Source code for beast.physicsmodel.creategrid

Create extinguished grid more segmented dealing with large grids with enough

All functions are now transformed into generators. As a result, any function
allows computation of a grid in an arbitrary number of chunks. This offers the
possibility to generate grids that cannot fit in memory.

.. note::

    * dependencies have also been updated accordingly.

    * likelihood computations need to be updated to allow computations even if
      the full grid does not fit in memory
import numpy as np
import copy

from astropy import units
from tqdm import tqdm

from beast.physicsmodel.stars import stellib
from beast.physicsmodel.grid import SpectralGrid, SEDGrid
from beast.physicsmodel.priormodel import PriorDustModel

# from beast.external.eztables import Table
from astropy.table import Table
from import generator
from import helpers

from beast.observationmodel.noisemodel import absflux_covmat

__all__ = [

[docs]@generator def gen_spectral_grid_from_stellib_given_points( osl, pts, bounds=dict(dlogT=0.1, dlogg=0.3), chunksize=0 ): """ Generator that reinterpolates a given stellar spectral library on to an Isochrone grid It will iterate over a list of `pts` points and generate `chunksize` models until all the list of points is processed Parameters ---------- osl: stellib.stellib a stellar library pts: dict like structure of points dictionary like or named data structure of points to interpolate at must contain logg, logT, logL, and Z bounds: dict, optional (default={dlogT:0.1, dlogg:0.3}) sensitivity to extrapolation (see grid.get_stellib_boundaries) chunksize: int, optional (default=0) number of models to generate at each cycle. If default <= 0, all models will be returned at once. Returns ------- g: SpectralGrid Spectral grid (in memory) containing the requested list of stars and associated spectra """ helpers.type_checker("osl", osl, stellib.Stellib) if chunksize <= 0: yield osl.gen_spectral_grid_from_given_points(pts, bounds=bounds) else: try: # Yield successive n-sized chunks from l, assuming we can take # slices of the iterator for chunk_slice in helpers.chunks(list(range(len(pts))), chunksize): chunk_pts = pts[chunk_slice] yield osl.gen_spectral_grid_from_given_points(chunk_pts, bounds=bounds) except Exception as e: # chunks may not work on this as pts is most likely a Table print(e) for chunk_pts in helpers.chunks(pts, chunksize): yield osl.gen_spectral_grid_from_given_points(chunk_pts, bounds=bounds)
def _make_dust_fA_valid_points_generator(it, min_Rv, max_Rv): """ compute the allowed points based on the R(V) versus f_A plane duplicates effort for all A(V) values, but it is quick compared to other steps .. note:: on 2.74: SMC extinction implies f_A = 0. and Rv = 2.74 Parameters ---------- it: an iterable an initial sequence of points that will be trimmed to only valid ones min_Rv: float lower Rv limit max_Rv: float upper Rv limit Returns ------- npts: int the actual number of valid points pts: generator a generator that only produce valid points """ itn = copy.copy(it) npts = 0 def is_valid(ak, rk, fk): return ( fk / max_Rv + (1.0 - fk) / 2.74 <= 1.0 / rk <= fk * 1.0 / min_Rv + (1.0 - fk) / 2.74 ) # explore the full list once # not very time consuming for ak, rk, fk in itn: if is_valid(ak, rk, fk): npts += 1 # make the iterator pts = ( (float(ak), float(rk), float(fk)) for ak, rk, fk in it if is_valid(ak, rk, fk) ) return npts, pts 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.zeros(N, dtype=float) # Existing columns keys0 = list(g0.keys()) for key in keys0: cols[key] = np.zeros(N, dtype=float) n_sed_points = g0.seds.shape[1] new_seds = np.zeros((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 = 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
[docs]@generator 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="disk") 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 # setup the dust prior models av_prior = PriorDustModel(av_prior_model) rv_prior = PriorDustModel(rv_prior_model) if with_fA: fA_prior = PriorDustModel(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: 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.zeros(N, dtype=float), "Rv": np.zeros(N, dtype=float)} if with_fA: cols["Rv_A"] = np.zeros(N, dtype=float) cols["f_A"] = np.zeros(N, dtype=float) keys = list(g0.keys()) for key in keys: cols[key] = np.zeros(N, dtype=float) n_filters = len(filter_names) _seds = np.zeros((N, n_filters), dtype=float) if absflux_cov: n_offdiag = ((n_filters ** 2) - n_filters) / 2 _cov_diag = np.zeros((N, n_filters), dtype=float) _cov_offdiag = np.zeros((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 = av_prior(Av) * rv_prior(Rv) * fA_prior(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 = av_prior(Av) * rv_prior(Rv) 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.zeros(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 = SEDGrid( _lamb, seds=_seds, cov_diag=_cov_diag, cov_offdiag=_cov_offdiag, grid=Table(cols), backend="memory", ) else: g = SEDGrid(_lamb, seds=_seds, grid=Table(cols), backend="memory") g.header["filters"] = " ".join(filter_names) yield g
[docs]def add_spectral_properties( specgrid, filternames=None, filters=None, callables=None, nameformat=None, filterLib=None, ): """ Addon spectral calculations to spectral grids to extract in the fitting routines Parameters ---------- specgrid: SpectralGrid instance instance of the spectral grid filternames: sequence(str) compute the integrated values through given filters in the library filters: sequence(Filters) sequence of filter instances from which extract integrated values callables: sequence(callable) sequence of functions to apply onto the spectral grid assuming storing results is internally processed by the individual functions nameformat: str naming format to adopt for filternames and filters default value is '{0:s}_0' where the value will be the filter name filterLib: str full filename to the filter library hd5 file Returns ------- specgrid: SpectralGrid instance instance of the input spectral grid which will include more properties """ if nameformat is None: nameformat = "{0:s}_0" if filternames is not None: temp = specgrid.getSEDs(filternames, extLaw=None, filterLib=filterLib) logtempseds = np.array(temp.seds) indxs = np.where(temp.seds > 0) if len(indxs) > 0: logtempseds[indxs] = np.log10(temp.seds[indxs]) indxs = np.where(temp.seds <= 0) if len(indxs) > 0: logtempseds[indxs] = -100.0 for i, fk in enumerate(filternames): specgrid.grid["log" + nameformat.format(fk)] = logtempseds[:, i] del temp if filters is not None: temp = specgrid.getSEDs(filters, extLaw=None) logtempseds = np.array(temp.seds) indxs = np.where(temp.seds > 0) if len(indxs) > 0: logtempseds[indxs] = np.log10(temp.seds[indxs]) indxs = np.where(temp.seds <= 0) if len(indxs) > 0: logtempseds[indxs] = -100.0 for i, fk in enumerate(filters): specgrid.grid["log" + nameformat.format(] = logtempseds[:, i] del temp if callables is not None: for fn in callables: fn(specgrid) return specgrid
[docs]def calc_absflux_cov_matrices(specgrid, sedgrid, filter_names): """ Calculate the absflux covariance matrices for each model Must be done on the full spectrum of each model to account for the changing combined spectral response due to the model SED and the filter response curve. Parameters ---------- specgrid: SpectralGrid instance instance of the spectral grid containing the full spectrum fluxes sedgrid: SpectralGrid instance instance of the spectral grid containing the band SED fluxes Returns ------- absflux_covmat : """ # get the fractional absflux covariance matrix absflux_cov_mats = absflux_covmat.hst_frac_matrix( filter_names, spectrum=(specgrid.lamb[:], specgrid.seds) ) # setup the output quantities n_models = specgrid.seds.shape[0] n_filters = len(filter_names) n_offdiag = ((n_filters ** 2) - n_filters) / 2 cov_diag = np.zeros((n_models, n_filters), dtype=np.float64) cov_offdiag = np.zeros((n_models, n_offdiag), dtype=np.float64) # pack the resulting covariance matrices into diganonal and # non-diagnonal terms # much more efficient for use later in combining with AST results # and fitting # also convert from fractional to physical flux units m = 0 cov_diag[:, n_filters - 1] = absflux_cov_mats[ :, n_filters - 1, n_filters - 1 ] * np.square(sedgrid.seds[:, n_filters - 1]) for k in range(n_filters - 1): cov_diag[:, k] = absflux_cov_mats[:, k, k] * np.square(sedgrid.seds[:, k]) for ll in range(k + 1, n_filters): cov_offdiag[:, m] = ( absflux_cov_mats[:, k, ll] * sedgrid.seds[:, k] * sedgrid.seds[:, ll] ) m += 1 return (cov_diag, cov_offdiag)