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 remove_filters_from_files(catfile, physgrid, obsgrid, outbase, rm_filters):
# remove the requested filters from the catalog file
cat = Table.read(catfile)
for cfilter in rm_filters:
colname = "{}_rate".format(cfilter)
if colname in cat.colnames:
cat.remove_column(colname)
else:
print("{} not in catalog file".format(colname))
cat.write("{}_cat.fits".format(outbase), overwrite=True)
# get the sed grid and process
g0 = FileSEDGrid(physgrid, backend="cache")
filters = g0.header["filters"].split(" ")
shortfilters = [(cfilter.split("_"))[-1].lower() for cfilter in filters]
nlamb = []
nfilters = []
rindxs = []
for csfilter, clamb, cfilter in zip(shortfilters, g0.lamb, filters):
if csfilter not in rm_filters:
nlamb.append(clamb)
nfilters.append(cfilter)
else:
rindxs.append(shortfilters.index(csfilter))
nseds = np.delete(g0.seds, rindxs, 1)
print("orig filters: {}".format(" ".join(filters)))
print(" new filters: {}".format(" ".join(nfilters)))
g = SpectralGrid(np.array(nlamb),
seds=nseds,
grid=g0.grid,
backend="memory")
g.grid.header["filters"] = " ".join(nfilters)
g.writeHDF("{}_sed.grid.hd5".format(outbase))
# get and process the observation model
obsgrid = noisemodel.get_noisemodelcat(obsgrid)
with tables.open_file("{}_noisemodel.grid.hd5".format(outbase),
"w") as outfile:
outfile.create_array(outfile.root, "bias",
np.delete(obsgrid.root.bias, rindxs, 1))
outfile.create_array(outfile.root, "error",
np.delete(obsgrid.root.error, rindxs, 1))
outfile.create_array(
outfile.root,
"completeness",
np.delete(obsgrid.root.completeness, rindxs, 1),
)
def remove_filters_from_files(catfile,
physgrid,
obsgrid,
outbase,
rm_filters):
# remove the requested filters from the catalog file
cat = Table.read(catfile)
for cfilter in rm_filters:
colname = '{}_rate'.format(cfilter)
if colname in cat.colnames:
cat.remove_column(colname)
else:
print('{} not in catalog file'.format(colname))
cat.write('{}_cat.fits'.format(outbase), overwrite=True)
# get the sed grid and process
g0 = FileSEDGrid(physgrid, backend='cache')
filters = g0.header['filters'].split(' ')
shortfilters = [(cfilter.split('_'))[-1].lower() for cfilter in filters]
nlamb = []
nfilters = []
rindxs = []
for csfilter, clamb, cfilter in zip(shortfilters, g0.lamb, filters):
if csfilter not in rm_filters:
nlamb.append(clamb)
nfilters.append(cfilter)
else:
rindxs.append(shortfilters.index(csfilter))
nseds = np.delete(g0.seds, rindxs, 1)
print('orig filters: {}'.format(' '.join(filters)))
print(' new filters: {}'.format(' '.join(nfilters)))
g = SpectralGrid(np.array(nlamb), seds=nseds,
grid=g0.grid, backend='memory')
g.grid.header['filters'] = ' '.join(nfilters)
g.writeHDF('{}_sed.grid.hd5'.format(outbase))
# get and process the observation model
obsgrid = noisemodel.get_noisemodelcat(obsgrid)
with tables.open_file('{}_noisemodel.grid.hd5'.format(outbase), 'w') \
as outfile:
outfile.create_array(outfile.root, 'bias',
np.delete(obsgrid.root.bias, rindxs, 1))
outfile.create_array(outfile.root, 'error',
np.delete(obsgrid.root.error, rindxs, 1))
outfile.create_array(outfile.root, 'completeness',
np.delete(obsgrid.root.completeness, rindxs, 1))
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 = SpectralGrid(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_splinter_noisemodel(frac_unc):
# make super simplified model SED grid
lamb = np.linspace(1000.0, 4000, 4)
seds = np.logspace(-4, -3, 4)[None, :] * np.array([1, 1.5])[:, None]
modelsedgrid = SpectralGrid(
lamb=lamb, seds=seds, grid=[1], backend="memory" # dummy input for now
)
# make splinter noisemodel
noise_fname = "/tmp/splinter_example_noisemodel_{:.2f}.grid.hd5".format(frac_unc)
make_splinter_noise_model(noise_fname, modelsedgrid, frac_unc=frac_unc)
# read entire noisemodel back in
noisemodel = h5py.File(noise_fname)
# read the estimated sigma and check if close to manually computed errors
sigma = noisemodel["error"]
np.testing.assert_allclose(sigma, frac_unc * seds)
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_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 = SpectralGrid(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 gen_subgrid(i, sub_name):
sub_g_pspec = SpectralGrid(sub_name)
sub_seds_fname = "{}seds.gridsub{}.hd5".format(file_prefix, i)
# 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
(sub_seds_fname, sub_g_seds) = make_extinguished_sed_grid(
datamodel.project,
sub_g_pspec,
datamodel.filters,
extLaw=datamodel.extLaw,
av=datamodel.avs,
rv=datamodel.rvs,
fA=datamodel.fAs,
rv_prior_model=datamodel.rv_prior_model,
av_prior_model=datamodel.av_prior_model,
fA_prior_model=datamodel.fA_prior_model,
add_spectral_properties_kwargs=extra_kwargs,
seds_fname=sub_seds_fname,
)
return sub_seds_fname
def remove_filters_from_files(
catfile,
physgrid=None,
obsgrid=None,
outbase=None,
physgrid_outfile=None,
rm_filters=None,
beast_filt=None,
):
"""
Remove filters from catalog, physics grid, and/or obsmodel grid. This has
two primary use cases:
1. When making simulated observations, you want to test how your fit quality
changes with different combinations of filters. In that case, put in
files for both `physgrid` and `obsgrid`. Set `rm_filters` to the
filter(s) you wish to remove, and they will be removed both from those
and from the catalog file. The three new files will be output with the
name prefix set in `outbase`.
2. When running the BEAST, you have a master physics model grid with all
filters present in the survey, but some fields don't have observations in
all of those filters. In that case, put the master grid in `physgrid`
and set `rm_filters` to None. The catalog will be used to determine the
filters to remove (if any). `obsgrid` should be left as None, because in
this use case, the obsmodel grid has not yet been generated. The output
physics model grid will be named using the filename in `physgrid_outfile`
(if given) or with the prefix in `outbase`.
Parameters
----------
catfile : string
file name of photometry catalog
physgrid : string (default=None)
If set, remove filters from this physics model grid
obsgrid : string (default=None)
If set, remove filters from this obsmodel grid
outbase : string (default=None)
Path+file to prepend to all output file names. Useful for case 1 above.
physgrid_outfile : string (default=None)
Path+name of the output physics model grid. Useful for case 2 above.
rm_filters : string or list of strings (default=None)
If set, these are the filters to remove from all of the files. If not
set, only the filters present in catfile will be retained in physgrid
and/or obsgrid.
beast_filt : list of strings
Sometimes there is ambiguity in the filter name (e.g., the grid has
both HST_ACS_WFC_F475W and HST_WFC3_F475W, and the filter name is
F475W). Set this to the BEAST filter name to resolve any
ambiguities. For example, ['HST_WFC3_F475W', 'HST_WFC3_F814W'] ensures
that these are the names used for F475W and F814W.
"""
# read in the photometry catalog
cat = Table.read(catfile)
# if rm_filters set, remove the requested filters from the catalog
if rm_filters is not None:
for cfilter in np.atleast_1d(rm_filters):
colname = "{}_rate".format(cfilter)
if colname.upper() in cat.colnames:
cat.remove_column(colname.upper())
elif colname.lower() in cat.colnames:
cat.remove_column(colname.lower())
else:
print("{} not in catalog file".format(colname))
cat.write("{}_cat.fits".format(outbase), overwrite=True)
# if rm_filters not set, extract the filter names that are present
if rm_filters is None:
cat_filters = [f[:-5].upper() for f in cat.colnames if f[-4:].lower() == "rate"]
# if beast_filt is set, make a list of the short versions
if beast_filt is not None:
beast_filt_short = [(f.split("_"))[-1].upper() for f in beast_filt]
# if physgrid set, process the SED grid
if physgrid is not None:
# read in the sed grid
g0 = FileSEDGrid(physgrid, backend="cache")
# extract info
filters = g0.header["filters"].split(" ")
shortfilters = [(cfilter.split("_"))[-1].upper() for cfilter in filters]
rindxs = []
rgridcols = []
# loop through filters and determine what needs deleting
for csfilter, cfilter in zip(shortfilters, filters):
# --------------------------
# if the user chose the filters to remove
if rm_filters is not None:
# if the current filter is in the list of filters to remove
if csfilter in np.atleast_1d(rm_filters):
# if there's a list of BEAST instrument+filter references
if beast_filt is not None:
# if the current filter is in the list of BEAST references
if csfilter in beast_filt_short:
# if it's the same instrument, delete it
# (if it's not the same instrument, keep it)
if beast_filt[beast_filt_short.index(csfilter)] == cfilter:
rindxs.append(filters.index(cfilter))
for grid_col in g0.grid.colnames:
if cfilter in grid_col:
rgridcols.append(grid_col)
# if the current filter isn't in the BEAST ref list, delete it
else:
rindxs.append(filters.index(cfilter))
for grid_col in g0.grid.colnames:
if cfilter in grid_col:
rgridcols.append(grid_col)
# if there isn't a list of BEAST refs, delete it
else:
rindxs.append(filters.index(cfilter))
for grid_col in g0.grid.colnames:
if cfilter in grid_col:
rgridcols.append(grid_col)
# --------------------------
# if the removed filters are determined from the catalog file
if rm_filters is None:
# if the current filter is present in the catalog filters
if csfilter in cat_filters:
# if there's a list of BEAST instrument+filter references
# (if there isn't a list of BEAST refs, keep it)
if beast_filt is not None:
# if the current filter is in the list of BEAST references
# (if the current filter isn't in the BEAST ref list, keep it)
if csfilter in beast_filt_short:
# if it's not the same instrument, delete it
# (if it's the same instrument, keep it)
if beast_filt[beast_filt_short.index(csfilter)] != cfilter:
rindxs.append(filters.index(cfilter))
for grid_col in g0.grid.colnames:
if cfilter in grid_col:
rgridcols.append(grid_col)
# if the current filter isn't in the catalog filters, delete it
else:
rindxs.append(filters.index(cfilter))
for grid_col in g0.grid.colnames:
if cfilter in grid_col:
rgridcols.append(grid_col)
# delete column(s)
nseds = np.delete(g0.seds, rindxs, 1)
nlamb = np.delete(g0.lamb, rindxs, 0)
nfilters = np.delete(filters, rindxs, 0)
for rcol in rgridcols:
g0.grid.delCol(rcol)
print("orig filters: {}".format(" ".join(filters)))
print(" new filters: {}".format(" ".join(nfilters)))
# save the modified grid
g = SpectralGrid(np.array(nlamb), seds=nseds, grid=g0.grid, backend="memory")
g.grid.header["filters"] = " ".join(nfilters)
if physgrid_outfile is not None:
g.writeHDF(physgrid_outfile)
elif outbase is not None:
g.writeHDF("{}_seds.grid.hd5".format(outbase))
else:
raise ValueError("Need to set either outbase or physgrid_outfile")
# if obsgrid set, process the observation model
if obsgrid is not None:
obsgrid = noisemodel.get_noisemodelcat(obsgrid)
with tables.open_file("{}_noisemodel.grid.hd5".format(outbase), "w") as outfile:
outfile.create_array(
outfile.root, "bias", np.delete(obsgrid["bias"], rindxs, 1)
)
outfile.create_array(
outfile.root, "error", np.delete(obsgrid["error"], rindxs, 1)
)
outfile.create_array(
outfile.root,
"completeness",
np.delete(obsgrid["completeness"], rindxs, 1),
)
def make_extinguished_grid(
spec_grid,
filter_names,
extLaw,
avs,
rvs,
fAs=None,
av_prior_model={"name": "flat"},
rv_prior_model={"name": "flat"},
fA_prior_model={"name": "flat"},
chunksize=0,
add_spectral_properties_kwargs=None,
absflux_cov=False,
filterLib=None,
):
"""
Extinguish spectra and extract an SEDGrid through given series of filters
(all wavelengths in stellar SEDs and filter response functions are assumed
to be in Angstroms)
Parameters
----------
spec_grid: string or grid.SpectralGrid
if string:
spec_grid is the filename to the grid file with stellar spectra
the backend to load this grid will be the minimal invasive: 'HDF'
if possible, 'cache' otherwise.
if not a string, expecting the corresponding SpectralGrid instance
(backend already setup)
filter_names: list
list of filter names according to the filter lib
Avs: sequence
Av values to iterate over
av_prior_model: list
list including prior model name and parameters
Rvs: sequence
Rv values to iterate over
rv_prior_model: list
list including prior model name and parameters
fAs: sequence (optional)
f_A values to iterate over
f_A can be omitted if the extinction Law does not use it or allow
fixed values
fA_prior_model: list
list including prior model name and parameters
chunksize: int, optional (default=0)
number of extinction model variations to generate at each cycle.
Note that this means len(spec_grid * chunksize)
If default <= 0, all models will be returned at once.
filterLib: str
full filename to the filter library hd5 file
add_spectral_properties_kwargs: dict
keyword arguments to call :func:`add_spectral_properties` at each
iteration to add model properties from the spectra into the grid
property table
asbflux_cov: boolean
set to calculate the absflux covariance matrices for each model
(can be very slow!!! But it is the right thing to do)
Returns
-------
g: grid.SpectralGrid
final grid of reddened SEDs and models
"""
# Check inputs
# ============
# get the stellar grid (no dust yet)
# if string is provided try to load the most memory efficient backend
# otherwise use a cache-type backend (load only when needed)
if isinstance(spec_grid, str):
ext = spec_grid.split(".")[-1]
if ext in ["hdf", "hd5", "hdf5"]:
g0 = SpectralGrid(spec_grid, backend="hdf")
else:
g0 = SpectralGrid(spec_grid, backend="cache")
else:
helpers.type_checker("spec_grid", spec_grid, SpectralGrid)
g0 = spec_grid
# Tag fA usage
if fAs is None:
with_fA = False
else:
with_fA = True
# get the min/max R(V) values necessary for the grid point definition
min_Rv = min(rvs)
max_Rv = max(rvs)
# Create the sampling mesh
# ========================
# basically the dot product from all input 1d vectors
# setup interation over the full dust parameter grid
if with_fA:
dustpriors = PriorWeightsDust(avs, av_prior_model, rvs, rv_prior_model,
fAs, fA_prior_model)
it = np.nditer(np.ix_(avs, rvs, fAs))
niter = np.size(avs) * np.size(rvs) * np.size(fAs)
npts, pts = _make_dust_fA_valid_points_generator(it, min_Rv, max_Rv)
# Pet the user
print("""number of initially requested points = {0:d}
number of valid points = {1:d} (based on restrictions in R(V)
versus f_A plane)
""".format(niter, npts))
if npts == 0:
raise AttributeError("No valid points")
else:
dustpriors = PriorWeightsDust(avs, av_prior_model, rvs, rv_prior_model,
[1.0], fA_prior_model)
it = np.nditer(np.ix_(avs, rvs))
npts = np.size(avs) * np.size(rvs)
pts = ((float(ak), float(rk)) for ak, rk in it)
# Generate the Grid
# =================
N0 = len(g0.grid)
N = N0 * npts
if chunksize <= 0:
print("Generating a final grid of {0:d} points".format(N))
else:
print("Generating a final grid of {0:d} points in {1:d}" +
" pieces".format(N, int(float(N0) / chunksize + 1.0)))
if chunksize <= 0:
chunksize = npts
if add_spectral_properties_kwargs is not None:
nameformat = add_spectral_properties_kwargs.pop("nameformat",
"{0:s}") + "_wd"
for chunk_pts in helpers.chunks(pts, chunksize):
# iter over chunks of models
# setup chunk outputs
cols = {"Av": np.empty(N, dtype=float), "Rv": np.empty(N, dtype=float)}
if with_fA:
cols["Rv_A"] = np.empty(N, dtype=float)
cols["f_A"] = np.empty(N, dtype=float)
keys = list(g0.keys())
for key in keys:
cols[key] = np.empty(N, dtype=float)
n_filters = len(filter_names)
_seds = np.empty((N, n_filters), dtype=float)
if absflux_cov:
n_offdiag = ((n_filters**2) - n_filters) / 2
_cov_diag = np.empty((N, n_filters), dtype=float)
_cov_offdiag = np.empty((N, n_offdiag), dtype=float)
for count, pt in enumerate(tqdm(chunk_pts, desc="SED grid")):
if with_fA:
Av, Rv, f_A = pt
dust_prior_weight = dustpriors.get_weight(Av, Rv, f_A)
Rv_MW = extLaw.get_Rv_A(Rv, f_A)
r = g0.applyExtinctionLaw(extLaw,
Av=Av,
Rv=Rv,
f_A=f_A,
inplace=False)
# add extra "spectral bands" if requested
if add_spectral_properties_kwargs is not None:
r = add_spectral_properties(
r,
nameformat=nameformat,
filterLib=filterLib,
**add_spectral_properties_kwargs)
temp_results = r.getSEDs(filter_names, filterLib=filterLib)
# adding the dust parameters to the models
cols["Av"][N0 * count:N0 * (count + 1)] = Av
cols["Rv"][N0 * count:N0 * (count + 1)] = Rv
cols["f_A"][N0 * count:N0 * (count + 1)] = f_A
cols["Rv_A"][N0 * count:N0 * (count + 1)] = Rv_MW
else:
Av, Rv = pt
dust_prior_weight = dustpriors.get_weight(Av, Rv, 1.0)
r = g0.applyExtinctionLaw(extLaw, Av=Av, Rv=Rv, inplace=False)
if add_spectral_properties_kwargs is not None:
r = add_spectral_properties(
r,
nameformat=nameformat,
filterLib=filterLib,
**add_spectral_properties_kwargs)
temp_results = r.getSEDs(filter_names, filterLib=filterLib)
# adding the dust parameters to the models
cols["Av"][N0 * count:N0 * (count + 1)] = Av
cols["Rv"][N0 * count:N0 * (count + 1)] = Rv
# get new attributes if exist
for key in list(temp_results.grid.keys()):
if key not in keys:
k1 = N0 * count
k2 = N0 * (count + 1)
cols.setdefault(key, np.empty(
N, dtype=float))[k1:k2] = temp_results.grid[key]
# compute the fractional absflux covariance matrices
if absflux_cov:
absflux_covmats = calc_absflux_cov_matrices(
r, temp_results, filter_names)
_cov_diag[N0 * count:N0 * (count + 1)] = absflux_covmats[0]
_cov_offdiag[N0 * count:N0 * (count + 1)] = absflux_covmats[1]
# assign the extinguished SEDs to the output object
_seds[N0 * count:N0 * (count + 1)] = temp_results.seds[:]
# copy the rest of the parameters
for key in keys:
cols[key][N0 * count:N0 * (count + 1)] = g0.grid[key]
# multiply existing prior weights by the dust prior weight
cols["weight"][N0 * count:N0 * (count + 1)] *= dust_prior_weight
cols["prior_weight"][N0 * count:N0 *
(count + 1)] *= dust_prior_weight
if count == 0:
cols["lamb"] = temp_results.lamb[:]
_lamb = cols.pop("lamb")
# free the memory of temp_results
# del temp_results
# del tempgrid
# Ship
if absflux_cov:
g = SpectralGrid(
_lamb,
seds=_seds,
cov_diag=_cov_diag,
cov_offdiag=_cov_offdiag,
grid=Table(cols),
backend="memory",
)
else:
g = SpectralGrid(_lamb,
seds=_seds,
grid=Table(cols),
backend="memory")
g.grid.header["filters"] = " ".join(filter_names)
yield g
def apply_distance_grid(specgrid, distances, redshift=0):
"""
Distances are applied to the spectral grid by copying the grid and
applying a scaling factor.
Parameters
----------
project: str
project name
specgrid: grid.SpectralGrid object
spectral grid to transform
distances: list of float
Distances at which models should be shifted
0 means absolute magnitude.
Expecting pc units
redshift: float
Redshift to which wavelengths should be shifted
Default is 0 (rest frame)
"""
g0 = specgrid
# Current length of the grid
N0 = len(g0.grid)
N = N0 * len(distances)
# Make singleton list if a single distance is given
if not hasattr(distances, "__iter__"):
_distances = [distances]
else:
_distances = distances
# Add distance column if multiple distances are specified
cols = {}
cols["distance"] = np.empty(N, dtype=float)
# Existing columns
keys0 = list(g0.keys())
for key in keys0:
cols[key] = np.empty(N, dtype=float)
n_sed_points = g0.seds.shape[1]
new_seds = np.empty((N, n_sed_points), dtype=float)
for count, distance in enumerate(tqdm(_distances, desc="Distance grid")):
# The range where the current distance points will live
distance_slice = slice(N0 * count, N0 * (count + 1))
# The seds default to 10 pc.
# Therefore, scale them with (d / (10 pc))**(-2).
distance_pc = distance.to(units.pc).value
new_seds[distance_slice, :] = g0.seds / (0.1 * distance_pc)**2
# Fill in the distance in the distance column
cols["distance"][distance_slice] = distance_pc
# Copy the old columns
for key in keys0:
cols[key][distance_slice] = g0.grid[key]
# apply redshift
g0.lamb = g0.lamb * (1.0 + redshift)
# New object
g = SpectralGrid(g0.lamb,
seds=new_seds,
grid=Table(cols),
backend="memory")
return g
def trim_models(
sedgrid,
sedgrid_noisemodel,
obsdata,
sed_outname,
noisemodel_outname,
sigma_fac=3.0,
n_detected=4,
inFlux=True,
trunchen=False,
):
"""
For a given set of observations, there will be models that are so
bright or faint that they will always have ~0 probability of fitting
the data. This program trims those models out of the SED grid
so that time is not spent calculating model points that are always
zero probability.
Parameters
----------
sedgrid: grid.SEDgrid instance
model grid
sedgrid_noisemodel: beast noisemodel instance
noise model data
obsdata: Observation object instance
observation catalog
sed_outname: str
name for output sed file
noisemodel_outname: str
name for output noisemodel file
sigma_fac: float
factor for trimming the upper and lower range of grid so that
the model range cuts off sigma_fac above and below the brightest
and faintest models, respectively (default: 3.)
n_detected: int
minimum number of bands where ASTs yielded a detection for
a given model, if fewer detections than n_detected this model
gets eliminated (default: 4)
inFlux: boolean
if true data are in fluxes (default: True)
trunchen: boolean
if true use the trunchen noise model (default: False)
"""
# Store the brigtest and faintest fluxes in each band (for data and asts)
n_filters = len(obsdata.filters)
min_data = np.zeros(n_filters)
max_data = np.zeros(n_filters)
min_models = np.zeros(n_filters)
max_models = np.zeros(n_filters)
for k, filtername in enumerate(obsdata.filters):
sfiltname = obsdata.data.resolve_alias(filtername)
if inFlux:
min_data[k] = np.amin(obsdata.data[sfiltname] *
obsdata.vega_flux[k])
max_data[k] = np.amax(obsdata.data[sfiltname] *
obsdata.vega_flux[k])
else:
min_data[k] = np.amin(10**(-0.4 * obsdata.data[sfiltname]) *
obsdata.vega_flux[k])
max_data[k] = np.amax(10**(-0.4 * obsdata.data[sfiltname]) *
obsdata.vega_flux[k])
min_models[k] = np.amin(sedgrid.seds[:, k])
max_models[k] = np.amax(sedgrid.seds[:, k])
# first remove all models that have any band with fluxes below the
# faintest ASTs run
# when the noisemodel was computed, models with fluxes below the
# faintest ASTs were tagged with a negative error/uncertainty
# identify the models that have been detected in enough bands
# the idea here is that if the ASTs are not measured that means
# that *none* were recovered and this implies
# that no model with these values would be recovered and thus the
# probability should always be zero
model_unc = sedgrid_noisemodel.root.error[:]
above_ast = model_unc > 0
sum_above_ast = np.sum(above_ast, axis=1)
indxs, = np.where(sum_above_ast >= n_detected)
# cache the noisemodel values
model_bias = sedgrid_noisemodel.root.bias[:]
model_unc = np.fabs(sedgrid_noisemodel.root.error[:])
model_compl = sedgrid_noisemodel.root.completeness[:]
if trunchen:
model_q_norm = sedgrid_noisemodel.root.q_norm[:]
model_icov_diag = sedgrid_noisemodel.root.icov_diag[:]
model_icov_offdiag = sedgrid_noisemodel.root.icov_offdiag[:]
if len(indxs) <= 0:
raise ValueError("no models are brighter than the minimum ASTs run")
n_ast_indxs = len(indxs)
# Find models with fluxes (with margin) between faintest and brightest data
for k in range(n_filters):
print("working on filter # = ", k)
# Get upper and lower values for the models given the noise model
# sigma_fac defaults to 3.
model_val = sedgrid.seds[indxs, k] + model_bias[indxs, k]
model_down = model_val - sigma_fac * model_unc[indxs, k]
model_up = model_val + sigma_fac * model_unc[indxs, k]
nindxs, = np.where((model_up >= min_data[k])
& (model_down <= max_data[k]))
if len(nindxs) > 0:
indxs = indxs[nindxs]
if len(indxs) == 0:
raise ValueError("no models that are within the data range")
print("number of original models = ", len(sedgrid.seds[:, 0]))
print("number of ast trimmed models = ", n_ast_indxs)
print("number of trimmed models = ", len(indxs))
# Save the grid
print("Writing trimmed sedgrid to disk into {0:s}".format(sed_outname))
cols = {}
for key in list(sedgrid.grid.keys()):
cols[key] = sedgrid.grid[key][indxs]
# New column to save the index of the model in the full grid
cols["fullgrid_idx"] = indxs.astype(int)
g = SpectralGrid(sedgrid.lamb,
seds=sedgrid.seds[indxs],
grid=Table(cols),
backend="memory")
filternames = obsdata.filters
g.grid.header["filters"] = " ".join(filternames)
# trimmed grid name
g.writeHDF(sed_outname)
# save the trimmed noise model
print("Writing trimmed noisemodel to disk into {0:s}".format(
noisemodel_outname))
with tables.open_file(noisemodel_outname, "w") as outfile:
outfile.create_array(outfile.root, "bias", model_bias[indxs])
outfile.create_array(outfile.root, "error", model_unc[indxs])
outfile.create_array(outfile.root, "completeness", model_compl[indxs])
if trunchen:
outfile.create_array(outfile.root, "q_norm", model_q_norm[indxs])
outfile.create_array(outfile.root, "icov_diag",
model_icov_diag[indxs])
outfile.create_array(outfile.root, "icov_offdiag",
model_icov_offdiag[indxs])
def add_stellar_priors(
project,
specgrid,
distance_prior_model={"name": "flat"},
age_prior_model={"name": "flat"},
mass_prior_model={"name": "kroupa"},
met_prior_model={"name": "flat"},
verbose=True,
priors_fname=None,
info_fname=None,
**kwargs,
):
"""
make_priors -- compute the weights for the stellar priors
Parameters
----------
project: str
project name
specgrid: SpectralGrid object
spectral grid to transform
distance_prior_model: dict
dict including prior model name and parameters
age_prior_model: dict
dict including prior model name and parameters
mass_prior_model: dict
dict including prior model name and parameters
met_prior_model: dict
dict including prior model name and parameters
priors_fname: str
full filename to which to save the spectral grid with priors
info_fname : str
Set to specify the filename to save beast info to, otherwise
saved to project/project_beast_info.asdf
Returns
-------
fname: str
name of saved file
g: SpectralGrid object
spectral grid to transform
"""
if priors_fname is None:
priors_fname = "%s/%s_spec_w_priors.grid.hd5" % (project, project)
if not os.path.isfile(priors_fname):
if verbose:
print("Make Prior Weights")
compute_distance_age_mass_metallicity_weights(
specgrid.grid,
distance_prior_model=distance_prior_model,
age_prior_model=age_prior_model,
mass_prior_model=mass_prior_model,
met_prior_model=met_prior_model,
**kwargs,
)
# write to disk
if hasattr(specgrid, "write"):
specgrid.write(priors_fname)
else:
for gk in specgrid:
gk.write(priors_fname, append=True)
# save info to the beast info file
info = {
"distance_prior_model": distance_prior_model,
"age_prior_model": age_prior_model,
"mass_prior_model": mass_prior_model,
"met_prior_model": met_prior_model,
}
if info_fname is None:
info_fname = f"{project}/{project}_beast_info.asdf"
add_to_beast_info_file(info_fname, info)
# read in spectralgrid from file (possible not needed, need to check)
g = SpectralGrid(priors_fname, backend="memory")
return (priors_fname, g)
def make_spectral_grid(
project,
oiso,
osl=None,
bounds={},
verbose=True,
spec_fname=None,
distance=10,
distance_unit=units.pc,
redshift=0.0,
filterLib=None,
add_spectral_properties_kwargs=None,
extLaw=None,
**kwargs,
):
"""
The spectral grid is generated using the stellar parameters by
interpolation of the isochrones and the generation of spectra into the
physical units
Parameters
----------
project: str
project name
oiso: isochrone.Isochrone object
set of isochrones to use
osl: stellib.Stellib object
Spectral library to use (default stellib.Kurucz)
distance: float or list of float
distances at which models should be shifted, specified as a
single number or as [min, max, step]
0 means absolute magnitude.
distance_unit: astropy length unit or mag
distances will be evenly spaced in this unit
therefore, specifying a distance grid in mag units will lead to
a log grid
redshift: float
Redshift to which wavelengths should be shifted
Default is 0 (rest frame)
spec_fname: str
full filename to save the spectral grid into
filterLib: str
full filename to the filter library hd5 file
extLaw: extinction.ExtLaw (default=None)
if set, only save the spectrum for the wavelengths over which the
extinction law is valid
add_spectral_properties_kwargs: dict
keyword arguments to call :func:`add_spectral_properties`
to add model properties from the spectra into the grid property table
Returns
-------
fname: str
name of saved file
g: grid.SpectralGrid object
spectral grid to transform
"""
if spec_fname is None:
spec_fname = "%s/%s_spec_grid.hd5" % (project, project)
# remove the isochrone points with logL=-9.999
oiso.data = oiso[oiso["logL"] > -9]
if not os.path.isfile(spec_fname):
osl = osl or stellib.Kurucz()
# filter extrapolations of the grid with given sensitivities in
# logg and logT
if "dlogT" not in bounds:
bounds["dlogT"] = 0.1
if "dlogg" not in bounds:
bounds["dlogg"] = 0.3
# make the spectral grid
if verbose:
print("Make spectra")
g = creategrid.gen_spectral_grid_from_stellib_given_points(
osl, oiso.data, bounds=bounds)
# Construct the distances array. Turn single value into
# 1-element list if single distance is given.
_distance = np.atleast_1d(distance)
if len(_distance) == 3:
mindist, maxdist, stepdist = _distance
distances = np.arange(mindist, maxdist + stepdist, stepdist)
elif len(_distance) == 1:
distances = np.array(_distance)
else:
raise ValueError(
"distance needs to be (min, max, step) or single number")
# calculate the distances in pc
if distance_unit == units.mag:
distances = np.power(10, distances / 5.0 + 1) * units.pc
else:
distances = (distances * distance_unit).to(units.pc)
print("applying {} distances".format(len(distances)))
if verbose:
print(
"Adding spectral properties:",
add_spectral_properties_kwargs is not None,
)
if add_spectral_properties_kwargs is not None:
nameformat = (
add_spectral_properties_kwargs.pop("nameformat", "{0:s}") +
"_nd")
# Apply the distances to the stars. Seds already at 10 pc, need
# multiplication by the square of the ratio to this distance.
# TODO: Applying the distances might have to happen in chunks
# for larger grids.
def apply_distance_and_spectral_props(g):
# distance
g = creategrid.apply_distance_grid(g, distances, redshift=redshift)
# spectral props
if add_spectral_properties_kwargs is not None:
g = creategrid.add_spectral_properties(
g,
nameformat=nameformat,
filterLib=filterLib,
**add_spectral_properties_kwargs,
)
# extinction
if extLaw is not None:
ext_law_range_A = 1e4 / np.array(extLaw.x_range)
valid_lambda = np.where((g.lamb > np.min(ext_law_range_A))
&
(g.lamb < np.max(ext_law_range_A)))[0]
g.lamb = g.lamb[valid_lambda]
g.seds = g.seds[:, valid_lambda]
return g
# Perform the extensions defined above and Write to disk
if hasattr(g, "write"):
g = apply_distance_and_spectral_props(g)
g.write(spec_fname)
else:
for gk in g:
gk = apply_distance_and_spectral_props(gk)
gk.write(spec_fname, append=True)
g = SpectralGrid(spec_fname, backend="memory")
return (spec_fname, g)
def add_stellar_priors(project, specgrid,
distance_prior_model={'name': 'flat'},
age_prior_model={'name': 'flat'},
mass_prior_model={'name': 'kroupa'},
met_prior_model={'name': 'flat'},
verbose=True,
priors_fname=None,
**kwargs):
"""
make_priors -- compute the weights for the stellar priors
Parameters
----------
project: str
project name
specgrid: SpectralGrid object
spectral grid to transform
distance_prior_model: dict
dict including prior model name and parameters
age_prior_model: dict
dict including prior model name and parameters
mass_prior_model: dict
dict including prior model name and parameters
met_prior_model: dict
dict including prior model name and parameters
priors_fname: str
full filename to which to save the spectral grid with priors
Returns
-------
fname: str
name of saved file
g: SpectralGrid object
spectral grid to transform
"""
if priors_fname is None:
priors_fname = "%s/%s_spec_w_priors.grid.hd5" % (project, project)
if not os.path.isfile(priors_fname):
if verbose:
print("Make Prior Weights")
compute_distance_age_mass_metallicity_weights(
specgrid.grid,
distance_prior_model=distance_prior_model,
age_prior_model=age_prior_model,
mass_prior_model=mass_prior_model,
met_prior_model=met_prior_model,
**kwargs)
# write to disk
if hasattr(specgrid, "write"):
specgrid.write(priors_fname)
else:
for gk in specgrid:
gk.write(priors_fname, append=True)
g = SpectralGrid(priors_fname, backend="memory")
return (priors_fname, g)