MeasureDefectsCombinedTaskConfig¶

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

Bases: MeasureDefectsTaskConfig

Configuration for measuring defects from combined exposures.

Attributes Summary

`badOnAndOffPixelColumnThreshold`	If BPC is the set of all the bad pixels in a given column (not necessarily consecutive) and the size of BPC is at least 'badOnAndOffPixelColumnThreshold', all the pixels between the pixels that satisfy minY (BPC) and maxY (BPC) will be marked as bad, with 'Y' being the long axis of the amplifier (and 'X' the other axis, which for a column is a constant for all pixels in the set BPC).
`badPixelsToFillColumnThreshold`	If the number of bad pixels in an amplifier column is above this threshold then the full amplifier column will be marked bad.
`biasThreshold`	If thresholdType==``VALUE``, bias threshold (in ADU) to define hot/bright pixels in bias frame.
`connections`	Field which refers to a dynamically added configuration class which is based on a PipelineTaskConnections class.
`darkCurrentThreshold`	If thresholdType=``VALUE``, dark current threshold (in e-/sec) to define hot/bright pixels in dark images.
`doVampirePixels`	Search for vampire pixels (bright pixels surrounded by ring of low flux) in ComCam flatBootstrap and mask the area arount them.
`fracThresholdFlat`	If thresholdType=``VALUE``, fractional threshold to define cold/dark pixels in flat images (fraction of the mean value per amplifier).Unused if thresholdType==``STDEV``.
`goodPixelColumnGapThreshold`	Size, in pixels, of usable consecutive pixels in a column with on and off bad pixels (see 'badOnAndOffPixelColumnThreshold').
`history`
`nPixBorderLeftRight`	Number of pixels to exclude from left & right of image when looking for defects.
`nPixBorderUpDown`	Number of pixels to exclude from top & bottom of image when looking for defects.
`nSigmaBright`	If thresholdType=``STDEV``, number of sigma above mean for bright/hot pixel detection.
`nSigmaDark`	If thresholdType=``STDEV``, number of sigma below mean for dark/cold pixel detection.
`radiusVampirePixels`	Radius (in pixels) of the area to mask around ComCam flatBootstrap bright pixels.
`saturatedColumnDilationRadius`	Dilation radius (along rows) to use to expand saturated columns to mitigate glow.
`saturatedColumnMask`	Saturated mask plane for dilation.
`saturatedPixelsToFillColumnThreshold`	If the number of saturated pixels in an amplifier column is above this threshold then the full amplifier column will be marked bad.
`saveLogOutput`	Flag to enable/disable saving of log output for a task, enabled by default.
`thresholdType`	Defects threshold type: `STDEV` or `VALUE`.
`thresholdVampirePixels`	Pixel value threshold to find bright pixels in ComCam flatBootstrap.

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

badOnAndOffPixelColumnThreshold¶: If BPC is the set of all the bad pixels in a given column (not necessarily consecutive) and the size of BPC is at least ‘badOnAndOffPixelColumnThreshold’, all the pixels between the pixels that satisfy minY (BPC) and maxY (BPC) will be marked as bad, with ‘Y’ being the long axis of the amplifier (and ‘X’ the other axis, which for a column is a constant for all pixels in the set BPC). If there are more than ‘goodPixelColumnGapThreshold’ consecutive non-bad pixels in BPC, an exception to the above is made and those consecutive ‘goodPixelColumnGapThreshold’ are not marked as bad. (int, default 50)

badPixelsToFillColumnThreshold¶: If the number of bad pixels in an amplifier column is above this threshold then the full amplifier column will be marked bad. This operation is performed after any merging of blinking columns performed with badOnAndOffPixelColumnThreshold. If thisvalue is less than 0 then no bad column filling will be performed. (float, default -1)

biasThreshold¶: If thresholdType==``VALUE``, bias threshold (in ADU) to define hot/bright pixels in bias frame. Unused if thresholdType==``STDEV``. (float, default 1000.0)

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

darkCurrentThreshold¶: If thresholdType=``VALUE``, dark current threshold (in e-/sec) to define hot/bright pixels in dark images. Unused if thresholdType==``STDEV``. (float, default 5)

doVampirePixels¶: Search for vampire pixels (bright pixels surrounded by ring of low flux) in ComCam flatBootstrap and mask the area arount them. (bool, default False)

fracThresholdFlat¶: If thresholdType=``VALUE``, fractional threshold to define cold/dark pixels in flat images (fraction of the mean value per amplifier).Unused if thresholdType==``STDEV``. (float, default 0.8)

goodPixelColumnGapThreshold¶: Size, in pixels, of usable consecutive pixels in a column with on and off bad pixels (see ‘badOnAndOffPixelColumnThreshold’). (int, default 30)

history¶: Read-only history.

nPixBorderLeftRight¶: Number of pixels to exclude from left & right of image when looking for defects. (int, default 0)

nPixBorderUpDown¶: Number of pixels to exclude from top & bottom of image when looking for defects. (int, default 0)

nSigmaBright¶: If thresholdType=``STDEV``, number of sigma above mean for bright/hot pixel detection. The default value was found to be appropriate for some LSST sensors in DM-17490. Unused if thresholdType==``VALUE`` (float, default 4.8)

nSigmaDark¶: If thresholdType=``STDEV``, number of sigma below mean for dark/cold pixel detection. The default value was found to be appropriate for some LSST sensors in DM-17490. Unused if thresholdType==``VALUE`` (float, default -5.0)

radiusVampirePixels¶: Radius (in pixels) of the area to mask around ComCam flatBootstrap bright pixels. (int, default 8)

saturatedColumnDilationRadius¶: Dilation radius (along rows) to use to expand saturated columns to mitigate glow. (int, default 0)

saturatedColumnMask¶: Saturated mask plane for dilation. (str, default 'SAT')

saturatedPixelsToFillColumnThreshold¶: If the number of saturated pixels in an amplifier column is above this threshold then the full amplifier column will be marked bad. If this value is less than 0then no saturated column filling will be performed. (int, default -1)

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

thresholdType¶

Defects threshold type: STDEV or VALUE. If VALUE, cold pixels will be found in flats, and hot pixels in darks. If STDEV, cold and hot pixels will be found in flats, and hot pixels in darks. (str, default 'STDEV')

Allowed values:

'STDEV': Use a multiple of the image standard deviation to determine detection threshold.
'VALUE': Use pixel value to determine detection threshold.
'None': Field is optional

thresholdVampirePixels¶: Pixel value threshold to find bright pixels in ComCam flatBootstrap. (float, default 1.9)

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

MeasureDefectsCombinedTaskConfig¶