MakeKernelConfig¶

class lsst.ip.diffim.MakeKernelConfig¶

Bases: lsst.ip.diffim.PsfMatchConfig

Attributes Summary

`afwBackgroundConfig`	Controlling the Afw background fitting (`SubtractBackgroundConfig`, default `<class 'lsst.meas.algorithms.subtractBackground.SubtractBackgroundConfig'>`)
`badMaskPlanes`	Mask planes to ignore when calculating diffim statistics Options: NO_DATA EDGE SAT BAD CR INTRP (`List`, default `('NO_DATA', 'EDGE', 'SAT')`)
`calculateKernelUncertainty`	Calculate kernel and background uncertainties for each kernel candidate? This comes from the inverse of the covariance matrix.
`candidateCoreRadius`	Radius for calculation of stats in ‘core’ of KernelCandidate diffim.
`candidateResidualMeanMax`	Rejects KernelCandidates yielding bad difference image quality.
`candidateResidualStdMax`	Rejects KernelCandidates yielding bad difference image quality.
`checkConditionNumber`	Test for maximum condition number when inverting a kernel matrix.
`conditionNumberType`	Use singular values (SVD) or eigen values (EIGENVALUE) to determine condition number (`str`, default `'EIGENVALUE'`)
`constantVarianceWeighting`	Use constant variance weighting in single kernel fitting? In some cases this is better for bright star residuals.
`detectionConfig`	Controlling the detection of sources for kernel building (`DetectionConfig`, default `<class 'lsst.ip.diffim.psfMatch.DetectionConfig'>`)
`fitForBackground`	Include terms (including kernel cross terms) for background in ip_diffim (`bool`, default `False`)
`history`
`iterateSingleKernel`	Remake KernelCandidate using better variance estimate after first pass? Primarily useful when convolving a single-depth image, otherwise not necessary.
`kernel`	kernel type (`ConfigInstanceDict`, default `'AL'`)
`kernelBasisSet`	Type of basis set for PSF matching kernel.
`kernelSize`	Number of rows/columns in the convolution kernel; should be odd-valued.
`kernelSizeFwhmScaling`	Multiplier of the largest AL Gaussian basis sigma to get the kernel bbox (pixel) size.
`kernelSizeMax`	Maximum kernel bbox (pixel) size.
`kernelSizeMin`	Minimum kernel bbox (pixel) size.
`kernelSumClipping`	Do sigma clipping on the ensemble of kernel sums (`bool`, default `True`)
`maxConditionNumber`	Maximum condition number for a well conditioned matrix (`float`, default `50000000.0`)
`maxKsumSigma`	Maximum allowed sigma for outliers from kernel sum distribution.
`maxSpatialConditionNumber`	Maximum condition number for a well conditioned spatial matrix (`float`, default `10000000000.0`)
`maxSpatialIterations`	Maximum number of iterations for rejecting bad KernelCandidates in spatial fitting (`int`, default `3`)
`nStarPerCell`	Number of KernelCandidates in each SpatialCell to use in the spatial fitting (`int`, default `3`)
`numPrincipalComponents`	Number of principal components to use for Pca basis, including the mean kernel if requested.
`scaleByFwhm`	Scale kernelSize, alardGaussians by input Fwhm (`bool`, default `True`)
`selectDetection`	Initial detections used to feed stars to kernel fitting (`ConfigurableInstance`, default `<class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>`)
`selectMeasurement`	Initial measurements used to feed stars to kernel fitting (`ConfigurableInstance`, default `<class 'lsst.meas.base.sfm.SingleFrameMeasurementConfig'>`)
`singleKernelClipping`	Do sigma clipping on each raw kernel candidate (`bool`, default `True`)
`sizeCellX`	Size (rows) in pixels of each SpatialCell for spatial modeling (`int`, default `128`)
`sizeCellY`	Size (columns) in pixels of each SpatialCell for spatial modeling (`int`, default `128`)
`spatialBgOrder`	Spatial order of differential background variation (`int`, default `1`)
`spatialKernelClipping`	Do sigma clipping after building the spatial model (`bool`, default `True`)
`spatialKernelOrder`	Spatial order of convolution kernel variation (`int`, default `2`)
`spatialModelType`	Type of spatial functions for kernel and background (`str`, default `'chebyshev1'`)
`subtractMeanForPca`	Subtract off the mean feature before doing the Pca (`bool`, default `True`)
`useAfwBackground`	Use afw background subtraction instead of ip_diffim (`bool`, default `False`)
`useBicForKernelBasis`	Use Bayesian Information Criterion to select the number of bases going into the kernel (`bool`, default `False`)
`useCoreStats`	Use the core of the footprint for the quality statistics, instead of the entire footprint.
`usePcaForSpatialKernel`	Use Pca to reduce the dimensionality of the kernel basis sets.
`warpingConfig`	Config for warping exposures to a common alignment (`WarperConfig`, default `<class 'lsst.afw.math._warper.WarperConfig'>`)

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

afwBackgroundConfig¶: Controlling the Afw background fitting (SubtractBackgroundConfig, default <class 'lsst.meas.algorithms.subtractBackground.SubtractBackgroundConfig'>)

badMaskPlanes¶: Mask planes to ignore when calculating diffim statistics Options: NO_DATA EDGE SAT BAD CR INTRP (List, default ('NO_DATA', 'EDGE', 'SAT'))

calculateKernelUncertainty¶: Calculate kernel and background uncertainties for each kernel candidate? This comes from the inverse of the covariance matrix. Warning: regularization can cause problems for this step. (bool, default False)

candidateCoreRadius¶: Radius for calculation of stats in ‘core’ of KernelCandidate diffim. Total number of pixels used will be (2*radius)**2. This is used both for ‘core’ diffim quality as well as ranking of KernelCandidates by their total flux in this core (int, default 3)

candidateResidualMeanMax¶: Rejects KernelCandidates yielding bad difference image quality. Used by BuildSingleKernelVisitor, AssessSpatialKernelVisitor. Represents average over pixels of (image/sqrt(variance)). (float, default 0.25)

candidateResidualStdMax¶: Rejects KernelCandidates yielding bad difference image quality. Used by BuildSingleKernelVisitor, AssessSpatialKernelVisitor. Represents stddev over pixels of (image/sqrt(variance)). (float, default 1.5)

checkConditionNumber¶: Test for maximum condition number when inverting a kernel matrix. Anything above maxConditionNumber is not used and the candidate is set as BAD. Also used to truncate inverse matrix in estimateBiasedRisk. However, if you are doing any deconvolution you will want to turn this off, or use a large maxConditionNumber (bool, default False)

conditionNumberType¶

Use singular values (SVD) or eigen values (EIGENVALUE) to determine condition number (str, default 'EIGENVALUE')

Allowed values:

'SVD': Use singular values
'EIGENVALUE': Use eigen values (faster)
'None': Field is optional

constantVarianceWeighting¶: Use constant variance weighting in single kernel fitting? In some cases this is better for bright star residuals. (bool, default True)

detectionConfig¶: Controlling the detection of sources for kernel building (DetectionConfig, default <class 'lsst.ip.diffim.psfMatch.DetectionConfig'>)

fitForBackground¶: Include terms (including kernel cross terms) for background in ip_diffim (bool, default False)

history¶

iterateSingleKernel¶: Remake KernelCandidate using better variance estimate after first pass? Primarily useful when convolving a single-depth image, otherwise not necessary. (bool, default False)

kernel¶: kernel type (ConfigInstanceDict, default 'AL')

kernelBasisSet¶

Type of basis set for PSF matching kernel. (str, default 'alard-lupton')

Allowed values:

'alard-lupton'

Alard-Lupton sum-of-gaussians basis set,

The first term has no spatial variation
The kernel sum is conserved
You may want to turn off ‘usePcaForSpatialKernel’

'delta-function'

Delta-function kernel basis set,

You may enable the option useRegularization
You should seriously consider usePcaForSpatialKernel, which will also enable kernel sum conservation for the delta function kernels

'None'

Field is optional

kernelSize¶: Number of rows/columns in the convolution kernel; should be odd-valued. Modified by kernelSizeFwhmScaling if scaleByFwhm = true (int, default 21)

kernelSizeFwhmScaling¶: Multiplier of the largest AL Gaussian basis sigma to get the kernel bbox (pixel) size. (float, default 6.0)

kernelSizeMax¶: Maximum kernel bbox (pixel) size. (int, default 35)

kernelSizeMin¶: Minimum kernel bbox (pixel) size. (int, default 21)

kernelSumClipping¶: Do sigma clipping on the ensemble of kernel sums (bool, default True)

maxConditionNumber¶: Maximum condition number for a well conditioned matrix (float, default 50000000.0)

maxKsumSigma¶: Maximum allowed sigma for outliers from kernel sum distribution. Used to reject variable objects from the kernel model (float, default 3.0)

maxSpatialConditionNumber¶: Maximum condition number for a well conditioned spatial matrix (float, default 10000000000.0)

maxSpatialIterations¶: Maximum number of iterations for rejecting bad KernelCandidates in spatial fitting (int, default 3)

nStarPerCell¶: Number of KernelCandidates in each SpatialCell to use in the spatial fitting (int, default 3)

numPrincipalComponents¶: Number of principal components to use for Pca basis, including the mean kernel if requested. (int, default 5)

scaleByFwhm¶: Scale kernelSize, alardGaussians by input Fwhm (bool, default True)

selectDetection¶: Initial detections used to feed stars to kernel fitting (ConfigurableInstance, default <class 'lsst.meas.algorithms.detection.SourceDetectionConfig'>)

selectMeasurement¶: Initial measurements used to feed stars to kernel fitting (ConfigurableInstance, default <class 'lsst.meas.base.sfm.SingleFrameMeasurementConfig'>)

singleKernelClipping¶: Do sigma clipping on each raw kernel candidate (bool, default True)

sizeCellX¶: Size (rows) in pixels of each SpatialCell for spatial modeling (int, default 128)

sizeCellY¶: Size (columns) in pixels of each SpatialCell for spatial modeling (int, default 128)

spatialBgOrder¶: Spatial order of differential background variation (int, default 1)

spatialKernelClipping¶: Do sigma clipping after building the spatial model (bool, default True)

spatialKernelOrder¶: Spatial order of convolution kernel variation (int, default 2)

spatialModelType¶

Type of spatial functions for kernel and background (str, default 'chebyshev1')

Allowed values:

'chebyshev1': Chebyshev polynomial of the first kind
'polynomial': Standard x,y polynomial
'None': Field is optional

subtractMeanForPca¶: Subtract off the mean feature before doing the Pca (bool, default True)

useAfwBackground¶: Use afw background subtraction instead of ip_diffim (bool, default False)

useBicForKernelBasis¶: Use Bayesian Information Criterion to select the number of bases going into the kernel (bool, default False)

useCoreStats¶: Use the core of the footprint for the quality statistics, instead of the entire footprint. WARNING: if there is deconvolution we probably will need to turn this off (bool, default False)

usePcaForSpatialKernel¶: Use Pca to reduce the dimensionality of the kernel basis sets. This is particularly useful for delta-function kernels. Functionally, after all Cells have their raw kernels determined, we run a Pca on these Kernels, re-fit the Cells using the eigenKernels and then fit those for spatial variation using the same technique as for Alard-Lupton kernels. If this option is used, the first term will have no spatial variation and the kernel sum will be conserved. (bool, default False)

warpingConfig¶: Config for warping exposures to a common alignment (WarperConfig, default <class 'lsst.afw.math._warper.WarperConfig'>)

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.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:

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.

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:

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.

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:	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`).

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:

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.

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:	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`.

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:	values : `list` List of field values.

See also

lsst.pex.config.Config.itervalues

Navigation

MakeKernelConfig¶