ScarletDeblendConfig¶

class lsst.meas.extensions.scarlet.ScarletDeblendConfig¶

Bases: lsst.pex.config.Config

MultibandDeblendConfig

Configuration for the multiband deblender. The parameters are organized by the parameter types, which are - Stopping Criteria: Used to determine if the fit has converged - Position Fitting Criteria: Used to fit the positions of the peaks - Constraints: Used to apply constraints to the peaks and their components - Other: Parameters that don’t fit into the above categories

Attributes Summary

`backgroundThresh`	Fraction of background to use for a sparsity threshold.
`badMask`	Whether or not to process isolated sources in the deblender (`List`, default `['BAD', 'CR', 'NO_DATA', 'SAT', 'SUSPECT', 'EDGE']`)
`catchFailures`	If True, catch exceptions thrown by the deblender, log them, and set a flag on the parent, instead of letting them propagate up (`bool`, default `True`)
`ciDeblendChildRange`	Only deblend parent Footprints with a number of peaks in the (inclusive) range indicated.If `useCiLimits==False` then this parameter is ignored.
`ciNumParentsToDeblend`	Only use the first `ciNumParentsToDeblend` parent footprints with a total peak count within `ciDebledChildRange`.
`columnInheritance`	Columns to pass from the parent to the child.
`convolutionType`	Type of convolution to render the model to the observations.
`fallback`	Whether or not to fallback to a smaller number of components if a source does not initialize (`bool`, default `True`)
`history`
`loggingInterval`	Interval (in seconds) to log messages (at VERBOSE level) while deblending sources.
`maskLimits`	Mask planes with the corresponding limit on the fraction of masked pixels.
`maxFootprintArea`	Maximum area for footprints before they are ignored as large; non-positive means no threshold applied (`int`, default `1000000`)
`maxFootprintSize`	Maximum linear dimension for footprints before they are ignored as large; non-positive means no threshold applied (`int`, default `0`)
`maxIter`	Maximum number of iterations to deblend a single parent (`int`, default `300`)
`maxNumberOfPeaks`	Only deblend the brightest maxNumberOfPeaks peaks in the parent (<= 0: unlimited) (`int`, default `0`)
`maxProxIter`	Maximum number of proximal operator iterations inside of each iteration of the optimizer.
`maxSpectrumCutoff`	Maximum number of pixels * number of sources in a blend.
`minFootprintAxisRatio`	Minimum axis ratio for footprints before they are ignored as large; non-positive means no threshold applied (`float`, default `0.0`)
`minIter`	Minimum number of iterations before the optimizer is allowed to stop.
`minSNR`	Minimum Signal to noise to accept the source.Sources with lower flux will be initialized with the PSF but updated like an ordinary ExtendedSource (known in scarlet as a `CompactSource`).
`modelPsfSigma`	Define sigma for the model frame PSF (`float`, default `0.8`)
`modelPsfSize`	Model PSF side length in pixels (`int`, default `11`)
`morphImage`	The type of image to use for initializing the morphology.
`morphThresh`	Fraction of background RMS a pixel must haveto be included in the initial morphology (`float`, default `1`)
`notDeblendedMask`	Mask name for footprints not deblended, or None (`str`, default `'NOT_DEBLENDED'`)
`optimizer`	The optimizer to use for fitting parameters and is only used when version=’lite’ (`str`, default `'adaprox'`)
`processSingles`	Whether or not to process isolated sources in the deblender (`bool`, default `True`)
`pseudoColumns`	Names of flags which should never be deblended.
`relativeError`	Change in the loss function between iterations to exit fitter.
`saveTemplates`	Whether or not to save the SEDs and templates (`bool`, default `True`)
`setSpectra`	Whether or not to solve for the best-fit spectra during initialization.
`sourceModel`	How to determine which model to use for sources, from - ‘single’: use a single component for all sources - ‘double’: use a bulge disk model for all sources - ‘compact’: use a single component model, initialzed with a point source morphology, for all sources - ‘point’: use a point-source model for all sources - ‘fit: use a PSF fitting model to determine the number of components (not yet implemented) Deprecated: This field will be deprecated when the default for `version` is changed to `lite`.
`statsMask`	Mask planes to ignore when performing statistics (`List`, default `['SAT', 'INTRP', 'NO_DATA']`)
`useCiLimits`	Limit the number of sources deblended for CI to prevent long build times (`bool`, default `False`)
`useWeights`	Whether or not use use inverse variance weighting.If `useWeights` is `False` then flat weights are used (`bool`, default `True`)
`version`	The version of scarlet to use.
`waveletScales`	Number of wavelet scales to use for wavelet initialization.

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.
`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

backgroundThresh¶: Fraction of background to use for a sparsity threshold. This prevents sources from growing unrealistically outside the parent footprint while still modeling flux correctly for bright sources. (float, default 0.25)

badMask¶: Whether or not to process isolated sources in the deblender (List, default ['BAD', 'CR', 'NO_DATA', 'SAT', 'SUSPECT', 'EDGE'])

catchFailures¶: If True, catch exceptions thrown by the deblender, log them, and set a flag on the parent, instead of letting them propagate up (bool, default True)

ciDeblendChildRange¶: Only deblend parent Footprints with a number of peaks in the (inclusive) range indicated.If useCiLimits==False then this parameter is ignored. (List, default [5, 10])

ciNumParentsToDeblend¶: Only use the first ciNumParentsToDeblend parent footprints with a total peak count within ciDebledChildRange. If useCiLimits==False then this parameter is ignored. (int, default 10)

columnInheritance¶: Columns to pass from the parent to the child. The key is the name of the column for the parent record, the value is the name of the column to use for the child. (Dict, default {'deblend_nChild': 'deblend_parentNChild', 'deblend_nPeaks': 'deblend_parentNPeaks', 'deblend_spectrumInitFlag': 'deblend_spectrumInitFlag', 'deblend_blendConvergenceFailedFlag': 'deblend_blendConvergenceFailedFlag'})

convolutionType¶: Type of convolution to render the model to the observations. - ‘fft’: perform convolutions in Fourier space - ‘real’: peform convolutions in real space. (str, default 'fft')

fallback¶: Whether or not to fallback to a smaller number of components if a source does not initialize (bool, default True)

history¶

loggingInterval¶: Interval (in seconds) to log messages (at VERBOSE level) while deblending sources. (int, default 600)

maskLimits¶: Mask planes with the corresponding limit on the fraction of masked pixels. Sources violating this limit will not be deblended. (Dict, default {})

maxFootprintArea¶: Maximum area for footprints before they are ignored as large; non-positive means no threshold applied (int, default 1000000)

maxFootprintSize¶: Maximum linear dimension for footprints before they are ignored as large; non-positive means no threshold applied (int, default 0)

maxIter¶: Maximum number of iterations to deblend a single parent (int, default 300)

maxNumberOfPeaks¶: Only deblend the brightest maxNumberOfPeaks peaks in the parent (<= 0: unlimited) (int, default 0)

maxProxIter¶: Maximum number of proximal operator iterations inside of each iteration of the optimizer. This config field is only used if version=’lite’ and optimizer=’adaprox’. (int, default 1)

maxSpectrumCutoff¶: Maximum number of pixels * number of sources in a blend. This is different than maxFootprintArea because this isn’t the footprint area but the area of the bounding box that contains the footprint, and is also multiplied by the number ofsources in the footprint. This prevents large skinny blends with a high density of sources from running out of memory. If maxSpectrumCutoff == -1 then there is no cutoff. (int, default 1000000)

minFootprintAxisRatio¶: Minimum axis ratio for footprints before they are ignored as large; non-positive means no threshold applied (float, default 0.0)

minIter¶: Minimum number of iterations before the optimizer is allowed to stop. (int, default 1)

minSNR¶: Minimum Signal to noise to accept the source.Sources with lower flux will be initialized with the PSF but updated like an ordinary ExtendedSource (known in scarlet as a CompactSource). (float, default 50)

modelPsfSigma¶: Define sigma for the model frame PSF (float, default 0.8)

modelPsfSize¶: Model PSF side length in pixels (int, default 11)

morphImage¶

The type of image to use for initializing the morphology. Must be either ‘chi2’ or ‘wavelet’. (str, default 'chi2')

Allowed values:

'chi2': Initialize sources on a chi^2 image made from all available bands
'wavelet': Initialize sources using a wavelet decomposition of the chi^2 image
'None': Field is optional

morphThresh¶: Fraction of background RMS a pixel must haveto be included in the initial morphology (float, default 1)

notDeblendedMask¶: Mask name for footprints not deblended, or None (str, default 'NOT_DEBLENDED')

optimizer¶

The optimizer to use for fitting parameters and is only used when version=’lite’ (str, default 'adaprox')

Allowed values:

'adaprox': Proximal ADAM optimization
'fista': Accelerated proximal gradient method
'None': Field is optional

processSingles¶: Whether or not to process isolated sources in the deblender (bool, default True)

pseudoColumns¶: Names of flags which should never be deblended. (List, default ['merge_peak_sky', 'sky_source'])

relativeError¶: Change in the loss function between iterations to exit fitter. Typically this is 1e-2 if measurements will be made on the flux re-distributed models and 1e-4 when making measurements on the models themselves. (float, default 0.01)

saveTemplates¶: Whether or not to save the SEDs and templates (bool, default True)

setSpectra¶: Whether or not to solve for the best-fit spectra during initialization. This makes initialization slightly longer, as it requires a convolution to set the optimal spectra, but results in a much better initial log-likelihood and reduced total runtime, with convergence in fewer iterations.This option is only used when peaks*area < maxSpectrumCutoff will use the improved initialization. (bool, default True)

sourceModel¶: How to determine which model to use for sources, from - ‘single’: use a single component for all sources - ‘double’: use a bulge disk model for all sources - ‘compact’: use a single component model, initialzed with a point source morphology, for all sources - ‘point’: use a point-source model for all sources - ‘fit: use a PSF fitting model to determine the number of components (not yet implemented) Deprecated: This field will be deprecated when the default for version is changed to lite. (str, default 'double')

statsMask¶: Mask planes to ignore when performing statistics (List, default ['SAT', 'INTRP', 'NO_DATA'])

useCiLimits¶: Limit the number of sources deblended for CI to prevent long build times (bool, default False)

useWeights¶: Whether or not use use inverse variance weighting.If useWeights is False then flat weights are used (bool, default True)

version¶

The version of scarlet to use. (str, default 'lite')

Allowed values:

'scarlet': main scarlet version (likely to be deprecated soon)
'lite': Optimized version of scarlet for survey data from a single instrument
'None': Field is optional

waveletScales¶: Number of wavelet scales to use for wavelet initialization. This field is only used when version`='lite' and `morphImage`='wavelet'. (`int, default 5)

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.

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, bytes, or compiled string

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

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.

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:

code : str, bytes, 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.

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.

saveToString(skipImports=False)¶

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

Parameters:	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.
Returns:	code : `str` A code string readable by `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:	values : `list` List of field values.

See also

lsst.pex.config.Config.itervalues

Navigation

ScarletDeblendConfig¶