SafeClipAssembleCoaddConfig¶

class lsst.pipe.tasks.assembleCoadd.SafeClipAssembleCoaddConfig(*args, **kw)¶

Bases: AssembleCoaddConfig

Configuration parameters for the SafeClipAssembleCoaddTask.

Attributes Summary

`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`)
`clipDetection`	Detect sources on difference between unclipped and clipped coadd (`ConfigurableInstance`, default `<class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>`)
`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`	Field which refers to a dynamically added configuration class which is based on a PipelineTaskConnections class.
`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).
`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`)
`doPsfMatch`	Match to modelPsf? Deprecated.
`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.
`matchingKernelSize`	Size in pixels of matching kernel.
`maxClipFootOverlapDouble`	Maximum fractional overlap of clipped footprints with visit DETECTED when considering two visits (`float`, default `0.15`)
`minBigOverlap`	Minimum number of pixels in footprint to use DETECTED mask from the single visits when labeling clipped footprints (`int`, default `100`)
`minClipFootOverlap`	Minimum fractional overlap of clipped footprint with visit DETECTED to be clipped (`float`, default `0.6`)
`minClipFootOverlapDouble`	Minimum fractional overlap of clipped footprints with visit DETECTED to be clipped when two visits overlap (`float`, default `0.45`)
`minClipFootOverlapSingle`	Minimum fractional overlap of clipped footprint with visit DETECTED to be clipped when only one visit overlaps (`float`, default `0.5`)
`modelPsf`	Model Psf factory (`ConfigurableInstance`, default `<class 'lsst.meas.algorithms.gaussianPsfFactory.GaussianPsfFactory'>`)
`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.
`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.
`statistic`	Main stacking statistic for aggregating over the epochs.
`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.
`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`()	Set default values for clipDetection.
`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

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)

clipDetection¶: Detect sources on difference between unclipped and clipped coadd (ConfigurableInstance, default <class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>)

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

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)

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)

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

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¶: Read-only 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})

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

maxClipFootOverlapDouble¶: Maximum fractional overlap of clipped footprints with visit DETECTED when considering two visits (float, default 0.15)

minBigOverlap¶: Minimum number of pixels in footprint to use DETECTED mask from the single visits when labeling clipped footprints (int, default 100)

minClipFootOverlap¶: Minimum fractional overlap of clipped footprint with visit DETECTED to be clipped (float, default 0.6)

minClipFootOverlapDouble¶: Minimum fractional overlap of clipped footprints with visit DETECTED to be clipped when two visits overlap (float, default 0.45)

minClipFootOverlapSingle¶: Minimum fractional overlap of clipped footprint with visit DETECTED to be clipped when only one visit overlaps (float, default 0.5)

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

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)

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)

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

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 True)

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:

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:

itemsdict_items

Iterator of tuples for each configuration. Tuple items are:

Field name.
Field value.

keys()¶

Get field names.

Returns:

namesdict_keys: 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:

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)¶

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

Parameters:

streamfile-like object, str, bytes, or compiled string

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.

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)¶

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

Parameters:

codestr, bytes, or compiled string

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.

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.
root: 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()¶

Set default values for clipDetection.

Notes

The numeric values for these configuration parameters were empirically determined, future work may further refine them.

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:

valuesdict_values: Iterator of field values.

Navigation

SafeClipAssembleCoaddConfig¶