I/O

HDF5 writer for summary statistics with units and provenance metadata.

class sum_stat.io.writer.SummaryStatWriter(path, mode='w')[source]

Bases: object

Write summary statistics to an HDF5 file with full units and provenance.

Each statistic occupies a named group (e.g. "angular_2pcf/DESI_BGS"). Every dataset carries unit and description attributes. Every group carries an estimator and survey provenance attributes. The cosmology is serialised inside each group so the file is self-contained.

Parameters:

path (str or Path) – Output HDF5 file path.
mode (str) – "w" to overwrite, "a" to append to an existing file.

Parameters:

path (str | Path)
mode (str)

Examples

>>> writer = SummaryStatWriter("results.h5")
>>> writer.write_twopcf("angular_2pcf/BGS", theta, w, cov, edges, "landy-szalay", cosmo, {})
>>> writer.close()

close()[source]

Close the HDF5 file.

Return type:: None

write_cl(group, ell_eff, cl, nl, cov, bin_edges, meta)[source]

Write angular power spectrum C_ℓ.

Parameters:

group (str) – HDF5 group path, e.g. "cl/DESI_BGS".
ell_eff (ndarray, shape (n_ell,)) – Effective multipole per bin.
cl (ndarray, shape (n_ell,)) – Angular power spectrum [sr].
nl (ndarray, shape (n_ell,)) – Shot noise power spectrum [sr].
cov (ndarray, shape (n_ell, n_ell)) – Covariance matrix [sr^2].
bin_edges (ndarray, shape (n_ell+1,)) – Multipole bin edges.
meta (dict)

Parameters:

group (str)
ell_eff (ndarray)
cl (ndarray)
nl (ndarray)
cov (ndarray)
bin_edges (ndarray)
meta (dict[str, Any])

Return type:

None

write_esd(group, rp_centres, delta_sigma, cov, bin_edges, cosmo, meta)[source]

Write excess surface mass density ΔΣ(r_p).

Parameters:

group (str) – HDF5 group path, e.g. "esd/DESI_BGS_KiDS".
rp_centres (ndarray, shape (n_bins,)) – Projected separation bin centres [Mpc].
delta_sigma (ndarray, shape (n_bins,)) – ΔΣ(r_p) [M_sun/pc^2].
cov (ndarray, shape (n_bins, n_bins)) – Jackknife covariance matrix [(M_sun/pc^2)^2].
bin_edges (ndarray, shape (n_bins+1,)) – Projected separation bin edges [Mpc].
cosmo (FlatLambdaCDM)
meta (dict) – Should include lens_survey, source_survey, m_bias, R_mean, photo_z_correction, boost_correction flags.

Parameters:

group (str)
rp_centres (ndarray)
delta_sigma (ndarray)
cov (ndarray)
bin_edges (ndarray)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])

Return type:

None

write_knn(group, r_centres, F_k, F_k_poisson, bin_edges, k_values, cosmo, meta)[source]

Write kNN-CDF summary statistics.

Parameters:

group (str) – HDF5 group path, e.g. "knn/DESI_BGS".
r_centres (ndarray, shape (n_r,)) – Separation bin centres [Mpc].
F_k (ndarray, shape (n_k, n_r)) – Empirical kNN-CDF for each k in k_values.
F_k_poisson (ndarray, shape (n_k, n_r)) – Erlang (Poisson) reference CDF for each k.
bin_edges (ndarray, shape (n_r+1,)) – Separation bin edges [Mpc].
k_values (ndarray, shape (n_k,)) – Neighbor orders used (e.g. [1, 2, 3, 4, 5]).
cosmo (FlatLambdaCDM)
meta (dict) – Extra attributes (estimator, n_query, n_gal, survey, etc.).

Parameters:

group (str)
r_centres (ndarray)
F_k (ndarray)
F_k_poisson (ndarray)
bin_edges (ndarray)
k_values (ndarray)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])

Return type:

None

write_lf(group, mag_centres, phi, phi_err, cov, bin_edges, cosmo, meta)[source]

Write a luminosity function.

Parameters:

group (str) – HDF5 group path, e.g. "lf/DESI_BGS_r".
mag_centres (ndarray, shape (n_bins,)) – Magnitude bin centres [mag].
phi (ndarray, shape (n_bins,)) – Luminosity function [Mpc^-3 mag^-1].
phi_err (ndarray, shape (n_bins,)) – Uncertainty on phi [Mpc^-3 mag^-1].
cov (ndarray, shape (n_bins, n_bins)) – Covariance matrix [(Mpc^-3 mag^-1)^2].
bin_edges (ndarray, shape (n_bins+1,)) – Magnitude bin edges [mag].
cosmo (FlatLambdaCDM) – Cosmology used for the V_max calculation.
meta (dict) – Extra attributes stored on the group (e.g. estimator, band, z_min, z_max).

Parameters:

group (str)
mag_centres (ndarray)
phi (ndarray)
phi_err (ndarray)
cov (ndarray)
bin_edges (ndarray)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])

Return type:

None

write_multipoles(group, s_centres, xi_dict, cov, bin_edges, cosmo, meta, sep_unit='Mpc/h')[source]

Write redshift-space multipoles ξ_ℓ(s).

Parameters:

group (str) – HDF5 group path.
s_centres (ndarray, shape (n_bins,)) – Separation bin centres.
xi_dict (dict) – Keys are multipole orders (0, 2, 4); values are shape (n_bins,).
cov (ndarray, shape (n_ell*n_bins, n_ell*n_bins)) – Stacked covariance matrix.
bin_edges (ndarray, shape (n_bins+1,)) – Separation bin edges.
cosmo (FlatLambdaCDM)
meta (dict)
sep_unit (str)

Parameters:

group (str)
s_centres (ndarray)
xi_dict (dict[int, ndarray])
cov (ndarray)
bin_edges (ndarray)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])
sep_unit (str)

Return type:

None

write_pk(group, k_centres, pk_dict, cov, bin_edges, cosmo, meta)[source]

Write power spectrum P(k) or multipoles P_ℓ(k).

Parameters:

group (str) – HDF5 group path, e.g. "pk3d/DESI_BGS".
k_centres (ndarray, shape (n_k,)) – Wavenumber bin centres [h/Mpc].
pk_dict (dict) – Keys are multipole orders (0, 2, 4); values are shape (n_k,) [Mpc/h]^3.
cov (ndarray, shape (n_ell*n_k, n_ell*n_k)) – Stacked covariance matrix [(Mpc/h)^6].
bin_edges (ndarray, shape (n_k+1,)) – Wavenumber bin edges [h/Mpc].
cosmo (FlatLambdaCDM)
meta (dict)

Parameters:

group (str)
k_centres (ndarray)
pk_dict (dict[int, ndarray])
cov (ndarray)
bin_edges (ndarray)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])

Return type:

None

write_smf(group, mstar_centres, phi, phi_err, cov, bin_edges, cosmo, meta)[source]

Write a stellar mass function.

Parameters:

group (str) – HDF5 group path, e.g. "smf/DESI_BGS".
mstar_centres (ndarray, shape (n_bins,)) – log10(M_*/M_sun) bin centres [dex].
phi (ndarray, shape (n_bins,)) – Stellar mass function [Mpc^-3 dex^-1].
phi_err (ndarray, shape (n_bins,)) – Uncertainty [Mpc^-3 dex^-1].
cov (ndarray, shape (n_bins, n_bins)) – Covariance matrix [(Mpc^-3 dex^-1)^2].
bin_edges (ndarray, shape (n_bins+1,)) – log10(M_*/M_sun) bin edges [dex].
cosmo (FlatLambdaCDM)
meta (dict)

Parameters:

group (str)
mstar_centres (ndarray)
phi (ndarray)
phi_err (ndarray)
cov (ndarray)
bin_edges (ndarray)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])

Return type:

None

write_twopcf(group, sep_centres, xi, cov, bin_edges, estimator, cosmo, meta, sep_unit='Mpc', xi_unit='dimensionless')[source]

Write a two-point correlation function.

Handles w(θ), ξ(r), w_p(r_p), and individual multipoles ξ_ℓ(s).

Parameters:

group (str) – HDF5 group path, e.g. "angular_2pcf/DESI_BGS".
sep_centres (ndarray, shape (n_bins,)) – Separation bin centres.
xi (ndarray, shape (n_bins,)) – Correlation function values.
cov (ndarray, shape (n_bins, n_bins)) – Covariance matrix.
bin_edges (ndarray, shape (n_bins+1,)) – Separation bin edges.
estimator (str) – Name of the estimator (e.g. "landy-szalay").
cosmo (FlatLambdaCDM)
meta (dict) – Extra attributes (e.g. pi_max_Mpc, ell, survey area).
sep_unit (str) – Physical unit string for separation axis (e.g. "arcmin", "Mpc").
xi_unit (str) – Physical unit string for correlation values.

Parameters:

group (str)
sep_centres (ndarray)
xi (ndarray)
cov (ndarray)
bin_edges (ndarray)
estimator (str)
cosmo (FlatLambdaCDM)
meta (dict[str, Any])
sep_unit (str)
xi_unit (str)

Return type:

None

HDF5 reader for summary statistics, reconstructing astropy Quantities.

class sum_stat.io.reader.SummaryStatReader(path)[source]

Bases: object

Read summary statistics from an HDF5 file written by SummaryStatWriter.

Parameters:: path (str or Path) – Path to the HDF5 file.
Parameters:: path (str | Path)

Examples

>>> reader = SummaryStatReader("results.h5")
>>> groups = reader.list_statistics()
>>> result = reader.read_esd("esd/DESI_BGS_KiDS")
>>> result["delta_sigma"]   # ndarray in M_sun/pc^2
>>> result["cov"]           # covariance matrix
>>> result["cosmology"]     # FlatLambdaCDM instance
>>> reader.close()

close()[source]

Close the HDF5 file.

Return type:: None

cosmology(group)[source]

Reconstruct the astropy cosmology stored in a group.

Parameters:: group (str) – HDF5 group path containing a cosmology subgroup.
Returns:: FlatLambdaCDM
Parameters:: group (str)
Return type:: FlatLambdaCDM

list_statistics()[source]

Return all leaf group paths (summary-statistic groups) in the file.

Returns:: paths (list of str)
Return type:: list[str]

read_cl(group)[source]

Read an angular power spectrum group.

Parameters:: group (str)
Return type:: dict

read_esd(group)[source]

Read an excess surface mass density group.

Parameters:: group (str)
Return type:: dict

read_lf(group)[source]

Read a luminosity function group.

Returns:: dict with keys (M_centres, bin_edges, phi, phi_err, cov,) – cosmology (FlatLambdaCDM), attrs (dict).
Parameters:: group (str)
Return type:: dict

read_multipoles(group)[source]

Read a multipoles group, returning xi0, xi2, xi4 if present.

Parameters:: group (str)
Return type:: dict

read_pk(group)[source]

Read a power spectrum group, returning pk0, pk2, pk4 if present.

Parameters:: group (str)
Return type:: dict

read_smf(group)[source]

Read a stellar mass function group.

Parameters:: group (str)
Return type:: dict

read_twopcf(group)[source]

Read a two-point correlation function group.

Parameters:: group (str)
Return type:: dict