JointcalConfig

class lsst.jointcal.JointcalConfig

Bases: lsst.pipe.base.PipelineTaskConfig

Configuration for JointcalTask

Attributes Summary

allowLineSearch	Allow a line search during minimization, if it is reasonable for the model (models with a significant non-linear component, e.g.
applyColorTerms	Apply photometric color terms to reference stars?Requires that colorterms be set to a ColortermLibrary (bool, default False)
astrometryChipOrder	Order of the per-chip transform for the constrained astrometry model.
astrometryDoRankUpdate	Do the rank update step during minimization (should not change the astrometry fit).
astrometryModel	Type of model to fit to astrometry (str, default 'constrained')
astrometryOutlierRelativeTolerance	Convergence tolerance for outlier rejection threshold when fitting astrometry.
astrometryRefObjLoader	Reference object loader for astrometric fit (ConfigurableInstance, default <class 'lsst.meas.algorithms.loadIndexedReferenceObjects.LoadIndexedReferenceObjectsConfig'>)
astrometryReferenceErr	Uncertainty on reference catalog coordinates [mas] to use in place of the coord_*Err fields.
astrometryReferenceSelector	How to down-select the loaded astrometry reference catalog.
astrometrySimpleOrder	Polynomial order for fitting the simple astrometry model.
astrometryVisitOrder	Order of the per-visit transform for the constrained astrometry model.
coaddName	Type of coadd, typically deep or goodSeeing Deprecated: Only applies to gen2; will be removed when gen2 support is removed (DM-20572).
colorterms	Library of photometric reference catalog name to color term dict.
connections	Configurations describing the connections of the PipelineTask to datatypes (Connections, default <class 'lsst.pipe.base.config.Connections'>)
debugOutputPath	Path to write debug output files to.
detailedProfile	Output separate profiling information for different parts of jointcal, e.g.
doAstrometry	Fit astrometry and write the fitted result.
doPhotometry	Fit photometry and write the fitted result.
history
matchCut	Matching radius between fitted and reference stars (arcseconds) (float, default 3.0)
maxAstrometrySteps	Maximum number of minimize iterations to take when fitting astrometry.
maxPhotometrySteps	Maximum number of minimize iterations to take when fitting photometry.
minMeasuredStarsPerCcd	Minimum number of measuredStars per ccdImage before printing warnings (int, default 100)
minMeasurements	Minimum number of associated measured stars for a fitted star to be included in the fit (int, default 2)
minRefStarsPerCcd	Minimum number of measuredStars per ccdImage before printing warnings (int, default 30)
outlierRejectSigma	How many sigma to reject outliers at during minimization.
photometryDoRankUpdate	Do the rank update step during minimization.
photometryErrorPedestal	Systematic term to apply to the measured error on flux or magnitude as a fraction of source flux or magnitude delta (e.g.
photometryModel	Type of model to fit to photometry (str, default 'constrainedMagnitude')
photometryRefObjLoader	Reference object loader for photometric fit (ConfigurableInstance, default <class 'lsst.meas.algorithms.loadIndexedReferenceObjects.LoadIndexedReferenceObjectsConfig'>)
photometryReferenceSelector	How to down-select the loaded photometry reference catalog.
photometryVisitOrder	Order of the per-visit polynomial transform for the constrained photometry model.
positionErrorPedestal	Systematic term to apply to the measured position error (pixels) (float, default 0.02)
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.
sourceFluxType	Source flux field to use in source selection and to get fluxes from the catalog.
sourceSelector	How to select sources for cross-matching (RegistryInstanceDict, default 'science')
useInputWcs	Use the input calexp WCSs to initialize a SimpleAstrometryModel.
writeChi2FilesInitialFinal	Write .csv files containing the contributions to chi2 for the initialization and final fit.
writeChi2FilesOuterLoop	Write .csv files containing the contributions to chi2 for the outer fit loop.
writeInitMatrix	Write the pre/post-initialization Hessian and gradient to text files, for debugging.
writeInitialModel	Write the pre-initialization model to text files, for debugging.

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

allowLineSearch

Allow a line search during minimization, if it is reasonable for the model (models with a significant non-linear component, e.g. constrainedPhotometry). (bool, default False)

applyColorTerms

Apply photometric color terms to reference stars?Requires that colorterms be set to a ColortermLibrary (bool, default False)

astrometryChipOrder

Order of the per-chip transform for the constrained astrometry model. (int, default 1)

astrometryDoRankUpdate

Do the rank update step during minimization (should not change the astrometry fit). Skipping this can help deal with models that are too non-linear. (bool, default True)

astrometryModel

Type of model to fit to astrometry (str, default 'constrained')

Allowed values:

'simple'

One polynomial per ccd

'constrained'

One polynomial per ccd, and one polynomial per visit

'None'

Field is optional

astrometryOutlierRelativeTolerance

Convergence tolerance for outlier rejection threshold when fitting astrometry. Iterations will stop when the fractional change in the chi2 cut level is below this value. If tolerance is set to zero, iterations will continue until there are no more outliers. We suggest a value of 0.002as a balance between a shorter minimization runtime and achieving a final fitted model that isclose to the solution found when removing all outliers. (float, default 0)

astrometryRefObjLoader

Reference object loader for astrometric fit (ConfigurableInstance, default <class 'lsst.meas.algorithms.loadIndexedReferenceObjects.LoadIndexedReferenceObjectsConfig'>)

astrometryReferenceErr

Uncertainty on reference catalog coordinates [mas] to use in place of the coord_*Err fields. If None, then raise an exception if the reference catalog is missing coordinate errors. If specified, overrides any existing coord_*Err values. (float, default None)

astrometryReferenceSelector

How to down-select the loaded astrometry reference catalog. (ConfigurableInstance, default <class 'lsst.meas.algorithms.sourceSelector.ReferenceSourceSelectorConfig'>)

astrometrySimpleOrder

Polynomial order for fitting the simple astrometry model. (int, default 3)

astrometryVisitOrder

Order of the per-visit transform for the constrained astrometry model. (int, default 5)

coaddName

Type of coadd, typically deep or goodSeeing Deprecated: Only applies to gen2; will be removed when gen2 support is removed (DM-20572). (str, default 'deep')

colorterms

Library of photometric reference catalog name to color term dict. (ColortermLibrary, default <class 'lsst.pipe.tasks.colorterms.ColortermLibrary'>)

connections

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

debugOutputPath

Path to write debug output files to. Used by writeInitialModel, writeChi2Files*, writeInitMatrix. (str, default '.')

detailedProfile

Output separate profiling information for different parts of jointcal, e.g. data read, fitting (bool, default False)

doAstrometry

Fit astrometry and write the fitted result. (bool, default True)

doPhotometry

Fit photometry and write the fitted result. (bool, default True)

history

matchCut

Matching radius between fitted and reference stars (arcseconds) (float, default 3.0)

maxAstrometrySteps

Maximum number of minimize iterations to take when fitting astrometry. (int, default 20)

maxPhotometrySteps

Maximum number of minimize iterations to take when fitting photometry. (int, default 20)

minMeasuredStarsPerCcd

Minimum number of measuredStars per ccdImage before printing warnings (int, default 100)

minMeasurements

Minimum number of associated measured stars for a fitted star to be included in the fit (int, default 2)

minRefStarsPerCcd

Minimum number of measuredStars per ccdImage before printing warnings (int, default 30)

outlierRejectSigma

How many sigma to reject outliers at during minimization. (float, default 5.0)

photometryDoRankUpdate

Do the rank update step during minimization. Skipping this can help deal with models that are too non-linear. (bool, default True)

photometryErrorPedestal

Systematic term to apply to the measured error on flux or magnitude as a fraction of source flux or magnitude delta (e.g. 0.05 is 5% of flux or +50 millimag). (float, default 0.0)

photometryModel

Type of model to fit to photometry (str, default 'constrainedMagnitude')

Allowed values:

'simpleFlux'

One constant zeropoint per ccd and visit, fitting in flux space.

'constrainedFlux'

Constrained zeropoint per ccd, and one polynomial per visit, fitting in flux space.

'simpleMagnitude'

One constant zeropoint per ccd and visit, fitting in magnitude space.

'constrainedMagnitude'

Constrained zeropoint per ccd, and one polynomial per visit, fitting in magnitude space.

'None'

Field is optional

photometryRefObjLoader

Reference object loader for photometric fit (ConfigurableInstance, default <class 'lsst.meas.algorithms.loadIndexedReferenceObjects.LoadIndexedReferenceObjectsConfig'>)

photometryReferenceSelector

How to down-select the loaded photometry reference catalog. (ConfigurableInstance, default <class 'lsst.meas.algorithms.sourceSelector.ReferenceSourceSelectorConfig'>)

photometryVisitOrder

Order of the per-visit polynomial transform for the constrained photometry model. (int, default 7)

positionErrorPedestal

Systematic term to apply to the measured position error (pixels) (float, default 0.02)

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)

sourceFluxType

Source flux field to use in source selection and to get fluxes from the catalog. (str, default 'apFlux_12_0')

sourceSelector

How to select sources for cross-matching (RegistryInstanceDict, default 'science')

useInputWcs

Use the input calexp WCSs to initialize a SimpleAstrometryModel. (bool, default True)

writeChi2FilesInitialFinal

Write .csv files containing the contributions to chi2 for the initialization and final fit. Output files will be written to config.debugOutputPath and will be of the form astrometry_[initial|final]_chi2-TRACT-FILTER. (`bool, default False)

writeChi2FilesOuterLoop

Write .csv files containing the contributions to chi2 for the outer fit loop. Output files will be written to config.debugOutputPath and will be of the form astrometry_init-NN_chi2-TRACT-FILTER. (bool, default False)

writeInitMatrix

Write the pre/post-initialization Hessian and gradient to text files, for debugging. Output files will be written to config.debugOutputPath and will be of the form ‘astrometry_[pre|post]init-TRACT-FILTER-mat.txt’. Note that these files are the dense versions of the matrix, and so may be very large. (bool, default False)

writeInitialModel

Write the pre-initialization model to text files, for debugging. Output files will be written to config.debugOutputPath and will be of the form initial_astrometry_model-TRACT_FILTER.txt. (bool, default False)

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 : dict_items

Iterator of tuples for each configuration. Tuple items are:

0. Field name.
1. Field value.

keys()

Get field names.

Returns:

names : dict_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:

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.

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.

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.

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 : dict_values

Iterator of field values.