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

`ampOffset`	Amp offset correction task.
`assembleCcd`	CCD assembly task.
`binFactor1`	Binning factor for first binned exposure.
`binFactor2`	Binning factor for second binned exposure.
`brighterFatterApplyGain`	Should the gain be applied when applying the brighter-fatter correction? (`bool`, default `True`)
`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.
`brighterFatterThreshold`	Threshold used to stop iterating the brighter-fatter correction.
`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.
`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`)
`doCorrectGains`	Apply temperature correction to the gains? (`bool`, default `False`)
`doCrosstalk`	Apply intra-CCD crosstalk correction? (`bool`, default `True`)
`doDark`	Apply dark frame correction.
`doDefect`	Apply correction for CCD defects, e.g.
`doDeferredCharge`	Apply deferred charge correction? (`bool`, default `True`)
`doDiffNonLinearCorrection`	Do differential non-linearity correction? (`bool`, default `False`)
`doFlat`	Apply flat field correction.
`doHeaderProvenance`	Write calibration identifiers into output exposure header.
`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 `False`)
`doVariance`	Calculate variance? (`bool`, default `True`)
`doWidenSaturationTrails`	Widen bleed trails based on their width.
`expectWcs`	Expect input science images to have a WCS (set False for e.g.
`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.
`history`
`isrStats`	Task to calculate additional statistics.
`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.
`nominalGain`	Nominal gain to use if no PTC is supplied.
`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.
`suspectMaskName`	Name of mask plane to use for suspect pixels.

Methods Summary

`applyConfigOverrides`(instrument, ...)	Apply config overrides to this config instance.
`compare`(other[, shortcut, rtol, atol, output])	Compare this configuration to another `Config` for equality.
`formatHistory`(name, **kwargs)	Format a configuration field's history to a human-readable format.
`freeze`()	Make this config, and all subconfigs, read-only.
`items`()	Get configurations as `(field name, field value)` pairs.
`keys`()	Get field names.
`load`(filename[, root])	Modify this config in place by executing the Python code in a configuration file.
`loadFromStream`(stream[, root, filename, ...])	Modify this Config in place by executing the Python code in the provided stream.
`loadFromString`(code[, root, filename, ...])	Modify this Config in place by executing the Python code in the provided string.
`names`()	Get all the field names in the config, recursively.
`save`(filename[, root])	Save a Python script to the named file, which, when loaded, reproduces this config.
`saveToStream`(outfile[, root, skipImports])	Save a configuration file to a stream, which, when loaded, reproduces this config.
`saveToString`([skipImports])	Return the Python script form of this configuration as an executable string.
`setDefaults`()	Subclass hook for computing defaults.
`toDict`()	Make a dictionary of field names and their values.
`update`(**kw)	Update values of fields specified by the keyword arguments.
`validate`()	Validate the Config, raising an exception if invalid.
`values`()	Get field values.

Attributes Documentation

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'>)

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)

brighterFatterApplyGain¶: Should the gain be applied when applying the brighter-fatter correction? (bool, default True)

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 0)

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. (int, default 10)

brighterFatterThreshold¶: Threshold used to stop iterating the brighter-fatter correction. 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)

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'>)

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)

doCorrectGains¶: Apply temperature correction to the gains? (bool, default False)

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)

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

doHeaderProvenance¶: Write calibration identifiers into output exposure header. (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. (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 doSaturationInterpolation=True (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 False)

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

doWidenSaturationTrails¶: Widen bleed trails based on their width. (bool, default True)

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)

history¶: Read-only history.

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

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

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')

nominalGain¶: Nominal gain to use if no PTC is supplied. (float, default 1.7)

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)

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

Methods Documentation

applyConfigOverrides(instrument: Instrument | None, taskDefaultName: str, pipelineConfigs: Iterable[ConfigIR] | None, parameters: ParametersIR, label: str) → None¶

Apply config overrides to this config instance.

Parameters:

instrumentInstrument or None: An instance of the Instrument specified in a pipeline. If None then the pipeline did not specify and instrument.
taskDefaultNamestr: The default name associated with the Task class. This may be used with instrumental overrides.
pipelineConfigsIterable of ConfigIR: An iterable of ConfigIR objects that contain overrides to apply to this config instance.
parametersParametersIR: Parameters defined in a Pipeline which are used in formatting of config values across multiple Task in a pipeline.
labelstr: The label associated with this class’s Task in a pipeline.

compare(other, shortcut=True, rtol=1e-08, atol=1e-08, output=None)¶

Compare this configuration to another Config for equality.

Parameters:

otherlsst.pex.config.Config: Other Config object to compare against this config.
shortcutbool, optional: If True, return as soon as an inequality is found. Default is True.
rtolfloat, optional: Relative tolerance for floating point comparisons.
atolfloat, optional: Absolute tolerance for floating point comparisons.
outputcallable, optional: A callable that takes a string, used (possibly repeatedly) to report inequalities.

Returns:

isEqualbool: True when the two lsst.pex.config.Config instances are equal. False if there is an inequality.

See also

lsst.pex.config.compareConfigs

Notes

Unselected targets of RegistryField fields and unselected choices of ConfigChoiceField fields are not considered by this method.

Floating point comparisons are performed by numpy.allclose.

formatHistory(name, **kwargs)¶

Format a configuration field’s history to a human-readable format.

Parameters:

namestr: Name of a Field in this config.
**kwargs: Keyword arguments passed to lsst.pex.config.history.format.

Returns:

historystr: A string containing the formatted history.

See also

lsst.pex.config.history.format

freeze()¶: Make this config, and all subconfigs, read-only.

items()¶

Get configurations as (field name, field value) pairs.

Returns:

itemsItemsView

Iterator of tuples for each configuration. Tuple items are:

Field name.
Field value.

keys()¶

Get field names.

Returns:

namesKeysView: List of lsst.pex.config.Field names.

load(filename, root='config')¶

Modify this config in place by executing the Python code in a configuration file.

Parameters:

filenamestr

Name of the configuration file. A configuration file is Python module.

rootstr, optional

Name of the variable in file that refers to the config being overridden.

For example, the value of root is "config" and the file contains:

config.myField = 5

Then this config’s field myField is set to 5.

See also

lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString
lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString

loadFromStream(stream, root='config', filename=None, extraLocals=None)¶

Modify this Config in place by executing the Python code in the provided stream.

Parameters:

streamfile-like object, str, bytes, or CodeType

Stream containing configuration override code. If this is a code object, it should be compiled with mode="exec".

rootstr, optional

Name of the variable in file that refers to the config being overridden.

For example, the value of root is "config" and the file contains:

config.myField = 5

Then this config’s field myField is set to 5.

filenamestr, optional

Name of the configuration file, or None if unknown or contained in the stream. Used for error reporting.

extraLocalsdict of str to object, optional

Any extra variables to include in local scope when loading.

See also

lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromString
lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString

Notes

For backwards compatibility reasons, this method accepts strings, bytes and code objects as well as file-like objects. New code should use loadFromString instead for most of these types.

loadFromString(code, root='config', filename=None, extraLocals=None)¶

Modify this Config in place by executing the Python code in the provided string.

Parameters:

codestr, bytes, or CodeType

Stream containing configuration override code.

rootstr, optional

Name of the variable in file that refers to the config being overridden.

For example, the value of root is "config" and the file contains:

config.myField = 5

Then this config’s field myField is set to 5.

filenamestr, optional

Name of the configuration file, or None if unknown or contained in the stream. Used for error reporting.

extraLocalsdict of str to object, optional

Any extra variables to include in local scope when loading.

Raises:

ValueError: Raised if a key in extraLocals is the same value as the value of the root argument.

See also

lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString

names()¶

Get all the field names in the config, recursively.

Returns:

nameslist of str: Field names.

save(filename, root='config')¶

Save a Python script to the named file, which, when loaded, reproduces this config.

Parameters:

filenamestr: Desination filename of this configuration.
rootstr, optional: Name to use for the root config variable. The same value must be used when loading (see lsst.pex.config.Config.load).

See also

lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.saveToString
lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString

saveToStream(outfile, root='config', skipImports=False)¶

Save a configuration file to a stream, which, when loaded, reproduces this config.

Parameters:

outfilefile-like object: Destination file object write the config into. Accepts strings not bytes.
rootstr, optional: Name to use for the root config variable. The same value must be used when loading (see lsst.pex.config.Config.load).
skipImportsbool, optional: If True then do not include import statements in output, this is to support human-oriented output from pipetask where additional clutter is not useful.

See also

lsst.pex.config.Config.save
lsst.pex.config.Config.saveToString
lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString

saveToString(skipImports=False)¶

Return the Python script form of this configuration as an executable string.

Parameters:

skipImportsbool, optional: If True then do not include import statements in output, this is to support human-oriented output from pipetask where additional clutter is not useful.

Returns:

codestr: A code string readable by loadFromString.

See also

lsst.pex.config.Config.save
lsst.pex.config.Config.saveToStream
lsst.pex.config.Config.load
lsst.pex.config.Config.loadFromStream
lsst.pex.config.Config.loadFromString

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.

toDict()¶

Make a dictionary of field names and their values.

Returns:

dict_dict: Dictionary with keys that are Field names. Values are Field values.

See also

lsst.pex.config.Field.toDict

Notes

This method uses the toDict method of individual fields. Subclasses of Field may need to implement a toDict method for this method to work.

update(**kw)¶

Update values of fields specified by the keyword arguments.

Parameters:

**kw: Keywords are configuration field names. Values are configuration field values.

Notes

The __at and __label keyword arguments are special internal keywords. They are used to strip out any internal steps from the history tracebacks of the config. Do not modify these keywords to subvert a Config instance’s history.

Examples

This is a config with three fields:

>>> from lsst.pex.config import Config, Field
>>> class DemoConfig(Config):
...     fieldA = Field(doc='Field A', dtype=int, default=42)
...     fieldB = Field(doc='Field B', dtype=bool, default=True)
...     fieldC = Field(doc='Field C', dtype=str, default='Hello world')
...
>>> config = DemoConfig()

These are the default values of each field:

>>> for name, value in config.iteritems():
...     print(f"{name}: {value}")
...
fieldA: 42
fieldB: True
fieldC: 'Hello world'

Using this method to update fieldA and fieldC:

>>> config.update(fieldA=13, fieldC='Updated!')

Now the values of each field are:

>>> for name, value in config.iteritems():
...     print(f"{name}: {value}")
...
fieldA: 13
fieldB: True
fieldC: 'Updated!'

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.

values()¶

Get field values.

Returns:

valuesValuesView: Iterator of field values.

Navigation

IsrTaskLSSTConfig¶