from picca.delta_extraction.astronomical_objects.desi_forest import DesiForest
from picca.delta_extraction.astronomical_objects.desi_pk1d_forest import DesiPk1dForest
from picca.delta_extraction.astronomical_objects.forest import Forest
from picca.delta_extraction.data import Data, defaults, accepted_options
from picca.delta_extraction.errors import DataError
from picca.delta_extraction.quasar_catalogues.desi_quasar_catalogue import DesiQuasarCatalogue
from picca.delta_extraction.quasar_catalogues.desi_quasar_catalogue import (
accepted_options as accepted_options_quasar_catalogue)
from picca.delta_extraction.quasar_catalogues.desi_quasar_catalogue import (
defaults as defaults_quasar_catalogue)
from picca.delta_extraction.utils import ACCEPTED_BLINDING_STRATEGIES
from picca.delta_extraction.utils_pk1d import spectral_resolution_desi, exp_diff_desi
from picca.delta_extraction.utils import update_accepted_options, update_default_options
accepted_options = update_accepted_options(accepted_options,
accepted_options_quasar_catalogue)
accepted_options = update_accepted_options(
accepted_options,
["blinding", "num processors", "use non-coadded spectra", "wave solution"])
defaults = update_default_options(
defaults, {
"delta lambda": 0.8,
"delta log lambda": 3e-4,
"blinding": "corr_yshift",
"use non-coadded spectra": False,
"wave solution": "lin",
})
defaults = update_default_options(defaults, defaults_quasar_catalogue)
"""This module defines the class Dr16FixedEtaExpectedFlux"""
import logging
import fitsio
import numpy as np
from scipy.interpolate import interp1d
from picca.delta_extraction.errors import ExpectedFluxError
from picca.delta_extraction.expected_fluxes.dr16_expected_flux import Dr16ExpectedFlux
from picca.delta_extraction.expected_fluxes.dr16_expected_flux import (
defaults, accepted_options)
from picca.delta_extraction.utils import update_accepted_options, update_default_options
accepted_options = update_accepted_options(accepted_options, ["eta value"])
accepted_options = update_accepted_options(
accepted_options,
["limit eta", "use constant weight", "use ivar as weight"],
remove=True)
defaults = update_default_options(defaults, {
"eta value": 1.0,
})
class Dr16FixedEtaExpectedFlux(Dr16ExpectedFlux):
"""Class to the expected flux similar to Dr16ExpectedFlux but fixing eta
Methods
-------
(see Dr16ExpectedFlux in py/picca/delta_extraction/expected_fluxes/dr16_expected_flux.py)
__init__
import numpy as np
from scipy.interpolate import interp1d
from picca.delta_extraction.astronomical_objects.forest import Forest
from picca.delta_extraction.astronomical_objects.pk1d_forest import Pk1dForest
from picca.delta_extraction.errors import ExpectedFluxError
from picca.delta_extraction.expected_flux import ExpectedFlux, defaults, accepted_options
from picca.delta_extraction.expected_fluxes.utils import compute_continuum
from picca.delta_extraction.least_squares.least_squares_var_stats import (
LeastsSquaresVarStats, FUDGE_REF)
from picca.delta_extraction.utils import (find_bins, update_accepted_options,
update_default_options)
accepted_options = update_accepted_options(accepted_options, [
"force stack delta to zero", "limit eta", "limit var lss",
"min num qso in fit", "num iterations", "order", "use constant weight",
"use ivar as weight"
])
defaults = update_default_options(
defaults, {
"force stack delta to zero": True,
"limit eta": (0.5, 1.5),
"limit var lss": (0., 0.3),
"num iterations": 5,
"min num qso in fit": 100,
"order": 1,
"use constant weight": False,
"use ivar as weight": False,
})
"""This module defines the class Dr16FixedEtaVarlssExpectedFlux"""
from picca.delta_extraction.expected_fluxes.dr16_fixed_eta_expected_flux import (
Dr16FixedEtaExpectedFlux)
from picca.delta_extraction.expected_fluxes.dr16_fixed_eta_expected_flux import (
defaults, accepted_options)
from picca.delta_extraction.expected_fluxes.dr16_fixed_varlss_expected_flux import (
Dr16FixedVarlssExpectedFlux)
from picca.delta_extraction.expected_fluxes.dr16_fixed_varlss_expected_flux import (
defaults as defaults2, accepted_options as accepted_options2)
from picca.delta_extraction.utils import update_accepted_options, update_default_options
accepted_options = update_accepted_options(accepted_options, accepted_options2)
accepted_options = update_accepted_options(accepted_options, [
"limit eta", "limit var lss", "use constant weight", "use ivar as weight"
],
remove=True)
defaults = update_default_options(defaults, defaults2)
class Dr16FixedEtaVarlssExpectedFlux(Dr16FixedEtaExpectedFlux,
Dr16FixedVarlssExpectedFlux):
"""Class to the expected flux similar to Dr16ExpectedFlux but fixing both
eta and var_lss
Methods
-------
(see Dr16FixedEtaExpectedFlux in
py/picca/delta_extraction/expected_fluxes/dr16_fix_eta_expected_flux.py)
(see Dr16FixedVarlssExpectedFlux in
py/picca/delta_extraction/expected_fluxes/dr16_fix_varlss_expected_flux.py)
"""This module defines the class Dr16FixedFudgeExpectedFlux"""
import logging
import fitsio
import numpy as np
from scipy.interpolate import interp1d
from picca.delta_extraction.errors import ExpectedFluxError
from picca.delta_extraction.expected_fluxes.dr16_expected_flux import Dr16ExpectedFlux
from picca.delta_extraction.expected_fluxes.dr16_expected_flux import (
defaults, accepted_options)
from picca.delta_extraction.utils import update_accepted_options, update_default_options
accepted_options = update_accepted_options(accepted_options, ["fudge value"])
accepted_options = update_accepted_options(
accepted_options, ["use constant weight", "use ivar as weight"],
remove=True)
defaults = update_default_options(defaults, {
"fudge value": 0.0,
})
class Dr16FixedFudgeExpectedFlux(Dr16ExpectedFlux):
"""Class to the expected flux similar to Dr16ExpectedFlux but fixing the
fudge factor
Methods
-------
(see Dr16ExpectedFlux in py/picca/delta_extraction/expected_fluxes/dr16_expected_flux.py)
__init__
import numpy as np
import fitsio
from picca.delta_extraction.astronomical_objects.sdss_forest import SdssForest
from picca.delta_extraction.astronomical_objects.sdss_pk1d_forest import SdssPk1dForest
from picca.delta_extraction.data import Data, defaults, accepted_options
from picca.delta_extraction.errors import DataError
from picca.delta_extraction.quasar_catalogues.drq_catalogue import DrqCatalogue
from picca.delta_extraction.quasar_catalogues.drq_catalogue import defaults as defaults_drq
from picca.delta_extraction.quasar_catalogues.drq_catalogue import (
accepted_options as accepted_options_quasar_catalogue)
from picca.delta_extraction.utils_pk1d import exp_diff, spectral_resolution
from picca.delta_extraction.utils import update_accepted_options, update_default_options
accepted_options = update_accepted_options(accepted_options,
accepted_options_quasar_catalogue)
accepted_options = update_accepted_options(accepted_options, ["rebin", "mode"])
accepted_options = update_accepted_options(
accepted_options,
["delta lambda", "delta log lambda", "delta lambda rest frame"],
remove=True)
defaults = update_default_options(defaults, {
"mode": "spplate",
"rebin": 3,
})
defaults = update_default_options(defaults, defaults_drq)
class SdssData(Data):
"""Reads the spectra from SDSS and formats its data as a list of
"""This module defines the class DesiQuasarCatalogue to read z_truth
files from DESI
"""
import logging
from astropy.table import Table
import fitsio
import healpy
import numpy as np
from picca.delta_extraction.errors import QuasarCatalogueError
from picca.delta_extraction.quasar_catalogue import QuasarCatalogue, accepted_options
from picca.delta_extraction.utils import update_accepted_options
accepted_options = update_accepted_options(
accepted_options, ["catalogue", "in_nside", "keep surveys"])
defaults = {
"keep surveys": "all",
"in_nside": "64",
}
accepted_surveys = ["sv1", "sv2", "sv3", "main", "special", "all"]
class DesiQuasarCatalogue(QuasarCatalogue):
"""Reads the z_truth catalogue from DESI
Methods
-------
(see QuasarCatalogue in py/picca/delta_extraction/quasar_catalogue.py)
"""This module defines the class DrqCatalogue to read SDSS
DRQX Catalogues
"""
import glob
import logging
from astropy.table import Table, join
import numpy as np
from picca.delta_extraction.errors import QuasarCatalogueError
from picca.delta_extraction.quasar_catalogue import QuasarCatalogue, accepted_options
from picca.delta_extraction.utils import update_accepted_options
accepted_options = update_accepted_options(accepted_options, [
"best obs", "BI max", "drq catalogue", "input directory", "keep BAL",
"spAll"
])
defaults = {
"best obs": False,
"keep BAL": False,
}
class DrqCatalogue(QuasarCatalogue):
"""Read the DRQ quasar catalogue SDSS
Methods
-------
(see QuasarCatalogue in py/picca/delta_extraction/quasar_catalogue.py)
__init__
import fitsio
import numpy as np
from scipy.interpolate import interp1d
import healpy
from pkg_resources import resource_filename
from picca.delta_extraction.astronomical_objects.forest import Forest
from picca.delta_extraction.astronomical_objects.pk1d_forest import Pk1dForest
from picca.delta_extraction.errors import ExpectedFluxError
from picca.delta_extraction.expected_flux import ExpectedFlux, defaults, accepted_options
from picca.delta_extraction.utils import (find_bins, update_accepted_options,
update_default_options)
accepted_options = update_accepted_options(accepted_options, [
"input directory", "raw statistics file", "use constant weight",
"num bins variance"
])
defaults = update_default_options(defaults, {
"raw statistics file": "",
"use constant weight": False,
})
IN_NSIDE = 16
class TrueContinuum(ExpectedFlux):
"""Class to compute the expected flux using the true unabsorbed contiuum
for mocks.
It uses var_lss pre-computed from mocks and the mean flux modeled from a
2nd order polinomial in effective optical depth.
