CompareWarpAssembleCoaddConfig¶

class lsst.pipe.tasks.assembleCoadd.CompareWarpAssembleCoaddConfig¶

Bases: lsst.pipe.tasks.assembleCoadd.AssembleCoaddConfig

Attributes Summary

`assembleStaticSkyModel`	Task to assemble an artifact-free, PSF-matched Coadd to serve as a naive/first-iteration model of the static sky.
`badMaskPlanes`	Mask planes that, if set, the associated pixel should not be included in the coaddTempExp.
`brightObjectMaskName`	Name of mask bit used for bright objects (`str`, default `'BRIGHT_OBJECT'`)
`calcErrorFromInputVariance`	Calculate coadd variance from input variance by stacking statistic.Passed to StatisticsControl.setCalcErrorFromInputVariance() (`bool`, default `True`)
`clipIter`	Number of iterations of outlier rejection; ignored if non-clipping statistic selected.
`coaddName`	Coadd name: typically one of deep or goodSeeing.
`coaddPsf`	Configuration for CoaddPsf (`CoaddPsfConfig`, default `<class 'lsst.meas.algorithms.coaddPsf.coaddPsf.CoaddPsfConfig'>`)
`connections`	Configurations describing the connections of the PipelineTask to datatypes (`Connections`, default `<class 'lsst.pipe.base.config.Connections'>`)
`detect`	Detect outlier sources on difference between each psfMatched warp and static sky model (`ConfigurableInstance`, default `<class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>`)
`detectTemplate`	Detect sources on static sky model.
`doApplyExternalPhotoCalib`	Whether to apply external photometric calibration via an `lsst.afw.image.PhotoCalib` object.
`doApplyExternalSkyWcs`	Whether to apply external astrometric calibration via an `lsst.afw.geom.SkyWcs` object.
`doAttachTransmissionCurve`	Attach a piecewise TransmissionCurve for the coadd? (requires all input Exposures to have TransmissionCurves).
`doFilterMorphological`	Filter artifact candidates based on morphological criteria, i.g.
`doInputMap`	Create a bitwise map of coadd inputs (`bool`, default `False`)
`doInterp`	Interpolate over NaN pixels? Also extrapolate, if necessary, but the results are ugly.
`doMaskBrightObjects`	Set mask and flag bits for bright objects? (`bool`, default `False`)
`doNImage`	Create image of number of contributing exposures for each pixel (`bool`, default `False`)
`doOnlineForMean`	Perform online coaddition when statistic=”MEAN” to save memory? (`bool`, default `False`)
`doPrefilterArtifacts`	Ignore artifact candidates that are mostly covered by the bad pixel mask, because they will be excluded anyway.
`doPreserveContainedBySource`	Rescue artifacts from clipping that completely lie within a footprint detectedon the PsfMatched Template Coadd.
`doPsfMatch`	Match to modelPsf? Deprecated.
`doScaleWarpVariance`	Rescale Warp variance plane using empirical noise? (`bool`, default `True`)
`doSelectVisits`	Coadd only visits selected by a SelectVisitsTask (`bool`, default `False`)
`doSigmaClip`	Perform sigma clipped outlier rejection with MEANCLIP statistic? (DEPRECATED) (`bool`, default `False`)
`doUsePsfMatchedPolygons`	Use ValidPolygons from shrunk Psf-Matched Calexps? Should be set to True by CompareWarp only.
`doWrite`	Persist coadd? (`bool`, default `True`)
`externalPhotoCalibName`	Type of external PhotoCalib if `doApplyExternalPhotoCalib` is True.
`externalSkyWcsName`	Type of external SkyWcs if `doApplyExternalSkyWcs` is True.
`hasFakes`	Should be set to True if fake sources have been inserted into the input data.
`history`
`includeCalibVar`	Add photometric calibration variance to warp variance plane.
`inputMapper`	Input map creation subtask.
`inputRecorder`	Subtask that helps fill CoaddInputs catalogs added to the final Exposure (`ConfigurableInstance`, default `<class 'lsst.pipe.tasks.coaddInputRecorder.CoaddInputRecorderConfig'>`)
`interpImage`	Task to interpolate (and extrapolate) over NaN pixels (`ConfigurableInstance`, default `<class 'lsst.pipe.tasks.interpImage.InterpImageConfig'>`)
`maskPropagationThresholds`	Threshold (in fractional weight) of rejection at which we propagate a mask plane to the coadd; that is, we set the mask bit on the coadd if the fraction the rejected frames would have contributed exceeds this value.
`maskStreaks`	Detect streaks on difference between each psfMatched warp and static sky model.
`matchingKernelSize`	Size in pixels of matching kernel.
`maxFractionEpochsHigh`	Fraction of local number of epochs (N) to use as effective maxNumEpochs for high N.
`maxFractionEpochsLow`	Fraction of local number of epochs (N) to use as effective maxNumEpochs for low N.
`maxNumEpochs`	Charactistic maximum local number of epochs/visits in which an artifact candidate can appear and still be masked.
`modelPsf`	Model Psf factory (`ConfigurableInstance`, default `<class 'lsst.meas.algorithms.gaussianPsfFactory.GaussianPsfFactory'>`)
`prefilterArtifactsMaskPlanes`	Prefilter artifact candidates that are mostly covered by these bad mask planes.
`prefilterArtifactsRatio`	Prefilter artifact candidates with less than this fraction overlapping good pixels (`float`, default `0.05`)
`removeMaskPlanes`	Mask planes to remove before coadding (`List`, default `['NOT_DEBLENDED']`)
`saveLogOutput`	Flag to enable/disable saving of log output for a task, enabled by default.
`saveMetadata`	Flag to enable/disable metadata saving for a task, enabled by default.
`scaleWarpVariance`	Rescale variance on warps (`ConfigurableInstance`, default `<class 'lsst.pipe.tasks.scaleVariance.ScaleVarianceConfig'>`)
`scaleZeroPoint`	Task to adjust the photometric zero point of the coadd temp exposures (`ConfigurableInstance`, default `<class 'lsst.pipe.tasks.scaleZeroPoint.ScaleZeroPointConfig'>`)
`select`	Image selection subtask.
`sigmaClip`	Sigma for outlier rejection; ignored if non-clipping statistic selected.
`spatialThreshold`	Unitless fraction of pixels defining how much of the outlier region has to meet the temporal criteria.
`statistic`	Main stacking statistic for aggregating over the epochs.
`streakMaskName`	Name of mask bit used for streaks (`str`, default `'STREAK'`)
`subregionSize`	Width, height of stack subregion size; make small enough that a full stack of images will fit into memory at once.
`useGlobalExternalPhotoCalib`	When using doApplyExternalPhotoCalib, use ‘global’ calibrations that are not run per-tract.
`useGlobalExternalSkyWcs`	When using doApplyExternalSkyWcs, use ‘global’ calibrations that are not run per-tract.
`warpType`	Warp name: one of ‘direct’ or ‘psfMatched’ (`str`, default `'direct'`)

Methods Summary

`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.
`iteritems`()	Iterate over (field name, field value) pairs.
`iterkeys`()	Iterate over field names
`itervalues`()	Iterate over field values.
`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.
`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.
`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

assembleStaticSkyModel¶: Task to assemble an artifact-free, PSF-matched Coadd to serve as a naive/first-iteration model of the static sky. (ConfigurableInstance, default <class 'lsst.pipe.tasks.assembleCoadd.AssembleCoaddConfig'>)

badMaskPlanes¶: Mask planes that, if set, the associated pixel should not be included in the coaddTempExp. (List, default ('NO_DATA',))

brightObjectMaskName¶: Name of mask bit used for bright objects (str, default 'BRIGHT_OBJECT')

calcErrorFromInputVariance¶: Calculate coadd variance from input variance by stacking statistic.Passed to StatisticsControl.setCalcErrorFromInputVariance() (bool, default True)

clipIter¶: Number of iterations of outlier rejection; ignored if non-clipping statistic selected. (int, default 2)

coaddName¶: Coadd name: typically one of deep or goodSeeing. (str, default 'deep')

coaddPsf¶: Configuration for CoaddPsf (CoaddPsfConfig, default <class 'lsst.meas.algorithms.coaddPsf.coaddPsf.CoaddPsfConfig'>)

connections¶: Configurations describing the connections of the PipelineTask to datatypes (Connections, default <class 'lsst.pipe.base.config.Connections'>)

detect¶: Detect outlier sources on difference between each psfMatched warp and static sky model (ConfigurableInstance, default <class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>)

detectTemplate¶: Detect sources on static sky model. Only used if doPreserveContainedBySource is True (ConfigurableInstance, default <class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>)

doApplyExternalPhotoCalib¶: Whether to apply external photometric calibration via an lsst.afw.image.PhotoCalib object. Uses the externalPhotoCalibName field to determine which calibration to load. (bool, default False)

doApplyExternalSkyWcs¶: Whether to apply external astrometric calibration via an lsst.afw.geom.SkyWcs object. Uses externalSkyWcsName field to determine which calibration to load. (bool, default False)

doAttachTransmissionCurve¶: Attach a piecewise TransmissionCurve for the coadd? (requires all input Exposures to have TransmissionCurves). (bool, default False)

doFilterMorphological¶: Filter artifact candidates based on morphological criteria, i.g. those that appear to be streaks. (bool, default False)

doInputMap¶: Create a bitwise map of coadd inputs (bool, default False)

doInterp¶: Interpolate over NaN pixels? Also extrapolate, if necessary, but the results are ugly. (bool, default True)

doMaskBrightObjects¶: Set mask and flag bits for bright objects? (bool, default False)

doNImage¶: Create image of number of contributing exposures for each pixel (bool, default False)

doOnlineForMean¶: Perform online coaddition when statistic=”MEAN” to save memory? (bool, default False)

doPrefilterArtifacts¶: Ignore artifact candidates that are mostly covered by the bad pixel mask, because they will be excluded anyway. This prevents them from contributing to the outlier epoch count image and potentially being labeled as persistant.’Mostly’ is defined by the config ‘prefilterArtifactsRatio’. (bool, default True)

doPreserveContainedBySource¶: Rescue artifacts from clipping that completely lie within a footprint detectedon the PsfMatched Template Coadd. Replicates a behavior of SafeClip. (bool, default True)

doPsfMatch¶: Match to modelPsf? Deprecated. Sets makePsfMatched=True, makeDirect=False (bool, default False)

doScaleWarpVariance¶: Rescale Warp variance plane using empirical noise? (bool, default True)

doSelectVisits¶: Coadd only visits selected by a SelectVisitsTask (bool, default False)

doSigmaClip¶: Perform sigma clipped outlier rejection with MEANCLIP statistic? (DEPRECATED) (bool, default False)

doUsePsfMatchedPolygons¶: Use ValidPolygons from shrunk Psf-Matched Calexps? Should be set to True by CompareWarp only. (bool, default False)

doWrite¶: Persist coadd? (bool, default True)

externalPhotoCalibName¶

Type of external PhotoCalib if doApplyExternalPhotoCalib is True. This field is only used for Gen2 middleware. (str, default 'jointcal')

Allowed values:

'jointcal': Use jointcal_photoCalib
'fgcm': Use fgcm_photoCalib
'fgcm_tract': Use fgcm_tract_photoCalib
'None': Field is optional

externalSkyWcsName¶

Type of external SkyWcs if doApplyExternalSkyWcs is True. This field is only used for Gen2 middleware. (str, default 'jointcal')

Allowed values:

'jointcal': Use jointcal_wcs
'None': Field is optional

hasFakes¶: Should be set to True if fake sources have been inserted into the input data. (bool, default False)

history¶

includeCalibVar¶: Add photometric calibration variance to warp variance plane. (bool, default False)

inputMapper¶: Input map creation subtask. (ConfigurableInstance, default <class 'lsst.pipe.tasks.healSparseMapping.HealSparseInputMapConfig'>)

inputRecorder¶: Subtask that helps fill CoaddInputs catalogs added to the final Exposure (ConfigurableInstance, default <class 'lsst.pipe.tasks.coaddInputRecorder.CoaddInputRecorderConfig'>)

interpImage¶: Task to interpolate (and extrapolate) over NaN pixels (ConfigurableInstance, default <class 'lsst.pipe.tasks.interpImage.InterpImageConfig'>)

maskPropagationThresholds¶: Threshold (in fractional weight) of rejection at which we propagate a mask plane to the coadd; that is, we set the mask bit on the coadd if the fraction the rejected frames would have contributed exceeds this value. (Dict, default {'SAT': 0.1})

maskStreaks¶: Detect streaks on difference between each psfMatched warp and static sky model. Only used if doFilterMorphological is True. Adds a mask plane to an exposure, with the mask plane name set bystreakMaskName (ConfigurableInstance, default <class 'lsst.pipe.tasks.maskStreaks.MaskStreaksConfig'>)

matchingKernelSize¶: Size in pixels of matching kernel. Must be odd. (int, default 21)

maxFractionEpochsHigh¶

Fraction of local number of epochs (N) to use as effective maxNumEpochs for high N. Effective maxNumEpochs = min(maxFractionEpochsLow * N, maxNumEpochs + maxFractionEpochsHigh * N) (float, default 0.03)

Valid Range = [0.0,1.0)

maxFractionEpochsLow¶

Fraction of local number of epochs (N) to use as effective maxNumEpochs for low N. Effective maxNumEpochs = min(maxFractionEpochsLow * N, maxNumEpochs + maxFractionEpochsHigh * N) (float, default 0.4)

Valid Range = [0.0,1.0)

maxNumEpochs¶: Charactistic maximum local number of epochs/visits in which an artifact candidate can appear and still be masked. The effective maxNumEpochs is a broken linear function of local number of epochs (N): min(maxFractionEpochsLow*N, maxNumEpochs + maxFractionEpochsHigh*N). For each footprint detected on the image difference between the psfMatched warp and static sky model, if a significant fraction of pixels (defined by spatialThreshold) are residuals in more than the computed effective maxNumEpochs, the artifact candidate is deemed persistant rather than transient and not masked. (int, default 2)

modelPsf¶: Model Psf factory (ConfigurableInstance, default <class 'lsst.meas.algorithms.gaussianPsfFactory.GaussianPsfFactory'>)

prefilterArtifactsMaskPlanes¶: Prefilter artifact candidates that are mostly covered by these bad mask planes. (List, default ('NO_DATA', 'BAD', 'SAT', 'SUSPECT'))

prefilterArtifactsRatio¶: Prefilter artifact candidates with less than this fraction overlapping good pixels (float, default 0.05)

removeMaskPlanes¶: Mask planes to remove before coadding (List, default ['NOT_DEBLENDED'])

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

saveMetadata¶: Flag to enable/disable metadata saving for a task, enabled by default. (bool, default True)

scaleWarpVariance¶: Rescale variance on warps (ConfigurableInstance, default <class 'lsst.pipe.tasks.scaleVariance.ScaleVarianceConfig'>)

scaleZeroPoint¶: Task to adjust the photometric zero point of the coadd temp exposures (ConfigurableInstance, default <class 'lsst.pipe.tasks.scaleZeroPoint.ScaleZeroPointConfig'>)

select¶: Image selection subtask. (ConfigurableInstance, default <class 'lsst.pex.config.config.Config'>)

sigmaClip¶: Sigma for outlier rejection; ignored if non-clipping statistic selected. (float, default 3.0)

spatialThreshold¶

Unitless fraction of pixels defining how much of the outlier region has to meet the temporal criteria. If 0, clip all. If 1, clip none. (float, default 0.5)

Valid Range = [0.0,1.0]

statistic¶: Main stacking statistic for aggregating over the epochs. (str, default 'MEANCLIP')

streakMaskName¶: Name of mask bit used for streaks (str, default 'STREAK')

subregionSize¶: Width, height of stack subregion size; make small enough that a full stack of images will fit into memory at once. (List, default (2000, 2000))

useGlobalExternalPhotoCalib¶: When using doApplyExternalPhotoCalib, use ‘global’ calibrations that are not run per-tract. When False, use per-tract photometric calibration files. (bool, default True)

useGlobalExternalSkyWcs¶: When using doApplyExternalSkyWcs, use ‘global’ calibrations that are not run per-tract. When False, use per-tract wcs files. (bool, default False)

warpType¶: Warp name: one of ‘direct’ or ‘psfMatched’ (str, default 'direct')

Methods Documentation

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

Compare this configuration to another Config for equality.

Parameters:

other : lsst.pex.config.Config: Other Config object to compare against this config.
shortcut : bool, optional: If True, return as soon as an inequality is found. Default is True.
rtol : float, optional: Relative tolerance for floating point comparisons.
atol : float, optional: Absolute tolerance for floating point comparisons.
output : callable, optional: A callable that takes a string, used (possibly repeatedly) to report inequalities.

Returns:

isEqual : bool: 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:	name : `str` Name of a `Field` in this config. kwargs Keyword arguments passed to `lsst.pex.config.history.format`.
Returns:	history : `str` 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:	items : `list` List of tuples for each configuration. Tuple items are: Field name. Field value.

See also

lsst.pex.config.Config.iteritems

iteritems()¶

Iterate over (field name, field value) pairs.

Yields:	item : `tuple` Tuple items are: Field name. Field value.

See also

lsst.pex.config.Config.items

iterkeys()¶

Iterate over field names

Yields:	key : `str` A field’s key (attribute name).

See also

lsst.pex.config.Config.values

itervalues()¶

Iterate over field values.

Yields:	value : obj A field value.

See also

lsst.pex.config.Config.values

keys()¶

Get field names.

Returns:	names : `list` List of `lsst.pex.config.Field` names.

See also

lsst.pex.config.Config.iterkeys

load(filename, root='config')¶

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

Parameters:

filename : str

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

root : str, 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.

Deprecated: For backwards compatibility, older config files that use root="root" instead of root="config" will be loaded with a warning printed to sys.stderr. This feature will be removed at some point.

See also

lsst.pex.config.Config.loadFromStream, lsst.pex.config.Config.save, lsst.pex.config.Config.saveFromStream

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

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

Parameters:

stream : file-like object, str, or compiled string

Stream containing configuration override code.

root : str, 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.

Deprecated: For backwards compatibility, older config files that use root="root" instead of root="config" will be loaded with a warning printed to sys.stderr. This feature will be removed at some point.

filename : str, optional

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

See also

lsst.pex.config.Config.load, lsst.pex.config.Config.save, lsst.pex.config.Config.saveFromStream

names()¶

Get all the field names in the config, recursively.

Returns:	names : `list` of `str` Field names.

save(filename, root='config')¶

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

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

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

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

Parameters:

outfile : file-like object: Destination file object write the config into. Accepts strings not bytes.
root: Name to use for the root config variable. The same value must be used when loading (see lsst.pex.config.Config.load).
skipImports : bool, 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.

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:	values : `list` List of field values.

See also

lsst.pex.config.Config.itervalues

Navigation

CompareWarpAssembleCoaddConfig¶