Index

_

_accepted_colums_map (Delta attribute) _accepted_delta_columns (Delta attribute) _accepted_extnames (in module qsonic.catalog) _accepted_targetid_keys (Delta attribute) _accepted_wave_columns (Delta attribute) _add_healpix() (in module qsonic.catalog) _blinding (Spectrum attribute) _check_hdu() (Delta static method) _check_required_columns() (in module qsonic.catalog) _coadd_reso() (Delta method) _coadd_wave (Spectrum attribute) _continuum_costfn() (PiccaContinuumModel method) _denom (PiccaContinuumFitter attribute) _dwave (Spectrum attribute) _eta_calibate_ivar() (PiccaContinuumFitter method) _fast_eval_interp1d_cubic() (in module qsonic.mathtools) _fast_eval_interp1d_lin() (in module qsonic.mathtools) _fast_weighted_vector_bincount() (in module qsonic.picca_continuum) _fit_array_shape_assert() (VarLSSFitter method) _fits_colnames (Spectrum attribute) _get_block_covariance() (SubsampleCov method) _get_fiducial_interp() (PiccaContinuumFitter method) _get_wave_bin_slice_params() (VarLSSFitter method) _get_xdiff() (SubsampleCov method) _iminuit_minimizer() (PiccaContinuumModel method) _interp (FluxStacker attribute) _interp_rf (FluxStacker attribute) _is_normalized (SubsampleCov attribute) _isample (SubsampleCov attribute) _istart (SubsampleCov attribute) _logic_true() (in module qsonic.mpi_utils)

_normalize() (SubsampleCov method) _normalize_flux() (PiccaContinuumFitter method) _one_function() (in module qsonic.mathtools) _optional_columns (in module qsonic.catalog) _prime_catalog() (in module qsonic.catalog) _project_normalize_meancont() (PiccaContinuumFitter method) _read() (FluxCalibrator method) (in module qsonic.catalog) (NoiseCalibrator method) _read_catalog() (DLAMask static method) _read_continua() (InputContinuumModel method) _read_continua_one_file() (InputContinuumModel method) _read_onehealpix_file() (in module qsonic.io) _read_onehealpix_file_onlyreso() (in module qsonic.io) _read_true_continuum() (in module qsonic.io) _required_columns (in module qsonic.catalog) _required_data_columns (in module qsonic.catalog) _required_tile_columns (in module qsonic.catalog) _scipy_l_bfgs_b_minimizer() (PiccaContinuumModel method) _set_coadd_wave() (Spectrum static method) _set_continuum_model() (PiccaContinuumFitter method) _set_forest_related_parameters() (Spectrum method) _set_meanflux_varlss_interps() (PiccaContinuumFitter method) _set_rsnr() (Spectrum method) _set_wave() (Spectrum static method) _smooth_fit_results() (VarLSSFitter method) _spline_cubic_natural() (in module qsonic.mathtools) _spline_cubic_notaknot() (in module qsonic.mathtools) _validate_adjust_column_names() (in module qsonic.catalog) _wave (Spectrum attribute) _zero_function() (in module qsonic.mathtools)

A

A12_lya (DLAMask attribute) A12_lyb (DLAMask attribute) accepted_zcolnames (DLAMask attribute) add() (FluxStacker method) (VarLSSFitter method) add_calibration_parser() (in module qsonic.calibration) add_io_parser() (in module qsonic.io) add_mask_parser() (in module qsonic.masks) add_measurement() (SubsampleCov method) add_picca_continuum_parser() (in module qsonic.picca_continuum) add_wave_region_parser() (in module qsonic.spectrum)

aij_coeff (DLAMask attribute) all_measurements (SubsampleCov attribute) all_weights (SubsampleCov attribute) allreduce() (SubsampleCov method) apply() (BALMask static method) (DLAMask method) (FluxCalibrator method) (NoiseCalibrator method) (SkyMask method) apply_masks() (in module qsonic.scripts.qsonic_fit) args_logic_fnc_qsonic_fit() (in module qsonic.scripts.qsonic_fit)

B

balance_load() (in module qsonic.mpi_utils) BALMask (class in qsonic.masks)

BaseContinuumModel (class in qsonic.continuum_models) blinding_not_set() (Spectrum static method) block_covariance_of_square() (in module qsonic.mathtools)

C

c_cms (DLAMask attribute) calc_continuum_chi2() (Spectrum method) calculate() (FluxStacker method) calculate_subsampler_stats() (VarLSSFitter method) check_catalog() (BALMask static method) close() (MPISaver method) coadd() (Delta method) coadd_arms_forest() (Spectrum method) column_names (SkyMask attribute)

comm (FluxStacker attribute) (PiccaContinuumFitter attribute) (VarLSSFitter attribute) construct_interp() (VarLSSFitter method) cont (Delta attribute) cont_order (PiccaContinuumFitter attribute) cont_params (Spectrum attribute) cov_var_delta (VarLSSFitter property) covariance (SubsampleCov attribute)

D

dec (Delta property) (Spectrum property) Delta (class in qsonic.spectrum) delta (Delta attribute) DLAMask (class in qsonic.masks)

drop_arm() (Spectrum method) drop_short_arms() (Spectrum method) dwave (Spectrum property) dwobs (FluxStacker attribute) dwrf (FluxStacker attribute)

E

e_var_centers (VarLSSFitter property) e_var_delta (VarLSSFitter property) eta_calib_ivar (PiccaContinuumFitter attribute)

eta_interp (NoiseCalibrator attribute) (PiccaContinuumFitter attribute) expected_columns (BALMask attribute)

F

f12_lya (DLAMask attribute) f12_lyb (DLAMask attribute) FastCubic1DInterp (class in qsonic.mathtools) FastLinear1DInterp (class in qsonic.mathtools) fft_gaussian_smooth() (in module qsonic.mathtools) fit() (VarLSSFitter method) fit_continua() (PiccaContinuumFitter method) fit_continuum() (BaseContinuumModel method) (InputContinuumModel method) (PiccaContinuumModel method) (TrueContinuumModel method) fit_eta (PiccaContinuumFitter attribute)

fit_final_varlss() (PiccaContinuumFitter method) flux_interp (FluxCalibrator attribute) flux_stacker (PiccaContinuumFitter attribute) FluxCalibrator (class in qsonic.calibration) FluxStacker (class in qsonic.picca_continuum) forestflux (Spectrum property) forestivar (Spectrum property) forestivar_sm (Spectrum property) forestreso (Spectrum property) forestwave (Spectrum property) forestweight (Spectrum property) from_dictionary() (Spectrum class method)

G

generate_spectra_list_from_data() (in module qsonic.spectrum) get_all_dlas() (DLAMask static method) get_continuum_model() (PiccaContinuumModel method) get_dla_flux() (DLAMask static method) get_effective_meansnr() (Spectrum method) get_mean() (SubsampleCov method) get_mean_n_cov() (SubsampleCov method) get_mean_n_var() (SubsampleCov method)

get_median_outlier_mask() (in module qsonic.mathtools) get_optical_depth() (DLAMask static method) get_parser() (in module qsonic.scripts.qsonic_calib) (in module qsonic.scripts.qsonic_coadd_deltas) (in module qsonic.scripts.qsonic_fit) get_real_size() (Spectrum method) get_smooth_ivar() (in module qsonic.mathtools) get_spectra_reader_function() (in module qsonic.io)

H

H_tepper_garcia() (DLAMask static method)

header (Delta attribute) hpix (Spectrum property)

I

init_spectra() (BaseContinuumModel method) (InputContinuumModel method) (PiccaContinuumModel method) (TrueContinuumModel method)

InputContinuumModel (class in qsonic.continuum_models) is_long() (Spectrum method) iterate() (PiccaContinuumFitter method) ivar (Delta attribute) ivar_edges (VarLSSFitter attribute)

L

LIGHT_SPEED (in module qsonic.masks)

lines (BALMask attribute)

M

main() (in module qsonic.scripts.qsonic_calib) (in module qsonic.scripts.qsonic_coadd_deltas) (in module qsonic.scripts.qsonic_fit) me (DLAMask attribute) mean (SubsampleCov attribute) mean_delta (VarLSSFitter property) mean_resolution() (Spectrum method) mean_snr (Delta attribute) (Spectrum attribute) meancont_interp (PiccaContinuumFitter attribute) meanflux_interp (PiccaContinuumFitter attribute) min_num_pix (VarLSSFitter attribute) min_num_qso (VarLSSFitter attribute) minimizer (PiccaContinuumModel attribute) minlength (VarLSSFitter attribute) model (PiccaContinuumFitter attribute) module qsonic.calibration qsonic.catalog qsonic.continuum_models qsonic.io qsonic.masks qsonic.mathtools qsonic.mpi_utils qsonic.picca_continuum qsonic.scripts.qsonic_calib qsonic.scripts.qsonic_coadd_deltas qsonic.scripts.qsonic_fit qsonic.spectrum

mpi_continuum_fitting() (in module qsonic.scripts.qsonic_fit) mpi_fnc_bcast() (in module qsonic.mpi_utils) mpi_get_local_queue() (in module qsonic.catalog) mpi_noise_flux_calibrate() (in module qsonic.scripts.qsonic_fit) mpi_parse() (in module qsonic.mpi_utils) mpi_rank (PiccaContinuumFitter attribute) (VarLSSFitter attribute) mpi_read_all_deltas() (in module qsonic.scripts.qsonic_calib) mpi_read_calibrate_mask_select_spectra() (in module qsonic.scripts.qsonic_fit) mpi_read_exposures_after() (in module qsonic.scripts.qsonic_fit) mpi_read_masks() (in module qsonic.scripts.qsonic_fit) mpi_read_quasar_catalog() (in module qsonic.catalog) mpi_read_spectra_local_queue() (in module qsonic.scripts.qsonic_fit) mpi_run_all() (in module qsonic.scripts.qsonic_calib) (in module qsonic.scripts.qsonic_fit) mpi_set_targetid_list_to_remove() (in module qsonic.scripts.qsonic_calib) mpi_stack_fluxes() (in module qsonic.scripts.qsonic_calib) MPISaver (class in qsonic.mpi_utils) mypoly1d() (in module qsonic.mathtools)

N

nbins (PiccaContinuumFitter attribute) niterations (PiccaContinuumFitter attribute) NoiseCalibrator (class in qsonic.calibration) normalize_stacked_flux (PiccaContinuumFitter attribute)

num_pixels (VarLSSFitter property) num_qso (VarLSSFitter property) nwbins (FluxStacker attribute) nwrfbins (FluxStacker attribute)

O

outdir (PiccaContinuumFitter attribute)

P

PiccaContinuumFitter (class in qsonic.picca_continuum)

PiccaContinuumModel (class in qsonic.continuum_models)

Q

qe (DLAMask attribute) qsonic.calibration module qsonic.catalog module qsonic.continuum_models module qsonic.io module qsonic.masks module qsonic.mathtools module

qsonic.mpi_utils module qsonic.picca_continuum module qsonic.scripts.qsonic_calib module qsonic.scripts.qsonic_coadd_deltas module qsonic.scripts.qsonic_fit module qsonic.spectrum module

R

ra (Delta property) (Spectrum property) read_deltas() (in module qsonic.io) read_dirs_to_dict() (in module qsonic.scripts.qsonic_coadd_deltas) read_onehealpix_file_data_coadd() (in module qsonic.io) read_onehealpix_file_data_uncoadd() (in module qsonic.io) read_onehealpix_file_mock() (in module qsonic.io) read_onetile_coaddfile_data() (in module qsonic.io) read_quasar_catalog() (in module qsonic.catalog) read_resolution_matrices_onehealpix_data() (in module qsonic.io)

remove_nonforest_pixels() (Spectrum method) remove_short_spectra() (in module qsonic.scripts.qsonic_fit) reset() (FastCubic1DInterp method) (FastLinear1DInterp method) (FluxStacker method) (SubsampleCov method) (VarLSSFitter method) reso (Delta attribute) rfwave (PiccaContinuumFitter attribute) rsnr (Spectrum attribute)

S

save() (PiccaContinuumFitter method) save_contchi2_catalog() (PiccaContinuumFitter method) save_deltas() (in module qsonic.io) set_blinding() (Spectrum static method) set_forest_region() (Spectrum method) set_forest_weight() (Spectrum method) set_smooth_forestivar() (Spectrum method) simple_coadd() (Spectrum method) SkyMask (class in qsonic.masks) slice() (Spectrum method) Spectrum (class in qsonic.spectrum) sqrt_2 (in module qsonic.masks) sqrt_pi (in module qsonic.masks)

stack_spectra() (BaseContinuumModel method) (InputContinuumModel method) (PiccaContinuumModel method) (TrueContinuumModel method) stacked_flux (FluxStacker property) stacked_flux_rf (FluxStacker property) stacks_residual_flux() (BaseContinuumModel method) (InputContinuumModel method) (PiccaContinuumModel method) (TrueContinuumModel method) std_flux_rf (FluxStacker property) SubsampleCov (class in qsonic.mathtools) subsampler (VarLSSFitter attribute)

T

targetid (Delta attribute) (Spectrum property)

TrueContinuumModel (class in qsonic.continuum_models)

U

update_mean_cont() (PiccaContinuumFitter method)

update_var_lss_eta() (PiccaContinuumFitter method)

V

valid_spectra() (in module qsonic.spectrum) var2_delta (VarLSSFitter property) var_centers (VarLSSFitter property) var_delta (VarLSSFitter property) variance (SubsampleCov attribute)

variance_function() (VarLSSFitter static method) varlss_fitter (PiccaContinuumFitter attribute) varlss_interp (PiccaContinuumFitter attribute) VarLSSFitter (class in qsonic.picca_continuum) voigt_tepper_garcia() (DLAMask static method)

W

wave (Delta attribute) (Spectrum property) wave_lya_A (DLAMask attribute) WAVE_LYA_A (Spectrum attribute) wave_lyb_A (DLAMask attribute) waveobs (FluxStacker attribute) (VarLSSFitter attribute) waverf0 (FluxStacker attribute)

weight (Delta attribute) weights (FluxStacker property) write() (Delta method) (MPISaver method) (Spectrum method) (VarLSSFitter method) write_one_hpx() (in module qsonic.scripts.qsonic_coadd_deltas) wvalid_bins (VarLSSFitter attribute)

Z

z_qso (Spectrum property)