ParallelOverscanCorrectionTaskConfig¶

class lsst.ip.isr.ParallelOverscanCorrectionTaskConfig(*args, **kw)¶

Bases: OverscanCorrectionTaskConfigBase

Attributes Summary

`doAbsoluteMaxDeviation`	Apply the maxDeviation to the absolute value of the deviation? If False, this will be a one-sided cut for positive-only deviations (typically for parallel overscan subtraction.
`doMedianSmoothingOutlierRejection`	Do column-by-column median smoothing outlier rejection? Columns that are rejected in this way will be grown by parallelOverscanMaskedColumnGrowSize.
`doParallelOverscanSaturation`	Mask saturated pixels in parallel overscan region? (`bool`, default `True`)
`fitType`	The method for fitting the overscan bias level.
`history`
`leadingToSkip`	Number of leading values to skip in parallel overscan correction.
`maskPlanes`	Mask planes to reject when measuring overscan (`List`, default `['BAD', 'SAT']`)
`maxDeviation`	Maximum deviation from median (in ADU) to mask in overscan correction; Will be applied to the absolute deviation if doAbsoluteMaxDeviation=True.
`medianSmoothingKernel`	Kernel (pixels) to use to smooth the parallel overscan columns.
`medianSmoothingOutlierThreshold`	Outlier threshold after parallel median smoothing (adu).
`numSigmaClip`	Rejection threshold (sigma) for collapsing overscan before fit (`float`, default `3.0`)
`order`	Order of polynomial to fit if overscan fit type is a polynomial, or number of spline knots if overscan fit type is a spline.
`overscanIsInt`	Treat overscan as an integer image for purposes of fitType=MEDIAN and fitType=MEDIAN_PER_ROW.
`parallelOverscanFraction`	When the parallel overscan region median is greater than parallelOverscanFraction and the imaging region median is greater than parallelOverscanImageThreshold then parallel overscan subtraction will be turned off, as this is usually due to the region being flooded with spillover from a super-saturated flat.
`parallelOverscanImageThreshold`	When the parallel overscan region median is greater than parallelOverscanFraction and the imaging region median is greater than parallelOverscanImageThreshold then parallel overscan subtraction will be turned off, as this is usually due to the region being flooded with spillover from a super-saturated flat.
`parallelOverscanMaskGrowSize`	Grow the SAT mask in the parallel overscan region by this many pixels.
`parallelOverscanMaskedColumnGrowSize`	When a full column is masked in the parallel overscan (at less than saturation) the mask should be grown by this many pixels.
`parallelOverscanSaturationLevel`	The saturation level (adu) to use if not specified in call to maskParallelOverscanAmp.
`parallelOverscanSaturationLevelAdjustmentFactor`	The parallel overscan saturation level may be below that of the data region.
`trailingToSkip`	Number of trailing values to skip in parallel overscan correction.

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

doAbsoluteMaxDeviation¶: Apply the maxDeviation to the absolute value of the deviation? If False, this will be a one-sided cut for positive-only deviations (typically for parallel overscan subtraction. (bool, default True)

doMedianSmoothingOutlierRejection¶: Do column-by-column median smoothing outlier rejection? Columns that are rejected in this way will be grown by parallelOverscanMaskedColumnGrowSize. (bool, default True)

doParallelOverscanSaturation¶: Mask saturated pixels in parallel overscan region? (bool, default True)

fitType¶

The method for fitting the overscan bias level. (str, default 'MEDIAN')

Allowed values:

'POLY': Fit ordinary polynomial to the longest axis of the overscan region
'CHEB': Fit Chebyshev polynomial to the longest axis of the overscan region
'LEG': Fit Legendre polynomial to the longest axis of the overscan region
'NATURAL_SPLINE': Fit natural spline to the longest axis of the overscan region
'CUBIC_SPLINE': Fit cubic spline to the longest axis of the overscan region
'AKIMA_SPLINE': Fit Akima spline to the longest axis of the overscan region
'MEAN': Correct using the mean of the overscan region
'MEANCLIP': Correct using a clipped mean of the overscan region
'MEDIAN': Correct using the median of the overscan region
'MEDIAN_PER_ROW': Correct using the median per row of the overscan region
'MEAN_PER_ROW': Correct using the mean per row of the overscan region
'None': Field is optional

history¶: Read-only history.

leadingToSkip¶: Number of leading values to skip in parallel overscan correction. (int, default 0)

maskPlanes¶: Mask planes to reject when measuring overscan (List, default ['BAD', 'SAT'])

maxDeviation¶: Maximum deviation from median (in ADU) to mask in overscan correction; Will be applied to the absolute deviation if doAbsoluteMaxDeviation=True. (float, default 1000.0)

medianSmoothingKernel¶: Kernel (pixels) to use to smooth the parallel overscan columns. Must be odd. (int, default 5)

medianSmoothingOutlierThreshold¶: Outlier threshold after parallel median smoothing (adu). This is applied only to positive outliers. (float, default 5.0)

numSigmaClip¶: Rejection threshold (sigma) for collapsing overscan before fit (float, default 3.0)

order¶: Order of polynomial to fit if overscan fit type is a polynomial, or number of spline knots if overscan fit type is a spline. (int, default 1)

overscanIsInt¶: Treat overscan as an integer image for purposes of fitType=MEDIAN and fitType=MEDIAN_PER_ROW. (bool, default True)

parallelOverscanFraction¶: When the parallel overscan region median is greater than parallelOverscanFraction and the imaging region median is greater than parallelOverscanImageThreshold then parallel overscan subtraction will be turned off, as this is usually due to the region being flooded with spillover from a super-saturated flat. (float, default 0.5)

parallelOverscanImageThreshold¶: When the parallel overscan region median is greater than parallelOverscanFraction and the imaging region median is greater than parallelOverscanImageThreshold then parallel overscan subtraction will be turned off, as this is usually due to the region being flooded with spillover from a super-saturated flat. (float, default 10000.0)

parallelOverscanMaskGrowSize¶: Grow the SAT mask in the parallel overscan region by this many pixels. This value was determined from the ITL chip in the LATISS camera. (int, default 7)

parallelOverscanMaskedColumnGrowSize¶: When a full column is masked in the parallel overscan (at less than saturation) the mask should be grown by this many pixels. This value is determined from ITL chips in LATISS and LSSTCam. (int, default 2)

parallelOverscanSaturationLevel¶: The saturation level (adu) to use if not specified in call to maskParallelOverscanAmp. This should be low enough to capture all possible amplifiers for defect detection. (float, default 20000.0)

parallelOverscanSaturationLevelAdjustmentFactor¶: The parallel overscan saturation level may be below that of the data region. This factor is applied to the amplifier saturation value when evaluating saturation in the parallel overscan region. (float, default 0.75)

trailingToSkip¶: Number of trailing values to skip in parallel overscan correction. (int, default 0)

Methods Documentation

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

ParallelOverscanCorrectionTaskConfig¶