ScarletDeblendConfig

class lsst.meas.extensions.scarlet.ScarletDeblendConfig(*args, **kw)

Bases: 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.

maxAreaTimesPeaks

Maximum rectangular footprint area * nPeaks in the footprint.

maxFootprintArea

Maximum area for footprints before they are ignored as large; non-positive means no threshold applied (int, default 100000)

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 200)

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.

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

Read-only history.

loggingInterval

Interval (in seconds) to log messages (at VERBOSE level) while deblending sources. Deprecated: This field is no longer used and will be removed in v25. (int, default 600)

maskLimits

Mask planes with the corresponding limit on the fraction of masked pixels. Sources violating this limit will not be deblended. If the fraction is 0 then the limit is a single pixel. (Dict, default {})

maxAreaTimesPeaks

Maximum rectangular footprint area * nPeaks in the footprint. This was introduced in DM-33690 to prevent fields that are crowded or have a LSB galaxy that causes memory intensive initialization in scarlet from dominating the overall runtime and/or causing the task to run out of memory. (<= 0: unlimited) (int, default 10000000)

maxFootprintArea

Maximum area for footprints before they are ignored as large; non-positive means no threshold applied (int, default 100000)

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 200)

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:
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.

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.

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:

  1. Field name.

  2. 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.

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.

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.

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).

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.

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.

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.

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.