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PIPE2D-1592: fitPfsFluxReference: Don't use low-SNR flux standards #369

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PIPE2D-1592: fitPfsFluxReference: Don't use low-SNR flux standards #369

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61 changes: 61 additions & 0 deletions python/pfs/drp/stella/fitPfsFluxReference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
import copy
import dataclasses
import math
import warnings

from typing import Literal, overload
from collections.abc import Generator, Mapping, Sequence
Expand Down Expand Up @@ -146,6 +147,22 @@ class FitPfsFluxReferenceConfig(PipelineTaskConfig, pipelineConnections=FitPfsFl
doc="Right ends of wavelength ranges ignored (because e.g. of strong atmospheric absorption)"
" when comparing middle-resolution observation spectra to models.",
)
cutoffSNR = Field(
dtype=float,
default=10,
doc="Minimally required pixel-wise S/N of observed spectra."
" Spectra with S/N worse than this value will be discarded.",
)
cutoffSNRRangeLeft = Field(
dtype=float,
default=840,
doc="Left edge of the wavelength range in which S/N is averaged to be compared with ``cutoffSNR``",
)
cutoffSNRRangeRight = Field(
dtype=float,
default=880,
doc="Right edge of the wavelength range in which S/N is averaged to be compared with ``cutoffSNR``",
)
badMask = ListField(
dtype=str, default=["BAD", "SAT", "CR", "NO_DATA", "SUSPECT"], doc="Mask planes for bad pixels"
)
Expand Down Expand Up @@ -402,6 +419,14 @@ def selectPfsConfig(pfsConfig: PfsConfig, flagName: str, isGood: Sequence[bool])
return goodConfig

pfsConfig = selectPfsConfig(pfsConfig, "ABSENT_FIBER", np.isin(pfsConfig.fiberId, pfsMerged.fiberId))

pfsMerged = removeBadSpectra(
pfsMerged,
self.config.cutoffSNR,
(self.config.cutoffSNRRangeLeft, self.config.cutoffSNRRangeRight),
)
pfsConfig = selectPfsConfig(pfsConfig, "LOW_SNR_FIBER", np.isin(pfsConfig.fiberId, pfsMerged.fiberId))

pfsConfig = selectPfsConfig(pfsConfig, "BAD_FIBER", (pfsConfig.fiberStatus == FiberStatus.GOOD))
pfsConfig = selectPfsConfig(
pfsConfig,
Expand Down Expand Up @@ -1996,6 +2021,42 @@ def removeBadFluxes(
pfsConfig.totalFluxErr = totalFluxErrArrays


def removeBadSpectra(
pfsMerged: PfsMerged,
cutoffSNR: float,
cutoffSNRRange: tuple[float, float],
) -> PfsMerged:
"""Remove bad spectra from ``pfsMerged``.

Spectra are bad if their average pixel-wise S/N is worse than ``cutoffSNR``.

Parameters
----------
pfsMerged : `PfsMerged`
Merged spectra from exposure.
cutoffSNR : `float`
Cut-off S/N.
cutoffSNRRange : `tuple` [`float`, `float`]
Wavelength range (nm) in which pixel-wise S/N is averaged to be compared
with ``cutoffSNR``.

Returns
-------
pfsMerged : `PfsMerged`
PfsMerged from which bad spectra have been removed.
"""
left, right = cutoffSNRRange
good = np.zeros(shape=(len(pfsMerged),), dtype=bool)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
for i in range(len(pfsMerged)):
sampleIndex = (left <= pfsMerged.wavelength[i]) & (pfsMerged.wavelength[i] <= right)
snr = pfsMerged.flux[i, sampleIndex] / np.sqrt(pfsMerged.covar[i, 0, sampleIndex])
good[i] = np.nanmedian(snr) >= cutoffSNR

return pfsMerged[good]


def promoteSimpleSpectrumToFiberArray(spectrum: PfsSimpleSpectrum, snr: float) -> PfsFiberArray:
"""Promote an instance of PfsSimpleSpectrum to PfsFiberArray.

Expand Down