modesedgrid
modelsedgrid = SEDGrid(self.seds_fname_cache)
# read in the noise model just created
noisemodel_vals = noisemodel.get_noisemodelcat(self.noise_fname_cache)
# trim the model sedgrid
seds_trim_fname = tempfile.NamedTemporaryFile(suffix=".hd5").name
noise_trim_fname = tempfile.NamedTemporaryFile(suffix=".hd5").name
trim_models(
modelsedgrid,
noisemodel_vals,
obsdata,
seds_trim_fname,
noise_trim_fname,
sigma_fac=3.0,
)
# compare the new to the cached version
compare_hdf5(self.seds_trim_fname_cache, seds_trim_fname, ctype="seds")
compare_hdf5(self.noise_trim_fname_cache,
noise_trim_fname,
ctype="noise")
def test_make_extinguished_sed_grid(self):
"""
Generate the extinguished SED grid using a cached version of the
spectral grid with priors and compare the result to a cached version.
"""
g_pspec = SpectralGrid(self.priors_fname_cache, backend="memory")
# generate the SED grid by integrating the filter response functions
# effect of dust extinction applied before filter integration
# also computes the dust priors as weights
seds_fname = tempfile.NamedTemporaryFile(suffix=".hd5").name
infoname = tempfile.NamedTemporaryFile(suffix=".asdf").name
(seds_fname, g) = make_extinguished_sed_grid(
"test",
g_pspec,
self.settings.filters,
seds_fname=seds_fname,
extLaw=self.settings.extLaw,
av=self.settings.avs,
rv=self.settings.rvs,
fA=self.settings.fAs,
rv_prior_model=self.settings.rv_prior_model,
av_prior_model=self.settings.av_prior_model,
fA_prior_model=self.settings.fA_prior_model,
add_spectral_properties_kwargs=self.settings.
add_spectral_properties_kwargs,
info_fname=infoname,
)
# compare the new to the cached version
compare_hdf5(self.seds_fname_cache, seds_fname)
def test_make_kurucz_tlusty_spectral_grid(self):
"""
Generate the spectral grid based on Kurucz and Tlusty stellar atmosphere
models based on a cached set of isochrones and compare the result to a cached
version.
"""
# read in the cached isochrones
oiso = ezIsoch(self.iso_fname_cache)
# calculate the redshift
redshift = (self.settings.velocity / const.c).decompose().value
# make the spectral grid
spec_fname = tempfile.NamedTemporaryFile(suffix=".hd5").name
(spec_fname, g) = make_spectral_grid(
"test",
oiso,
osl=self.settings.osl,
redshift=redshift,
distance=self.settings.distances,
distance_unit=self.settings.distance_unit,
spec_fname=spec_fname,
# filterLib=filter_fname,
extLaw=self.settings.extLaw,
add_spectral_properties_kwargs=self.settings.
add_spectral_properties_kwargs,
)
# compare the new to the cached version
compare_hdf5(self.spec_fname_cache, spec_fname)
def test_create_physicsmodel_with_subgrid(self):
"""
Test create_physicsmodel.py, assuming two subgrids
"""
# run create_physicsmodel
create_physicsmodel.create_physicsmodel(
self.settings_sg, nsubs=self.settings_sg.n_subgrid, nprocs=1)
# check that files match
# - isochrones
table_cache = Table.read(
self.iso_fname_cache,
format="ascii.csv",
comment="#",
delimiter=",",
)
table_new = Table.read(
"beast_metal_small_subgrids/beast_metal_small_subgrids_iso.csv",
format="ascii.csv",
comment="#",
delimiter=",",
)
compare_tables(table_cache, table_new)
# - spectra with priors
compare_hdf5(
self.priors_fname_cache,
"./beast_metal_small_subgrids/beast_metal_small_subgrids_spec_w_priors.grid.hd5",
)
compare_hdf5(
self.priors_sub0_fname_cache,
"beast_metal_small_subgrids/beast_metal_small_subgrids_spec_w_priors.gridsub0.hd5",
)
compare_hdf5(
self.priors_sub1_fname_cache,
"beast_metal_small_subgrids/beast_metal_small_subgrids_spec_w_priors.gridsub1.hd5",
)
# - SEDs grid
compare_hdf5(
self.seds_sub0_fname_cache,
"beast_metal_small_subgrids/beast_metal_small_subgrids_seds.gridsub0.hd5",
)
compare_hdf5(
self.seds_sub1_fname_cache,
"beast_metal_small_subgrids/beast_metal_small_subgrids_seds.gridsub1.hd5",
)
# - list of subgrids
with open("./beast_metal_small_subgrids/subgrid_fnames.txt") as f:
temp = f.read()
subgrid_list = [x for x in temp.split("\n") if x != ""]
expected_list = [
"beast_metal_small_subgrids/beast_metal_small_subgrids_seds.gridsub0.hd5",
"beast_metal_small_subgrids/beast_metal_small_subgrids_seds.gridsub1.hd5",
]
assert subgrid_list == expected_list, "subgrid_fnames.txt has incorrect content"
def test_make_kurucz_tlusty_spectral_grid():
# download the needed files
kurucz_fname = download_rename("kurucz2004.grid.fits")
tlusty_fname = download_rename("tlusty.lowres.grid.fits")
filter_fname = download_rename("filters.hd5")
iso_fname = download_rename("beast_example_phat_iso.csv")
# download cached version of spectral grid
spec_fname_cache = download_rename("beast_example_phat_spec_grid.hd5")
################
# generate the same spectral grid from the code
# read in the cached isochrones
oiso = ezIsoch(iso_fname)
# define the distance
distances = [24.47]
distance_unit = units.mag
velocity = -300 * units.km / units.s
redshift = (velocity / const.c).decompose().value
# define the spectral libraries to use
osl = stellib.Tlusty(filename=tlusty_fname) + stellib.Kurucz(
filename=kurucz_fname)
# define the extinction curve to use
extLaw = extinction.Gordon16_RvFALaw()
filters = [
"HST_WFC3_F275W",
"HST_WFC3_F336W",
"HST_ACS_WFC_F475W",
"HST_ACS_WFC_F814W",
"HST_WFC3_F110W",
"HST_WFC3_F160W",
]
add_spectral_properties_kwargs = dict(filternames=filters)
spec_fname = "/tmp/beast_example_phat_spec_grid.hd5"
spec_fname, g = make_spectral_grid(
"test",
oiso,
osl=osl,
redshift=redshift,
distance=distances,
distance_unit=distance_unit,
spec_fname=spec_fname,
filterLib=filter_fname,
extLaw=extLaw,
add_spectral_properties_kwargs=add_spectral_properties_kwargs,
)
# compare the new to the cached version
compare_hdf5(spec_fname_cache, spec_fname)
def test_trim_grid():
# download the needed files
vega_fname = download_rename("vega.hd5")
seds_fname = download_rename("beast_example_phat_seds.grid.hd5")
noise_fname = download_rename("beast_example_phat_noisemodel.grid.hd5")
obs_fname = download_rename("b15_4band_det_27_A.fits")
# download cached version of noisemodel on the sed grid
noise_trim_fname_cache = download_rename(
"beast_example_phat_noisemodel_trim.grid.hd5")
seds_trim_fname_cache = download_rename(
"beast_example_phat_seds_trim.grid.hd5")
################
# read in the observed data
filters = [
"HST_WFC3_F275W",
"HST_WFC3_F336W",
"HST_ACS_WFC_F475W",
"HST_ACS_WFC_F814W",
"HST_WFC3_F110W",
"HST_WFC3_F160W",
]
basefilters = ["F275W", "F336W", "F475W", "F814W", "F110W", "F160W"]
obs_colnames = [f.lower() + "_rate" for f in basefilters]
obsdata = Observations(obs_fname,
filters,
obs_colnames,
vega_fname=vega_fname)
# get the modesedgrid
modelsedgrid = SEDGrid(seds_fname)
# read in the noise model just created
noisemodel_vals = noisemodel.get_noisemodelcat(noise_fname)
# trim the model sedgrid
seds_trim_fname = "beast_example_phat_seds_trim.grid.hd5"
noise_trim_fname = seds_trim_fname.replace("_seds", "_noisemodel")
trim_models(
modelsedgrid,
noisemodel_vals,
obsdata,
seds_trim_fname,
noise_trim_fname,
sigma_fac=3.0,
)
# compare the new to the cached version
compare_hdf5(seds_trim_fname_cache, seds_trim_fname, ctype="seds")
compare_hdf5(noise_trim_fname_cache, noise_trim_fname, ctype="noise")
def test_trim_grid():
# download the needed files
vega_fname = download_rename('vega.hd5')
seds_fname = download_rename('beast_example_phat_seds.grid.hd5')
noise_fname = download_rename('beast_example_phat_noisemodel.hd5')
obs_fname = download_rename('b15_4band_det_27_A.fits')
# download cached version of noisemodel on the sed grid
noise_trim_fname_cache = download_rename(
'beast_example_phat_noisemodel_trim.grid.hd5')
seds_trim_fname_cache = download_rename(
'beast_example_phat_seds_trim.grid.hd5')
################
# read in the observed data
filters = [
'HST_WFC3_F275W', 'HST_WFC3_F336W', 'HST_ACS_WFC_F475W',
'HST_ACS_WFC_F814W', 'HST_WFC3_F110W', 'HST_WFC3_F160W'
]
basefilters = ['F275W', 'F336W', 'F475W', 'F814W', 'F110W', 'F160W']
obs_colnames = [f.lower() + '_rate' for f in basefilters]
obsdata = get_obscat(obs_fname,
filters,
obs_colnames,
vega_fname=vega_fname)
# get the modesedgrid
modelsedgrid = FileSEDGrid(seds_fname)
# read in the noise model just created
noisemodel_vals = noisemodel.get_noisemodelcat(noise_fname)
# trim the model sedgrid
seds_trim_fname = 'beast_example_phat_sed_trim.grid.hd5'
noise_trim_fname = seds_trim_fname.replace('_sed', '_noisemodel')
trim_models(modelsedgrid,
noisemodel_vals,
obsdata,
seds_trim_fname,
noise_trim_fname,
sigma_fac=3.)
# compare the new to the cached version
compare_hdf5(seds_trim_fname_cache, seds_trim_fname, ctype='seds')
compare_hdf5(noise_trim_fname_cache, noise_trim_fname, ctype='noise')
def test_make_kurucz_tlusty_spectral_grid():
# download the needed files
kurucz_fname = download_rename('kurucz2004.grid.fits')
tlusty_fname = download_rename('tlusty.lowres.grid.fits')
filter_fname = download_rename('filters.hd5')
iso_fname = download_rename('beast_example_phat_iso.csv')
# download cached version of spectral grid
spec_fname_cache = download_rename('beast_example_phat_spec_grid.hd5')
################
# generate the same spectral grid from the code
# read in the cached isochrones
oiso = ezIsoch(iso_fname)
# define the distance
distances = [24.47]
distance_unit = units.mag
velocity = -300 * units.km / units.s
redshift = (velocity / const.c).decompose().value
# define the spectral libraries to use
osl = stellib.Tlusty(filename=tlusty_fname) \
+ stellib.Kurucz(filename=kurucz_fname)
filters = [
'HST_WFC3_F275W', 'HST_WFC3_F336W', 'HST_ACS_WFC_F475W',
'HST_ACS_WFC_F814W', 'HST_WFC3_F110W', 'HST_WFC3_F160W'
]
add_spectral_properties_kwargs = dict(filternames=filters)
spec_fname = '/tmp/beast_example_phat_spec_grid.hd5'
spec_fname, g = make_spectral_grid(
'test',
oiso,
osl=osl,
redshift=redshift,
distance=distances,
distance_unit=distance_unit,
spec_fname=spec_fname,
filterLib=filter_fname,
add_spectral_properties_kwargs=add_spectral_properties_kwargs)
# compare the new to the cached version
compare_hdf5(spec_fname_cache, spec_fname)
def test_create_obsmodel_no_subgrid(self):
"""
Test create_obsmodel.py, assuming no subgrids
"""
print("running test_create_obsmodel_no_subgrid")
# run create_obsmodel
create_obsmodel.create_obsmodel(
self.settings, use_sd=False, nsubs=self.settings.n_subgrid, nprocs=1,
)
# check that files match
compare_hdf5(
self.noise_fname_cache,
"beast_metal_small/beast_metal_small_noisemodel.grid.hd5",
)
def test_make_extinguished_sed_grid():
# download the needed files
priors_fname = download_rename("beast_example_phat_spec_w_priors.grid.hd5")
filter_fname = download_rename("filters.hd5")
# download cached version of sed grid
seds_fname_cache = download_rename("beast_example_phat_seds.grid.hd5")
################
# generate the same extinguished SED grid from the code
# Add in the filters
filters = [
"HST_WFC3_F275W",
"HST_WFC3_F336W",
"HST_ACS_WFC_F475W",
"HST_ACS_WFC_F814W",
"HST_WFC3_F110W",
"HST_WFC3_F160W",
]
add_spectral_properties_kwargs = dict(filternames=filters)
g_pspec = grid.FileSpectralGrid(priors_fname, backend="memory")
# generate the SED grid by integrating the filter response functions
# effect of dust extinction applied before filter integration
# also computes the dust priors as weights
seds_fname = "/tmp/beast_example_phat_sed.grid.hd5"
seds_fname, g_seds = make_extinguished_sed_grid(
"test",
g_pspec,
filters,
seds_fname=seds_fname,
filterLib=filter_fname,
extLaw=extinction.Gordon16_RvFALaw(),
av=[0.0, 10.055, 1.0],
rv=[2.0, 6.0, 1.0],
fA=[0.0, 1.0, 0.25],
av_prior_model={"name": "flat"},
rv_prior_model={"name": "flat"},
fA_prior_model={"name": "flat"},
add_spectral_properties_kwargs=add_spectral_properties_kwargs,
)
# compare the new to the cached version
compare_hdf5(seds_fname_cache, seds_fname)
def test_add_stellar_priors_to_spectral_grid():
# download the needed files
gspec_fname = download_rename("beast_example_phat_spec_grid.hd5")
# download cached version of spectral grid with priors
priors_fname_cache = download_rename("beast_example_phat_spec_w_priors.grid.hd5")
###############
# generate the spectral grid with stellar priors from the code
gspec_fname = "/tmp/beast_example_phat_spec_grid.hd5"
specgrid = grid.FileSpectralGrid(gspec_fname, backend="memory")
priors_fname = "/tmp/beast_example_phat_spec_w_priors.grid.hd5"
priors_fname, g = add_stellar_priors("test", specgrid, priors_fname=priors_fname)
# compare the new to the cached version
compare_hdf5(priors_fname_cache, priors_fname)
def test_toothpick_noisemodel(self):
"""
Generate the nosiemodel (aka observationmodel) using a cached version of
the artifical star test results (ASTs) and compare the result to a cached
version.
"""
# get the modelsedgrid on which to generate the noisemodel
modelsedgrid = SEDGrid(self.seds_fname_cache)
# generate the AST noise model
noise_fname = tempfile.NamedTemporaryFile(suffix=".hd5").name
noisemodel.make_toothpick_noise_model(
noise_fname,
self.asts_fname_cache,
modelsedgrid,
absflux_a_matrix=self.settings.absflux_a_matrix,
)
# compare the new to the cached version
compare_hdf5(self.noise_fname_cache, noise_fname)
def test_add_stellar_priors_to_spectral_grid(self):
"""
Add the stellar priors to the a cached spectral grid and compare
it to the cached version.
"""
specgrid = SpectralGrid(self.spec_fname_cache, backend="memory")
priors_fname = tempfile.NamedTemporaryFile(suffix=".hd5").name
infoname = tempfile.NamedTemporaryFile(suffix=".asdf").name
priors_fname, g = add_stellar_priors(
"test",
specgrid,
priors_fname=priors_fname,
age_prior_model=self.settings.age_prior_model,
mass_prior_model=self.settings.mass_prior_model,
met_prior_model=self.settings.met_prior_model,
distance_prior_model=self.settings.distance_prior_model,
info_fname=infoname,
)
# compare the new to the cached version
compare_hdf5(self.priors_fname_cache, priors_fname)
def test_create_obsmodel_with_subgrid(self):
"""
Test create_obsmodel.py, assuming two subgrids
"""
print("running test_create_obsmodel_with_subgrid")
# run create_obsmodel
create_obsmodel.create_obsmodel(
self.settings_sg,
use_sd=False,
nsubs=self.settings_sg.n_subgrid,
nprocs=1,
use_rate=False,
)
# check that files match
compare_hdf5(
self.noise_sub0_fname_cache,
"beast_example_phat_subgrids/beast_example_phat_subgrids_noisemodel.gridsub0.hd5",
)
compare_hdf5(
self.noise_sub1_fname_cache,
"beast_example_phat_subgrids/beast_example_phat_subgrids_noisemodel.gridsub1.hd5",
)