PhotonTransferCurveExtractConfig¶

class lsst.cp.pipe.PhotonTransferCurveExtractConfig(*args, **kw)¶

Bases: PhotonTransferCurveExtractConfigBase

Attributes Summary

`auxiliaryHeaderKeys`	Auxiliary header keys to store with the PTC dataset.
`binSize`	Bin the image by this factor in both dimensions.
`connections`	Field which refers to a dynamically added configuration class which is based on a PipelineTaskConnections class.
`detectorMeasurementRegion`	Region of each exposure where to perform the calculations (amplifier or full image).
`doExtractPhotodiodeData`	Extract photodiode data? (`bool`, default `False`)
`doGain`	Calculate a gain per input flat pair.
`doKsHistMeasurement`	Do the Ks test of gaussianity? If False, kspValue will be filled with all 1.0s.
`doVignetteFunctionRegionSelection`	Use vignette function to select PTC region? (`bool`, default `False`)
`edgeMaskLevel`	Mask edge pixels in which coordinate frame: DETECTOR or AMP? (`str`, default `'DETECTOR'`)
`efdPhotodiodeSeries`	EFD series to use to get photodiode values.
`efdSalIndex`	EFD SAL Index to select electrometer.
`gainCorrectionType`	Correction type for the gain.
`history`
`ksHistLimitMultiplier`	Number of sigma (as predicted from the mean value) to compute KS test histogram.
`ksHistMinDataValues`	Minimum number of good data values to compute KS test histogram.
`ksHistNBins`	Number of bins for the KS test histogram.
`maskNameList`	Mask list to exclude from statistics calculations.
`matchExposuresByFluxKeyword`	Header keyword for flux if matchExposuresType is FLUX.
`matchExposuresType`	Match input exposures by time, flux, or expId (`str`, default `'TIME'`)
`maximumRangeCovariancesAstier`	Maximum range of covariances as in Astier+19 (`int`, default `8`)
`minNumberGoodPixelsForCovariance`	Minimum number of acceptable good pixels per amp to calculate the covariances (via FFT or direclty).
`nIterSigmaClipPtc`	Number of sigma-clipping iterations for afwMath.StatisticsControl() (`int`, default `3`)
`nSigmaClipPtc`	Sigma cut for afwMath.StatisticsControl() (`float`, default `5.5`)
`numEdgeSuspect`	Number of edge pixels to be flagged as untrustworthy.
`photodiodeCurrentScale`	Scale factor to apply to photodiode current values for the `CHARGE_SUM`, `TRIMMED_SUM`, and `MEAN` integration methods.
`photodiodeIntegrationMethod`	Integration method for photodiode monitoring data.
`saveLogOutput`	Flag to enable/disable saving of log output for a task, enabled by default.
`thresholdDiffAfwVarVsCov00`	If the absolute fractional differece between afwMath.VARIANCECLIP and Cov00 for a region of a difference image is greater than this threshold (percentage), a warning will be issued.
`useEfdPhotodiodeData`	Extract photodiode values from EFD? (`bool`, default `False`)
`vignetteFunctionPolynomialCoeffs`
`vignetteFunctionRegionSelectionMinimumPixels`	Minumum number of pixels to select for vignette function region selection.
`vignetteFunctionRegionSelectionPercent`	Vignetting function variation over the focal plane that is determined to be satisfactory.

Methods Summary

`applyConfigOverrides`(instrument, ...)	Apply config overrides to this config instance.
`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

auxiliaryHeaderKeys¶: Auxiliary header keys to store with the PTC dataset. (List, default [])

binSize¶: Bin the image by this factor in both dimensions. (int, default 1)

connections: pexConfig.ConfigField¶: Field which refers to a dynamically added configuration class which is based on a PipelineTaskConnections class.

detectorMeasurementRegion¶

Region of each exposure where to perform the calculations (amplifier or full image). (str, default 'AMP')

Allowed values:

'AMP': Amplifier of the detector.
'FULL': Full image.
'None': Field is optional

doExtractPhotodiodeData¶: Extract photodiode data? (bool, default False)

doGain¶: Calculate a gain per input flat pair. (bool, default True)

doKsHistMeasurement¶: Do the Ks test of gaussianity? If False, kspValue will be filled with all 1.0s. (bool, default False)

doVignetteFunctionRegionSelection¶: Use vignette function to select PTC region? (bool, default False)

edgeMaskLevel¶

Mask edge pixels in which coordinate frame: DETECTOR or AMP? (str, default 'DETECTOR')

Allowed values:

'DETECTOR': Mask only the edges of the full detector.
'AMP': Mask edges of each amplifier.
'None': Field is optional

efdPhotodiodeSeries¶: EFD series to use to get photodiode values. (str, default 'lsst.sal.Electrometer.logevent_logMessage')

efdSalIndex¶: EFD SAL Index to select electrometer. This is 101 for mainTel, 201 for auxTel. (int, default 201)

gainCorrectionType¶

Correction type for the gain. (str, default 'FULL')

Allowed values:

'NONE': No correction.
'SIMPLE': First order correction.
'FULL': Second order correction.
'None': Field is optional

history¶: Read-only history.

ksHistLimitMultiplier¶: Number of sigma (as predicted from the mean value) to compute KS test histogram. (float, default 8.0)

ksHistMinDataValues¶: Minimum number of good data values to compute KS test histogram. (int, default 100)

ksHistNBins¶: Number of bins for the KS test histogram. (int, default 100)

maskNameList¶: Mask list to exclude from statistics calculations. (List, default ['SUSPECT', 'BAD', 'NO_DATA', 'SAT'])

matchExposuresByFluxKeyword¶: Header keyword for flux if matchExposuresType is FLUX. (str, default 'CCOBFLUX')

matchExposuresType¶

Match input exposures by time, flux, or expId (str, default 'TIME')

Allowed values:

'TIME': Match exposures by reported exposure time. Entries that are within 5e-3 seconds.
'FLUX': Match exposures by target flux. Use header keyword in matchExposuresByFluxKeyword to find the flux.
'EXPID': Match exposures by exposure ID.
'None': Field is optional

maximumRangeCovariancesAstier¶: Maximum range of covariances as in Astier+19 (int, default 8)

minNumberGoodPixelsForCovariance¶: Minimum number of acceptable good pixels per amp to calculate the covariances (via FFT or direclty). (int, default 10000)

nIterSigmaClipPtc¶: Number of sigma-clipping iterations for afwMath.StatisticsControl() (int, default 3)

nSigmaClipPtc¶: Sigma cut for afwMath.StatisticsControl() (float, default 5.5)

numEdgeSuspect¶: Number of edge pixels to be flagged as untrustworthy. (int, default 0)

photodiodeCurrentScale¶: Scale factor to apply to photodiode current values for the CHARGE_SUM, TRIMMED_SUM, and MEAN integration methods. (float, default -1.0)

photodiodeIntegrationMethod¶

Integration method for photodiode monitoring data. (str, default 'TRIMMED_SUM')

Allowed values:

'DIRECT_SUM': Use numpy’s trapezoid integrator on all photodiode readout entries
'TRIMMED_SUM': Use numpy’s trapezoid integrator, clipping the leading and trailing entries, which are nominally at zero baseline level.
'CHARGE_SUM': Treat the current values as integrated charge over the sampling interval and simply sum the values, after subtracting a baseline level.
'MEAN': {‘Take the average of the photodiode measurements and multiply by the exposure time.’}
'None': Field is optional

saveLogOutput¶: Flag to enable/disable saving of log output for a task, enabled by default. (bool, default True)

thresholdDiffAfwVarVsCov00¶: If the absolute fractional differece between afwMath.VARIANCECLIP and Cov00 for a region of a difference image is greater than this threshold (percentage), a warning will be issued. (float, default 1.0)

useEfdPhotodiodeData¶: Extract photodiode values from EFD? (bool, default False)

vignetteFunctionPolynomialCoeffs¶

vignetteFunctionRegionSelectionMinimumPixels¶: Minumum number of pixels to select for vignette function region selection. (int, default 250000)

vignetteFunctionRegionSelectionPercent¶: Vignetting function variation over the focal plane that is determined to be satisfactory. If this does not yield vignetteFunctionRegionSelectionMinimumPixels then this will be increased until vignetteFunctionRegionSelectionMinimumPixels is reached. (float, default 2.0)

Methods Documentation

applyConfigOverrides(instrument: Instrument | None, taskDefaultName: str, pipelineConfigs: Iterable[ConfigIR] | None, parameters: ParametersIR, label: str) → None¶

Apply config overrides to this config instance.

Parameters:

instrumentInstrument or None: An instance of the Instrument specified in a pipeline. If None then the pipeline did not specify and instrument.
taskDefaultNamestr: The default name associated with the Task class. This may be used with instrumental overrides.
pipelineConfigsIterable of ConfigIR: An iterable of ConfigIR objects that contain overrides to apply to this config instance.
parametersParametersIR: Parameters defined in a Pipeline which are used in formatting of config values across multiple Task in a pipeline.
labelstr: The label associated with this class’s Task in a pipeline.

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.

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:

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.

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:

itemsItemsView

Iterator of tuples for each configuration. Tuple items are:

Field name.
Field value.

keys()¶

Get field names.

Returns:

namesKeysView: 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:

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.

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, extraLocals=None)¶

Modify this Config in place by executing the Python code in the provided stream.

Parameters:

streamfile-like object, str, bytes, or CodeType

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.

extraLocalsdict of str to object, optional

Any extra variables to include in local scope when loading.

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, extraLocals=None)¶

Modify this Config in place by executing the Python code in the provided string.

Parameters:

codestr, bytes, or CodeType

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.

extraLocalsdict of str to object, optional

Any extra variables to include in local scope when loading.

Raises:

ValueError: Raised if a key in extraLocals is the same value as the value of the root argument.

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:

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).

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:

outfilefile-like object: Destination file object write the config into. Accepts strings not bytes.
rootstr, optional: 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.

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:

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.

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:

valuesValuesView: Iterator of field values.

Navigation

PhotonTransferCurveExtractConfig¶