IsrTaskLSSTConfig#

class lsst.ip.isr.IsrTaskLSSTConfig(*args, **kw)#

Bases: PipelineTaskConfig

Configuration parameters for IsrTaskLSST.

Items are grouped in the order in which they are executed by the task.

Attributes Summary

`ampNoiseThreshold`	Maximum amplifier noise (e-) that is allowed before an amp is masked as bad.
`ampOffset`	Amp offset correction task.
`assembleCcd`	CCD assembly task.
`badAmps`	List of bad amps that should be masked as BAD in the defect code.
`binFactor1`	Binning factor for first binned exposure.
`binFactor2`	Binning factor for second binned exposure.
`binning`	Task to bin the exposure.
`brighterFatterCorrectionMethod`	The method for brighter-fatter correction.
`brighterFatterFwhmForInterpolation`	FWHM of PSF in arcseconds used for interpolation in brighter-fatter correction (currently unused).
`brighterFatterLevel`	The level at which to correct for brighter-fatter.
`brighterFatterMaskGrowSize`	Number of pixels to grow the masks listed in config.brighterFatterMaskListToInterpolate when brighter-fatter correction is applied.
`brighterFatterMaskListToInterpolate`	List of mask planes that should be interpolated over when applying the brighter-fatter correction.
`brighterFatterMaxIter`	Maximum number of iterations for the brighter-fatter correction for the COULTON18* correction types (`int`, default `10`)
`brighterFatterThreshold`	Threshold used to stop iterating the brighter-fatter correction for the COULTON18* correction types.
`bssVoltageKeyword`	Back-side bias voltage header keyword.
`bssVoltageMinimum`	Minimum back-side bias voltage.
`cameraKeywordsToCompare`	List of header keywords to compare between exposure and calibrations.
`connections`	Field which refers to a dynamically added configuration class which is based on a PipelineTaskConnections class.
`crosstalk`	Intra-CCD crosstalk correction.
`defaultSaturationSource`	Source to retrieve default amp-level saturation values.
`defaultSuspectSource`	Source to retrieve default amp-level suspect values.
`deferredChargeCorrection`	Deferred charge correction task.
`doAmpOffset`	Calculate amp offset corrections? (`bool`, default `False`)
`doApplyGains`	Apply gains to the image? (`bool`, default `True`)
`doAssembleCcd`	Assemble amp-level exposures into a ccd-level exposure? (`bool`, default `True`)
`doBias`	Apply bias frame correction? (`bool`, default `True`)
`doBinnedExposures`	Should binned exposures be calculated? (`bool`, default `False`)
`doBootstrap`	Is this task to be run in a `bootstrap` fashion that does not require a PTC or full calibrations? (`bool`, default `False`)
`doBrighterFatter`	Apply the brighter-fatter correction? (`bool`, default `True`)
`doCalculateStatistics`	Should additional ISR statistics be calculated? (`bool`, default `True`)
`doCheckUnprocessableData`	Check if this image is completely unprocessable due to all bad amps.
`doCorrectGains`	Apply gain corrections from detector restarts? (`bool`, default `True`)
`doCrosstalk`	Apply intra-CCD crosstalk correction? (`bool`, default `True`)
`doDark`	Apply dark frame correction.
`doDefect`	Apply correction for CCD defects, e.g. hot pixels? (`bool`, default `True`).
`doDeferredCharge`	Apply deferred charge correction? (`bool`, default `True`)
`doDiffNonLinearCorrection`	Do differential non-linearity correction? (`bool`, default `False`)
`doE2VEdgeBleedMask`	Mask flag-like edge bleeds from saturated columns in E2V amplifiers.
`doFlat`	Apply flat field correction.
`doHeaderProvenance`	Write calibration identifiers into output exposure header.
`doITLDipMask`	Apply `ITL dip` masking.
`doITLEdgeBleedMask`	Mask edge bleeds from saturated columns in ITL amplifiers.
`doITLSatSagMask`	Mask columns presenting saturation sag.
`doInterpolate`	Interpolate masked pixels? (`bool`, default `True`)
`doLinearize`	Correct for nonlinearity of the detector's response? (`bool`, default `True`)
`doNanMasking`	Mask non-finite (NAN, inf) pixels.
`doRaiseOnCalibMismatch`	Should IsrTaskLSST halt if exposure and calibration header values do not match? (`bool`, default `False`)
`doSaturation`	Mask saturated pixels? NB: this is totally independent of the interpolation option - this is ONLY setting the bits in the mask.
`doSaveInterpPixels`	Save a copy of the pre-interpolated pixel values? (`bool`, default `False`)
`doSetBadRegions`	Should we set the level of all BAD patches of the chip to the chip's average value? (`bool`, default `True`)
`doStandardStatistics`	Should standard image quality statistics be calculated? (`bool`, default `True`)
`doSuspect`	Mask suspect pixels? (`bool`, default `True`)
`doVariance`	Calculate variance? (`bool`, default `True`)
`doWidenSaturationTrails`	Widen bleed trails based on their width.
`e2vEdgeBleedSatMaxArea`	Maximum limit of saturated cores footprint area to apply edgebleed masking in E2V amplifiers.
`e2vEdgeBleedSatMinArea`	Minimum limit of saturated cores footprint area to apply edgebleed masking in E2V amplifiers.
`e2vEdgeBleedYMax`	Height in pixels of edge bleed masking in E2V amplifiers (widthis the width of the amplifier).
`expectWcs`	Expect input science images to have a WCS (set False for e.g. spectrographs).
`flatScalingType`	The method for scaling the flat on the fly.
`flatUserScale`	If flatScalingType is 'USER' then scale flat by this amount; ignored otherwise.
`growSaturationFootprintSize`	Number of pixels by which to grow the saturation footprints.
`hvBiasKeyword`	Back-side bias voltage on/off header keyword.
`isrStats`	Task to calculate additional statistics.
`itlDipMaskPlanes`	Mask plane to use for ITL dip pixels.
`itlEdgeBleedModelConstant`	Constant in the edge bleed exponential decay model.
`itlEdgeBleedSatMaxArea`	Maximum limit for saturated cores footprint area.
`itlEdgeBleedSatMinArea`	Minimum limit for saturated cores footprint area.
`itlEdgeBleedThreshold`	Sky background threshold for edge bleed detection.
`maskListToInterpolate`	List of mask planes that should be interpolated.
`maskNegativeVariance`	Mask pixels that claim a negative variance.
`masking`	Masking task.
`negativeVarianceMaskName`	Mask plane to use to mark pixels with negative variance, if `maskNegativeVariance` is True.
`overscanCamera`	Per-detector and per-amplifier overscan configurations.
`qa`	QA related configuration options.
`saturatedMaskName`	Name of mask plane to use in saturation detection and interpolation.
`saveLogOutput`	Flag to enable/disable saving of log output for a task, enabled by default.
`serialOverscanMedianShiftSigmaThreshold`	Number of sigma difference from per-amp overscan median (as compared to PTC) to check if an amp is in a different state than the baseline PTC calib and should be marked BAD.
`suspectMaskName`	Name of mask plane to use for suspect pixels.
`useGainsFrom`	Where to retrieve the gains.
`useLegacyInterp`	Use the legacy interpolation algorithm.

Methods Summary

`setDefaults`()	Subclass hook for computing defaults.
`validate`()	Validate the Config, raising an exception if invalid.

Attributes Documentation

ampNoiseThreshold#: Maximum amplifier noise (e-) that is allowed before an amp is masked as bad. Set to np.inf/np.nan to turn off noise checking. (float, default 25.0)

ampOffset#: Amp offset correction task. (ConfigurableInstance, default <class 'lsst.ip.isr.ampOffset.AmpOffsetConfig'>)

assembleCcd#: CCD assembly task. (ConfigurableInstance, default <class 'lsst.ip.isr.assembleCcdTask.AssembleCcdConfig'>)

badAmps#: List of bad amps that should be masked as BAD in the defect code. Value should be of form {detector_name}_{amp_name}, e.g. R42_S21_C07. Only used if doDefect is True. (List, default [])

binFactor1#: Binning factor for first binned exposure. This is intended for a finely binned output. (int, default 8)

binFactor2#: Binning factor for second binned exposure. This is intended for a coarsely binned output. (int, default 64)

binning#: Task to bin the exposure. (ConfigurableInstance, default <class 'lsst.ip.isr.binImageDataTask.BinImageDataConfig'>)

brighterFatterCorrectionMethod#

The method for brighter-fatter correction. (str, default 'COULTON18')

Allowed values:

'COULTON18': Coulton et al. 2018 BF correction with kernel
'COULTON18_FLUX_CONSERVING': Coulton et al. 2018 BF correction with kernel + Flux conserving corrections
'ASTIER23': Astier & Regenault 2023 electrostatic BF correction
'None': Field is optional

brighterFatterFwhmForInterpolation#: FWHM of PSF in arcseconds used for interpolation in brighter-fatter correction (currently unused). (float, default 1.0)

brighterFatterLevel#

The level at which to correct for brighter-fatter. (str, default 'DETECTOR')

Allowed values:

'AMP': Every amplifier treated separately.
'DETECTOR': One kernel per detector.
'None': Field is optional

brighterFatterMaskGrowSize#: Number of pixels to grow the masks listed in config.brighterFatterMaskListToInterpolate when brighter-fatter correction is applied. (int, default 2)

brighterFatterMaskListToInterpolate#: List of mask planes that should be interpolated over when applying the brighter-fatter correction. (List, default ['SAT', 'BAD', 'NO_DATA', 'UNMASKEDNAN'])

brighterFatterMaxIter#: Maximum number of iterations for the brighter-fatter correction for the COULTON18* correction types (int, default 10)

brighterFatterThreshold#: Threshold used to stop iterating the brighter-fatter correction for the COULTON18* correction types. It is the absolute value of the difference between the current corrected image and the one from the previous iteration summed over all the pixels. (float, default 1000)

bssVoltageKeyword#: Back-side bias voltage header keyword. Only checked if doCheckUnprocessableData is True and bssVoltageMinimum is greater than 0. (str, default 'BSSVBS')

bssVoltageMinimum#: Minimum back-side bias voltage. Below this the detector is off and an UnprocessableDataError will be logged. Check will be skipped if doCheckUnprocessableData is False or if value is less than or equal to 0. (float, default 5.0)

cameraKeywordsToCompare#: List of header keywords to compare between exposure and calibrations. (List, default [])

connections: pexConfig.ConfigField#: Field which refers to a dynamically added configuration class which is based on a PipelineTaskConnections class.

crosstalk#: Intra-CCD crosstalk correction. (ConfigurableInstance, default <class 'lsst.ip.isr.crosstalk.CrosstalkConfig'>)

defaultSaturationSource#

Source to retrieve default amp-level saturation values. (str, default 'PTCTURNOFF')

Allowed values:

'NONE': No default saturation values; only config overrides will be used.
'CAMERAMODEL': Use the default from the camera model (old defaults).
'PTCTURNOFF': Use the ptcTurnoff value as the saturation level.
'None': Field is optional

defaultSuspectSource#

Source to retrieve default amp-level suspect values. (str, default 'PTCTURNOFF')

Allowed values:

'NONE': No default suspect values; only config overrides will be used.
'CAMERAMODEL': Use the default from the camera model (old defaults).
'PTCTURNOFF': Use the ptcTurnoff value as the suspect level.
'None': Field is optional

deferredChargeCorrection#: Deferred charge correction task. (ConfigurableInstance, default <class 'lsst.ip.isr.deferredCharge.DeferredChargeConfig'>)

doAmpOffset#: Calculate amp offset corrections? (bool, default False)

doApplyGains#: Apply gains to the image? (bool, default True)

doAssembleCcd#: Assemble amp-level exposures into a ccd-level exposure? (bool, default True)

doBias#: Apply bias frame correction? (bool, default True)

doBinnedExposures#: Should binned exposures be calculated? (bool, default False)

doBootstrap#: Is this task to be run in a bootstrap fashion that does not require a PTC or full calibrations? (bool, default False)

doBrighterFatter#: Apply the brighter-fatter correction? (bool, default True)

doCalculateStatistics#: Should additional ISR statistics be calculated? (bool, default True)

doCheckUnprocessableData#: Check if this image is completely unprocessable due to all bad amps. (bool, default True)

doCorrectGains#: Apply gain corrections from detector restarts? (bool, default True)

doCrosstalk#: Apply intra-CCD crosstalk correction? (bool, default True)

doDark#: Apply dark frame correction. (bool, default True)

doDefect#: Apply correction for CCD defects, e.g. hot pixels? (bool, default True)

doDeferredCharge#: Apply deferred charge correction? (bool, default True)

doDiffNonLinearCorrection#: Do differential non-linearity correction? (bool, default False)

doE2VEdgeBleedMask#: Mask flag-like edge bleeds from saturated columns in E2V amplifiers. (bool, default True)

doFlat#: Apply flat field correction. (bool, default True)

doHeaderProvenance#: Write calibration identifiers into output exposure header. (bool, default True)

doITLDipMask#: Apply ITL dip masking. The itlDipMaskPlane mask plane will be added even if this configuration is False. (bool, default True)

doITLEdgeBleedMask#: Mask edge bleeds from saturated columns in ITL amplifiers. (bool, default True)

doITLSatSagMask#: Mask columns presenting saturation sag. (bool, default True)

doInterpolate#: Interpolate masked pixels? (bool, default True)

doLinearize#: Correct for nonlinearity of the detector’s response? (bool, default True)

doNanMasking#: Mask non-finite (NAN, inf) pixels. The UNMASKEDNAN mask plane will be added even if this configuration is False. (bool, default True)

doRaiseOnCalibMismatch#: Should IsrTaskLSST halt if exposure and calibration header values do not match? (bool, default False)

doSaturation#: Mask saturated pixels? NB: this is totally independent of the interpolation option - this is ONLY setting the bits in the mask. To have them interpolated make sure doInterpolate=True and maskListToInterpolate includes SAT. (bool, default True)

doSaveInterpPixels#: Save a copy of the pre-interpolated pixel values? (bool, default False)

doSetBadRegions#: Should we set the level of all BAD patches of the chip to the chip’s average value? (bool, default True)

doStandardStatistics#: Should standard image quality statistics be calculated? (bool, default True)

doSuspect#: Mask suspect pixels? (bool, default True)

doVariance#: Calculate variance? (bool, default True)

doWidenSaturationTrails#: Widen bleed trails based on their width. (bool, default False)

e2vEdgeBleedSatMaxArea#: Maximum limit of saturated cores footprint area to apply edgebleed masking in E2V amplifiers. (int, default 100000)

e2vEdgeBleedSatMinArea#: Minimum limit of saturated cores footprint area to apply edgebleed masking in E2V amplifiers. (int, default 10000)

e2vEdgeBleedYMax#: Height in pixels of edge bleed masking in E2V amplifiers (widthis the width of the amplifier). (int, default 350)

expectWcs#: Expect input science images to have a WCS (set False for e.g. spectrographs). (bool, default True)

flatScalingType#

The method for scaling the flat on the fly. (str, default 'USER')

Allowed values:

'USER': Scale by flatUserScale
'MEAN': Scale by the inverse of the mean
'MEDIAN': Scale by the inverse of the median
'None': Field is optional

flatUserScale#: If flatScalingType is ‘USER’ then scale flat by this amount; ignored otherwise. (float, default 1.0)

growSaturationFootprintSize#: Number of pixels by which to grow the saturation footprints. (int, default 1)

hvBiasKeyword#: Back-side bias voltage on/off header keyword. Only checked if doCheckUnprocessableData is True and bssVoltageMinimum is greater than 0. (str, default 'HVBIAS')

isrStats#: Task to calculate additional statistics. (ConfigurableInstance, default <class 'lsst.ip.isr.isrStatistics.IsrStatisticsTaskConfig'>)

itlDipMaskPlanes#: Mask plane to use for ITL dip pixels. (List, default ['SUSPECT', 'ITL_DIP'])

itlEdgeBleedModelConstant#: Constant in the edge bleed exponential decay model. (float, default 0.02)

itlEdgeBleedSatMaxArea#: Maximum limit for saturated cores footprint area. (int, default 100000)

itlEdgeBleedSatMinArea#: Minimum limit for saturated cores footprint area. (int, default 10000)

itlEdgeBleedThreshold#: Sky background threshold for edge bleed detection. (float, default 5000.0)

maskListToInterpolate#: List of mask planes that should be interpolated. (List, default ['SAT', 'BAD', 'UNMASKEDNAN'])

maskNegativeVariance#: Mask pixels that claim a negative variance. This likely indicates a failure in the measurement of the overscan at an edge due to the data falling off faster than the overscan model can account for it. (bool, default True)

masking#: Masking task. (ConfigurableInstance, default <class 'lsst.ip.isr.masking.MaskingConfig'>)

negativeVarianceMaskName#: Mask plane to use to mark pixels with negative variance, if maskNegativeVariance is True. (str, default 'BAD')

overscanCamera#: Per-detector and per-amplifier overscan configurations. (OverscanCameraConfig, default <class 'lsst.ip.isr.overscanAmpConfig.OverscanCameraConfig'>)

qa#: QA related configuration options. (IsrQaConfig, default <class 'lsst.ip.isr.isrQa.IsrQaConfig'>)

saturatedMaskName#: Name of mask plane to use in saturation detection and interpolation. (str, default 'SAT')

saveLogOutput#: Flag to enable/disable saving of log output for a task, enabled by default. (bool, default True)

serialOverscanMedianShiftSigmaThreshold#: Number of sigma difference from per-amp overscan median (as compared to PTC) to check if an amp is in a different state than the baseline PTC calib and should be marked BAD. Set to np.inf/np.nan to turn off overscan median checking. (float, default inf)

suspectMaskName#: Name of mask plane to use for suspect pixels. (str, default 'SUSPECT')

useGainsFrom#

Where to retrieve the gains. Unused if doBootstrap is True. (str, default 'PTC')

Allowed values:

'PTC': Use the gains from the inputPtc calibration.
'LINEARIZER': Use the gains from the linearizer calibration.
'None': Field is optional

useLegacyInterp#: Use the legacy interpolation algorithm. If False use Gaussian Process. (bool, default True)

Methods Documentation

setDefaults()#: Subclass hook for computing defaults.

Notes#

Derived Config classes that must compute defaults rather than using the Field instances’s defaults should do so here. To correctly use inherited defaults, implementations of setDefaults must call their base class’s setDefaults.

validate()#

Validate the Config, raising an exception if invalid.

Raises#

lsst.pex.config.FieldValidationError: Raised if verification fails.

Notes#

The base class implementation performs type checks on all fields by calling their validate methods.

Complex single-field validation can be defined by deriving new Field types. For convenience, some derived lsst.pex.config.Field-types (ConfigField and ConfigChoiceField) are defined in lsst.pex.config that handle recursing into subconfigs.

Inter-field relationships should only be checked in derived Config classes after calling this method, and base validation is complete.