matcherSourceSelector.py

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#
# 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
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# 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.
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# the GNU General Public License along with this program.  If not,
# see <https://www.lsstcorp.org/LegalNotices/>.
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import numpy as np

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


class MatcherSourceSelectorConfig(BaseSourceSelectorConfig):
    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=40,
    )
    excludePixelFlags = pexConfig.Field(
        dtype=bool,
        doc="Exclude objects that have saturated, interpolated, or edge "
            "pixels using PixelFlags. For matchOptimisticB set this to False "
            "to recover previous matcher selector behavior.",
        default=True,
    )


@pexConfig.registerConfigurable("matcher", sourceSelectorRegistry)
class MatcherSourceSelectorTask(BaseSourceSelectorTask):
    """Select sources that are useful for matching.

    Good matching sources have high signal/noise, are non-blended. They need not
    be PSF sources, just have reliable centroids.

    Distinguished from astrometrySourceSelector because it is more lenient
    (i.e. not checking footprints or bad flags).
    """
    ConfigClass = MatcherSourceSelectorConfig

    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 matching.

        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)

        good = self._isUsable(sourceCat)
        if self.config.excludePixelFlags:
            good = good & self._isGood(sourceCat)
        return Struct(selected=good)

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

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

    def _isParent(self, sourceCat):
        """Return True for each source that is the parent source."""
        test = (sourceCat.get(self.parentKey) == 0)
        return test

    def _hasCentroid(self, sourceCat):
        """Return True for each source that has a valid centroid"""
        return np.isfinite(sourceCat.get(self.centroidXKey)) \
            & np.isfinite(sourceCat.get(self.centroidYKey)) \
            & ~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.fluxKey)/sourceCat.get(self.fluxErrKey) > 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 instFlux (of the type specified in this object's constructor)
        - have adequate signal-to-noise
        """
        return self._hasCentroid(sourceCat) \
            & self._isParent(sourceCat) \
            & self._goodSN(sourceCat) \
            & ~sourceCat.get(self.fluxFlagKey)

    def _isGood(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:
        - Not be on a CCD edge.
        - Not have an interpolated pixel within 3x3 around their centroid.
        - Not have a saturated pixel in their footprint.
        """
        return ~sourceCat.get(self.edgeKey) & \
               ~sourceCat.get(self.interpolatedCenterKey) & \
               ~sourceCat.get(self.saturatedKey)