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.
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)

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. (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:

0. Field name.

1. 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.