astrometrySourceSelector.py

Go to the documentation of this file.

#
# LSST Data Management System
#
# Copyright 2008-2017  AURA/LSST.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# 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 LSST License Statement and
# the GNU General Public License along with this program.  If not,
# see <https://www.lsstcorp.org/LegalNotices/>.
#
"""Select sources that are useful for astrometry.

Such sources have good signal-to-noise, are well centroided, not blended,
and not flagged with a handful of "bad" flags.
"""

import numpy as np

import lsst.pex.config as pexConfig
from .sourceSelector import BaseSourceSelectorConfig, BaseSourceSelectorTask, sourceSelectorRegistry
from lsst.pipe.base import Struct
from functools import reduce


class AstrometrySourceSelectorConfig(BaseSourceSelectorConfig):
    badFlags = pexConfig.ListField(
        doc="List of flags which cause a source to be rejected as bad",
        dtype=str,
        default=[
            "base_PixelFlags_flag_edge",
            "base_PixelFlags_flag_interpolatedCenter",
            "base_PixelFlags_flag_saturatedCenter",
            "base_PixelFlags_flag_crCenter",
            "base_PixelFlags_flag_bad",
        ],
    )
    sourceFluxType = pexConfig.Field(
        doc="Type of source flux; typically one of Ap or Psf",
        dtype=str,
        default="Ap",
    )
    minSnr = pexConfig.Field(
        dtype=float,
        doc="Minimum allowed signal-to-noise ratio for sources used for matching "
        "(in the flux specified by sourceFluxType); <= 0 for no limit",
        default=10,
    )


@pexConfig.registerConfigurable("astrometry", sourceSelectorRegistry)
class AstrometrySourceSelectorTask(BaseSourceSelectorTask):
    """Select sources that are useful for astrometry.

    Good astrometry sources have high signal/noise, are non-blended, and
    did not have certain "bad" flags set during source extraction. They need not
    be PSF sources, just have reliable centroids.
    """
    ConfigClass = AstrometrySourceSelectorConfig

    def __init__(self, *args, **kwargs):
        BaseSourceSelectorTask.__init__(self, *args, **kwargs)

    def selectSources(self, sourceCat, matches=None, exposure=None):
        """Return a selection of sources that are useful for astrometry.

        Parameters:
        -----------
        sourceCat : `lsst.afw.table.SourceCatalog`
            Catalog of sources to select from.
            This catalog must be contiguous in memory.
        matches : `list` of `lsst.afw.table.ReferenceMatch` or None
            Ignored in this SourceSelector.
        exposure : `lsst.afw.image.Exposure` or None
            The exposure the catalog was built from; used for debug display.

        Return
        ------
        struct : `lsst.pipe.base.Struct`
            The struct contains the following data:

            - selected : `array` of `bool``
                Boolean array of sources that were selected, same length as
                sourceCat.
        """
        self._getSchemaKeys(sourceCat.schema)

        bad = reduce(lambda x, y: np.logical_or(x, sourceCat.get(y)), self.config.badFlags, False)
        good = self._isGood(sourceCat)
        return Struct(selected=good & ~bad)

    def _getSchemaKeys(self, schema):
        """Extract and save the necessary keys from schema with asKey."""
        self.parentKey = schema["parent"].asKey()
        self.nChildKey = schema["deblend_nChild"].asKey()
        self.centroidXKey = schema["slot_Centroid_x"].asKey()
        self.centroidYKey = schema["slot_Centroid_y"].asKey()
        self.centroidXErrKey = schema["slot_Centroid_xErr"].asKey()
        self.centroidYErrKey = schema["slot_Centroid_yErr"].asKey()
        self.centroidFlagKey = schema["slot_Centroid_flag"].asKey()

        self.edgeKey = schema["base_PixelFlags_flag_edge"].asKey()
        self.interpolatedCenterKey = schema["base_PixelFlags_flag_interpolatedCenter"].asKey()
        self.saturatedKey = schema["base_PixelFlags_flag_saturated"].asKey()

        fluxPrefix = "slot_%sFlux_" % (self.config.sourceFluxType,)
        self.instFluxKey = schema[fluxPrefix + "instFlux"].asKey()
        self.fluxFlagKey = schema[fluxPrefix + "flag"].asKey()
        self.instFluxErrKey = schema[fluxPrefix + "instFluxErr"].asKey()

    def _isMultiple(self, sourceCat):
        """Return True for each source that is likely multiple sources."""
        test = (sourceCat.get(self.parentKey) != 0) | (sourceCat.get(self.nChildKey) != 0)
        # have to currently manage footprints on a source-by-source basis.
        for i, cat in enumerate(sourceCat):
            footprint = cat.getFootprint()
            test[i] |= (footprint is not None) and (len(footprint.getPeaks()) > 1)
        return test

    def _hasCentroid(self, sourceCat):
        """Return True for each source that has a valid centroid"""
        def checkNonfiniteCentroid():
            """Return True for sources with non-finite centroids."""
            return ~np.isfinite(sourceCat.get(self.centroidXKey)) | \
                ~np.isfinite(sourceCat.get(self.centroidYKey))
        assert ~checkNonfiniteCentroid().any(), \
            "Centroids not finite for %d unflagged sources." % (checkNonfiniteCentroid().sum())
        return np.isfinite(sourceCat.get(self.centroidXErrKey)) \
            & np.isfinite(sourceCat.get(self.centroidYErrKey)) \
            & ~sourceCat.get(self.centroidFlagKey)

    def _goodSN(self, sourceCat):
        """Return True for each source that has Signal/Noise > config.minSnr."""
        if self.config.minSnr <= 0:
            return True
        else:
            with np.errstate(invalid="ignore"):  # suppress NAN warnings
                return sourceCat.get(self.instFluxKey)/sourceCat.get(self.instFluxErrKey) > self.config.minSnr

    def _isUsable(self, sourceCat):
        """
        Return True for each source that is usable for matching, even if it may
        have a poor centroid.

        For a source to be usable it must:
        - have a valid centroid
        - not be deblended
        - have a valid flux (of the type specified in this object's constructor)
        - have adequate signal-to-noise
        """

        return self._hasCentroid(sourceCat) \
            & ~self._isMultiple(sourceCat) \
            & self._goodSN(sourceCat) \
            & ~sourceCat.get(self.fluxFlagKey)

    def _isGood(self, sourceCat):
        """
        Return True for each source that is usable for matching and likely has a
        good centroid.

        The additional tests for a good centroid, beyond isUsable, are:
        - not interpolated in the center
        - not saturated
        - not near the edge
        """

        return self._isUsable(sourceCat) \
            & ~sourceCat.get(self.saturatedKey) \
            & ~sourceCat.get(self.interpolatedCenterKey) \
            & ~sourceCat.get(self.edgeKey)

    def _isBadFlagged(self, source):
        """Return True if any of config.badFlags are set for this source."""
        return any(source.get(flag) for flag in self.config.badFlags)