references.py

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#!/usr/bin/env python
#
# LSST Data Management System
# Copyright 2008-2015 AURA/LSST.
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"""
Subtasks for creating the reference catalogs used in forced measurement.
"""

import lsst.afw.geom
import lsst.pex.config
import lsst.pipe.base

__all__ = ("BaseReferencesTask", "CoaddSrcReferencesTask")


class BaseReferencesConfig(lsst.pex.config.Config):
    removePatchOverlaps = lsst.pex.config.Field(
        doc="Only include reference sources for each patch that lie within the patch's inner bbox",
        dtype=bool,
        default=True
    )
    filter = lsst.pex.config.Field(
        doc="Bandpass for reference sources; None indicates chi-squared detections.",
        dtype=str,
        optional=True
    )


class BaseReferencesTask(lsst.pipe.base.Task):
    """!
    Base class for forced photometry subtask that retrieves reference sources.

    BaseReferencesTask defines the required API for the references task, which includes:
      - getSchema(butler)
      - fetchInPatches(butler, tract, filter, patchList)
      - fetchInBox(self, butler, tract, filter, bbox, wcs)
      - the removePatchOverlaps config option

    It also provides the subset() method, which may be of use to derived classes when
    reimplementing fetchInBox.
    """

    ConfigClass = BaseReferencesConfig

    def __init__(self, butler=None, schema=None, **kwargs):
        """!Initialize the task.

        BaseReferencesTask and its subclasses take two keyword arguments beyond the usual Task arguments:
         - schema: the Schema of the reference catalog
         - butler: a butler that will allow the task to load its Schema from disk.
        At least one of these arguments must be present; if both are, schema takes precedence.
        """
        lsst.pipe.base.Task.__init__(self, **kwargs)

    def getSchema(self, butler):
        """!
        Return the schema for the reference sources.

        Must be available even before any data has been processed.
        """
        raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")

    def getWcs(self, dataRef):
        """!
        Return the WCS for reference sources.  The given dataRef must include the tract in its dataId.
        """
        raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")

    def fetchInBox(self, dataRef, bbox, wcs):
        """!
        Return reference sources that overlap a region defined by a pixel-coordinate bounding box
        and corresponding Wcs.

        @param[in] dataRef    ButlerDataRef; the implied data ID must contain the 'tract' key.
        @param[in] bbox       a afw.geom.Box2I or Box2D that defines the region in pixel coordinates
        @param[in] wcs        afw.image.Wcs that maps the bbox to sky coordinates

        @return an iterable of reference sources

        It is not required that the returned object be a SourceCatalog; it may be any Python iterable
        containing SourceRecords (including a lazy iterator).

        The returned set of sources should be complete and close to minimal.
        """
        raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")

    def fetchInPatches(self, dataRef, patchList):
        """!
        Return reference sources that overlap a region defined by one or more SkyMap patches.

        @param[in] dataRef    ButlerDataRef; the implied data ID must contain the 'tract' key.
        @param[in] patchList  list of skymap.PatchInfo instances for which to fetch reference sources

        @return an iterable of reference sources

        It is not required that the returned object be a SourceCatalog; it may be any Python sequence
        containing SourceRecords (including a lazy iterator).

        The returned set of sources should be complete and close to minimal.  If
        config.removePatchOverlaps is True, only sources within each patch's "inner" bounding box
        should be returned.
        """
        raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")

    def subset(self, sources, bbox, wcs):
        """!
        Filter sources to contain only those within the given box, defined in the coordinate system
        defined by the given Wcs.

        @param[in] sources     input iterable of SourceRecords
        @param[in] bbox        bounding box with which to filter reference sources (Box2I or Box2D)
        @param[in] wcs         afw.image.Wcs that defines the coordinate system of bbox

        Instead of filtering sources directly via their positions, we filter based on the positions
        of parent objects, then include or discard all children based on their parent's status.  This
        is necessary to support ReplaceWithNoise in measurement, which requires all child sources have
        their parent present.

        @return an iterable of filtered reference sources

        This is not a part of the required BaseReferencesTask interface; it's a convenience function
        used in implementing fetchInBox that may be of use to subclasses.
        """
        boxD = lsst.afw.geom.Box2D(bbox)
        # We're passed an arbitrary iterable, but we need a catalog so we can iterate
        # over parents and then children.
        catalog = lsst.afw.table.SourceCatalog(self.schema)
        catalog.extend(sources)
        # catalog must be sorted by parent ID for lsst.afw.table.getChildren to work
        catalog.sort(lsst.afw.table.SourceTable.getParentKey())
        # Iterate over objects that have no parent.
        for parent in catalog.getChildren(0):
            pixel = wcs.skyToPixel(parent.getCoord())
            if boxD.contains(pixel):
                yield parent
                for child in catalog.getChildren(parent.getId()):
                    yield child


class CoaddSrcReferencesConfig(BaseReferencesTask.ConfigClass):
    coaddName = lsst.pex.config.Field(
        doc="Coadd name: typically one of deep or goodSeeing.",
        dtype=str,
        default="deep",
    )

    def validate(self):
        if (self.coaddName == "chiSquared") != (self.filter is None):
            raise lsst.pex.config.FieldValidationError(
                field=CoaddSrcReferencesConfig.coaddName,
                config=self,
                msg="filter may be None if and only if coaddName is chiSquared"
            )


class CoaddSrcReferencesTask(BaseReferencesTask):
    """!
    A references task implementation that loads the coadd_datasetSuffix dataset directly from
    disk using the butler.
    """

    ConfigClass = CoaddSrcReferencesConfig
    datasetSuffix = "src"  # Suffix to add to "Coadd_" for dataset name

    def __init__(self, butler=None, schema=None, **kwargs):
        """! Initialize the task.
        Additional keyword arguments (forwarded to BaseReferencesTask.__init__):
         - schema: the schema of the detection catalogs used as input to this one
         - butler: a butler used to read the input schema from disk, if schema is None
        The task will set its own self.schema attribute to the schema of the output merged catalog.
        """
        BaseReferencesTask.__init__(self, butler=butler, schema=schema, **kwargs)
        if schema is None:
            assert butler is not None, "No butler nor schema provided"
            schema = butler.get("{}Coadd_{}_schema".format(self.config.coaddName, self.datasetSuffix),
                                immediate=True).getSchema()
        self.schema = schema

    def getWcs(self, dataRef):
        """Return the WCS for reference sources.  The given dataRef must include the tract in its dataId.
        """
        skyMap = dataRef.get(self.config.coaddName + "Coadd_skyMap", immediate=True)
        return skyMap[dataRef.dataId["tract"]].getWcs()

    def fetchInPatches(self, dataRef, patchList):
        """!
        An implementation of BaseReferencesTask.fetchInPatches that loads 'coadd_' + datasetSuffix
        catalogs using the butler.

        The given dataRef must include the tract in its dataId.
        """
        dataset = "{}Coadd_{}".format(self.config.coaddName, self.datasetSuffix)
        tract = dataRef.dataId["tract"]
        butler = dataRef.butlerSubset.butler
        for patch in patchList:
            dataId = {'tract': tract, 'patch': "%d,%d" % patch.getIndex()}
            if self.config.filter is not None:
                dataId['filter'] = self.config.filter

            if not butler.datasetExists(dataset, dataId):
                raise lsst.pipe.base.TaskError("Reference %s doesn't exist" % (dataId,))
            self.log.info("Getting references in %s" % (dataId,))
            catalog = butler.get(dataset, dataId, immediate=True)
            if self.config.removePatchOverlaps:
                bbox = lsst.afw.geom.Box2D(patch.getInnerBBox())
                for source in catalog:
                    if bbox.contains(source.getCentroid()):
                        yield source
            else:
                for source in catalog:
                    yield source

    def fetchInBox(self, dataRef, bbox, wcs, pad=0):
        """!
        Return reference sources that overlap a region defined by a pixel-coordinate bounding box
        and corresponding Wcs.

        @param[in] dataRef    ButlerDataRef; the implied data ID must contain the 'tract' key.
        @param[in] bbox       a afw.geom.Box2I or Box2D that defines the region in pixel coordinates
        @param[in] wcs        afw.image.Wcs that maps the bbox to sky coordinates
        @param[in] pad        a buffer to grow the bounding box by after catalogs have been loaded, but
                              before filtering them to include just the given bounding box.

        @return an iterable of reference sources
        """
        skyMap = dataRef.get(self.config.coaddName + "Coadd_skyMap", immediate=True)
        tract = skyMap[dataRef.dataId["tract"]]
        coordList = [wcs.pixelToSky(corner) for corner in lsst.afw.geom.Box2D(bbox).getCorners()]
        self.log.info("Getting references in region with corners %s [degrees]" %
                      ", ".join("(%s)" % (coord.getPosition(lsst.afw.geom.degrees),) for coord in coordList))
        patchList = tract.findPatchList(coordList)
        # After figuring out which patch catalogs to read from the bbox, pad out the bbox if desired
        # But don't add any new patches while padding
        if pad:
            bbox.grow(pad)
        return self.subset(self.fetchInPatches(dataRef, patchList), bbox, wcs)


class MultiBandReferencesConfig(CoaddSrcReferencesTask.ConfigClass):

    def validate(self):
        if self.filter is not None:
            raise lsst.pex.config.FieldValidationError(
                field=MultiBandReferencesConfig.filter,
                config=self,
                msg="Filter should not be set for the multiband processing scheme")
        # Delegate to ultimate base class, because the direct one has a check we don't want.
        BaseReferencesTask.ConfigClass.validate(self)


class MultiBandReferencesTask(CoaddSrcReferencesTask):
    """Loads references from the multiband processing scheme"""
    ConfigClass = MultiBandReferencesConfig
    datasetSuffix = "ref"