Inheritance diagram for lsst.obs.decam.crosstalk.DecamCrosstalkTask:

Public Member Functions
	run (self, exposure, crosstalk=None, crosstalkSources=None, isTrimmed=None, camera=None, parallelOverscanRegion=None, detectorConfig=None, fullAmplifier=False, gains=None, badAmpDict=None, ignoreVariance=False)

Static Public Attributes
	ConfigClass = CrosstalkConfig

Static Protected Attributes
str	_DefaultName = 'isrCrosstalk'

Detailed Description

Remove crosstalk from a raw DECam image.

This was a gen2-only task, as crosstalk code is all in ip_isr.

Definition at line 45 of file crosstalk.py.

Member Function Documentation

◆ run()

lsst.ip.isr.crosstalk.CrosstalkTask.run	(	self,
		exposure,
		crosstalk = None,
		crosstalkSources = None,
		isTrimmed = None,
		camera = None,
		parallelOverscanRegion = None,
		detectorConfig = None,
		fullAmplifier = False,
		gains = None,
		badAmpDict = None,
		ignoreVariance = False )

inherited

Apply intra-detector crosstalk correction

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure for which to remove crosstalk.
crosstalkCalib : `lsst.ip.isr.CrosstalkCalib`, optional
    External crosstalk calibration to apply.  Constructed from
    detector if not found.
crosstalkSources : `defaultdict`, optional
    Image data for other detectors that are sources of
    crosstalk in exposure.  The keys are expected to be names
    of the other detectors, with the values containing
    `lsst.afw.image.Exposure` at the same level of processing
    as ``exposure``.
    The default for intra-detector crosstalk here is None.
isTrimmed : `bool`, optional
    This option has been deprecated and does not do anything.
    It will be removed after v29.
camera : `lsst.afw.cameraGeom.Camera`, optional
    Camera associated with this exposure.  Only used for
    inter-chip matching.
parallelOverscanRegion : `bool`, optional
    This option has been deprecated and will be removed after v29.
detectorConfig : `lsst.ip.isr.OverscanDetectorConfig`, optional
    This option has been deprecated and will be removed after v29.
fullAmplifier : `bool`, optional
    Use full amplifier and not just imaging region.
gains : `dict` [`str`, `float`], optional
    Dictionary of amp name to gain.  Required if there is a unit
    mismatch between the exposure and the crosstalk matrix.
badAmpDict : `dict` [`str`, `bool`], optional
    Dictionary to identify bad amplifiers that should not be
    source or target for crosstalk correction.
ignoreVariance : `bool`, optional
    Ignore variance plane when applying crosstalk?

Raises
------
RuntimeError
    Raised if called for a detector that does not have a
    crosstalk correction.  Also raised if the crosstalkSource
    is not an expected type.

Reimplemented in lsst.ip.isr.crosstalk.NullCrosstalkTask.

Definition at line 1011 of file crosstalk.py.

    ):
        """Apply intra-detector crosstalk correction
 
        Parameters
        ----------
        exposure : `lsst.afw.image.Exposure`
            Exposure for which to remove crosstalk.
        crosstalkCalib : `lsst.ip.isr.CrosstalkCalib`, optional
            External crosstalk calibration to apply.  Constructed from
            detector if not found.
        crosstalkSources : `defaultdict`, optional
            Image data for other detectors that are sources of
            crosstalk in exposure.  The keys are expected to be names
            of the other detectors, with the values containing
            `lsst.afw.image.Exposure` at the same level of processing
            as ``exposure``.
            The default for intra-detector crosstalk here is None.
        isTrimmed : `bool`, optional
            This option has been deprecated and does not do anything.
            It will be removed after v29.
        camera : `lsst.afw.cameraGeom.Camera`, optional
            Camera associated with this exposure.  Only used for
            inter-chip matching.
        parallelOverscanRegion : `bool`, optional
            This option has been deprecated and will be removed after v29.
        detectorConfig : `lsst.ip.isr.OverscanDetectorConfig`, optional
            This option has been deprecated and will be removed after v29.
        fullAmplifier : `bool`, optional
            Use full amplifier and not just imaging region.
        gains : `dict` [`str`, `float`], optional
            Dictionary of amp name to gain.  Required if there is a unit
            mismatch between the exposure and the crosstalk matrix.
        badAmpDict : `dict` [`str`, `bool`], optional
            Dictionary to identify bad amplifiers that should not be
            source or target for crosstalk correction.
        ignoreVariance : `bool`, optional
            Ignore variance plane when applying crosstalk?
 
        Raises
        ------
        RuntimeError
            Raised if called for a detector that does not have a
            crosstalk correction.  Also raised if the crosstalkSource
            is not an expected type.
        """
        # TODO: Remove on DM-48394
        if isTrimmed is not None:
            warnings.warn(
                "The isTrimmed option has been deprecated and will be removed after v29.",
                FutureWarning,
            )
        isTrimmed = isTrimmedImage(exposure.maskedImage, exposure.getDetector())
 
        # TODO: Remove on DM-48394
        if parallelOverscanRegion is not None:
            warnings.warn(
                "The parallelOverscanRegion option has been deprecated and will be removed after v29.",
                FutureWarning,
            )
        if detectorConfig is not None:
            warnings.warn(
                "The detectorConfig option has been deprecated and will be removed after v29.",
                FutureWarning,
            )
 
        if not crosstalk:
            crosstalk = CrosstalkCalib(log=self.log)
            crosstalk = crosstalk.fromDetector(exposure.getDetector(),
                                               coeffVector=self.config.crosstalkValues)
        if not crosstalk.log:
            crosstalk.log = self.log
 
        doSqrCrosstalk = self.config.doQuadraticCrosstalkCorrection
 
        if doSqrCrosstalk and crosstalk.coeffsSqr is None:
            raise RuntimeError("Attempted to perform NL crosstalk correction without NL "
                               "crosstalk coefficients.")
        if doSqrCrosstalk:
            crosstalkCoeffsSqr = crosstalk.coeffsSqr
        else:
            crosstalkCoeffsSqr = None
 
        if not crosstalk.hasCrosstalk:
            raise RuntimeError("Attempted to correct crosstalk without crosstalk coefficients.")
 
        # Get the exposure units; defaults to adu.
        exposureUnits = exposure.metadata.get("LSST ISR UNITS", "adu")
        invertGains = False
        gainApply = False
        if crosstalk.crosstalkRatiosUnits != exposureUnits:
            detector = exposure.getDetector()
 
            if gains is None and np.all(crosstalk.fitGains == 0.0):
                raise RuntimeError(
                    f"Unit mismatch between exposure ({exposureUnits}) and "
                    f"crosstalk ratios ({crosstalk.crosstalkRatiosUnits}) and "
                    "no gains were supplied or available in crosstalk calibration.",
                )
            elif gains is None:
                self.log.info("Using crosstalk calib fitGains for gain corrections.")
                gains = {}
                for i, amp in enumerate(detector):
                    gains[amp.getName()] = crosstalk.fitGains[i]
 
            # Check individual gains for finite-ness.
            gainArray = np.zeros(len(detector))
            for i, amp in enumerate(detector):
                gainArray[i] = gains[amp.getName()]
            badGains = (~np.isfinite(gainArray) | (gainArray == 0.0))
            if np.any(badGains):
                if np.all(badGains):
                    raise RuntimeError("No valid (finite, non-zero) gains found for crosstalk correction.")
 
                badAmpNames = [amp.getName() for i, amp in enumerate(detector) if badGains[i]]
 
                self.log.warning("Illegal gain value found for %d amplifiers %r in crosstalk correction; "
                                 "substituting with median gain.", badGains.sum(), badAmpNames)
                medGain = np.median(gainArray[~badGains])
                gainArray[badGains] = medGain
                for i, amp in enumerate(detector):
                    gains[amp.getName()] = gainArray[i]
 
            gainApply = True
 
            if crosstalk.crosstalkRatiosUnits == "adu":
                invertGains = True
 
            if exposureUnits == "adu":
                self.log.info("Temporarily applying gains to perform crosstalk correction "
                              "because crosstalk is in electron units and exposure is in "
                              "adu units.")
            else:
                self.log.info("Temporarily un-applying gains to perform crosstalk correction "
                              "because crosstalk is in adu units and exposure is in "
                              "electron units.")
 
        self.log.info("Applying crosstalk correction.")
 
        with gainContext(
                exposure,
                exposure.image,
                gainApply,
                gains=gains,
                invert=invertGains,
                isTrimmed=isTrimmed,
        ):
            crosstalk.subtractCrosstalk(
                exposure,
                crosstalkCoeffs=crosstalk.coeffs,
                crosstalkCoeffsSqr=crosstalkCoeffsSqr,
                crosstalkCoeffsValid=crosstalk.coeffValid,
                minPixelToMask=self.config.minPixelToMask,
                doSubtrahendMasking=self.config.doSubtrahendMasking,
                crosstalkStr=self.config.crosstalkMaskPlane,
                backgroundMethod=self.config.crosstalkBackgroundMethod,
                doSqrCrosstalk=doSqrCrosstalk,
                fullAmplifier=fullAmplifier,
                badAmpDict=badAmpDict,
                ignoreVariance=ignoreVariance,
            )
 
        if crosstalk.interChip:
            if crosstalkSources:
                # Parse crosstalkSources: Identify which detectors we have
                # available
                if isinstance(crosstalkSources[0], lsst.afw.image.Exposure):
                    # Received afwImage.Exposure
                    sourceNames = [exp.getDetector().getName() for exp in crosstalkSources]
                elif isinstance(crosstalkSources[0], lsst.daf.butler.DeferredDatasetHandle):
                    # Received dafButler.DeferredDatasetHandle
                    detectorList = [source.dataId['detector'] for source in crosstalkSources]
                    sourceNames = [camera[detectorId].getName() for detectorId in detectorList]
                else:
                    raise RuntimeError("Unknown object passed as crosstalk sources.",
                                       type(crosstalkSources[0]))
 
                for detName in crosstalk.interChip:
                    if detName not in sourceNames:
                        self.log.warning("Crosstalk lists %s, not found in sources: %s",
                                         detName, sourceNames)
                        continue
                    # Get the coefficients.
                    interChipCoeffs = crosstalk.interChip[detName]
 
                    sourceExposure = crosstalkSources[sourceNames.index(detName)]
                    if isinstance(sourceExposure, lsst.daf.butler.DeferredDatasetHandle):
                        # Dereference the dafButler.DeferredDatasetHandle.
                        sourceExposure = sourceExposure.get()
                    if not isinstance(sourceExposure, lsst.afw.image.Exposure):
                        raise RuntimeError("Unknown object passed as crosstalk sources.",
                                           type(sourceExposure))
 
                    if sourceExposure.getBBox() != exposure.getBBox():
                        raise RuntimeError(
                            "Mis-match between exposure bounding box and crosstalk source "
                            "exposure bounding box. Were these run with the same trim state?",
                        )
 
                    self.log.info("Correcting detector %s with ctSource %s",
                                  exposure.getDetector().getName(),
                                  sourceExposure.getDetector().getName())
                    crosstalk.subtractCrosstalk(
                        exposure,
                        sourceExposure=sourceExposure,
                        crosstalkCoeffs=interChipCoeffs,
                        minPixelToMask=self.config.minPixelToMask,
                        crosstalkStr=self.config.crosstalkMaskPlane,
                        backgroundMethod=self.config.crosstalkBackgroundMethod,
                        ignoreVariance=ignoreVariance,
                    )
            else:
                self.log.warning("Crosstalk contains interChip coefficients, but no sources found!")
 
 

Member Data Documentation

◆ _DefaultName

str lsst.ip.isr.crosstalk.CrosstalkTask._DefaultName = 'isrCrosstalk'

staticprotectedinherited

Definition at line 1009 of file crosstalk.py.

◆ ConfigClass

lsst.ip.isr.crosstalk.CrosstalkTask.ConfigClass = CrosstalkConfig

staticinherited

Definition at line 1008 of file crosstalk.py.

The documentation for this class was generated from the following file:

/j/snowflake/release/lsstsw/stack/lsst-scipipe-10.0.0/Linux64/obs_decam/g0fba68d861+fcbc158cd0/python/lsst/obs/decam/crosstalk.py

Public Member Functions