psfexPsfDeterminer.py

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# This file is part of meas_extensions_psfex.
#
# 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.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
__all__ = (
    "PsfexPsfDeterminerConfig",
    "PsfexPsfDeterminerTask",
    "PsfexNoStarsError",
    "PsfexNoGoodStarsError",
    "PsfexTooFewGoodStarsError",
)
 
import os
import numpy as np
 
import lsst.daf.base as dafBase
import lsst.pex.config as pexConfig
import lsst.pex.exceptions as pexExcept
import lsst.geom as geom
import lsst.afw.geom.ellipses as afwEll
import lsst.afw.display as afwDisplay
import lsst.afw.image as afwImage
import lsst.afw.math as afwMath
import lsst.meas.algorithms as measAlg
import lsst.meas.algorithms.utils as maUtils
import lsst.meas.extensions.psfex as psfex
from lsst.pipe.base import AlgorithmError
 
 
class PsfexNoStarsError(AlgorithmError):
    """Raised if no stars are available for PSF determination."""
 
    def __init__(self) -> None:
        super().__init__("No psf candidates supplied.")
 
 
    def __init__(self) -> None: …
class PsfexNoStarsError(AlgorithmError): …
class PsfexNoGoodStarsError(AlgorithmError):
    """Raised if no "good" stars are available for PSF determination.
 
    Parameters
    ----------
    num_available_stars : `int`
        Number of available stars for PSF determination.
    """
 
    def __init__(self, num_available_stars) -> None:
        self._num_available_stars = num_available_stars
        super().__init__(f"No good psf candidates to pass to psfex out of {num_available_stars} available.")
 
    def __init__(self, num_available_stars) -> None: …
    @property
    def metadata(self) -> dict:
        return {
            "num_available_stars": self._num_available_stars,
        }
 
 
    def metadata(self) -> dict: …
class PsfexNoGoodStarsError(AlgorithmError): …
class PsfexTooFewGoodStarsError(AlgorithmError):
    """Raised if too few good stars are available for PSF determination.
 
    Parameters
    ----------
    num_available_stars : `int`
        Number of available stars for PSF determination.
    num_good_stars : `int`
        Number of good stars used for PSF determination.
    poly_ndim_initial : `int`
        Initial number of dependency parameters (dimensions) used in
        polynomial fitting.
    poly_ndim_final : `int`
        Final number of dependency parameters (dimensions) set in the PSFEx
        model after initializing the PSF structure.
    """
 
    def __init__(
        self,
        num_available_stars,
        num_good_stars,
        poly_ndim_initial,
        poly_ndim_final,
    ) -> None:
        self._num_available_stars = num_available_stars
        self._num_good_stars = num_good_stars
        self._poly_ndim_initial = poly_ndim_initial
        self._poly_ndim_final = poly_ndim_final
        super().__init__(
            f"Failed to determine psfex psf: too few good stars ({num_good_stars}) out of "
            f"{num_available_stars} available. To accommodate this low count, the polynomial dimension was "
            f"lowered from {poly_ndim_initial} to {poly_ndim_final}, which is not handled by the Science "
            "Pipelines code."
        )
 
    def __init__( …
    @property
    def metadata(self) -> dict:
        return {
            "num_available_stars": self._num_available_stars,
            "num_good_stars": self._num_good_stars,
            "poly_ndim_initial": self._poly_ndim_initial,
            "poly_ndim_final": self._poly_ndim_final,
        }
 
 
    def metadata(self) -> dict: …
class PsfexTooFewGoodStarsError(AlgorithmError): …
class PsfexPsfDeterminerConfig(measAlg.BasePsfDeterminerConfig):
    spatialOrder = pexConfig.Field[int](
        doc="specify spatial order for PSF kernel creation",
        default=2,
        check=lambda x: x >= 1,
    )
    sizeCellX = pexConfig.Field[int](
        doc="size of cell used to determine PSF (pixels, column direction)",
        default=256,
        #        minValue = 10,
        check=lambda x: x >= 10,
    )
    sizeCellY = pexConfig.Field[int](
        doc="size of cell used to determine PSF (pixels, row direction)",
        default=sizeCellX.default,
        #        minValue = 10,
        check=lambda x: x >= 10,
    )
    samplingSize = pexConfig.Field[float](
        doc="Resolution of the internal PSF model relative to the pixel size; "
        "e.g. 0.5 is equal to 2x oversampling",
        default=0.5,
    )
    badMaskBits = pexConfig.ListField[str](
        doc="List of mask bits which cause a source to be rejected as bad "
        "N.b. INTRP is used specially in PsfCandidateSet; it means \"Contaminated by neighbour\"",
        default=["INTRP", "SAT"],
    )
    psfexBasis = pexConfig.ChoiceField[str](
        doc="BASIS value given to psfex.  PIXEL_AUTO will use the requested samplingSize only if "
        "the FWHM < 3 pixels.  Otherwise, it will use samplingSize=1.  PIXEL will always use the "
        "requested samplingSize",
        allowed={
            "PIXEL": "Always use requested samplingSize",
            "PIXEL_AUTO": "Only use requested samplingSize when FWHM < 3",
        },
        default='PIXEL_AUTO',
        optional=False,
    )
    tolerance = pexConfig.Field[float](
        doc="tolerance of spatial fitting",
        default=1e-2,
    )
    lam = pexConfig.Field[float](
        doc="floor for variance is lam*data",
        default=0.05,
    )
    reducedChi2ForPsfCandidates = pexConfig.Field[float](
        doc="for psf candidate evaluation",
        default=2.0,
    )
    spatialReject = pexConfig.Field[float](
        doc="Rejection threshold (stdev) for candidates based on spatial fit",
        default=3.0,
    )
    recentroid = pexConfig.Field[bool](
        doc="Should PSFEX be permitted to recentroid PSF candidates?",
        default=False,
    )
    photometricFluxField = pexConfig.Field[str](
        doc="Flux field to use for photometric normalization. This overrides the "
            "``PHOTFLUX_KEY`` field for psfex. The associated flux error is "
            "derived by appending ``Err`` to this field.",
        default="base_CircularApertureFlux_9_0_instFlux",
    )
 
    def setDefaults(self):
        super().setDefaults()
        self.stampSize = 41
 
    def setDefaults(self): …
    def validate(self):
        super().validate()
        fluxFieldEnding = self.photometricFluxField.rpartition("_")[-1]
        if "_" not in self.photometricFluxField or not (
            fluxFieldEnding == "flux" or fluxFieldEnding.endswith("Flux")
        ):
            raise ValueError(
                "Expected `photometricFluxField` to end with '_flux' "
                f"or '_*Flux', but got '{self.photometricFluxField}'"
            )
 
 
    def validate(self): …
class PsfexPsfDeterminerConfig(measAlg.BasePsfDeterminerConfig): …
class PsfexPsfDeterminerTask(measAlg.BasePsfDeterminerTask):
    ConfigClass = PsfexPsfDeterminerConfig
 
    def determinePsf(self, exposure, psfCandidateList, metadata=None, flagKey=None):
        """Determine a PSFEX PSF model for an exposure given a list of PSF
        candidates.
 
        Parameters
        ----------
        exposure: `lsst.afw.image.Exposure`
            Exposure containing the PSF candidates.
        psfCandidateList: iterable of `lsst.meas.algorithms.PsfCandidate`
            Sequence of PSF candidates typically obtained by detecting sources
            and then running them through a star selector.
        metadata: metadata, optional
            A home for interesting tidbits of information.
        flagKey: `lsst.afw.table.Key`, optional
            Schema key used to mark sources actually used in PSF determination.
 
        Returns
        -------
        psf: `lsst.meas.extensions.psfex.PsfexPsf`
            The determined PSF.
        """
        psfCandidateList = self.downsampleCandidates(psfCandidateList)
 
        import lsstDebug
        display = lsstDebug.Info(__name__).display
        displayExposure = display and \
            lsstDebug.Info(__name__).displayExposure      # display the Exposure + spatialCells
        displayPsfComponents = display and \
            lsstDebug.Info(__name__).displayPsfComponents  # show the basis functions
        showBadCandidates = display and \
            lsstDebug.Info(__name__).showBadCandidates    # Include bad candidates (meaningless, methinks)
        displayResiduals = display and \
            lsstDebug.Info(__name__).displayResiduals     # show residuals
        displayPsfMosaic = display and \
            lsstDebug.Info(__name__).displayPsfMosaic     # show mosaic of reconstructed PSF(x,y)
        normalizeResiduals = lsstDebug.Info(__name__).normalizeResiduals
        afwDisplay.setDefaultMaskTransparency(75)
        # Normalise residuals by object amplitude
 
        mi = exposure.getMaskedImage()
 
        nCand = len(psfCandidateList)
        if nCand == 0:
            raise PsfexNoStarsError()
        #
        # How big should our PSF models be?
        #
        if display:                     # only needed for debug plots
            # construct and populate a spatial cell set
            bbox = mi.getBBox(afwImage.PARENT)
            psfCellSet = afwMath.SpatialCellSet(bbox, self.config.sizeCellX, self.config.sizeCellY)
        else:
            psfCellSet = None
 
        sizes = np.empty(nCand)
        for i, psfCandidate in enumerate(psfCandidateList):
            try:
                if psfCellSet:
                    psfCellSet.insertCandidate(psfCandidate)
            except Exception as e:
                self.log.error("Skipping PSF candidate %d of %d: %s", i, len(psfCandidateList), e)
                continue
 
            source = psfCandidate.getSource()
            quad = afwEll.Quadrupole(source.getIxx(), source.getIyy(), source.getIxy())
            rmsSize = quad.getTraceRadius()
            sizes[i] = rmsSize
 
        pixKernelSize = self.config.stampSize
        actualKernelSize = int(2*np.floor(0.5*pixKernelSize/self.config.samplingSize) + 1)
 
        if display:
            rms = np.median(sizes)
            self.log.debug("Median PSF RMS size=%.2f pixels (\"FWHM\"=%.2f)",
                           rms, 2*np.sqrt(2*np.log(2))*rms)
 
        self.log.trace("Psfex Kernel size=%.2f, Image Kernel Size=%.2f", actualKernelSize, pixKernelSize)
 
        # -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BEGIN PSFEX
        #
        # Insert the good candidates into the set
        #
        defaultsFile = os.path.join(os.environ["MEAS_EXTENSIONS_PSFEX_DIR"], "config", "default-lsst.psfex")
        args_md = dafBase.PropertySet()
        args_md.set("BASIS_TYPE", str(self.config.psfexBasis))
        args_md.set("PSFVAR_DEGREES", str(self.config.spatialOrder))
        args_md.set("PSF_SIZE", str(actualKernelSize))
        args_md.set("PSF_SAMPLING", str(self.config.samplingSize))
        args_md.set("PHOTFLUX_KEY", str(self.config.photometricFluxField))
        args_md.set("PHOTFLUXERR_KEY", str(self.config.photometricFluxField) + "Err")
        prefs = psfex.Prefs(defaultsFile, args_md)
        prefs.setCommandLine([])
        prefs.addCatalog("psfexPsfDeterminer")
 
        prefs.use()
        principalComponentExclusionFlag = bool(bool(psfex.Context.REMOVEHIDDEN)
                                               if False else psfex.Context.KEEPHIDDEN)
        context = psfex.Context(prefs.getContextName(), prefs.getContextGroup(),
                                prefs.getGroupDeg(), principalComponentExclusionFlag)
        psfSet = psfex.Set(context)
        psfSet.setVigSize(pixKernelSize, pixKernelSize)
        psfSet.setFwhm(2*np.sqrt(2*np.log(2))*np.median(sizes))
        psfSet.setRecentroid(self.config.recentroid)
 
        catindex, ext = 0, 0
        backnoise2 = afwMath.makeStatistics(mi.getImage(), afwMath.VARIANCECLIP).getValue()
        ccd = exposure.getDetector()
        if ccd:
            gain = np.mean(np.array([a.getGain() for a in ccd]))
        else:
            gain = 1.0
            self.log.warning("Setting gain to %g", gain)
 
        contextvalp = []
        for i, key in enumerate(context.getName()):
            if key[0] == ':':
                try:
                    contextvalp.append(exposure.getMetadata().getScalar(key[1:]))
                except KeyError as e:
                    raise RuntimeError("%s parameter not found in the header of %s" %
                                       (key[1:], prefs.getContextName())) from e
            else:
                try:
                    contextvalp.append(np.array([psfCandidateList[_].getSource().get(key)
                                                 for _ in range(nCand)]))
                except KeyError as e:
                    raise RuntimeError("%s parameter not found" % (key,)) from e
                psfSet.setContextname(i, key)
 
        if display:
            frame = 0
            if displayExposure:
                disp = afwDisplay.Display(frame=frame)
                disp.mtv(exposure, title="psf determination")
 
        badBits = mi.getMask().getPlaneBitMask(self.config.badMaskBits)
        fluxName = prefs.getPhotfluxRkey()
        fluxFlagName = fluxName.rpartition("_")[0] + "_flag"
 
        xpos, ypos = [], []
        for i, psfCandidate in enumerate(psfCandidateList):
            source = psfCandidate.getSource()
 
            # skip sources with bad centroids
            xc, yc = source.getX(), source.getY()
            if not np.isfinite(xc) or not np.isfinite(yc):
                continue
            # skip flagged sources
            if source.get(fluxFlagName):
                continue
            # skip nonfinite and negative sources
            flux = source.get(fluxName)
            if flux < 0 or not np.isfinite(flux):
                continue
 
            try:
                pstamp = psfCandidate.getMaskedImage(pixKernelSize, pixKernelSize).clone()
            except pexExcept.LengthError:
                self.log.warning("Could not get stamp image for psfCandidate: %s with kernel size: %s",
                                 psfCandidate, pixKernelSize)
                continue
 
            # From this point, we're configuring the "sample" (PSFEx's version
            # of a PSF candidate).
            # Having created the sample, we must proceed to configure it, and
            # then fini (finalize), or it will be malformed.
            try:
                sample = psfSet.newSample()
                sample.setCatindex(catindex)
                sample.setExtindex(ext)
                sample.setObjindex(i)
 
                imArray = pstamp.getImage().getArray()
                imArray[np.where(np.bitwise_and(pstamp.getMask().getArray(), badBits))] = \
                    -2*psfex.BIG
                sample.setVig(imArray)
 
                sample.setNorm(flux)
                sample.setBacknoise2(backnoise2)
                sample.setGain(gain)
                sample.setX(xc)
                sample.setY(yc)
                sample.setFluxrad(sizes[i])
 
                for j in range(psfSet.getNcontext()):
                    sample.setContext(j, float(contextvalp[j][i]))
            except Exception as e:
                self.log.error("Exception when processing sample at (%f,%f): %s", xc, yc, e)
                continue
            else:
                psfSet.finiSample(sample)
 
            xpos.append(xc)  # for QA
            ypos.append(yc)
 
        if displayExposure:
            with disp.Buffering():
                disp.dot("o", xc, yc, ctype=afwDisplay.CYAN, size=4)
 
        if psfSet.getNsample() == 0:
            raise PsfexNoGoodStarsError(num_available_stars=nCand)
 
        # ---- Update min and max and then the scaling
        for i in range(psfSet.getNcontext()):
            cmin = contextvalp[i].min()
            cmax = contextvalp[i].max()
            psfSet.setContextScale(i, cmax - cmin)
            psfSet.setContextOffset(i, (cmin + cmax)/2.0)
 
        # Don't waste memory!
        psfSet.trimMemory()
 
        # =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- END PSFEX
        #
        # Do a PSFEX decomposition of those PSF candidates
        #
        fields = []
        field = psfex.Field("Unknown")
        field.addExt(exposure.getWcs(), exposure.getWidth(), exposure.getHeight(), psfSet.getNsample())
        field.finalize()
 
        fields.append(field)
 
        sets = []
        sets.append(psfSet)
 
        psfex.makeit(fields, sets)
        psfs = field.getPsfs()
 
        # Flag which objects were actually used in psfex by
        good_indices = []
        for i in range(sets[0].getNsample()):
            index = sets[0].getSample(i).getObjindex()
            if index > -1:
                good_indices.append(index)
 
        if flagKey is not None:
            for i, psfCandidate in enumerate(psfCandidateList):
                source = psfCandidate.getSource()
                if i in good_indices:
                    source.set(flagKey, True)
 
        xpos = np.array(xpos)
        ypos = np.array(ypos)
        numGoodStars = len(good_indices)
        avgX, avgY = np.mean(xpos), np.mean(ypos)
 
        psf = psfex.PsfexPsf(psfs[0], geom.Point2D(avgX, avgY))
 
        # If there are too few stars, the PSFEx psf model will reduce the order
        # to 0, which the Science Pipelines code cannot handle (see
        # https://github.com/lsst/meas_extensions_psfex/blob/f0d5218b5446faf5e39edc30e31d2e6f673ef294/src/PsfexPsf.cc#L118
        # ).
        if (ndim := psf.getNdim()) == 0:
            raise PsfexTooFewGoodStarsError(
                num_available_stars=nCand,
                num_good_stars=numGoodStars,
                poly_ndim_initial=psfSet.getNcontext(),
                poly_ndim_final=ndim,
            )
 
        #
        # Display code for debugging
        #
        if display:
            assert psfCellSet is not None
 
            if displayExposure:
                maUtils.showPsfSpatialCells(exposure, psfCellSet, showChi2=True,
                                            symb="o", ctype=afwDisplay.YELLOW, ctypeBad=afwDisplay.RED,
                                            size=8, display=disp)
            if displayResiduals:
                disp4 = afwDisplay.Display(frame=4)
                maUtils.showPsfCandidates(exposure, psfCellSet, psf=psf, display=disp4,
                                          normalize=normalizeResiduals,
                                          showBadCandidates=showBadCandidates)
            if displayPsfComponents:
                disp6 = afwDisplay.Display(frame=6)
                maUtils.showPsf(psf, display=disp6)
            if displayPsfMosaic:
                disp7 = afwDisplay.Display(frame=7)
                maUtils.showPsfMosaic(exposure, psf, display=disp7, showFwhm=True)
                disp.scale('linear', 0, 1)
        #
        # Generate some QA information
        #
        # Count PSF stars
        #
        if metadata is not None:
            metadata["spatialFitChi2"] = np.nan
            metadata["numAvailStars"] = nCand
            metadata["numGoodStars"] = numGoodStars
            metadata["avgX"] = avgX
            metadata["avgY"] = avgY
 
        return psf, psfCellSet
 
 
    def determinePsf(self, exposure, psfCandidateList, metadata=None, flagKey=None): …
measAlg.psfDeterminerRegistry.register("psfex", PsfexPsfDeterminerTask)
class PsfexPsfDeterminerTask(measAlg.BasePsfDeterminerTask): …