Inheritance diagram for lsst.ip.isr.isrTask.IsrTask:

Public Member Functions
	__init__ (self, **kwargs)

	runQuantum (self, butlerQC, inputRefs, outputRefs)

	run (self, ccdExposure, *, camera=None, bias=None, linearizer=None, crosstalk=None, crosstalkSources=None, dark=None, flat=None, ptc=None, bfKernel=None, bfGains=None, defects=None, fringes=pipeBase.Struct(fringes=None), opticsTransmission=None, filterTransmission=None, sensorTransmission=None, atmosphereTransmission=None, detectorNum=None, strayLightData=None, illumMaskedImage=None, deferredChargeCalib=None)

	defineEffectivePtc (self, ptcDataset, detector, bfGains, overScans, metadata)

	ensureExposure (self, inputExp, camera=None, detectorNum=None)

	compareUnits (self, calibMetadata, calibName)

	convertIntToFloat (self, exposure)

	maskAmplifier (self, ccdExposure, amp, defects)

	overscanCorrection (self, ccdExposure, amp)

	updateVariance (self, ampExposure, amp, ptcDataset)

	maskNegativeVariance (self, exposure)

	darkCorrection (self, exposure, darkExposure, invert=False)

	doLinearize (self, detector)

	flatCorrection (self, exposure, flatExposure, invert=False)

	saturationDetection (self, exposure, amp)

	saturationInterpolation (self, exposure)

	suspectDetection (self, exposure, amp)

	maskDefect (self, exposure, defectBaseList)

	maskEdges (self, exposure, numEdgePixels=0, maskPlane="SUSPECT", level='DETECTOR')

	maskAndInterpolateDefects (self, exposure, defectBaseList)

	maskNan (self, exposure)

	maskAndInterpolateNan (self, exposure)

	measureBackground (self, exposure, IsrQaConfig=None)

	roughZeroPoint (self, exposure)

	flatContext (self, exp, flat, dark=None)

	makeBinnedImages (self, exposure)

	debugView (self, exposure, stepname)

Static Public Member Functions
	extractCalibDate (calib)

Public Attributes
	vignettePolygon

Static Public Attributes
	ConfigClass = IsrTaskConfig

Static Protected Attributes
str	_DefaultName = "isr"

Detailed Description

Apply common instrument signature correction algorithms to a raw frame.

The process for correcting imaging data is very similar from
camera to camera.  This task provides a vanilla implementation of
doing these corrections, including the ability to turn certain
corrections off if they are not needed.  The inputs to the primary
method, `run()`, are a raw exposure to be corrected and the
calibration data products. The raw input is a single chip sized
mosaic of all amps including overscans and other non-science
pixels.

The __init__ method sets up the subtasks for ISR processing, using
the defaults from `lsst.ip.isr`.

Parameters
----------
args : `list`
    Positional arguments passed to the Task constructor.
    None used at this time.
kwargs : `dict`, optional
    Keyword arguments passed on to the Task constructor.
    None used at this time.

Definition at line 997 of file isrTask.py.

Constructor & Destructor Documentation

◆ init()

lsst.ip.isr.isrTask.IsrTask.__init__	(		self,
		**	kwargs )

Definition at line 1024 of file isrTask.py.

Member Function Documentation

◆ compareUnits()

lsst.ip.isr.isrTask.IsrTask.compareUnits	(	self,
		calibMetadata,
		calibName )

Compare units from calibration to ISR units.

For the regular IsrTask this is used to confirm that calibs
suitable for IsrTaskLSST are not used with the old IsrTask.

Parameters
----------
calibMetadata : `lsst.daf.base.PropertyList`
    Calibration metadata from header.
calibName : `str`
    Calibration name for log message.

Definition at line 2102 of file isrTask.py.

◆ convertIntToFloat()

lsst.ip.isr.isrTask.IsrTask.convertIntToFloat	(		self,
			exposure )

Convert exposure image from uint16 to float.

If the exposure does not need to be converted, the input is
immediately returned.  For exposures that are converted to use
floating point pixels, the variance is set to unity and the
mask to zero.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
   The raw exposure to be converted.

Returns
-------
newexposure : `lsst.afw.image.Exposure`
   The input ``exposure``, converted to floating point pixels.

Raises
------
RuntimeError
    Raised if the exposure type cannot be converted to float.

Definition at line 2133 of file isrTask.py.

◆ darkCorrection()

lsst.ip.isr.isrTask.IsrTask.darkCorrection	(	self,
		exposure,
		darkExposure,
		invert = False )

Apply dark correction in place.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.
darkExposure : `lsst.afw.image.Exposure`
    Dark exposure of the same size as ``exposure``.
invert : `Bool`, optional
    If True, re-add the dark to an already corrected image.

Raises
------
RuntimeError
    Raised if either ``exposure`` or ``darkExposure`` do not
    have their dark time defined.

See Also
--------
lsst.ip.isr.isrFunctions.darkCorrection

Definition at line 2396 of file isrTask.py.

◆ debugView()

lsst.ip.isr.isrTask.IsrTask.debugView	(	self,
		exposure,
		stepname )

Utility function to examine ISR exposure at different stages.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to view.
stepname : `str`
    State of processing to view.

Definition at line 2868 of file isrTask.py.

◆ defineEffectivePtc()

lsst.ip.isr.isrTask.IsrTask.defineEffectivePtc	(	self,
		ptcDataset,
		detector,
		bfGains,
		overScans,
		metadata )

Define an effective Photon Transfer Curve dataset
with nominal gains and noise.

Parameters
----------
ptcDataset : `lsst.ip.isr.PhotonTransferCurveDataset`
    Input Photon Transfer Curve dataset.
detector : `lsst.afw.cameraGeom.Detector`
    Detector object.
bfGains : `dict`
    Gains from running the brighter-fatter code.
    A dict keyed by amplifier name for the detector
    in question.
overScans : `list` [`lsst.pipe.base.Struct`]
    List of overscanResults structures
metadata : `lsst.daf.base.PropertyList`
    Exposure metadata to update gain and read noise
    provenance.

Returns
-------
effectivePtc : `lsst.ip.isr.PhotonTransferCurveDataset`
    PTC dataset containing gains and readout noise
    values to be used throughout
    Instrument Signature Removal.

Definition at line 1878 of file isrTask.py.

◆ doLinearize()

lsst.ip.isr.isrTask.IsrTask.doLinearize	(		self,
			detector )

Check if linearization is needed for the detector cameraGeom.

Checks config.doLinearize and the linearity type of the first
amplifier.

Parameters
----------
detector : `lsst.afw.cameraGeom.Detector`
    Detector to get linearity type from.

Returns
-------
doLinearize : `Bool`
    If True, linearization should be performed.

Definition at line 2439 of file isrTask.py.

◆ ensureExposure()

lsst.ip.isr.isrTask.IsrTask.ensureExposure	(	self,
		inputExp,
		camera = None,
		detectorNum = None )

Ensure that the data returned by Butler is a fully constructed exp.

ISR requires exposure-level image data for historical reasons, so if we
did not recieve that from Butler, construct it from what we have,
modifying the input in place.

Parameters
----------
inputExp : `lsst.afw.image` image-type.
    The input data structure obtained from Butler.
    Can be  `lsst.afw.image.Exposure`,
    `lsst.afw.image.DecoratedImageU`,
    or `lsst.afw.image.ImageF`
camera : `lsst.afw.cameraGeom.camera`, optional
    The camera associated with the image.  Used to find the appropriate
    detector if detector is not already set.
detectorNum : `int`, optional
    The detector in the camera to attach, if the detector is not
    already set.

Returns
-------
inputExp : `lsst.afw.image.Exposure`
    The re-constructed exposure, with appropriate detector parameters.

Raises
------
TypeError
    Raised if the input data cannot be used to construct an exposure.

Definition at line 2023 of file isrTask.py.

◆ extractCalibDate()

lsst.ip.isr.isrTask.IsrTask.extractCalibDate ( calib )

static

Extract common calibration metadata values that will be written to
output header.

Parameters
----------
calib : `lsst.afw.image.Exposure` or `lsst.ip.isr.IsrCalib`
    Calibration to pull date information from.

Returns
-------
dateString : `str`
    Calibration creation date string to add to header.

Definition at line 2078 of file isrTask.py.

◆ flatContext()

lsst.ip.isr.isrTask.IsrTask.flatContext	(	self,
		exp,
		flat,
		dark = None )

Context manager that applies and removes flats and darks,
if the task is configured to apply them.

Parameters
----------
exp : `lsst.afw.image.Exposure`
    Exposure to process.
flat : `lsst.afw.image.Exposure`
    Flat exposure the same size as ``exp``.
dark : `lsst.afw.image.Exposure`, optional
    Dark exposure the same size as ``exp``.

Yields
------
exp : `lsst.afw.image.Exposure`
    The flat and dark corrected exposure.

Definition at line 2803 of file isrTask.py.

◆ flatCorrection()

lsst.ip.isr.isrTask.IsrTask.flatCorrection	(	self,
		exposure,
		flatExposure,
		invert = False )

Apply flat correction in place.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.
flatExposure : `lsst.afw.image.Exposure`
    Flat exposure of the same size as ``exposure``.
invert : `Bool`, optional
    If True, unflatten an already flattened image.

See Also
--------
lsst.ip.isr.isrFunctions.flatCorrection

Definition at line 2458 of file isrTask.py.

◆ makeBinnedImages()

lsst.ip.isr.isrTask.IsrTask.makeBinnedImages	(		self,
			exposure )

Make visualizeVisit style binned exposures.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to bin.

Returns
-------
bin1 : `lsst.afw.image.Exposure`
    Binned exposure using binFactor1.
bin2 : `lsst.afw.image.Exposure`
    Binned exposure using binFactor2.

Definition at line 2840 of file isrTask.py.

◆ maskAmplifier()

lsst.ip.isr.isrTask.IsrTask.maskAmplifier	(	self,
		ccdExposure,
		amp,
		defects )

Identify bad amplifiers, saturated and suspect pixels.

Parameters
----------
ccdExposure : `lsst.afw.image.Exposure`
    Input exposure to be masked.
amp : `lsst.afw.cameraGeom.Amplifier`
    Catalog of parameters defining the amplifier on this
    exposure to mask.
defects : `lsst.ip.isr.Defects`
    List of defects.  Used to determine if the entire
    amplifier is bad.

Returns
-------
badAmp : `Bool`
    If this is true, the entire amplifier area is covered by
    defects and unusable.

Definition at line 2170 of file isrTask.py.

◆ maskAndInterpolateDefects()

lsst.ip.isr.isrTask.IsrTask.maskAndInterpolateDefects	(	self,
		exposure,
		defectBaseList )

Mask and interpolate defects using mask plane "BAD", in place.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.
defectBaseList : defects-like
    List of defects to mask and interpolate. Can be
    `lsst.ip.isr.Defects` or `list` of `lsst.afw.image.DefectBase`.

See Also
--------
lsst.ip.isr.isrTask.maskDefect

Definition at line 2627 of file isrTask.py.

◆ maskAndInterpolateNan()

lsst.ip.isr.isrTask.IsrTask.maskAndInterpolateNan	(		self,
			exposure )

"Mask and interpolate NaN/infs using mask plane "UNMASKEDNAN",
in place.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.

See Also
--------
lsst.ip.isr.isrTask.maskNan

Definition at line 2679 of file isrTask.py.

◆ maskDefect()

lsst.ip.isr.isrTask.IsrTask.maskDefect	(	self,
		exposure,
		defectBaseList )

Mask defects using mask plane "BAD", in place.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.
defectBaseList : defect-type
    List of defects to mask. Can be of type  `lsst.ip.isr.Defects`
    or `list` of `lsst.afw.image.DefectBase`.

Notes
-----
Call this after CCD assembly, since defects may cross amplifier
boundaries.

Definition at line 2569 of file isrTask.py.

◆ maskEdges()

lsst.ip.isr.isrTask.IsrTask.maskEdges	(	self,
		exposure,
		numEdgePixels = 0,
		maskPlane = "SUSPECT",
		level = 'DETECTOR' )

Mask edge pixels with applicable mask plane.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.
numEdgePixels : `int`, optional
    Number of edge pixels to mask.
maskPlane : `str`, optional
    Mask plane name to use.
level : `str`, optional
    Level at which to mask edges.

Definition at line 2593 of file isrTask.py.

◆ maskNan()

lsst.ip.isr.isrTask.IsrTask.maskNan	(		self,
			exposure )

Mask NaNs using mask plane "UNMASKEDNAN", in place.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.

Notes
-----
We mask over all non-finite values (NaN, inf), including those
that are masked with other bits (because those may or may not be
interpolated over later, and we want to remove all NaN/infs).
Despite this behaviour, the "UNMASKEDNAN" mask plane is used to
preserve the historical name.

Definition at line 2653 of file isrTask.py.

◆ maskNegativeVariance()

lsst.ip.isr.isrTask.IsrTask.maskNegativeVariance	(		self,
			exposure )

Identify and mask pixels with negative variance values.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.

See Also
--------
lsst.ip.isr.isrFunctions.updateVariance

Definition at line 2380 of file isrTask.py.

◆ measureBackground()

lsst.ip.isr.isrTask.IsrTask.measureBackground	(	self,
		exposure,
		IsrQaConfig = None )

Measure the image background in subgrids, for quality control.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.
IsrQaConfig : `lsst.ip.isr.isrQa.IsrQaConfig`
    Configuration object containing parameters on which background
    statistics and subgrids to use.

Definition at line 2701 of file isrTask.py.

◆ overscanCorrection()

lsst.ip.isr.isrTask.IsrTask.overscanCorrection	(	self,
		ccdExposure,
		amp )

Apply overscan correction in place.

This method does initial pixel rejection of the overscan
region.  The overscan can also be optionally segmented to
allow for discontinuous overscan responses to be fit
separately.  The actual overscan subtraction is performed by
the `lsst.ip.isr.overscan.OverscanTask`, which is called here
after the amplifier is preprocessed.

Parameters
----------
ccdExposure : `lsst.afw.image.Exposure`
    Exposure to have overscan correction performed.
amp : `lsst.afw.cameraGeom.Amplifer`
    The amplifier to consider while correcting the overscan.

Returns
-------
overscanResults : `lsst.pipe.base.Struct`
    Result struct with components:

    ``imageFit``
        Value or fit subtracted from the amplifier image data.
        (scalar or `lsst.afw.image.Image`)
    ``overscanFit``
        Value or fit subtracted from the overscan image data.
        (scalar or `lsst.afw.image.Image`)
    ``overscanImage``
        Image of the overscan region with the overscan
        correction applied. This quantity is used to estimate
        the amplifier read noise empirically.
        (`lsst.afw.image.Image`)
    ``edgeMask``
        Mask of the suspect pixels. (`lsst.afw.image.Mask`)
    ``overscanMean``
        Median overscan fit value. (`float`)
    ``overscanSigma``
        Clipped standard deviation of the overscan after
        correction. (`float`)

Raises
------
RuntimeError
    Raised if the ``amp`` does not contain raw pixel information.

See Also
--------
lsst.ip.isr.overscan.OverscanTask

Definition at line 2247 of file isrTask.py.

◆ roughZeroPoint()

lsst.ip.isr.isrTask.IsrTask.roughZeroPoint	(		self,
			exposure )

Set an approximate magnitude zero point for the exposure.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.

Definition at line 2773 of file isrTask.py.

◆ run()

lsst.ip.isr.isrTask.IsrTask.run	(		self,
			ccdExposure,
		*	,
			camera = None,
			bias = None,
			linearizer = None,
			crosstalk = None,
			crosstalkSources = None,
			dark = None,
			flat = None,
			ptc = None,
			bfKernel = None,
			bfGains = None,
			defects = None,
			fringes = pipeBase.Struct(fringes=None),
			opticsTransmission = None,
			filterTransmission = None,
			sensorTransmission = None,
			atmosphereTransmission = None,
			detectorNum = None,
			strayLightData = None,
			illumMaskedImage = None,
			deferredChargeCalib = None )

Perform instrument signature removal on an exposure.

Steps included in the ISR processing, in order performed, are:

- saturation and suspect pixel masking
- overscan subtraction
- CCD assembly of individual amplifiers
- bias subtraction
- variance image construction
- linearization of non-linear response
- crosstalk masking
- brighter-fatter correction
- dark subtraction
- fringe correction
- stray light subtraction
- flat correction
- masking of known defects and camera specific features
- vignette calculation
- appending transmission curve and distortion model

Parameters
----------
ccdExposure : `lsst.afw.image.Exposure`
    The raw exposure that is to be run through ISR.  The
    exposure is modified by this method.
camera : `lsst.afw.cameraGeom.Camera`, optional
    The camera geometry for this exposure. Required if
    one or more of ``ccdExposure``, ``bias``, ``dark``, or
    ``flat`` does not have an associated detector.
bias : `lsst.afw.image.Exposure`, optional
    Bias calibration frame.
linearizer : `lsst.ip.isr.linearize.LinearizeBase`, optional
    Functor for linearization.
crosstalk : `lsst.ip.isr.crosstalk.CrosstalkCalib`, optional
    Calibration for crosstalk.
crosstalkSources : `list`, optional
    List of possible crosstalk sources.
dark : `lsst.afw.image.Exposure`, optional
    Dark calibration frame.
flat : `lsst.afw.image.Exposure`, optional
    Flat calibration frame.
ptc : `lsst.ip.isr.PhotonTransferCurveDataset`, optional
    Photon transfer curve dataset, with, e.g., gains
    and read noise.
bfKernel : `numpy.ndarray`, optional
    Brighter-fatter kernel.
bfGains : `dict` of `float`, optional
    Gains used to override the detector's nominal gains for the
    brighter-fatter correction. A dict keyed by amplifier name for
    the detector in question.
defects : `lsst.ip.isr.Defects`, optional
    List of defects.
fringes : `lsst.pipe.base.Struct`, optional
    Struct containing the fringe correction data, with
    elements:

    ``fringes``
        fringe calibration frame (`lsst.afw.image.Exposure`)
    ``seed``
        random seed derived from the ``ccdExposureId`` for random
        number generator (`numpy.uint32`)
opticsTransmission: `lsst.afw.image.TransmissionCurve`, optional
    A ``TransmissionCurve`` that represents the throughput of the,
    optics, to be evaluated in focal-plane coordinates.
filterTransmission : `lsst.afw.image.TransmissionCurve`
    A ``TransmissionCurve`` that represents the throughput of the
    filter itself, to be evaluated in focal-plane coordinates.
sensorTransmission : `lsst.afw.image.TransmissionCurve`
    A ``TransmissionCurve`` that represents the throughput of the
    sensor itself, to be evaluated in post-assembly trimmed detector
    coordinates.
atmosphereTransmission : `lsst.afw.image.TransmissionCurve`
    A ``TransmissionCurve`` that represents the throughput of the
    atmosphere, assumed to be spatially constant.
detectorNum : `int`, optional
    The integer number for the detector to process.
strayLightData : `object`, optional
    Opaque object containing calibration information for stray-light
    correction.  If `None`, no correction will be performed.
illumMaskedImage : `lsst.afw.image.MaskedImage`, optional
    Illumination correction image.

Returns
-------
result : `lsst.pipe.base.Struct`
    Result struct with component:

    ``exposure``
        The fully ISR corrected exposure.
        (`lsst.afw.image.Exposure`)
    ``outputExposure``
        An alias for ``exposure``. (`lsst.afw.image.Exposure`)
    ``ossThumb``
        Thumbnail image of the exposure after overscan subtraction.
        (`numpy.ndarray`)
    ``flattenedThumb``
        Thumbnail image of the exposure after flat-field correction.
        (`numpy.ndarray`)
    ``outputStatistics``
        Values of the additional statistics calculated.

Raises
------
RuntimeError
    Raised if a configuration option is set to `True`, but the
    required calibration data has not been specified.

Notes
-----
The current processed exposure can be viewed by setting the
appropriate `lsstDebug` entries in the ``debug.display``
dictionary.  The names of these entries correspond to some of
the `IsrTaskConfig` Boolean options, with the value denoting the
frame to use.  The exposure is shown inside the matching
option check and after the processing of that step has
finished.  The steps with debug points are:

* doAssembleCcd
* doBias
* doCrosstalk
* doBrighterFatter
* doDark
* doFringe
* doStrayLight
* doFlat

In addition, setting the ``postISRCCD`` entry displays the
exposure after all ISR processing has finished.

Definition at line 1192 of file isrTask.py.

◆ runQuantum()

lsst.ip.isr.isrTask.IsrTask.runQuantum	(	self,
		butlerQC,
		inputRefs,
		outputRefs )

Definition at line 1038 of file isrTask.py.

◆ saturationDetection()

lsst.ip.isr.isrTask.IsrTask.saturationDetection	(	self,
		exposure,
		amp )

Detect and mask saturated pixels in config.saturatedMaskName.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.  Only the amplifier DataSec is processed.
amp : `lsst.afw.cameraGeom.Amplifier`
    Amplifier detector data.

See Also
--------
lsst.ip.isr.isrFunctions.makeThresholdMask

Definition at line 2483 of file isrTask.py.

◆ saturationInterpolation()

lsst.ip.isr.isrTask.IsrTask.saturationInterpolation	(		self,
			exposure )

Interpolate over saturated pixels, in place.

This method should be called after `saturationDetection`, to
ensure that the saturated pixels have been identified in the
SAT mask.  It should also be called after `assembleCcd`, since
saturated regions may cross amplifier boundaries.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.

See Also
--------
lsst.ip.isr.isrTask.saturationDetection
lsst.ip.isr.isrFunctions.interpolateFromMask

Definition at line 2507 of file isrTask.py.

◆ suspectDetection()

lsst.ip.isr.isrTask.IsrTask.suspectDetection	(	self,
		exposure,
		amp )

Detect and mask suspect pixels in config.suspectMaskName.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
    Exposure to process.  Only the amplifier DataSec is processed.
amp : `lsst.afw.cameraGeom.Amplifier`
    Amplifier detector data.

See Also
--------
lsst.ip.isr.isrFunctions.makeThresholdMask

Notes
-----
Suspect pixels are pixels whose value is greater than
amp.getSuspectLevel(). This is intended to indicate pixels that may be
affected by unknown systematics; for example if non-linearity
corrections above a certain level are unstable then that would be a
useful value for suspectLevel. A value of `nan` indicates that no such
level exists and no pixels are to be masked as suspicious.

Definition at line 2533 of file isrTask.py.

◆ updateVariance()

lsst.ip.isr.isrTask.IsrTask.updateVariance	(	self,
		ampExposure,
		amp,
		ptcDataset )

Set the variance plane using the gain and read noise

The read noise is calculated from the ``overscanImage`` if the
``doEmpiricalReadNoise`` option is set in the configuration; otherwise
the value from the amplifier data is used.

Parameters
----------
ampExposure : `lsst.afw.image.Exposure`
    Exposure to process.
amp : `lsst.afw.cameraGeom.Amplifier` or `FakeAmp`
    Amplifier detector data.
ptcDataset : `lsst.ip.isr.PhotonTransferCurveDataset`
    Effective PTC dataset containing the gains and read noise.

See also
--------
lsst.ip.isr.isrFunctions.updateVariance

Definition at line 2345 of file isrTask.py.

Member Data Documentation

◆ _DefaultName

str lsst.ip.isr.isrTask.IsrTask._DefaultName = "isr"

staticprotected

Definition at line 1022 of file isrTask.py.

◆ ConfigClass

lsst.ip.isr.isrTask.IsrTask.ConfigClass = IsrTaskConfig