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 (str, default 'deep')
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 photometry.
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)
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 'astrometry')
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.
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.
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 (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 photometry. (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)

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 'Calib')

sourceSelector

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

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-FILTER1. (`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.

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.

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:

  1. Field name.
  2. Field value.
iteritems()

Iterate over (field name, field value) pairs.

Yields:
item : tuple

Tuple items are:

  1. Field name.
  2. Field value.
iterkeys()

Iterate over field names

Yields:
key : str

A field’s key (attribute name).

itervalues()

Iterate over field values.

Yields:
value : obj

A field value.

keys()

Get field names.

Returns:
names : list

List of lsst.pex.config.Field names.

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.save, lsst.pex.config.Config.saveFromStream

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, 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.save, lsst.pex.config.Config.saveFromStream

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.

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:
values : list

List of field values.