processCcdWithFakes.py

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"""
Insert fake sources into calexps
"""
from astropy.table import Table
 
import lsst.pex.config as pexConfig
import lsst.pipe.base as pipeBase
 
from .insertFakes import InsertFakesTask
from lsst.meas.base import PerTractCcdDataIdContainer
from lsst.afw.table import SourceTable
from lsst.obs.base import ExposureIdInfo
from lsst.pipe.base import PipelineTask, PipelineTaskConfig, CmdLineTask, PipelineTaskConnections
import lsst.pipe.base.connectionTypes as cT
import lsst.afw.table as afwTable
from lsst.pipe.tasks.calibrate import CalibrateTask
 
__all__ = ["ProcessCcdWithFakesConfig", "ProcessCcdWithFakesTask"]
 
 
class ProcessCcdWithFakesConnections(PipelineTaskConnections,
                                     dimensions=("skymap", "tract", "instrument", "visit", "detector"),
                                     defaultTemplates={"coaddName": "deep",
                                                       "wcsName": "jointcal",
                                                       "photoCalibName": "jointcal",
                                                       "fakesType": "fakes_"}):
 
    exposure = cT.Input(
        doc="Exposure into which fakes are to be added.",
        name="calexp",
        storageClass="ExposureF",
        dimensions=("instrument", "visit", "detector")
    )
 
    fakeCat = cT.Input(
        doc="Catalog of fake sources to draw inputs from.",
        name="{fakesType}fakeSourceCat",
        storageClass="DataFrame",
        dimensions=("tract", "skymap")
    )
 
    wcs = cT.Input(
        doc="WCS information for the input exposure.",
        name="{wcsName}_wcs",
        storageClass="Wcs",
        dimensions=("tract", "skymap", "instrument", "visit", "detector")
    )
 
    photoCalib = cT.Input(
        doc="Calib information for the input exposure.",
        name="{photoCalibName}_photoCalib",
        storageClass="PhotoCalib",
        dimensions=("tract", "skymap", "instrument", "visit", "detector")
    )
 
    icSourceCat = cT.Input(
        doc="Catalog of calibration sources",
        name="icSrc",
        storageClass="SourceCatalog",
        dimensions=("instrument", "visit", "detector")
    )
 
    sfdSourceCat = cT.Input(
        doc="Catalog of calibration sources",
        name="src",
        storageClass="SourceCatalog",
        dimensions=("instrument", "visit", "detector")
    )
 
    outputExposure = cT.Output(
        doc="Exposure with fake sources added.",
        name="{fakesType}calexp",
        storageClass="ExposureF",
        dimensions=("instrument", "visit", "detector")
    )
 
    outputCat = cT.Output(
        doc="Source catalog produced in calibrate task with fakes also measured.",
        name="{fakesType}src",
        storageClass="SourceCatalog",
        dimensions=("instrument", "visit", "detector"),
    )
 
    def __init__(self, *, config=None):
        super().__init__(config=config)
 
        if config.doApplyExternalSkyWcs is False:
            self.inputsinputs.remove("wcs")
        if config.doApplyExternalPhotoCalib is False:
            self.inputsinputs.remove("photoCalib")
 
 
class ProcessCcdWithFakesConfig(PipelineTaskConfig,
                                pipelineConnections=ProcessCcdWithFakesConnections):
    """Config for inserting fake sources
 
    Notes
    -----
    The default column names are those from the UW sims database.
    """
 
    doApplyExternalPhotoCalib = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="Whether to apply an external photometric calibration via an "
            "`lsst.afw.image.PhotoCalib` object. Uses the "
            "`externalPhotoCalibName` config option to determine which "
            "calibration to use."
    )
 
    externalPhotoCalibName = pexConfig.ChoiceField(
        doc="What type of external photo calib to use.",
        dtype=str,
        default="jointcal",
        allowed={"jointcal": "Use jointcal_photoCalib",
                 "fgcm": "Use fgcm_photoCalib",
                 "fgcm_tract": "Use fgcm_tract_photoCalib"}
    )
 
    doApplyExternalSkyWcs = pexConfig.Field(
        dtype=bool,
        default=False,
        doc="Whether to apply an external astrometric calibration via an "
            "`lsst.afw.geom.SkyWcs` object. Uses the "
            "`externalSkyWcsName` config option to determine which "
            "calibration to use."
    )
 
    externalSkyWcsName = pexConfig.ChoiceField(
        doc="What type of updated WCS calib to use.",
        dtype=str,
        default="jointcal",
        allowed={"jointcal": "Use jointcal_wcs"}
    )
 
    coaddName = pexConfig.Field(
        doc="The name of the type of coadd used",
        dtype=str,
        default="deep",
    )
 
    srcFieldsToCopy = pexConfig.ListField(
        dtype=str,
        default=("calib_photometry_reserved", "calib_photometry_used", "calib_astrometry_used",
                 "calib_psf_candidate", "calib_psf_used", "calib_psf_reserved"),
        doc=("Fields to copy from the `src` catalog to the output catalog "
             "for matching sources Any missing fields will trigger a "
             "RuntimeError exception.")
    )
 
    matchRadiusPix = pexConfig.Field(
        dtype=float,
        default=3,
        doc=("Match radius for matching icSourceCat objects to sourceCat objects (pixels)"),
    )
 
    calibrate = pexConfig.ConfigurableField(target=CalibrateTask,
                                            doc="The calibration task to use.")
 
    insertFakes = pexConfig.ConfigurableField(target=InsertFakesTask,
                                              doc="Configuration for the fake sources")
 
    def setDefaults(self):
        super().setDefaults()
        self.calibrate.measurement.plugins["base_PixelFlags"].masksFpAnywhere.append("FAKE")
        self.calibrate.measurement.plugins["base_PixelFlags"].masksFpCenter.append("FAKE")
        self.calibrate.doAstrometry = False
        self.calibrate.doWriteMatches = False
        self.calibrate.doPhotoCal = False
        self.calibrate.detection.reEstimateBackground = False
 
 
class ProcessCcdWithFakesTask(PipelineTask, CmdLineTask):
    """Insert fake objects into calexps.
 
    Add fake stars and galaxies to the given calexp, specified in the dataRef. Galaxy parameters are read in
    from the specified file and then modelled using galsim. Re-runs characterize image and calibrate image to
    give a new background estimation and measurement of the calexp.
 
    `ProcessFakeSourcesTask` inherits six functions from insertFakesTask that make images of the fake
    sources and then add them to the calexp.
 
    `addPixCoords`
        Use the WCS information to add the pixel coordinates of each source
        Adds an ``x`` and ``y`` column to the catalog of fake sources.
    `trimFakeCat`
        Trim the fake cat to about the size of the input image.
    `mkFakeGalsimGalaxies`
        Use Galsim to make fake double sersic galaxies for each set of galaxy parameters in the input file.
    `mkFakeStars`
        Use the PSF information from the calexp to make a fake star using the magnitude information from the
        input file.
    `cleanCat`
        Remove rows of the input fake catalog which have half light radius, of either the bulge or the disk,
        that are 0.
    `addFakeSources`
        Add the fake sources to the calexp.
 
    Notes
    -----
    The ``calexp`` with fake souces added to it is written out as the datatype ``calexp_fakes``.
    """
 
    _DefaultName = "processCcdWithFakes"
    ConfigClass = ProcessCcdWithFakesConfig
 
    def __init__(self, schema=None, butler=None, **kwargs):
        """Initalize things! This should go above in the class docstring
        """
 
        super().__init__(**kwargs)
 
        if schema is None:
            schema = SourceTable.makeMinimalSchema()
        self.schema = schema
        self.makeSubtask("insertFakes")
        self.makeSubtask("calibrate")
 
    def runDataRef(self, dataRef):
        """Read in/write out the required data products and add fake sources to the calexp.
 
        Parameters
        ----------
        dataRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef`
            Data reference defining the ccd to have fakes added to it.
            Used to access the following data products:
                calexp
                jointcal_wcs
                jointcal_photoCalib
 
        Notes
        -----
        Uses the calibration and WCS information attached to the calexp for the posistioning and calibration
        of the sources unless the config option config.externalPhotoCalibName or config.externalSkyWcsName
        are set then it uses the specified outputs. The config defualts for the column names in the catalog
        of fakes are taken from the University of Washington simulations database.
        Operates on one ccd at a time.
        """
        exposureIdInfo = dataRef.get("expIdInfo")
 
        if self.config.insertFakes.fakeType == "snapshot":
            fakeCat = dataRef.get("fakeSourceCat").toDataFrame()
        elif self.config.insertFakes.fakeType == "static":
            fakeCat = dataRef.get("deepCoadd_fakeSourceCat").toDataFrame()
        else:
            fakeCat = Table.read(self.config.insertFakes.fakeType).to_pandas()
 
        calexp = dataRef.get("calexp")
        if self.config.doApplyExternalSkyWcs:
            self.log.info("Using external wcs from " + self.config.externalSkyWcsName)
            wcs = dataRef.get(self.config.externalSkyWcsName + "_wcs")
        else:
            wcs = calexp.getWcs()
 
        if self.config.doApplyExternalPhotoCalib:
            self.log.info("Using external photocalib from " + self.config.externalPhotoCalibName)
            photoCalib = dataRef.get(self.config.externalPhotoCalibName + "_photoCalib")
        else:
            photoCalib = calexp.getPhotoCalib()
 
        icSourceCat = dataRef.get("icSrc", immediate=True)
        sfdSourceCat = dataRef.get("src", immediate=True)
 
        resultStruct = self.run(fakeCat, calexp, wcs=wcs, photoCalib=photoCalib,
                                exposureIdInfo=exposureIdInfo, icSourceCat=icSourceCat,
                                sfdSourceCat=sfdSourceCat)
 
        dataRef.put(resultStruct.outputExposure, "fakes_calexp")
        dataRef.put(resultStruct.outputCat, "fakes_src")
        return resultStruct
 
    def runQuantum(self, butlerQC, inputRefs, outputRefs):
        inputs = butlerQC.get(inputRefs)
        if 'exposureIdInfo' not in inputs.keys():
            expId, expBits = butlerQC.quantum.dataId.pack("visit_detector", returnMaxBits=True)
            inputs['exposureIdInfo'] = ExposureIdInfo(expId, expBits)
 
        if not self.config.doApplyExternalSkyWcs:
            inputs["wcs"] = inputs["exposure"].getWcs()
 
        if not self.config.doApplyExternalPhotoCalib:
            inputs["photoCalib"] = inputs["exposure"].getPhotoCalib()
 
        outputs = self.run(**inputs)
        butlerQC.put(outputs, outputRefs)
 
    @classmethod
    def _makeArgumentParser(cls):
        parser = pipeBase.ArgumentParser(name=cls._DefaultName)
        parser.add_id_argument("--id", "fakes_calexp", help="data ID with raw CCD keys [+ tract optionally], "
                               "e.g. --id visit=12345 ccd=1,2 [tract=0]",
                               ContainerClass=PerTractCcdDataIdContainer)
        return parser
 
    def run(self, fakeCat, exposure, wcs=None, photoCalib=None, exposureIdInfo=None, icSourceCat=None,
            sfdSourceCat=None):
        """Add fake sources to a calexp and then run detection, deblending and measurement.
 
        Parameters
        ----------
        fakeCat : `pandas.core.frame.DataFrame`
                    The catalog of fake sources to add to the exposure
        exposure : `lsst.afw.image.exposure.exposure.ExposureF`
                    The exposure to add the fake sources to
        wcs : `lsst.afw.geom.SkyWcs`
                    WCS to use to add fake sources
        photoCalib : `lsst.afw.image.photoCalib.PhotoCalib`
                    Photometric calibration to be used to calibrate the fake sources
        exposureIdInfo : `lsst.obs.base.ExposureIdInfo`
        icSourceCat : `lsst.afw.table.SourceCatalog`
                    Default : None
                    Catalog to take the information about which sources were used for calibration from.
        sfdSourceCat : `lsst.afw.table.SourceCatalog`
                    Default : None
                    Catalog produced by singleFrameDriver, needed to copy some calibration flags from.
 
        Returns
        -------
        resultStruct : `lsst.pipe.base.struct.Struct`
            contains : outputExposure : `lsst.afw.image.exposure.exposure.ExposureF`
                       outputCat : `lsst.afw.table.source.source.SourceCatalog`
 
        Notes
        -----
        Adds pixel coordinates for each source to the fakeCat and removes objects with bulge or disk half
        light radius = 0 (if ``config.cleanCat = True``). These columns are called ``x`` and ``y`` and are in
        pixels.
 
        Adds the ``Fake`` mask plane to the exposure which is then set by `addFakeSources` to mark where fake
        sources have been added. Uses the information in the ``fakeCat`` to make fake galaxies (using galsim)
        and fake stars, using the PSF models from the PSF information for the calexp. These are then added to
        the calexp and the calexp with fakes included returned.
 
        The galsim galaxies are made using a double sersic profile, one for the bulge and one for the disk,
        this is then convolved with the PSF at that point.
 
        If exposureIdInfo is not provided then the SourceCatalog IDs will not be globally unique.
        """
 
        if wcs is None:
            wcs = exposure.getWcs()
 
        if photoCalib is None:
            photoCalib = exposure.getPhotoCalib()
 
        self.insertFakes.run(fakeCat, exposure, wcs, photoCalib)
 
        # detect, deblend and measure sources
        if exposureIdInfo is None:
            exposureIdInfo = ExposureIdInfo()
        returnedStruct = self.calibrate.run(exposure, exposureIdInfo=exposureIdInfo)
        sourceCat = returnedStruct.sourceCat
 
        sourceCat = self.copyCalibrationFields(sfdSourceCat, sourceCat, self.config.srcFieldsToCopy)
 
        resultStruct = pipeBase.Struct(outputExposure=exposure, outputCat=sourceCat)
        return resultStruct
 
    def copyCalibrationFields(self, calibCat, sourceCat, fieldsToCopy):
        """Match sources in calibCat and sourceCat and copy the specified fields
 
        Parameters
        ----------
        calibCat : `lsst.afw.table.SourceCatalog`
            Catalog from which to copy fields.
        sourceCat : `lsst.afw.table.SourceCatalog`
            Catalog to which to copy fields.
        fieldsToCopy : `lsst.pex.config.listField.List`
            Fields to copy from calibCat to SoourceCat.
 
        Returns
        -------
        newCat : `lsst.afw.table.SourceCatalog`
            Catalog which includes the copied fields.
 
        The fields copied are those specified by `fieldsToCopy` that actually exist
        in the schema of `calibCat`.
 
        This version was based on and adapted from the one in calibrateTask.
        """
 
        # Make a new SourceCatalog with the data from sourceCat so that we can add the new columns to it
        sourceSchemaMapper = afwTable.SchemaMapper(sourceCat.schema)
        sourceSchemaMapper.addMinimalSchema(sourceCat.schema, True)
 
        calibSchemaMapper = afwTable.SchemaMapper(calibCat.schema, sourceCat.schema)
 
        # Add the desired columns from the option fieldsToCopy
        missingFieldNames = []
        for fieldName in fieldsToCopy:
            if fieldName in calibCat.schema:
                schemaItem = calibCat.schema.find(fieldName)
                calibSchemaMapper.editOutputSchema().addField(schemaItem.getField())
                schema = calibSchemaMapper.editOutputSchema()
                calibSchemaMapper.addMapping(schemaItem.getKey(), schema.find(fieldName).getField())
            else:
                missingFieldNames.append(fieldName)
        if missingFieldNames:
            raise RuntimeError(f"calibCat is missing fields {missingFieldNames} specified in "
                               "fieldsToCopy")
 
        if "calib_detected" not in calibSchemaMapper.getOutputSchema():
            self.calibSourceKey = calibSchemaMapper.addOutputField(afwTable.Field["Flag"]("calib_detected",
                                                                   "Source was detected as an icSource"))
        else:
            self.calibSourceKey = None
 
        schema = calibSchemaMapper.getOutputSchema()
        newCat = afwTable.SourceCatalog(schema)
        newCat.reserve(len(sourceCat))
        newCat.extend(sourceCat, sourceSchemaMapper)
 
        # Set the aliases so it doesn't complain.
        for k, v in sourceCat.schema.getAliasMap().items():
            newCat.schema.getAliasMap().set(k, v)
 
        select = newCat["deblend_nChild"] == 0
        matches = afwTable.matchXy(newCat[select], calibCat, self.config.matchRadiusPix)
        # Check that no sourceCat sources are listed twice (we already know
        # that each match has a unique calibCat source ID, due to using
        # that ID as the key in bestMatches)
        numMatches = len(matches)
        numUniqueSources = len(set(m[1].getId() for m in matches))
        if numUniqueSources != numMatches:
            self.log.warn("%d calibCat sources matched only %d sourceCat sources", numMatches,
                          numUniqueSources)
 
        self.log.info("Copying flags from calibCat to sourceCat for %s sources", numMatches)
 
        # For each match: set the calibSourceKey flag and copy the desired
        # fields
        for src, calibSrc, d in matches:
            if self.calibSourceKey:
                src.setFlag(self.calibSourceKey, True)
            # src.assign copies the footprint from calibSrc, which we don't want
            # (DM-407)
            # so set calibSrc's footprint to src's footprint before src.assign,
            # then restore it
            calibSrcFootprint = calibSrc.getFootprint()
            try:
                calibSrc.setFootprint(src.getFootprint())
                src.assign(calibSrc, calibSchemaMapper)
            finally:
                calibSrc.setFootprint(calibSrcFootprint)
 
        return newCat