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.
`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

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 : `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

JointcalConfig¶