calibrateImage.py

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# This file is part of pipe_tasks.
#
# Developed for the LSST Data Management System.
# This product includes software developed by the LSST Project
# (https://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
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# it under the terms of the GNU General Public License as published by
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__all__ = ["CalibrateImageTask", "CalibrateImageConfig", "NoPsfStarsToStarsMatchError",
           "AllCentroidsFlaggedError"]
 
import math
import numpy as np
import requests
import os
 
from lsst.afw.geom import SpanSet
import lsst.afw.table as afwTable
import lsst.afw.image as afwImage
import lsst.afw.math as afwMath
from lsst.ip.diffim.utils import evaluateMaskFraction, populate_sattle_visit_cache
import lsst.meas.algorithms
import lsst.meas.algorithms.installGaussianPsf
import lsst.meas.algorithms.measureApCorr
import lsst.meas.algorithms.setPrimaryFlags
from lsst.meas.algorithms.adaptive_thresholds import AdaptiveThresholdDetectionTask
import lsst.meas.base
import lsst.meas.astrom
import lsst.meas.deblender
import lsst.meas.extensions.shapeHSM
from lsst.obs.base import createInitialSkyWcs
import lsst.pex.config as pexConfig
import lsst.pipe.base as pipeBase
from lsst.pipe.base import connectionTypes
from lsst.utils.timer import timeMethod
 
from . import measurePsf, repair, photoCal, computeExposureSummaryStats, snapCombine, diffractionSpikeMask
 
 
class AllCentroidsFlaggedError(pipeBase.AlgorithmError):
    """Raised when there are no valid centroids during psf fitting.
    """
    def __init__(self, n_sources, psf_shape_ixx, psf_shape_iyy, psf_shape_ixy, psf_size):
        msg = (f"All source centroids (out of {n_sources}) flagged during PSF fitting. "
               "Original image PSF is likely unusable; best-fit PSF shape parameters: "
               f"Ixx={psf_shape_ixx}, Iyy={psf_shape_iyy}, Ixy={psf_shape_ixy}, size={psf_size}"
               )
        super().__init__(msg)
        self.n_sources = n_sources
        self.psf_shape_ixx = psf_shape_ixx
        self.psf_shape_iyy = psf_shape_iyy
        self.psf_shape_ixy = psf_shape_ixy
        self.psf_size = psf_size
 
    @property
    def metadata(self):
        return {"n_sources": self.n_sources,
                "psf_shape_ixx": self.psf_shape_ixx,
                "psf_shape_iyy": self.psf_shape_iyy,
                "psf_shape_ixy": self.psf_shape_ixy,
                "psf_size": self.psf_size
                }
 
 
class NoPsfStarsToStarsMatchError(pipeBase.AlgorithmError):
    """Raised when there are no matches between the psf_stars and stars
    catalogs.
    """
    def __init__(self, *, n_psf_stars, n_stars):
        msg = (f"No psf stars out of {n_psf_stars} matched {n_stars} calib stars."
               " Downstream processes probably won't have useful {calib_type} stars in this case."
               " Is `star_selector` too strict or is this a bad image?")
        super().__init__(msg)
        self.n_psf_stars = n_psf_stars
        self.n_stars = n_stars
 
    @property
    def metadata(self):
        return {"n_psf_stars": self.n_psf_stars,
                "n_stars": self.n_stars
                }
 
 
class CalibrateImageConnections(pipeBase.PipelineTaskConnections,
                                dimensions=("instrument", "visit", "detector")):
 
    astrometry_ref_cat = connectionTypes.PrerequisiteInput(
        doc="Reference catalog to use for astrometric calibration.",
        name="gaia_dr3_20230707",
        storageClass="SimpleCatalog",
        dimensions=("skypix",),
        deferLoad=True,
        multiple=True,
    )
    photometry_ref_cat = connectionTypes.PrerequisiteInput(
        doc="Reference catalog to use for photometric calibration.",
        name="ps1_pv3_3pi_20170110",
        storageClass="SimpleCatalog",
        dimensions=("skypix",),
        deferLoad=True,
        multiple=True
    )
    camera_model = connectionTypes.PrerequisiteInput(
        doc="Camera distortion model to use for astrometric calibration.",
        name="astrometry_camera",
        storageClass="Camera",
        dimensions=("instrument", "physical_filter"),
        isCalibration=True,
        minimum=0,  # Can fall back on WCS already attached to exposure.
    )
    exposures = connectionTypes.Input(
        doc="Exposure (or two snaps) to be calibrated, and detected and measured on.",
        name="postISRCCD",
        storageClass="Exposure",
        multiple=True,  # to handle 1 exposure or 2 snaps
        dimensions=["instrument", "exposure", "detector"],
    )
 
    background_flat = connectionTypes.PrerequisiteInput(
        name="flat",
        doc="Flat calibration frame used for background correction.",
        storageClass="ExposureF",
        dimensions=["instrument", "detector", "physical_filter"],
        isCalibration=True,
    )
    illumination_correction = connectionTypes.PrerequisiteInput(
        name="illuminationCorrection",
        doc="Illumination correction frame.",
        storageClass="Exposure",
        dimensions=["instrument", "detector", "physical_filter"],
        isCalibration=True,
    )
 
    # outputs
    initial_stars_schema = connectionTypes.InitOutput(
        doc="Schema of the output initial stars catalog.",
        name="initial_stars_schema",
        storageClass="SourceCatalog",
    )
 
    # TODO DM-38732: We want some kind of flag on Exposures/Catalogs to make
    # it obvious which components had failed to be computed/persisted.
    exposure = connectionTypes.Output(
        doc="Photometrically calibrated, background-subtracted exposure with fitted calibrations and "
            "summary statistics. To recover the original exposure, first add the background "
            "(`initial_pvi_background`), and then uncalibrate (divide by `initial_photoCalib_detector`).",
        name="initial_pvi",
        storageClass="ExposureF",
        dimensions=("instrument", "visit", "detector"),
    )
    stars = connectionTypes.Output(
        doc="Catalog of unresolved sources detected on the calibrated exposure.",
        name="initial_stars_detector",
        storageClass="ArrowAstropy",
        dimensions=["instrument", "visit", "detector"],
    )
    stars_footprints = connectionTypes.Output(
        doc="Catalog of unresolved sources detected on the calibrated exposure; "
            "includes source footprints.",
        name="initial_stars_footprints_detector",
        storageClass="SourceCatalog",
        dimensions=["instrument", "visit", "detector"],
    )
    applied_photo_calib = connectionTypes.Output(
        doc=(
            "Photometric calibration that was applied to exposure's pixels. "
            "This connection is disabled when do_calibrate_pixels=False."
        ),
        name="initial_photoCalib_detector",
        storageClass="PhotoCalib",
        dimensions=("instrument", "visit", "detector"),
    )
    background = connectionTypes.Output(
        doc="Background models estimated during calibration task; calibrated to be in nJy units.",
        name="initial_pvi_background",
        storageClass="Background",
        dimensions=("instrument", "visit", "detector"),
    )
    background_to_photometric_ratio = connectionTypes.Output(
        doc="Ratio of a background-flattened image to a photometric-flattened image. Only persisted "
            "if do_illumination_correction is True.",
        name="background_to_photometric_ratio",
        storageClass="Image",
        dimensions=("instrument", "visit", "detector"),
    )
 
    # Optional outputs
    mask = connectionTypes.Output(
        doc="The mask plane of the calibrated exposure, written as a separate "
            "output so that it can be passed to downstream tasks even if the "
            "exposure is removed to save storage.",
        name="preliminary_visit_mask",
        storageClass="Mask",
        dimensions=("instrument", "visit", "detector"),
    )
    psf_stars_footprints = connectionTypes.Output(
        doc="Catalog of bright unresolved sources detected on the exposure used for PSF determination; "
            "includes source footprints.",
        name="initial_psf_stars_footprints_detector",
        storageClass="SourceCatalog",
        dimensions=["instrument", "visit", "detector"],
    )
    psf_stars = connectionTypes.Output(
        doc="Catalog of bright unresolved sources detected on the exposure used for PSF determination.",
        name="initial_psf_stars_detector",
        storageClass="ArrowAstropy",
        dimensions=["instrument", "visit", "detector"],
    )
    astrometry_matches = connectionTypes.Output(
        doc="Source to reference catalog matches from the astrometry solver.",
        name="initial_astrometry_match_detector",
        storageClass="Catalog",
        dimensions=("instrument", "visit", "detector"),
    )
    photometry_matches = connectionTypes.Output(
        doc="Source to reference catalog matches from the photometry solver.",
        name="initial_photometry_match_detector",
        storageClass="Catalog",
        dimensions=("instrument", "visit", "detector"),
    )
 
    def __init__(self, *, config=None):
        super().__init__(config=config)
        if "psf_stars" not in config.optional_outputs:
            del self.psf_stars
        if "psf_stars_footprints" not in config.optional_outputs:
            del self.psf_stars_footprints
        if "astrometry_matches" not in config.optional_outputs:
            del self.astrometry_matches
        if "photometry_matches" not in config.optional_outputs:
            del self.photometry_matches
        if "mask" not in config.optional_outputs:
            del self.mask
        if not config.do_calibrate_pixels:
            del self.applied_photo_calib
        if not config.do_illumination_correction:
            del self.background_flat
            del self.illumination_correction
            del self.background_to_photometric_ratio
        if not config.useButlerCamera:
            del self.camera_model
 
 
class CalibrateImageConfig(pipeBase.PipelineTaskConfig, pipelineConnections=CalibrateImageConnections):
    optional_outputs = pexConfig.ListField(
        doc="Which optional outputs to save (as their connection name)?",
        dtype=str,
        # TODO: note somewhere to disable this for benchmarking, but should
        # we always have it on for production runs?
        default=["psf_stars", "psf_stars_footprints", "astrometry_matches", "photometry_matches", "mask"],
        optional=False
    )
 
    # To generate catalog ids consistently across subtasks.
    id_generator = lsst.meas.base.DetectorVisitIdGeneratorConfig.make_field()
 
    snap_combine = pexConfig.ConfigurableField(
        target=snapCombine.SnapCombineTask,
        doc="Task to combine two snaps to make one exposure.",
    )
 
    # subtasks used during psf characterization
    install_simple_psf = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.installGaussianPsf.InstallGaussianPsfTask,
        doc="Task to install a simple PSF model into the input exposure to use "
            "when detecting bright sources for PSF estimation.",
    )
    psf_repair = pexConfig.ConfigurableField(
        target=repair.RepairTask,
        doc="Task to repair cosmic rays on the exposure before PSF determination.",
    )
    psf_subtract_background = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.SubtractBackgroundTask,
        doc="Task to perform initial background subtraction, before first detection pass.",
    )
    psf_detection = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.SourceDetectionTask,
        doc="Task to detect sources for PSF determination."
    )
    do_adaptive_threshold_detection = pexConfig.Field(
        dtype=bool,
        default=True,
        doc="Implement the adaptive detection thresholding approach?",
    )
    psf_adaptive_threshold_detection = pexConfig.ConfigurableField(
        target=AdaptiveThresholdDetectionTask,
        doc="Task to adaptively detect sources for PSF determination.",
    )
    psf_source_measurement = pexConfig.ConfigurableField(
        target=lsst.meas.base.SingleFrameMeasurementTask,
        doc="Task to measure sources to be used for psf estimation."
    )
    psf_measure_psf = pexConfig.ConfigurableField(
        target=measurePsf.MeasurePsfTask,
        doc="Task to measure the psf on bright sources."
    )
    psf_normalized_calibration_flux = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.NormalizedCalibrationFluxTask,
        doc="Task to normalize the calibration flux (e.g. compensated tophats) "
            "for the bright stars used for psf estimation.",
    )
 
    # TODO DM-39203: we can remove aperture correction from this task once we
    # are using the shape-based star/galaxy code.
    measure_aperture_correction = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.measureApCorr.MeasureApCorrTask,
        doc="Task to compute the aperture correction from the bright stars."
    )
 
    # subtasks used during star measurement
    star_background = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.SubtractBackgroundTask,
        doc="Task to perform final background subtraction, just before photoCal.",
    )
    star_background_min_footprints = pexConfig.Field(
        dtype=int,
        default=3,
        doc="Minimum number of footprints in the detection mask for star_background measurement. "
            "This number will get adjusted to the fraction config.star_background_peak_fraction "
            "of the detected peaks if that number is larger. If the number of footprints is less "
            "than the minimum, the detection threshold is iteratively increased until the "
            "threshold is met.",
    )
    star_background_peak_fraction = pexConfig.Field(
        dtype=float,
        default=0.01,
        doc="The minimum number of footprints in the detection mask for star_background measurement. "
            "gets set to the maximum of this fraction of the detected peaks and the value set in "
            "config.star_background_min_footprints. If the number of footprints is less than the "
            "current minimum set, the detection threshold is iteratively increased until the "
            "threshold is met.",
    )
    star_detection = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.SourceDetectionTask,
        doc="Task to detect stars to return in the output catalog."
    )
    star_sky_sources = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.SkyObjectsTask,
        doc="Task to generate sky sources ('empty' regions where there are no detections).",
    )
    do_downsample_footprints = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="Downsample footprints prior to deblending to optimize speed?",
    )
    downsample_max_footprints = pexConfig.Field(
        dtype=int,
        default=1000,
        doc="Maximum number of non-sky-source footprints to use if do_downsample_footprints is True,",
    )
    star_deblend = pexConfig.ConfigurableField(
        target=lsst.meas.deblender.SourceDeblendTask,
        doc="Split blended sources into their components."
    )
    star_measurement = pexConfig.ConfigurableField(
        target=lsst.meas.base.SingleFrameMeasurementTask,
        doc="Task to measure stars to return in the output catalog."
    )
    star_normalized_calibration_flux = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.NormalizedCalibrationFluxTask,
        doc="Task to apply the normalization for calibration fluxes (e.g. compensated tophats) "
            "for the final output star catalog.",
    )
    star_apply_aperture_correction = pexConfig.ConfigurableField(
        target=lsst.meas.base.ApplyApCorrTask,
        doc="Task to apply aperture corrections to the selected stars."
    )
    star_catalog_calculation = pexConfig.ConfigurableField(
        target=lsst.meas.base.CatalogCalculationTask,
        doc="Task to compute extendedness values on the star catalog, "
            "for the star selector to remove extended sources."
    )
    star_set_primary_flags = pexConfig.ConfigurableField(
        target=lsst.meas.algorithms.setPrimaryFlags.SetPrimaryFlagsTask,
        doc="Task to add isPrimary to the catalog."
    )
    star_selector = lsst.meas.algorithms.sourceSelectorRegistry.makeField(
        default="science",
        doc="Task to select reliable stars to use for calibration."
    )
 
    # final calibrations and statistics
    astrometry = pexConfig.ConfigurableField(
        target=lsst.meas.astrom.AstrometryTask,
        doc="Task to perform astrometric calibration to fit a WCS.",
    )
    astrometry_ref_loader = pexConfig.ConfigField(
        dtype=lsst.meas.algorithms.LoadReferenceObjectsConfig,
        doc="Configuration of reference object loader for astrometric fit.",
    )
    photometry = pexConfig.ConfigurableField(
        target=photoCal.PhotoCalTask,
        doc="Task to perform photometric calibration to fit a PhotoCalib.",
    )
    photometry_ref_loader = pexConfig.ConfigField(
        dtype=lsst.meas.algorithms.LoadReferenceObjectsConfig,
        doc="Configuration of reference object loader for photometric fit.",
    )
    doMaskDiffractionSpikes = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="If True, load the photometric reference catalog again but select "
        "only bright stars. Use the bright star catalog to set the SPIKE "
        "mask for regions likely contaminated by diffraction spikes.",
    )
    diffractionSpikeMask = pexConfig.ConfigurableField(
        target=diffractionSpikeMask.DiffractionSpikeMaskTask,
        doc="Task to identify and mask the diffraction spikes of bright stars.",
    )
 
    compute_summary_stats = pexConfig.ConfigurableField(
        target=computeExposureSummaryStats.ComputeExposureSummaryStatsTask,
        doc="Task to to compute summary statistics on the calibrated exposure."
    )
 
    do_illumination_correction = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="If True, apply the illumination correction. This assumes that the "
            "input image has already been flat-fielded such that it is suitable "
            "for background subtraction.",
    )
 
    do_calibrate_pixels = pexConfig.Field(
        dtype=bool,
        default=True,
        doc=(
            "If True, apply the photometric calibration to the image pixels "
            "and background model, and attach an identity PhotoCalib to "
            "the output image to reflect this.  If False`, leave the image "
            "and background uncalibrated and attach the PhotoCalib that maps "
            "them to physical units."
        )
    )
 
    do_include_astrometric_errors = pexConfig.Field(
        dtype=bool,
        default=True,
        doc="If True, include astrometric errors in the output catalog.",
    )
 
    background_stats_ignored_pixel_masks = pexConfig.ListField(
        dtype=str,
        default=["SAT", "SUSPECT", "SPIKE"],
        doc="Pixel mask flags to ignore when calculating post-sky-subtraction "
            "background statistics. These are added to those ignored by the "
            "meas.algorithms.SubtractBackgroundConfig algorithm."
    )
 
    run_sattle = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="If True, the sattle service will populate a cache for later use "
            "in ip_diffim.detectAndMeasure alert verification."
    )
 
    sattle_historical = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="If re-running a pipeline that requires sattle, this should be set "
            "to True. This will populate sattle's cache with the historic data "
            "closest in time to the exposure.",
    )
 
    useButlerCamera = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="If True, use a camera distortion model generated elsewhere in "
            "the pipeline combined with the telescope boresight as a starting "
            "point for fitting the WCS, instead of using the WCS attached to "
            "the exposure, which is generated from the boresight and the "
            "camera model from the obs_* package."
    )
 
    background_stats_flux_column = pexConfig.Field(
        dtype=str,
        default="base_CircularApertureFlux_12_0_flux",
        doc="Column used to generate post-subtracted background stats."
    )
 
    def setDefaults(self):
        super().setDefaults()
 
        # Use a very broad PSF here, to thoroughly reject CRs.
        # TODO investigation: a large initial psf guess may make stars look
        # like CRs for very good seeing images.
        self.install_simple_psf.fwhm = 4
 
        # S/N>=50 sources for PSF determination, but detection to S/N=10.
        # The thresholdValue sets the minimum flux in a pixel to be included
        # in the footprint, while peaks are only detected when they are above
        # thresholdValue * includeThresholdMultiplier. The low thresholdValue
        # ensures that the footprints are large enough for the noise replacer
        # to mask out faint undetected neighbors that are not to be measured.
        self.psf_detection.thresholdValue = 10.0
        self.psf_detection.includeThresholdMultiplier = 5.0
        # TODO investigation: Probably want False here, but that may require
        # tweaking the background spatial scale, to make it small enough to
        # prevent extra peaks in the wings of bright objects.
        self.psf_detection.doTempLocalBackground = False
        self.psf_detection.reEstimateBackground = False
 
        # Minimal measurement plugins for PSF determination.
        # TODO DM-39203: We can drop GaussianFlux and PsfFlux, if we use
        # shapeHSM/moments for star/galaxy separation.
        # TODO DM-39203: we can remove aperture correction from this task
        # once we are using the shape-based star/galaxy code.
        self.psf_source_measurement.plugins = ["base_PixelFlags",
                                               "base_SdssCentroid",
                                               "ext_shapeHSM_HsmSourceMoments",
                                               "base_CircularApertureFlux",
                                               "base_GaussianFlux",
                                               "base_PsfFlux",
                                               "base_CompensatedTophatFlux",
                                               ]
        self.psf_source_measurement.slots.shape = "ext_shapeHSM_HsmSourceMoments"
        # Only measure apertures we need for PSF measurement.
        self.psf_source_measurement.plugins["base_CircularApertureFlux"].radii = [12.0]
        self.psf_source_measurement.plugins["base_CompensatedTophatFlux"].apertures = [12]
        # TODO DM-40843: Remove this line once this is the psfex default.
        self.psf_measure_psf.psfDeterminer["psfex"].photometricFluxField = \
            "base_CircularApertureFlux_12_0_instFlux"
 
        # No extendedness information available: we need the aperture
        # corrections to determine that.
        self.measure_aperture_correction.sourceSelector["science"].doUnresolved = False
        self.measure_aperture_correction.sourceSelector["science"].flags.good = ["calib_psf_used"]
        self.measure_aperture_correction.sourceSelector["science"].flags.bad = []
 
        # Detection for good S/N for astrometry/photometry and other
        # downstream tasks; detection mask to S/N>=5, but S/N>=10 peaks.
        self.star_detection.reEstimateBackground = False
        self.star_detection.thresholdValue = 5.0
        self.star_detection.includeThresholdMultiplier = 2.0
        self.star_measurement.plugins = ["base_PixelFlags",
                                         "base_SdssCentroid",
                                         "ext_shapeHSM_HsmSourceMoments",
                                         "ext_shapeHSM_HsmPsfMoments",
                                         "base_GaussianFlux",
                                         "base_PsfFlux",
                                         "base_CircularApertureFlux",
                                         "base_ClassificationSizeExtendedness",
                                         "base_CompensatedTophatFlux",
                                         ]
        self.star_measurement.slots.psfShape = "ext_shapeHSM_HsmPsfMoments"
        self.star_measurement.slots.shape = "ext_shapeHSM_HsmSourceMoments"
        # Only measure the apertures we need for star selection.
        self.star_measurement.plugins["base_CircularApertureFlux"].radii = [12.0]
        self.star_measurement.plugins["base_CompensatedTophatFlux"].apertures = [12]
 
        # We measure and apply the normalization aperture correction with
        # the psf_normalized_calibration_flux task, and we only apply the
        # normalization aperture correction for the full list of stars.
        self.star_normalized_calibration_flux.do_measure_ap_corr = False
 
        # Select stars with reliable measurements and no bad flags.
        self.star_selector["science"].doFlags = True
        self.star_selector["science"].doUnresolved = True
        self.star_selector["science"].doSignalToNoise = True
        self.star_selector["science"].signalToNoise.minimum = 10.0
        # Keep sky sources in the output catalog, even though they aren't
        # wanted for calibration.
        self.star_selector["science"].doSkySources = True
        # Set the flux and error fields
        self.star_selector["science"].signalToNoise.fluxField = "slot_CalibFlux_instFlux"
        self.star_selector["science"].signalToNoise.errField = "slot_CalibFlux_instFluxErr"
 
        # Use the affine WCS fitter (assumes we have a good camera geometry).
        self.astrometry.wcsFitter.retarget(lsst.meas.astrom.FitAffineWcsTask)
        # phot_g_mean is the primary Gaia band for all input bands.
        self.astrometry_ref_loader.anyFilterMapsToThis = "phot_g_mean"
 
        # Only reject sky sources; we already selected good stars.
        self.astrometry.sourceSelector["science"].doFlags = True
        self.astrometry.sourceSelector["science"].flags.good = []  # ["calib_psf_candidate"]
        # self.astrometry.sourceSelector["science"].flags.bad = []
        self.astrometry.sourceSelector["science"].doUnresolved = False
        self.astrometry.sourceSelector["science"].doIsolated = False
        self.astrometry.sourceSelector["science"].doRequirePrimary = False
        self.photometry.match.sourceSelection.doFlags = True
        self.photometry.match.sourceSelection.flags.bad = ["sky_source"]
        # Unset the (otherwise reasonable, but we've already made the
        # selections we want above) selection settings in PhotoCalTask.
        self.photometry.match.sourceSelection.doRequirePrimary = False
        self.photometry.match.sourceSelection.doUnresolved = False
 
    def validate(self):
        super().validate()
 
        # Ensure that the normalization calibration flux tasks
        # are configured correctly.
        if not self.psf_normalized_calibration_flux.do_measure_ap_corr:
            msg = ("psf_normalized_calibration_flux task must be configured with do_measure_ap_corr=True "
                   "or else the normalization and calibration flux will not be properly measured.")
            raise pexConfig.FieldValidationError(
                CalibrateImageConfig.psf_normalized_calibration_flux, self, msg,
            )
        if self.star_normalized_calibration_flux.do_measure_ap_corr:
            msg = ("star_normalized_calibration_flux task must be configured with do_measure_ap_corr=False "
                   "to apply the previously measured normalization to the full catalog of calibration "
                   "fluxes.")
            raise pexConfig.FieldValidationError(
                CalibrateImageConfig.star_normalized_calibration_flux, self, msg,
            )
 
        # Ensure base_LocalPhotoCalib and base_LocalWcs plugins are not run,
        # because they'd be running too early to pick up the fitted PhotoCalib
        # and WCS.
        if "base_LocalWcs" in self.psf_source_measurement.plugins.names:
            raise pexConfig.FieldValidationError(
                CalibrateImageConfig.psf_source_measurement,
                self,
                "base_LocalWcs cannot run CalibrateImageTask, as it would be run before the astrometry fit."
            )
        if "base_LocalWcs" in self.star_measurement.plugins.names:
            raise pexConfig.FieldValidationError(
                CalibrateImageConfig.star_measurement,
                self,
                "base_LocalWcs cannot run CalibrateImageTask, as it would be run before the astrometry fit."
            )
        if "base_LocalPhotoCalib" in self.psf_source_measurement.plugins.names:
            raise pexConfig.FieldValidationError(
                CalibrateImageConfig.psf_source_measurement,
                self,
                "base_LocalPhotoCalib cannot run CalibrateImageTask, "
                "as it would be run before the photometry fit."
            )
        if "base_LocalPhotoCalib" in self.star_measurement.plugins.names:
            raise pexConfig.FieldValidationError(
                CalibrateImageConfig.star_measurement,
                self,
                "base_LocalPhotoCalib cannot run CalibrateImageTask, "
                "as it would be run before the photometry fit."
            )
 
        # Check for illumination correction and background consistency.
        if self.do_illumination_correction:
            if not self.psf_subtract_background.doApplyFlatBackgroundRatio:
                raise pexConfig.FieldValidationError(
                    CalibrateImageConfig.psf_subtract_background,
                    self,
                    "CalibrateImageTask.psf_subtract_background must be configured with "
                    "doApplyFlatBackgroundRatio=True if do_illumination_correction=True."
                )
            if self.psf_detection.reEstimateBackground:
                if not self.psf_detection.doApplyFlatBackgroundRatio:
                    raise pexConfig.FieldValidationError(
                        CalibrateImageConfig.psf_detection,
                        self,
                        "CalibrateImageTask.psf_detection background must be configured with "
                        "doApplyFlatBackgroundRatio=True if do_illumination_correction=True."
                    )
            if self.star_detection.reEstimateBackground:
                if not self.star_detection.doApplyFlatBackgroundRatio:
                    raise pexConfig.FieldValidationError(
                        CalibrateImageConfig.star_detection,
                        self,
                        "CalibrateImageTask.star_detection background must be configured with "
                        "doApplyFlatBackgroundRatio=True if do_illumination_correction=True."
                    )
            if not self.star_background.doApplyFlatBackgroundRatio:
                raise pexConfig.FieldValidationError(
                    CalibrateImageConfig.star_background,
                    self,
                    "CalibrateImageTask.star_background background must be configured with "
                    "doApplyFlatBackgroundRatio=True if do_illumination_correction=True."
                )
 
        if self.run_sattle:
            if not os.getenv("SATTLE_URI_BASE"):
                raise pexConfig.FieldValidationError(CalibrateImageConfig.run_sattle, self,
                                                     "Sattle requested but URI environment variable not set.")
 
        if not self.do_adaptive_threshold_detection:
            if not self.psf_detection.reEstimateBackground:
                raise pexConfig.FieldValidationError(
                    CalibrateImageConfig.psf_detection,
                    self,
                    "If not using the adaptive threshold detection implementation (i.e. "
                    "config.do_adaptive_threshold_detection = False), CalibrateImageTask.psf_detection "
                    "background must be configured with "
                    "reEstimateBackground = True to maintain original behavior."
                )
            if not self.star_detection.reEstimateBackground:
                raise pexConfig.FieldValidationError(
                    CalibrateImageConfig.psf_detection,
                    self,
                    "If not using the adaptive threshold detection implementation "
                    "(i.e. config.do_adaptive_threshold_detection = False), "
                    "CalibrateImageTask.star_detection background must be configured "
                    "with reEstimateBackground = True to maintain original behavior."
                )
 
 
class CalibrateImageTask(pipeBase.PipelineTask):
    """Compute the PSF, aperture corrections, astrometric and photometric
    calibrations, and summary statistics for a single science exposure, and
    produce a catalog of brighter stars that were used to calibrate it.
 
    Parameters
    ----------
    initial_stars_schema : `lsst.afw.table.Schema`
        Schema of the initial_stars output catalog.
    """
    _DefaultName = "calibrateImage"
    ConfigClass = CalibrateImageConfig
 
    def __init__(self, initial_stars_schema=None, **kwargs):
        super().__init__(**kwargs)
        self.makeSubtask("snap_combine")
 
        # PSF determination subtasks
        self.makeSubtask("install_simple_psf")
        self.makeSubtask("psf_repair")
        self.makeSubtask("psf_subtract_background")
        self.psf_schema = afwTable.SourceTable.makeMinimalSchema()
        self.psf_schema.addField(
            'psf_max_value',
            type=np.float32,
            doc="PSF max value.",
        )
        afwTable.CoordKey.addErrorFields(self.psf_schema)
        self.makeSubtask("psf_detection", schema=self.psf_schema)
        self.makeSubtask("psf_source_measurement", schema=self.psf_schema)
        self.makeSubtask("psf_adaptive_threshold_detection")
        self.makeSubtask("psf_measure_psf", schema=self.psf_schema)
        self.makeSubtask("psf_normalized_calibration_flux", schema=self.psf_schema)
 
        self.makeSubtask("measure_aperture_correction", schema=self.psf_schema)
        self.makeSubtask("astrometry", schema=self.psf_schema)
 
        # star measurement subtasks
        if initial_stars_schema is None:
            initial_stars_schema = afwTable.SourceTable.makeMinimalSchema()
 
        # These fields let us track which sources were used for psf modeling,
        # astrometric fitting, and aperture correction calculations.
        self.psf_fields = ("calib_psf_candidate", "calib_psf_used", "calib_psf_reserved",
                           "calib_astrometry_used",
                           # TODO DM-39203:
                           # these can be removed once apcorr is gone.
                           "apcorr_slot_CalibFlux_used", "apcorr_base_GaussianFlux_used",
                           "apcorr_base_PsfFlux_used",)
        for field in self.psf_fields:
            item = self.psf_schema.find(field)
            initial_stars_schema.addField(item.getField())
        id_type = self.psf_schema["id"].asField().getTypeString()
        psf_max_value_type = self.psf_schema['psf_max_value'].asField().getTypeString()
        initial_stars_schema.addField("psf_id",
                                      type=id_type,
                                      doc="id of this source in psf_stars; 0 if there is no match.")
        initial_stars_schema.addField("psf_max_value",
                                      type=psf_max_value_type,
                                      doc="Maximum value in the star image used to train PSF.")
 
        afwTable.CoordKey.addErrorFields(initial_stars_schema)
        self.makeSubtask("star_background")
        self.makeSubtask("star_detection", schema=initial_stars_schema)
        self.makeSubtask("star_sky_sources", schema=initial_stars_schema)
        self.makeSubtask("star_deblend", schema=initial_stars_schema)
        self.makeSubtask("star_measurement", schema=initial_stars_schema)
        self.makeSubtask("star_normalized_calibration_flux", schema=initial_stars_schema)
 
        self.makeSubtask("star_apply_aperture_correction", schema=initial_stars_schema)
        self.makeSubtask("star_catalog_calculation", schema=initial_stars_schema)
        self.makeSubtask("star_set_primary_flags", schema=initial_stars_schema, isSingleFrame=True)
        self.makeSubtask("star_selector")
        self.makeSubtask("photometry", schema=initial_stars_schema)
        if self.config.doMaskDiffractionSpikes:
            self.makeSubtask("diffractionSpikeMask")
        self.makeSubtask("compute_summary_stats")
 
        # The final catalog will have calibrated flux columns, which we add to
        # the init-output schema by calibrating our zero-length catalog with an
        # arbitrary dummy PhotoCalib.  We also use this schema to initialize
        # the stars catalog in order to ensure it's the same even when we hit
        # an error (and write partial outputs) before calibrating the catalog
        # - note that calibrateCatalog will happily reuse existing output
        # columns.
        dummy_photo_calib = afwImage.PhotoCalib(1.0, 0, bbox=lsst.geom.Box2I())
        self.initial_stars_schema = dummy_photo_calib.calibrateCatalog(
            afwTable.SourceCatalog(initial_stars_schema)
        )
 
    def runQuantum(self, butlerQC, inputRefs, outputRefs):
        inputs = butlerQC.get(inputRefs)
        exposures = inputs.pop("exposures")
 
        id_generator = self.config.id_generator.apply(butlerQC.quantum.dataId)
 
        astrometry_loader = lsst.meas.algorithms.ReferenceObjectLoader(
            dataIds=[ref.datasetRef.dataId for ref in inputRefs.astrometry_ref_cat],
            refCats=inputs.pop("astrometry_ref_cat"),
            name=self.config.connections.astrometry_ref_cat,
            config=self.config.astrometry_ref_loader, log=self.log)
        self.astrometry.setRefObjLoader(astrometry_loader)
 
        photometry_loader = lsst.meas.algorithms.ReferenceObjectLoader(
            dataIds=[ref.datasetRef.dataId for ref in inputRefs.photometry_ref_cat],
            refCats=inputs.pop("photometry_ref_cat"),
            name=self.config.connections.photometry_ref_cat,
            config=self.config.photometry_ref_loader, log=self.log)
        self.photometry.match.setRefObjLoader(photometry_loader)
 
        if self.config.doMaskDiffractionSpikes:
            # Use the same photometry reference catalog for the bright star
            # mask.
            self.diffractionSpikeMask.setRefObjLoader(photometry_loader)
 
        if self.config.do_illumination_correction:
            background_flat = inputs.pop("background_flat")
            illumination_correction = inputs.pop("illumination_correction")
        else:
            background_flat = None
            illumination_correction = None
 
        camera_model = None
        if self.config.useButlerCamera:
            if "camera_model" in inputs:
                camera_model = inputs.pop("camera_model")
            else:
                self.log.warning("useButlerCamera=True, but camera is not available for filter %s. The "
                                 "astrometry fit will use the WCS already attached to the exposure.",
                                 exposures[0].filter.bandLabel)
 
        # This should not happen with a properly configured execution context.
        assert not inputs, "runQuantum got more inputs than expected"
 
        # Specify the fields that `annotate` needs below, to ensure they
        # exist, even as None.
        result = pipeBase.Struct(
            exposure=None,
            stars_footprints=None,
            psf_stars_footprints=None,
            background_to_photometric_ratio=None,
        )
        try:
            self.run(
                exposures=exposures,
                result=result,
                id_generator=id_generator,
                background_flat=background_flat,
                illumination_correction=illumination_correction,
                camera_model=camera_model,
            )
        except pipeBase.AlgorithmError as e:
            error = pipeBase.AnnotatedPartialOutputsError.annotate(
                e,
                self,
                result.exposure,
                result.psf_stars_footprints,
                result.stars_footprints,
                log=self.log
            )
            butlerQC.put(result, outputRefs)
            raise error from e
 
        butlerQC.put(result, outputRefs)
 
    @timeMethod
    def run(
        self,
        *,
        exposures,
        id_generator=None,
        result=None,
        background_flat=None,
        illumination_correction=None,
        camera_model=None,
    ):
        """Find stars and perform psf measurement, then do a deeper detection
        and measurement and calibrate astrometry and photometry from that.
 
        Parameters
        ----------
        exposures : `lsst.afw.image.Exposure` or \
                    `list` [`lsst.afw.image.Exposure`]
            Post-ISR exposure(s), with an initial WCS, VisitInfo, and Filter.
            Modified in-place during processing if only one is passed.
            If two exposures are passed, treat them as snaps and combine
            before doing further processing.
        id_generator : `lsst.meas.base.IdGenerator`, optional
            Object that generates source IDs and provides random seeds.
        result : `lsst.pipe.base.Struct`, optional
            Result struct that is modified to allow saving of partial outputs
            for some failure conditions. If the task completes successfully,
            this is also returned.
        background_flat : `lsst.afw.image.Exposure`, optional
            Background flat-field image.
        illumination_correction : `lsst.afw.image.Exposure`, optional
            Illumination correction image.
        camera_model : `lsst.afw.cameraGeom.Camera`, optional
            Camera to be used if constructing updated WCS.
 
        Returns
        -------
        result : `lsst.pipe.base.Struct`
            Results as a struct with attributes:
 
            ``exposure``
                Calibrated exposure, with pixels in nJy units.
                (`lsst.afw.image.Exposure`)
            ``stars``
                Stars that were used to calibrate the exposure, with
                calibrated fluxes and magnitudes.
                (`astropy.table.Table`)
            ``stars_footprints``
                Footprints of stars that were used to calibrate the exposure.
                (`lsst.afw.table.SourceCatalog`)
            ``psf_stars``
                Stars that were used to determine the image PSF.
                (`astropy.table.Table`)
            ``psf_stars_footprints``
                Footprints of stars that were used to determine the image PSF.
                (`lsst.afw.table.SourceCatalog`)
            ``background``
                Background that was fit to the exposure when detecting
                ``stars``. (`lsst.afw.math.BackgroundList`)
            ``applied_photo_calib``
                Photometric calibration that was fit to the star catalog and
                applied to the exposure. (`lsst.afw.image.PhotoCalib`)
                This is `None` if ``config.do_calibrate_pixels`` is `False`.
            ``astrometry_matches``
                Reference catalog stars matches used in the astrometric fit.
                (`list` [`lsst.afw.table.ReferenceMatch`] or
                `lsst.afw.table.BaseCatalog`).
            ``photometry_matches``
                Reference catalog stars matches used in the photometric fit.
                (`list` [`lsst.afw.table.ReferenceMatch`] or
                `lsst.afw.table.BaseCatalog`).
            ``mask``
                Copy of the mask plane of `exposure`.
                (`lsst.afw.image.Mask`)
        """
        if result is None:
            result = pipeBase.Struct()
        if id_generator is None:
            id_generator = lsst.meas.base.IdGenerator()
 
        result.exposure = self.snap_combine.run(exposures).exposure
        self.log.info("Initial PhotoCalib: %s", result.exposure.getPhotoCalib())
 
        result.exposure.metadata["LSST CALIB ILLUMCORR APPLIED"] = False
 
        # Check input image processing.
        if self.config.do_illumination_correction:
            if not result.exposure.metadata.get("LSST ISR FLAT APPLIED", False):
                raise pipeBase.InvalidQuantumError(
                    "Cannot use do_illumination_correction with an image that has not had a flat applied",
                )
 
        if camera_model:
            if camera_model.get(result.exposure.detector.getId()):
                self.log.info("Updating WCS with the provided camera model.")
                self._update_wcs_with_camera_model(result.exposure, camera_model)
            else:
                self.log.warning(
                    "useButlerCamera=True, but detector %s is not available in the provided camera. The "
                    "astrometry fit will use the WCS already attached to the exposure.",
                    result.exposure.detector.getId())
 
        result.background = None
        result.background_to_photometric_ratio = None
        summary_stat_catalog = None
        # Some exposure components are set to initial placeholder objects
        # while we try to bootstrap them.  If we fail before we fit for them,
        # we want to reset those components to None so the placeholders don't
        # masquerade as the real thing.
        have_fit_psf = False
        have_fit_astrometry = False
        have_fit_photometry = False
        try:
            result.background_to_photometric_ratio = self._apply_illumination_correction(
                result.exposure,
                background_flat,
                illumination_correction,
            )
 
            result.psf_stars_footprints, _, adaptive_det_res_struct = self._compute_psf(
                result,
                id_generator,
            )
            have_fit_psf = True
 
            # Check if all centroids have been flagged. This should happen
            # after the PSF is fit and recorded because even a junky PSF
            # model is informative.
            if result.psf_stars_footprints["slot_Centroid_flag"].all():
                psf_shape = result.exposure.psf.computeShape(result.exposure.psf.getAveragePosition())
                raise AllCentroidsFlaggedError(
                    n_sources=len(result.psf_stars_footprints),
                    psf_shape_ixx=psf_shape.getIxx(),
                    psf_shape_iyy=psf_shape.getIyy(),
                    psf_shape_ixy=psf_shape.getIxy(),
                    psf_size=psf_shape.getDeterminantRadius(),
                )
 
            if result.background is None:
                result.background = afwMath.BackgroundList()
 
            self._measure_aperture_correction(result.exposure, result.psf_stars_footprints)
            result.psf_stars = result.psf_stars_footprints.asAstropy()
            # Run astrometry using PSF candidate stars.
            # Update "the psf_stars" source coordinates with the current wcs.
            afwTable.updateSourceCoords(
                result.exposure.wcs,
                sourceList=result.psf_stars_footprints,
                include_covariance=self.config.do_include_astrometric_errors,
            )
            astrometry_matches, astrometry_meta = self._fit_astrometry(
                result.exposure, result.psf_stars_footprints
            )
            num_astrometry_matches = len(astrometry_matches)
            if "astrometry_matches" in self.config.optional_outputs:
                result.astrometry_matches = lsst.meas.astrom.denormalizeMatches(astrometry_matches,
                                                                                astrometry_meta)
            result.psf_stars = result.psf_stars_footprints.asAstropy()
 
            # Add diffraction spike mask here so it can be used (i.e. avoided)
            # in the adaptive background estimation.
            if self.config.doMaskDiffractionSpikes:
                self.diffractionSpikeMask.run(result.exposure)
 
            self.metadata['adaptive_threshold_value'] = float("nan")
            if self.config.do_adaptive_threshold_detection:
                self._remeasure_star_background(
                    result,
                    background_to_photometric_ratio=result.background_to_photometric_ratio,
                )
 
            # Run the stars_detection subtask for the photometric calibration.
            result.stars_footprints = self._find_stars(
                result.exposure,
                result.background,
                id_generator,
                background_to_photometric_ratio=result.background_to_photometric_ratio,
                adaptive_det_res_struct=adaptive_det_res_struct,
                num_astrometry_matches=num_astrometry_matches,
            )
            psf = result.exposure.getPsf()
            psfSigma = psf.computeShape(result.exposure.getBBox().getCenter()).getDeterminantRadius()
            self._match_psf_stars(result.psf_stars_footprints, result.stars_footprints,
                                  psfSigma=psfSigma)
 
            # Update the "stars" source coordinates with the current wcs.
            afwTable.updateSourceCoords(
                result.exposure.wcs,
                sourceList=result.stars_footprints,
                include_covariance=self.config.do_include_astrometric_errors,
            )
 
            summary_stat_catalog = result.stars_footprints
            result.stars = result.stars_footprints.asAstropy()
            self.metadata["star_count"] = np.sum(~result.stars["sky_source"])
 
            # Validate the astrometric fit. Send in the stars_footprints
            # catalog so that its coords get set to NaN if the fit is deemed
            # a failure.
            self.astrometry.check(result.exposure, result.stars_footprints, len(astrometry_matches))
            result.stars = result.stars_footprints.asAstropy()
            have_fit_astrometry = True
 
            result.stars_footprints, photometry_matches, \
                photometry_meta, photo_calib = self._fit_photometry(result.exposure, result.stars_footprints)
            have_fit_photometry = True
            self.metadata["photometry_matches_count"] = len(photometry_matches)
            # fit_photometry returns a new catalog, so we need a new astropy
            # table view.
            result.stars = result.stars_footprints.asAstropy()
            # summary stats don't make use of the calibrated fluxes, but we
            # might as well use the best catalog we've got in case that
            # changes, and help the old one get garbage-collected.
            summary_stat_catalog = result.stars_footprints
            if "photometry_matches" in self.config.optional_outputs:
                result.photometry_matches = lsst.meas.astrom.denormalizeMatches(photometry_matches,
                                                                                photometry_meta)
            if "mask" in self.config.optional_outputs:
                result.mask = result.exposure.mask.clone()
        except pipeBase.AlgorithmError:
            if not have_fit_psf:
                result.exposure.setPsf(None)
            if not have_fit_astrometry:
                result.exposure.setWcs(None)
            if not have_fit_photometry:
                result.exposure.setPhotoCalib(None)
            # Summary stat calculations can handle missing components
            # gracefully, but we want to run them as late as possible (but
            # still before we calibrate pixels, if we do that at all).
            # So we run them after we succeed or if we get an AlgorithmError.
            # We intentionally don't use 'finally' here because we don't
            # want to run them if we get some other kind of error.
            self._summarize(result.exposure, summary_stat_catalog, result.background)
            raise
        else:
            self._summarize(result.exposure, summary_stat_catalog, result.background)
 
        # Output post-subtraction background stats to task metadata:
        # Specify the pixels flags to ignore, starting with those ignored
        # by the subtraction.
        bgIgnoredPixelMasks = lsst.meas.algorithms.SubtractBackgroundConfig().ignoredPixelMask.list()
        for maskName in self.config.background_stats_ignored_pixel_masks:
            if (maskName in result.exposure.mask.getMaskPlaneDict().keys()
                    and maskName not in bgIgnoredPixelMasks):
                bgIgnoredPixelMasks += [maskName]
 
        statsCtrl = afwMath.StatisticsControl()
        statsCtrl.setAndMask(afwImage.Mask.getPlaneBitMask(bgIgnoredPixelMasks))
 
        statObj = afwMath.makeStatistics(result.exposure.getMaskedImage(), afwMath.MEDIAN, statsCtrl)
        median_bg, _ = statObj.getResult(afwMath.MEDIAN)
        self.metadata["bg_subtracted_skyPixel_instFlux_median"] = median_bg
 
        statObj = afwMath.makeStatistics(result.exposure.getMaskedImage(), afwMath.STDEV, statsCtrl)
        stdev_bg, _ = statObj.getResult(afwMath.STDEV)
        self.metadata["bg_subtracted_skyPixel_instFlux_stdev"] = stdev_bg
 
        self.metadata["bg_subtracted_skySource_flux_median"] = (
            np.median(result.stars[result.stars['sky_source']][self.config.background_stats_flux_column])
        )
        self.metadata["bg_subtracted_skySource_flux_stdev"] = (
            np.std(result.stars[result.stars['sky_source']][self.config.background_stats_flux_column])
        )
 
        if self.config.do_calibrate_pixels:
            self._apply_photometry(
                result.exposure,
                result.background,
                background_to_photometric_ratio=result.background_to_photometric_ratio,
            )
            result.applied_photo_calib = photo_calib
        else:
            result.applied_photo_calib = None
 
        self._recordMaskedPixelFractions(result.exposure)
 
        if self.config.run_sattle:
            # send boresight and timing information to sattle so the cache
            # is populated by the time we reach ip_diffim detectAndMeasure.
            try:
                populate_sattle_visit_cache(result.exposure.getInfo().getVisitInfo(),
                                            historical=self.config.sattle_historical)
                self.log.info('Successfully triggered load of sattle visit cache')
            except requests.exceptions.HTTPError:
                self.log.exception("Sattle visit cache update failed; continuing with image processing")
 
        return result
 
    def _apply_illumination_correction(self, exposure, background_flat, illumination_correction):
        """Apply the illumination correction to a background-flattened image.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure to convert to a photometric-flattened image.
        background_flat : `lsst.afw.image.Exposure`
            Flat image that had previously been applied to exposure.
        illumination_correction : `lsst.afw.image.Exposure`
            Illumination correction image to convert to photometric-flattened
            image.
 
        Returns
        -------
        background_to_photometric_ratio : `lsst.afw.image.Image`
            Ratio image to convert a photometric-flattened image to/from
            a background-flattened image. Will be None if task not
            configured to use the illumination correction.
        """
        if not self.config.do_illumination_correction:
            return None
 
        # From a raw image to a background-flattened image, we have:
        #   bfi = image / background_flat
        # From a raw image to a photometric-flattened image, we have:
        #   pfi = image / reference_flux_flat
        #   pfi = image / (dome_flat * illumination_correction),
        # where the illumination correction contains the jacobian
        # of the wcs, converting to fluence units.
        # Currently background_flat == dome_flat, so we have for the
        # "background_to_photometric_ratio", the ratio of the background-
        # flattened image to the photometric-flattened image:
        #   bfi / pfi = illumination_correction.
 
        background_to_photometric_ratio = illumination_correction.image.clone()
 
        # Dividing the ratio will convert a background-flattened image to
        # a photometric-flattened image.
        exposure.maskedImage /= background_to_photometric_ratio
 
        exposure.metadata["LSST CALIB ILLUMCORR APPLIED"] = True
 
        return background_to_photometric_ratio
 
    def _compute_psf(self, result, id_generator):
        """Find bright sources detected on an exposure and fit a PSF model to
        them, repairing likely cosmic rays before detection.
 
        Repair, detect, measure, and compute PSF twice, to ensure the PSF
        model does not include contributions from cosmic rays.
 
        Parameters
        ----------
        result : `lsst.pipe.base.Struct`
            Result struct that is modified to allow saving of partial outputs
            for some failure conditions. Should contain at least the following
            attributes:
 
            - exposure : `lsst.afw.image.Exposure`
                Exposure to detect and measure bright stars on.
            - background : `lsst.afw.math.BackgroundList` | `None`
                Background that was fit to the exposure during detection.
            - background_to_photometric_ratio : `lsst.afw.image.Image` | `None`
                Image to convert photometric-flattened image to
                background-flattened image.
        id_generator : `lsst.meas.base.IdGenerator`
            Object that generates source IDs and provides random seeds.
 
        Returns
        -------
        sources : `lsst.afw.table.SourceCatalog`
            Catalog of detected bright sources.
        cell_set : `lsst.afw.math.SpatialCellSet`
            PSF candidates returned by the psf determiner.
        adaptive_det_res_struct : `lsst.pipe.base.Struct`
            Result struct from the adaptive threshold detection.
 
        Notes
        -----
        This method modifies the exposure, background and
        background_to_photometric_ratio attributes of the result struct
        in-place.
        """
        def log_psf(msg, addToMetadata=False):
            """Log the parameters of the psf and background, with a prepended
            message. There is also the option to add the PSF sigma to the task
            metadata.
 
            Parameters
            ----------
            msg : `str`
                Message to prepend the log info with.
            addToMetadata : `bool`, optional
                Whether to add the final psf sigma value to the task
                metadata (the default is False).
            """
            position = result.exposure.psf.getAveragePosition()
            sigma = result.exposure.psf.computeShape(position).getDeterminantRadius()
            dimensions = result.exposure.psf.computeImage(position).getDimensions()
            if result.background is not None:
                median_background = np.median(result.background.getImage().array)
            else:
                median_background = 0.0
            self.log.info("%s sigma=%0.4f, dimensions=%s; median background=%0.2f",
                          msg, sigma, dimensions, median_background)
            if addToMetadata:
                self.metadata["final_psf_sigma"] = sigma
 
        self.log.info("First pass detection with Gaussian PSF FWHM=%s pixels",
                      self.config.install_simple_psf.fwhm)
        self.install_simple_psf.run(exposure=result.exposure)
 
        result.background = self.psf_subtract_background.run(
            exposure=result.exposure,
            backgroundToPhotometricRatio=result.background_to_photometric_ratio,
        ).background
        log_psf("Initial PSF:")
        self.psf_repair.run(exposure=result.exposure, keepCRs=True)
 
        table = afwTable.SourceTable.make(self.psf_schema, id_generator.make_table_id_factory())
        if not self.config.do_adaptive_threshold_detection:
            adaptive_det_res_struct = None
            # Re-estimate the background during this detection step, so that
            # measurement uses the most accurate background-subtraction.
            detections = self.psf_detection.run(
                table=table,
                exposure=result.exposure,
                background=result.background,
                backgroundToPhotometricRatio=result.background_to_photometric_ratio,
            )
        else:
            initialThreshold = self.config.psf_detection.thresholdValue
            initialThresholdMultiplier = self.config.psf_detection.includeThresholdMultiplier
            adaptive_det_res_struct = self.psf_adaptive_threshold_detection.run(
                table, result.exposure,
                initialThreshold=initialThreshold,
                initialThresholdMultiplier=initialThresholdMultiplier,
            )
            detections = adaptive_det_res_struct.detections
 
        self.metadata["initial_psf_positive_footprint_count"] = detections.numPos
        self.metadata["initial_psf_negative_footprint_count"] = detections.numNeg
        self.metadata["initial_psf_positive_peak_count"] = detections.numPosPeaks
        self.metadata["initial_psf_negative_peak_count"] = detections.numNegPeaks
        self.psf_source_measurement.run(detections.sources, result.exposure)
        psf_result = self.psf_measure_psf.run(exposure=result.exposure, sources=detections.sources)
 
        # This 2nd round of PSF fitting has been deemed unnecessary (and
        # sometimes even causing harm), so it is being skipped for the
        # adaptive threshold logic, but is left here for now to maintain
        # consistency with the previous logic for any users wanting to
        # revert to it.
        if not self.config.do_adaptive_threshold_detection:
            # Replace the initial PSF with something simpler for the second
            # repair/detect/measure/measure_psf step: this can help it
            # converge.
            self.install_simple_psf.run(exposure=result.exposure)
 
            log_psf("Rerunning with simple PSF:")
            # TODO investigation: Should we only re-run repair here, to use the
            # new PSF? Maybe we *do* need to re-run measurement with PsfFlux,
            # to use the fitted PSF?
            # TODO investigation: do we need a separate measurement task here
            # for the post-psf_measure_psf step, since we only want to do
            # PsfFlux and GaussianFlux *after* we have a PSF? Maybe that's not
            # relevant once DM-39203 is merged?
            self.psf_repair.run(exposure=result.exposure, keepCRs=True)
            # Re-estimate the background during this detection step, so that
            # measurement uses the most accurate background-subtraction.
            detections = self.psf_detection.run(
                table=table,
                exposure=result.exposure,
                background=result.background,
                backgroundToPhotometricRatio=result.background_to_photometric_ratio,
            )
            self.psf_source_measurement.run(detections.sources, result.exposure)
            psf_result = self.psf_measure_psf.run(exposure=result.exposure, sources=detections.sources)
        self.metadata["simple_psf_positive_footprint_count"] = detections.numPos
        self.metadata["simple_psf_negative_footprint_count"] = detections.numNeg
        self.metadata["simple_psf_positive_peak_count"] = detections.numPosPeaks
        self.metadata["simple_psf_negative_peak_count"] = detections.numNegPeaks
        log_psf("Final PSF:", addToMetadata=True)
 
        # Final repair with final PSF, removing cosmic rays this time.
        self.psf_repair.run(exposure=result.exposure)
        # Final measurement with the CRs removed.
        self.psf_source_measurement.run(detections.sources, result.exposure)
 
        # PSF is set on exposure; candidates are returned to use for
        # calibration flux normalization and aperture corrections.
        return detections.sources, psf_result.cellSet, adaptive_det_res_struct
 
    def _measure_aperture_correction(self, exposure, bright_sources):
        """Measure and set the ApCorrMap on the Exposure, using
        previously-measured bright sources.
 
        This function first normalizes the calibration flux and then
        the full set of aperture corrections are measured relative
        to this normalized calibration flux.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure to set the ApCorrMap on.
        bright_sources : `lsst.afw.table.SourceCatalog`
            Catalog of detected bright sources; modified to include columns
            necessary for point source determination for the aperture
            correction calculation.
        """
        norm_ap_corr_map = self.psf_normalized_calibration_flux.run(
            exposure=exposure,
            catalog=bright_sources,
        ).ap_corr_map
 
        ap_corr_map = self.measure_aperture_correction.run(exposure, bright_sources).apCorrMap
 
        # Need to merge the aperture correction map from the normalization.
        for key in norm_ap_corr_map:
            ap_corr_map[key] = norm_ap_corr_map[key]
 
        exposure.info.setApCorrMap(ap_corr_map)
 
    def _find_stars(self, exposure, background, id_generator, background_to_photometric_ratio=None,
                    adaptive_det_res_struct=None, num_astrometry_matches=None):
        """Detect stars on an exposure that has a PSF model, and measure their
        PSF, circular aperture, compensated gaussian fluxes.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure to detect and measure stars on.
        background : `lsst.afw.math.BackgroundList`
            Background that was fit to the exposure during detection;
            modified in-place during subsequent detection.
        id_generator : `lsst.meas.base.IdGenerator`
            Object that generates source IDs and provides random seeds.
        background_to_photometric_ratio : `lsst.afw.image.Image`, optional
            Image to convert photometric-flattened image to
            background-flattened image.
 
        Returns
        -------
        stars : `SourceCatalog`
            Sources that are very likely to be stars, with a limited set of
            measurements performed on them.
        """
        table = afwTable.SourceTable.make(self.initial_stars_schema.schema,
                                          id_generator.make_table_id_factory())
 
        maxAdaptiveDetIter = 8
        threshFactor = 0.2
        if adaptive_det_res_struct is not None:
            for adaptiveDetIter in range(maxAdaptiveDetIter):
                adaptiveDetectionConfig = lsst.meas.algorithms.SourceDetectionConfig()
                adaptiveDetectionConfig.reEstimateBackground = False
                adaptiveDetectionConfig.includeThresholdMultiplier = 2.0
                psfThreshold = (
                    adaptive_det_res_struct.thresholdValue*adaptive_det_res_struct.includeThresholdMultiplier
                )
                adaptiveDetectionConfig.thresholdValue = max(
                    self.config.star_detection.thresholdValue,
                    threshFactor*psfThreshold/adaptiveDetectionConfig.includeThresholdMultiplier
                )
                self.log.info("Using adaptive threshold detection (nIter = %d) with "
                              "thresholdValue = %.2f and multiplier = %.1f",
                              adaptiveDetIter, adaptiveDetectionConfig.thresholdValue,
                              adaptiveDetectionConfig.includeThresholdMultiplier)
                adaptiveDetectionTask = lsst.meas.algorithms.SourceDetectionTask(
                    config=adaptiveDetectionConfig
                )
                detections = adaptiveDetectionTask.run(
                    table=table,
                    exposure=exposure,
                    background=background,
                    backgroundToPhotometricRatio=background_to_photometric_ratio,
                )
                nFootprint = len(detections.sources)
                nPeak = 0
                nIsolated = 0
                for src in detections.sources:
                    nPeakSrc = len(src.getFootprint().getPeaks())
                    if nPeakSrc == 1:
                        nIsolated += 1
                    nPeak += nPeakSrc
                minIsolated = min(400, max(3, 0.005*nPeak, 0.6*num_astrometry_matches))
                if nFootprint > 0:
                    self.log.info("Adaptive threshold detection _find_stars nIter: %d; "
                                  "nPeak/nFootprint = %.2f (max is 800); nIsolated = %d (min is %.1f).",
                                  adaptiveDetIter, nPeak/nFootprint, nIsolated, minIsolated)
                    if nPeak/nFootprint > 800 or nIsolated < minIsolated:
                        threshFactor = max(0.01, 1.5*threshFactor)
                        self.log.warning("nPeak/nFootprint = %.2f (max is 800); nIsolated = %d "
                                         "(min is %.1f).", nPeak/nFootprint, nIsolated, minIsolated)
                    else:
                        break
                else:
                    threshFactor *= 0.75
                    self.log.warning("No footprints detected on image. Decreasing threshold "
                                     "factor to %.2f. and rerunning.", threshFactor)
        else:
            # Re-estimate the background during this detection step, so that
            # measurement uses the most accurate background-subtraction.
            detections = self.star_detection.run(
                table=table,
                exposure=exposure,
                background=background,
                backgroundToPhotometricRatio=background_to_photometric_ratio,
            )
        sources = detections.sources
        self.star_sky_sources.run(exposure.mask, id_generator.catalog_id, sources)
 
        n_sky_sources = np.sum(sources["sky_source"])
        if (self.config.do_downsample_footprints
           and (len(sources) - n_sky_sources) > self.config.downsample_max_footprints):
            if exposure.info.id is None:
                self.log.warning("Exposure does not have a proper id; using 0 seed for downsample.")
                seed = 0
            else:
                seed = exposure.info.id & 0xFFFFFFFF
 
            gen = np.random.RandomState(seed)
 
            # Isolate the sky sources before downsampling.
            indices = np.arange(len(sources))[~sources["sky_source"]]
            indices = gen.choice(
                indices,
                size=self.config.downsample_max_footprints,
                replace=False,
            )
            skyIndices, = np.where(sources["sky_source"])
            indices = np.concatenate((indices, skyIndices))
 
            self.log.info("Downsampling from %d to %d non-sky-source footprints.", len(sources), len(indices))
 
            sel = np.zeros(len(sources), dtype=bool)
            sel[indices] = True
            sources = sources[sel]
 
        # TODO investigation: Could this deblender throw away blends of
        # non-PSF sources?
        self.star_deblend.run(exposure=exposure, sources=sources)
        # The deblender may not produce a contiguous catalog; ensure
        # contiguity for subsequent tasks.
        if not sources.isContiguous():
            sources = sources.copy(deep=True)
 
        # Measure everything, and use those results to select only stars.
        self.star_measurement.run(sources, exposure)
        self.metadata["post_deblend_source_count"] = np.sum(~sources["sky_source"])
        self.metadata["failed_deblend_source_count"] = np.sum(
            ~sources["sky_source"] & sources["deblend_failed"]
        )
        self.metadata["saturated_source_count"] = np.sum(sources["base_PixelFlags_flag_saturated"])
        self.metadata["bad_source_count"] = np.sum(sources["base_PixelFlags_flag_bad"])
 
        # Run the normalization calibration flux task to apply the
        # normalization correction to create normalized
        # calibration fluxes.
        self.star_normalized_calibration_flux.run(exposure=exposure, catalog=sources)
        self.star_apply_aperture_correction.run(sources, exposure.apCorrMap)
        self.star_catalog_calculation.run(sources)
        self.star_set_primary_flags.run(sources)
 
        result = self.star_selector.run(sources)
        # The star selector may not produce a contiguous catalog.
        if not result.sourceCat.isContiguous():
            return result.sourceCat.copy(deep=True)
        else:
            return result.sourceCat
 
    def _match_psf_stars(self, psf_stars, stars, psfSigma=None):
        """Match calibration stars to psf stars, to identify which were psf
        candidates, and which were used or reserved during psf measurement
        and the astrometric fit.
 
        Parameters
        ----------
        psf_stars : `lsst.afw.table.SourceCatalog`
            PSF candidate stars that were sent to the psf determiner and
            used in the astrometric fit. Used to populate psf and astrometry
            related flag fields.
        stars : `lsst.afw.table.SourceCatalog`
            Stars that will be used for calibration; psf-related fields will
            be updated in-place.
 
        Notes
        -----
        This code was adapted from CalibrateTask.copyIcSourceFields().
        """
        control = afwTable.MatchControl()
        matchRadius = 3.0 if psfSigma is None else max(3.0, psfSigma)  # in pixels
        # Return all matched objects, to separate blends.
        control.findOnlyClosest = False
        matches = afwTable.matchXy(psf_stars, stars, matchRadius, control)
        deblend_key = stars.schema["deblend_nChild"].asKey()
        matches = [m for m in matches if m[1].get(deblend_key) == 0]
 
        # Because we had to allow multiple matches to handle parents, we now
        # need to prune to the best (closest) matches.
        # Closest matches is a dict of psf_stars source ID to Match record
        # (psf_stars source, sourceCat source, distance in pixels).
        best = {}
        for match_psf, match_stars, d in matches:
            match = best.get(match_psf.getId())
            if match is None or d <= match[2]:
                best[match_psf.getId()] = (match_psf, match_stars, d)
        matches = list(best.values())
        # We'll use this to construct index arrays into each catalog.
        ids = np.array([(match_psf.getId(), match_stars.getId()) for match_psf, match_stars, d in matches]).T
 
        if (n_matches := len(matches)) == 0:
            raise NoPsfStarsToStarsMatchError(n_psf_stars=len(psf_stars), n_stars=len(stars))
 
        self.log.info("%d psf/astrometry stars out of %d matched %d calib stars",
                      n_matches, len(psf_stars), len(stars))
        self.metadata["matched_psf_star_count"] = n_matches
 
        # Check that no stars sources are listed twice; we already know
        # that each match has a unique psf_stars id, due to using as the key
        # in best above.
        n_unique = len(set(m[1].getId() for m in matches))
        if n_unique != n_matches:
            self.log.warning("%d psf_stars matched only %d stars", n_matches, n_unique)
 
        # The indices of the IDs, so we can update the flag fields as arrays.
        idx_psf_stars = np.searchsorted(psf_stars["id"], ids[0])
        idx_stars = np.searchsorted(stars["id"], ids[1])
        for field in self.psf_fields:
            result = np.zeros(len(stars), dtype=bool)
            result[idx_stars] = psf_stars[field][idx_psf_stars]
            stars[field] = result
        stars['psf_id'][idx_stars] = psf_stars['id'][idx_psf_stars]
        stars['psf_max_value'][idx_stars] = psf_stars['psf_max_value'][idx_psf_stars]
 
    def _fit_astrometry(self, exposure, stars):
        """Fit an astrometric model to the data and return the reference
        matches used in the fit, and the fitted WCS.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure that is being fit, to get PSF and other metadata from.
            Modified to add the fitted skyWcs.
        stars : `SourceCatalog`
            Good stars selected for use in calibration, with RA/Dec coordinates
            computed from the pixel positions and fitted WCS.
 
        Returns
        -------
        matches : `list` [`lsst.afw.table.ReferenceMatch`]
            Reference/stars matches used in the fit.
        """
        initialWcs = exposure.wcs
        result = self.astrometry.run(stars, exposure)
 
        # Record astrometry stats to metadata
        self.metadata["astrometry_matches_count"] = len(result.matches)
        if exposure.wcs is not None:
            if initialWcs is not None:
                center = exposure.getBBox().getCenter()
                self.metadata['initial_to_final_wcs'] = (
                    initialWcs.pixelToSky(center).separation(
                        exposure.wcs.pixelToSky(center)
                    ).asArcseconds()
                )
            else:
                self.metadata['initial_to_final_wcs'] = float("nan")
            self.metadata['astrom_offset_mean'] = exposure.metadata['SFM_ASTROM_OFFSET_MEAN']
            self.metadata['astrom_offset_std'] = exposure.metadata['SFM_ASTROM_OFFSET_STD']
            self.metadata['astrom_offset_median'] = exposure.metadata['SFM_ASTROM_OFFSET_MEDIAN']
        else:
            self.metadata['initial_to_final_wcs'] = float("nan")
            self.metadata['astrom_offset_mean'] = float("nan")
            self.metadata['astrom_offset_std'] = float("nan")
            self.metadata['astrom_offset_median'] = float("nan")
 
        return result.matches, result.matchMeta
 
    def _fit_photometry(self, exposure, stars):
        """Fit a photometric model to the data and return the reference
        matches used in the fit, and the fitted PhotoCalib.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure that is being fit, to get PSF and other metadata from.
            Has the fit `lsst.afw.image.PhotoCalib` attached, with pixel values
            unchanged.
        stars : `lsst.afw.table.SourceCatalog`
            Good stars selected for use in calibration.
        background : `lsst.afw.math.BackgroundList`
            Background that was fit to the exposure during detection of the
            above stars.
 
        Returns
        -------
        calibrated_stars : `lsst.afw.table.SourceCatalog`
            Star catalog with flux/magnitude columns computed from the fitted
            photoCalib (instFlux columns are retained as well).
        matches : `list` [`lsst.afw.table.ReferenceMatch`]
            Reference/stars matches used in the fit.
        matchMeta : `lsst.daf.base.PropertyList`
            Metadata needed to unpersist matches, as returned by the matcher.
        photo_calib : `lsst.afw.image.PhotoCalib`
            Photometric calibration that was fit to the star catalog.
        """
        result = self.photometry.run(exposure, stars)
        calibrated_stars = result.photoCalib.calibrateCatalog(stars)
        exposure.setPhotoCalib(result.photoCalib)
        return calibrated_stars, result.matches, result.matchMeta, result.photoCalib
 
    def _apply_photometry(self, exposure, background, background_to_photometric_ratio=None):
        """Apply the photometric model attached to the exposure to the
        exposure's pixels and an associated background model.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure with the target `lsst.afw.image.PhotoCalib` attached.
            On return, pixel values will be calibrated and an identity
            photometric transform will be attached.
        background : `lsst.afw.math.BackgroundList`
            Background model to convert to nanojansky units in place.
        background_to_photometric_ratio : `lsst.afw.image.Image`, optional
            Image to convert photometric-flattened image to
            background-flattened image.
        """
        photo_calib = exposure.getPhotoCalib()
        exposure.maskedImage = photo_calib.calibrateImage(exposure.maskedImage)
        identity = afwImage.PhotoCalib(1.0,
                                       photo_calib.getCalibrationErr(),
                                       bbox=exposure.getBBox())
        exposure.setPhotoCalib(identity)
        exposure.metadata["BUNIT"] = "nJy"
 
        assert photo_calib._isConstant, \
            "Background calibration assumes a constant PhotoCalib; PhotoCalTask should always return that."
 
        for bg in background:
            # The statsImage is a view, but we can't assign to a function call
            # in python.
            binned_image = bg[0].getStatsImage()
            binned_image *= photo_calib.getCalibrationMean()
 
    def _summarize(self, exposure, stars, background):
        """Compute summary statistics on the exposure and update in-place the
        calibrations attached to it.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure that was calibrated, to get PSF and other metadata from.
            Should be in instrumental units with the photometric calibration
            attached.
            Modified to contain the computed summary statistics.
        stars : `SourceCatalog`
            Good stars selected used in calibration.
        background : `lsst.afw.math.BackgroundList`
            Background that was fit to the exposure during detection of the
            above stars.  Should be in instrumental units.
        """
        summary = self.compute_summary_stats.run(exposure, stars, background)
        exposure.info.setSummaryStats(summary)
 
    def _recordMaskedPixelFractions(self, exposure):
        """Record the fraction of all the pixels in an exposure
        that are masked with a given flag. Each fraction is
        recorded in the task metadata. One record per flag type.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.ExposureF`
            The target exposure to calculate masked pixel fractions for.
        """
 
        mask = exposure.mask
        maskPlanes = list(mask.getMaskPlaneDict().keys())
        for maskPlane in maskPlanes:
            self.metadata[f"{maskPlane.lower()}_mask_fraction"] = (
                evaluateMaskFraction(mask, maskPlane)
            )
 
    def _update_wcs_with_camera_model(self, exposure, cameraModel):
        """Replace the existing WCS with one generated using the pointing
        and the input camera model.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.ExposureF`
            The exposure whose WCS will be updated.
        cameraModel : `lsst.afw.cameraGeom.Camera`
            Camera to be used when constructing updated WCS.
        """
        detector = cameraModel[exposure.detector.getId()]
        newWcs = createInitialSkyWcs(exposure.visitInfo, detector)
        exposure.setWcs(newWcs)
 
    def _compute_mask_fraction(self, mask, mask_planes, bad_mask_planes):
        """Evaluate the fraction of masked pixels in a (set of) mask plane(s).
 
        Parameters
        ----------
        mask : `lsst.afw.image.Mask`
            The mask on which to evaluate the fraction.
        mask_planes : `list`, `str`
            The mask planes for which to evaluate the fraction.
        bad_mask_planes : `list`, `str`
            The mask planes to exclude from the computation.
 
        Returns
        -------
        detected_fraction : `float`
            The calculated fraction of masked pixels
        """
        bad_pixel_mask = afwImage.Mask.getPlaneBitMask(bad_mask_planes)
        n_good_pix = np.sum(mask.array & bad_pixel_mask == 0)
        if n_good_pix == 0:
            detected_fraction = float("nan")
            return detected_fraction
        detected_pixel_mask = afwImage.Mask.getPlaneBitMask(mask_planes)
        n_detected_pix = np.sum((mask.array & detected_pixel_mask != 0)
                                & (mask.array & bad_pixel_mask == 0))
        detected_fraction = n_detected_pix/n_good_pix
        return detected_fraction
 
    def _compute_per_amp_fraction(self, exposure, detected_fraction, mask_planes, bad_mask_planes):
        """Evaluate the maximum per-amplifier fraction of masked pixels.
 
        Parameters
        ----------
        exposure : `lsst.afw.image.ExposureF`
            The exposure on which to compute the per-amp masked fraction.
        detected_fraction : `float`
            The current detected_fraction of the ``mask_planes`` for the
            full detector.
        mask_planes : `list`, `str`
            The mask planes for which to evaluate the fraction.
        bad_mask_planes : `list`, `str`
            The mask planes to exclude from the computation.
 
        Returns
        -------
        n_above_max_per_amp : `int`
            The number of amplifiers with masked fractions above a maximum
            value (set by the current full-detector ``detected_fraction``).
        highest_detected_fraction_per_amp : `float`
            The highest value of the per-amplifier fraction of masked pixels.
        no_zero_det_amps : `bool`
            A boolean representing whether any of the amplifiers has zero
            masked pixels.
        """
        highest_detected_fraction_per_amp = -9.99
        n_above_max_per_amp = 0
        n_no_zero_det_amps = 0
        no_zero_det_amps = True
        amps = exposure.detector.getAmplifiers()
        if amps is not None:
            for ia, amp in enumerate(amps):
                amp_bbox = amp.getBBox()
                exp_bbox = exposure.getBBox()
                if not exp_bbox.contains(amp_bbox):
                    self.log.info("Bounding box of amplifier (%s) does not fit in exposure's "
                                  "bounding box (%s).  Skipping...", amp_bbox, exp_bbox)
                    continue
                sub_image = exposure.subset(amp.getBBox())
                detected_fraction_amp = self._compute_mask_fraction(sub_image.mask,
                                                                    mask_planes,
                                                                    bad_mask_planes)
                self.log.debug("Current detected fraction for amplifier %s = %.3f",
                               amp.getName(), detected_fraction_amp)
                if detected_fraction_amp < 0.002:
                    n_no_zero_det_amps += 1
                    if n_no_zero_det_amps > 2:
                        no_zero_det_amps = False
                        break
                highest_detected_fraction_per_amp = max(detected_fraction_amp,
                                                        highest_detected_fraction_per_amp)
                if highest_detected_fraction_per_amp > min(0.998, max(0.8, 3.0*detected_fraction)):
                    n_above_max_per_amp += 1
                    if n_above_max_per_amp > 2:
                        break
        else:
            self.log.info("No amplifier object for detector %d, so skipping per-amp "
                          "detection fraction checks.", exposure.detector.getId())
        return n_above_max_per_amp, highest_detected_fraction_per_amp, no_zero_det_amps
 
    def _remeasure_star_background(self, result, background_to_photometric_ratio=None):
        """Remeasure the exposure's background with iterative adaptive
        threshold detection.
 
        Parameters
        ----------
        result : `lsst.pipe.base.Struct`
            The current state of the result Strut from the run method of
            CalibrateImageTask.  Will be modified in place.
        background_to_photometric_ratio : `lsst.afw.image.Image`, optional
            Image to convert photometric-flattened image to
            background-flattened image.
 
        Returns
        -------
        result : `lsst.pipe.base.Struct`
            The modified result Struct with the new background subtracted.
        """
        # Restore the previously measured background and remeasure it
        # using an adaptive threshold detection iteration to ensure a
        # "Goldilocks Zone" for the fraction of detected pixels.
        backgroundOrig = result.background.clone()
        median_background_orig = np.median(backgroundOrig.getImage().array)
        self.log.info("Original median_background = %.2f", median_background_orig)
        result.exposure.image.array += result.background.getImage().array
        result.background = afwMath.BackgroundList()
 
        origMask = result.exposure.mask.clone()
        bad_mask_planes = ["BAD", "EDGE", "NO_DATA"]
        detected_mask_planes = ["DETECTED", "DETECTED_NEGATIVE"]
        detected_fraction_orig = self._compute_mask_fraction(result.exposure.mask,
                                                             detected_mask_planes,
                                                             bad_mask_planes)
        minDetFracForFinalBg = 0.02
        maxDetFracForFinalBg = 0.93
        # Dilate the current detected mask planes and don't clear
        # them in the detection step.
        nPixToDilate = 10
        maxAdaptiveDetIter = 10
        for dilateIter in range(maxAdaptiveDetIter):
            dilatedMask = origMask.clone()
            for maskName in detected_mask_planes:
                # Compute the grown detection mask plane using SpanSet
                detectedMaskBit = dilatedMask.getPlaneBitMask(maskName)
                detectedMaskSpanSet = SpanSet.fromMask(dilatedMask, detectedMaskBit)
                detectedMaskSpanSet = detectedMaskSpanSet.dilated(nPixToDilate)
                detectedMaskSpanSet = detectedMaskSpanSet.clippedTo(dilatedMask.getBBox())
                # Clear the detected mask plane
                detectedMask = dilatedMask.getMaskPlane(maskName)
                dilatedMask.clearMaskPlane(detectedMask)
                # Set the mask plane to the dilated one
                detectedMaskSpanSet.setMask(dilatedMask, detectedMaskBit)
 
            detected_fraction_dilated = self._compute_mask_fraction(dilatedMask,
                                                                    detected_mask_planes,
                                                                    bad_mask_planes)
            if detected_fraction_dilated < maxDetFracForFinalBg or nPixToDilate == 1:
                break
            else:
                nPixToDilate -= 1
 
        result.exposure.mask = dilatedMask
        self.log.warning("detected_fraction_orig = %.3f  detected_fraction_dilated = %.3f",
                         detected_fraction_orig, detected_fraction_dilated)
        n_above_max_per_amp = -99
        highest_detected_fraction_per_amp = float("nan")
 
        # Check the per-amplifier detection fractions.
        n_above_max_per_amp, highest_detected_fraction_per_amp, no_zero_det_amps = \
            self._compute_per_amp_fraction(result.exposure, detected_fraction_dilated,
                                           detected_mask_planes, bad_mask_planes)
        self.log.warning("Dilated mask: n_above_max_per_amp = %d, "
                         "highest_detected_fraction_per_amp = %.3f",
                         n_above_max_per_amp, highest_detected_fraction_per_amp)
 
        bgIgnoreMasksToAdd = ["SAT", "SUSPECT", "SPIKE"]
        detected_fraction = 1.0
        nFootprintTemp = 1e12
        starBackgroundDetectionConfig = lsst.meas.algorithms.SourceDetectionConfig()
        for maskName in bgIgnoreMasksToAdd:
            if (maskName in result.exposure.mask.getMaskPlaneDict().keys()
                    and maskName not in starBackgroundDetectionConfig.background.ignoredPixelMask):
                starBackgroundDetectionConfig.background.ignoredPixelMask += [maskName]
        starBackgroundDetectionConfig.doTempLocalBackground = False
        starBackgroundDetectionConfig.nSigmaToGrow = 70.0
        starBackgroundDetectionConfig.reEstimateBackground = False
        starBackgroundDetectionConfig.includeThresholdMultiplier = 1.0
        starBackgroundDetectionConfig.thresholdValue = max(2.0, 0.2*median_background_orig)
        starBackgroundDetectionConfig.thresholdType = "pixel_stdev"
 
        n_above_max_per_amp = -99
        highest_detected_fraction_per_amp = float("nan")
        doCheckPerAmpDetFraction = True
 
        minFootprints = self.config.star_background_min_footprints
        maxIter = 40
        for nIter in range(maxIter):
            currentThresh = starBackgroundDetectionConfig.thresholdValue
            nZeroEncountered = 0
            if nFootprintTemp == 0:
                zeroFactor = min(0.98, 0.9 + 0.01*nZeroEncountered)
                starBackgroundDetectionConfig.thresholdValue = zeroFactor*currentThresh
                self.log.warning("No footprints detected. Decreasing threshold to %.2f and rerunning.",
                                 starBackgroundDetectionConfig.thresholdValue)
                starBackgroundDetectionTask = lsst.meas.algorithms.SourceDetectionTask(
                    config=starBackgroundDetectionConfig)
                table = afwTable.SourceTable.make(self.initial_stars_schema.schema)
                tempDetections = starBackgroundDetectionTask.run(
                    table=table, exposure=result.exposure, clearMask=True)
                nFootprintTemp = len(tempDetections.sources)
                minFootprints = max(self.config.star_background_min_footprints,
                                    int(self.config.star_background_peak_fraction*tempDetections.numPosPeaks))
                minFootprints = min(200, minFootprints)
                nZeroEncountered += 1
                if nFootprintTemp >= minFootprints:
                    detected_fraction = self._compute_mask_fraction(result.exposure.mask,
                                                                    detected_mask_planes,
                                                                    bad_mask_planes)
                    self.log.info("nIter = %d, thresh = %.2f: Fraction of pixels marked as DETECTED or "
                                  "DETECTED_NEGATIVE in star_background_detection = %.3f "
                                  "(max is %.3f; min is %.3f)  nFootprint = %d (current min is %d)",
                                  nIter, starBackgroundDetectionConfig.thresholdValue,
                                  detected_fraction, maxDetFracForFinalBg, minDetFracForFinalBg,
                                  nFootprintTemp, minFootprints)
                    self.metadata['adaptive_threshold_value'] = starBackgroundDetectionConfig.thresholdValue
 
                    break
                else:
                    # Still not enough footprints, so make sure this loop is
                    # entered again.
                    if nFootprintTemp > 0 and nFootprintTemp < minFootprints:
                        nFootprintTemp = 0
                    continue
            if detected_fraction > maxDetFracForFinalBg or nFootprintTemp <= minFootprints:
                starBackgroundDetectionConfig.thresholdValue = 1.07*currentThresh
                if nFootprintTemp < minFootprints and detected_fraction > 0.9*maxDetFracForFinalBg:
                    if nFootprintTemp == 1:
                        starBackgroundDetectionConfig.thresholdValue = 1.4*currentThresh
                    else:
                        starBackgroundDetectionConfig.thresholdValue = 1.2*currentThresh
 
            if n_above_max_per_amp > 1:
                starBackgroundDetectionConfig.thresholdValue = 1.1*currentThresh
            if detected_fraction < minDetFracForFinalBg:
                starBackgroundDetectionConfig.thresholdValue = 0.8*currentThresh
            starBackgroundDetectionTask = lsst.meas.algorithms.SourceDetectionTask(
                config=starBackgroundDetectionConfig)
            table = afwTable.SourceTable.make(self.initial_stars_schema.schema)
            tempDetections = starBackgroundDetectionTask.run(
                table=table, exposure=result.exposure, clearMask=True)
            result.exposure.mask |= dilatedMask
            nFootprintTemp = len(tempDetections.sources)
            minFootprints = max(self.config.star_background_min_footprints,
                                int(self.config.star_background_peak_fraction*tempDetections.numPosPeaks))
            minFootprints = min(200, minFootprints)
            detected_fraction = self._compute_mask_fraction(result.exposure.mask, detected_mask_planes,
                                                            bad_mask_planes)
            self.log.info("nIter = %d, thresh = %.2f: Fraction of pixels marked as DETECTED or "
                          "DETECTED_NEGATIVE in star_background_detection = %.3f "
                          "(max is %.3f; min is %.3f)  nFootprint = %d (current min is %d)",
                          nIter, starBackgroundDetectionConfig.thresholdValue,
                          detected_fraction, maxDetFracForFinalBg, minDetFracForFinalBg,
                          nFootprintTemp, minFootprints)
            self.metadata['adaptive_threshold_value'] = starBackgroundDetectionConfig.thresholdValue
 
            n_amp = len(result.exposure.detector.getAmplifiers())
            if doCheckPerAmpDetFraction:  # detected_fraction < maxDetFracForFinalBg:
                n_above_max_per_amp, highest_detected_fraction_per_amp, no_zero_det_amps = \
                    self._compute_per_amp_fraction(result.exposure, detected_fraction,
                                                   detected_mask_planes, bad_mask_planes)
 
            if not no_zero_det_amps:
                starBackgroundDetectionConfig.thresholdValue = 0.95*currentThresh
 
            if (detected_fraction < maxDetFracForFinalBg and detected_fraction > minDetFracForFinalBg
                    and n_above_max_per_amp < int(0.75*n_amp)
                    and no_zero_det_amps
                    and nFootprintTemp >= minFootprints):
                if (n_above_max_per_amp < max(1, int(0.15*n_amp))
                        or detected_fraction < 0.85*maxDetFracForFinalBg):
                    break
                else:
                    self.log.warning("Making small tweak....")
                    starBackgroundDetectionConfig.thresholdValue = 1.05*currentThresh
            self.log.warning("n_above_max_per_amp = %d (abs max is %d)", n_above_max_per_amp, int(0.75*n_amp))
 
        detected_fraction = self._compute_mask_fraction(result.exposure.mask, detected_mask_planes,
                                                        bad_mask_planes)
        self.log.info("Fraction of pixels marked as DETECTED or DETECTED_NEGATIVE is now %.5f "
                      "(highest per amp section = %.5f)",
                      detected_fraction, highest_detected_fraction_per_amp)
 
        if detected_fraction > maxDetFracForFinalBg:
            result.exposure.mask = dilatedMask
            self.log.warning("Final fraction of pixels marked as DETECTED or DETECTED_NEGATIVE "
                             "was too large in star_background_detection = %.3f (max = %.3f). "
                             "Reverting to dilated mask from PSF detection...",
                             detected_fraction, maxDetFracForFinalBg)
            self.metadata['adaptive_threshold_value'] = float("nan")
        star_background = self.star_background.run(
            exposure=result.exposure,
            backgroundToPhotometricRatio=background_to_photometric_ratio,
        ).background
        result.background.append(star_background[0])
 
        median_background = np.median(result.background.getImage().array)
        self.log.info("New initial median_background = %.2f", median_background)
 
        # Perform one more round of background subtraction that is just an
        # overall pedestal (order = 0).  This is intended to account for
        # any potential gross oversubtraction imposed by the higher-order
        # subtraction.
        # Dilate DETECTED mask a bit more if it's below 50% detected.
        nPixToDilate = 2
        if detected_fraction < 0.5:
            dilatedMask = result.exposure.mask.clone()
            for maskName in detected_mask_planes:
                # Compute the grown detection mask plane using SpanSet
                detectedMaskBit = dilatedMask.getPlaneBitMask(maskName)
                detectedMaskSpanSet = SpanSet.fromMask(dilatedMask, detectedMaskBit)
                detectedMaskSpanSet = detectedMaskSpanSet.dilated(nPixToDilate)
                detectedMaskSpanSet = detectedMaskSpanSet.clippedTo(dilatedMask.getBBox())
                # Clear the detected mask plane
                detectedMask = dilatedMask.getMaskPlane(maskName)
                dilatedMask.clearMaskPlane(detectedMask)
                # Set the mask plane to the dilated one
                detectedMaskSpanSet.setMask(dilatedMask, detectedMaskBit)
 
            detected_fraction_dilated = self._compute_mask_fraction(dilatedMask,
                                                                    detected_mask_planes,
                                                                    bad_mask_planes)
            result.exposure.mask = dilatedMask
            self.log.debug("detected_fraction_orig = %.3f  detected_fraction_dilated = %.3f",
                           detected_fraction_orig, detected_fraction_dilated)
 
        bbox = result.exposure.getBBox()
 
        # Now measure a final background pedestal level (largely to account
        # for the over-subtraction often seen in the first pass, especially
        # in high fill-factor fields). Since the pedestal measurement can be
        # sensitive to the bin size, start an iteration with a small bin size,
        # then double it on each iteration until the relative or absolute
        # change criterion is met. If those are never achieved, the iteration
        # stops when the bin size gets bigger than the exposure's bounding box.
 
        # Initialize the parameters for the pedestal iteration.
        pedestalBackgroundConfig = lsst.meas.algorithms.SubtractBackgroundConfig()
        for maskName in bgIgnoreMasksToAdd:
            if (maskName in result.exposure.mask.getMaskPlaneDict().keys()
                    and maskName not in pedestalBackgroundConfig.ignoredPixelMask):
                pedestalBackgroundConfig.ignoredPixelMask += [maskName]
        pedestalBackgroundConfig.statisticsProperty = "MEDIAN"
        pedestalBackgroundConfig.approxOrderX = 0
        pedestalBackgroundConfig.binSize = min(32, int(math.ceil(max(bbox.width, bbox.height)/4.0)))
        self.log.info("Initial pedestal binSize = %d pixels", pedestalBackgroundConfig.binSize)
        cumulativePedestalLevel = 0.0
        # When the cumulative pedestal value changes by less than 5% from one
        # bin size to the next we assume we are converged.
        relativeStoppingCriterion = 0.05
        # When the cumulative pedestal value changes by less than 0.5 counts
        # (electrons or adu) from one bin size to the next, we assume we are
        # converged.
        absoluteStoppingCriterion = 0.5
        inPedestalIteration = True
        while inPedestalIteration:
            cumulativePedestalPrev = cumulativePedestalLevel
            pedestalBackgroundTask = lsst.meas.algorithms.SubtractBackgroundTask(
                config=pedestalBackgroundConfig)
            pedestalBackgroundList = pedestalBackgroundTask.run(
                exposure=result.exposure,
                background=result.background,
                backgroundToPhotometricRatio=background_to_photometric_ratio,
            ).background
            # Isolate the most recent pedestal background measured to log the
            # current computed value and add it to the cumulative value.
            pedestalBackground = afwMath.BackgroundList()
            pedestalBackground.append(pedestalBackgroundList[-1])
            pedestalBackgroundLevel = pedestalBackground.getImage().array[0, 0]
            cumulativePedestalLevel += pedestalBackgroundLevel
            absoluteDelta = abs(cumulativePedestalLevel - cumulativePedestalPrev)
            if cumulativePedestalPrev != 0.0:
                relativeDelta = abs(absoluteDelta/cumulativePedestalPrev)
            else:
                relativeDelta = 1.0
            self.log.info("Subtracted pedestalBackgroundLevel = %.4f (cumulative = %.4f; "
                          "relativeDelta = %.4f;  absoluteDelta = %.3f)",
                          pedestalBackgroundLevel, cumulativePedestalLevel,
                          relativeDelta, absoluteDelta)
 
            if (relativeDelta < relativeStoppingCriterion
                    or absoluteDelta < absoluteStoppingCriterion):
                # We are converged.
                inPedestalIteration = False
            else:
                # We have not yet converged; grow the bin size if possible.
                if pedestalBackgroundConfig.binSize*2 < 2*max(bbox.width, bbox.height):
                    pedestalBackgroundConfig.binSize = int(pedestalBackgroundConfig.binSize*2)
                    self.log.info("Increasing pedestal binSize to %d pixels and remeasuring.",
                                  pedestalBackgroundConfig.binSize)
                else:
                    # We have reached the maximum bin size.
                    self.log.warning("Reached maximum bin size. Exiting pedestal loop without meeting "
                                     "the convergence criteria (relativeDelta <= %.2f or "
                                     "absoluteDelta <= %.2f).",
                                     relativeStoppingCriterion, absoluteStoppingCriterion)
                    inPedestalIteration = False
        self.log.info("Final subtracted cumulativePedestalBackgroundLevel = %.4f", cumulativePedestalLevel)
 
        # Clear detected mask plane before final round of detection
        mask = result.exposure.mask
        for mp in detected_mask_planes:
            if mp not in mask.getMaskPlaneDict():
                mask.addMaskPlane(mp)
            mask &= ~mask.getPlaneBitMask(detected_mask_planes)
 
        return result