CfhtIsrTaskConfig

class lsst.obs.cfht.cfhtIsrTask.CfhtIsrTaskConfig

Bases: lsst.ip.isr.isrTask.IsrTaskConfig

Attributes Summary

assembleCcd	CCD assembly task (ConfigurableInstance, default <class 'lsst.ip.isr.assembleCcdTask.AssembleCcdConfig'>)
badStatistic	How to estimate the average value for BAD regions.
biasDataProductName	Name of the bias data product (str, default 'bias')
brighterFatterApplyGain	Should the gain be applied when applying the brighter fatter correction? (bool, default True)
brighterFatterKernelFile	Kernel file used for the brighter fatter correction (str, default '')
brighterFatterLevel	The level at which to correct for brighter-fatter.
brighterFatterMaxIter	Maximum number of iterations for the brighter fatter correction (int, default 10)
brighterFatterThreshold	Threshold used to stop iterating the brighter fatter correction.
crosstalk	Intra-CCD crosstalk correction (ConfigurableInstance, default <class 'lsst.ip.isr.crosstalk.CrosstalkConfig'>)
darkDataProductName	Name of the dark data product (str, default 'dark')
datasetType	Dataset type for input data; users will typically leave this alone, but camera-specific ISR tasks will override it (str, default 'raw')
defaultFluxMag0T1	Default value for fluxMag0T1 (for an unrecognized filter).
doAddDistortionModel	Apply a distortion model based on camera geometry to the WCS? (bool, default True)
doApplyGains	Correct the amplifiers for their gains instead of applying flat correction (bool, default False)
doAssembleCcd	Assemble amp-level exposures into a ccd-level exposure? (bool, default True)
doAssembleIsrExposures	Assemble amp-level calibration exposures into ccd-level exposure? (bool, default False)
doAttachTransmissionCurve	Construct and attach a wavelength-dependent throughput curve for this CCD image? (bool, default False)
doBias	Apply bias frame correction? (bool, default True)
doBrighterFatter	Apply the brighter fatter correction (bool, default False)
doCameraSpecificMasking	Mask camera-specific bad regions? (bool, default False)
doConvertIntToFloat	Convert integer raw images to floating point values? (bool, default True)
doCrosstalk	Apply intra-CCD crosstalk correction? (bool, default False)
doCrosstalkBeforeAssemble	Apply crosstalk correction before CCD assembly, and before trimming? (bool, default True)
doDark	Apply dark frame correction? (bool, default True)
doDefect	Apply correction for CCD defects, e.g.
doEmpiricalReadNoise	Calculate empirical read noise instead of value from AmpInfo data? (bool, default False)
doFlat	Apply flat field correction? (bool, default True)
doFringe	Apply fringe correction? (bool, default True)
doLinearize	Correct for nonlinearity of the detector’s response? (bool, default True)
doMeasureBackground	Measure the background level on the reduced image? (bool, default False)
doNanInterpAfterFlat	If True, ensure we interpolate NaNs after flat-fielding, even if we also have to interpolate them before flat-fielding.
doOverscan	Do overscan subtraction? (bool, default True)
doSaturation	Mask saturated pixels? (bool, default True)
doSaturationInterpolation	Perform interpolation over pixels masked as saturated? (bool, default True)
doSetBadRegions	Should we set the level of all BAD patches of the chip to the chip’s average value? (bool, default True)
doStrayLight	Subtract stray light in the y-band (due to encoder LEDs)? (bool, default False)
doSuspect	Mask suspect pixels? (bool, default True)
doTrimToMatchCalib	Trim raw data to match calibration bounding boxes? (bool, default False)
doTweakFlat	Tweak flats to match observed amplifier ratios? (bool, default False)
doUseAtmosphereTransmission	Load and use transmission_atmosphere (if doAttachTransmissionCurve is True)? (bool, default True)
doUseFilterTransmission	Load and use transmission_filter (if doAttachTransmissionCurve is True)? (bool, default True)
doUseOpticsTransmission	Load and use transmission_optics (if doAttachTransmissionCurve is True)? (bool, default True)
doUseSensorTransmission	Load and use transmission_sensor (if doAttachTransmissionCurve is True)? (bool, default True)
doVariance	Calculate variance? (bool, default True)
doVignette	Apply vignetting parameters? (bool, default False)
doWidenSaturationTrails	Widen bleed trails based on their width? (bool, default True)
doWrite	Persist postISRCCD? (bool, default True)
expectWcs	Expect input science images to have a WCS (set False for e.g.
fallbackFilterName	Fallback default filter name for calibrations.
flatDataProductName	Name of the flat data product (str, default 'flat')
flatScalingType	The method for scaling the flat on the fly.
flatUserScale	If flatScalingType is ‘USER’ then scale flat by this amount; ignored otherwise (float, default 1.0)
fluxMag0T1	The approximate flux of a zero-magnitude object in a one-second exposure, per filter.
fringe	Fringe subtraction task (ConfigurableInstance, default <class 'lsst.ip.isr.fringe.FringeConfig'>)
fringeAfterFlat	Do fringe subtraction after flat-fielding? (bool, default True)
fwhm	FWHM of PSF in arcseconds.
gain	The gain to use if no Detector is present in the Exposure (ignored if NaN) (float, default nan)
growSaturationFootprintSize	Number of pixels by which to grow the saturation footprints (int, default 1)
history
masking	Masking task.
normalizeGains	Normalize all the amplifiers in each CCD to have the same median value.
numEdgeSuspect	Number of edge pixels to be flagged as untrustworthy.
overscanBiasJump	Fit the overscan in a piecewise-fashion to correct for bias jumps? (bool, default False)
overscanBiasJumpDevices	List of devices that need piecewise overscan correction.
overscanBiasJumpKeyword	Header keyword containing information about devices.
overscanBiasJumpLocation	Location of bias jump along y-axis.
overscanFitType	The method for fitting the overscan bias level.
overscanIsInt	Treat overscan as an integer image for purposes of overscan.FitType=MEDIAN (bool, default True)
overscanMaxDev	Maximum deviation from the median for overscan (float, default 1000.0)
overscanNumLeadingColumnsToSkip	Number of columns to skip in overscan, i.e.
overscanNumSigmaClip	Rejection threshold (sigma) for collapsing overscan before fit (float, default 3.0)
overscanNumTrailingColumnsToSkip	Number of columns to skip in overscan, i.e.
overscanOrder	Order of polynomial or to fit if overscan fit type is a polynomial, or number of spline knots if overscan fit type is a spline.
qa	QA related configuration options.
readNoise	The read noise to use if no Detector is present in the Exposure (float, default 0.0)
safe	Safety margin for CFHT sensors gain determination (float, default 0.95)
saturatedMaskName	Name of mask plane to use in saturation detection and interpolation (str, default 'SAT')
saturation	The saturation level to use if no Detector is present in the Exposure (ignored if NaN) (float, default nan)
strayLight	y-band stray light correction (ConfigurableInstance, default <class 'lsst.ip.isr.straylight.StrayLightConfig'>)
suspectMaskName	Name of mask plane to use for suspect pixels (str, default 'SUSPECT')
vignette	Vignetting task.

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])	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

assembleCcd

CCD assembly task (ConfigurableInstance, default <class 'lsst.ip.isr.assembleCcdTask.AssembleCcdConfig'>)

badStatistic

How to estimate the average value for BAD regions. (str, default 'MEANCLIP')

Allowed values:

'MEANCLIP'

Correct using the (clipped) mean of good data

'MEDIAN'

Correct using the median of the good data

'None'

Field is optional

biasDataProductName

Name of the bias data product (str, default 'bias')

brighterFatterApplyGain

Should the gain be applied when applying the brighter fatter correction? (bool, default True)

brighterFatterKernelFile

Kernel file used for the brighter fatter correction (str, default '')

brighterFatterLevel

The level at which to correct for brighter-fatter. (str, default 'DETECTOR')

Allowed values:

'AMP'

Every amplifier treated separately.

'DETECTOR'

One kernel per detector

'None'

Field is optional

brighterFatterMaxIter

Maximum number of iterations for the brighter fatter correction (int, default 10)

brighterFatterThreshold

Threshold used to stop iterating the brighter fatter correction. It is the absolute value of the difference between the current corrected image and the one from the previous iteration summed over all the pixels. (float, default 1000)

crosstalk

Intra-CCD crosstalk correction (ConfigurableInstance, default <class 'lsst.ip.isr.crosstalk.CrosstalkConfig'>)

darkDataProductName

Name of the dark data product (str, default 'dark')

datasetType

Dataset type for input data; users will typically leave this alone, but camera-specific ISR tasks will override it (str, default 'raw')

defaultFluxMag0T1

Default value for fluxMag0T1 (for an unrecognized filter). (float, default 158489319246.11172)

doAddDistortionModel

Apply a distortion model based on camera geometry to the WCS? (bool, default True)

doApplyGains

Correct the amplifiers for their gains instead of applying flat correction (bool, default False)

doAssembleCcd

Assemble amp-level exposures into a ccd-level exposure? (bool, default True)

doAssembleIsrExposures

Assemble amp-level calibration exposures into ccd-level exposure? (bool, default False)

doAttachTransmissionCurve

Construct and attach a wavelength-dependent throughput curve for this CCD image? (bool, default False)

doBias

Apply bias frame correction? (bool, default True)

doBrighterFatter

Apply the brighter fatter correction (bool, default False)

doCameraSpecificMasking

Mask camera-specific bad regions? (bool, default False)

doConvertIntToFloat

Convert integer raw images to floating point values? (bool, default True)

doCrosstalk

Apply intra-CCD crosstalk correction? (bool, default False)

doCrosstalkBeforeAssemble

Apply crosstalk correction before CCD assembly, and before trimming? (bool, default True)

doDark

Apply dark frame correction? (bool, default True)

doDefect

Apply correction for CCD defects, e.g. hot pixels? (bool, default True)

doEmpiricalReadNoise

Calculate empirical read noise instead of value from AmpInfo data? (bool, default False)

doFlat

Apply flat field correction? (bool, default True)

doFringe

Apply fringe correction? (bool, default True)

doLinearize

Correct for nonlinearity of the detector’s response? (bool, default True)

doMeasureBackground

Measure the background level on the reduced image? (bool, default False)

doNanInterpAfterFlat

If True, ensure we interpolate NaNs after flat-fielding, even if we also have to interpolate them before flat-fielding. (bool, default False)

doOverscan

Do overscan subtraction? (bool, default True)

doSaturation

Mask saturated pixels? (bool, default True)

doSaturationInterpolation

Perform interpolation over pixels masked as saturated? (bool, default True)

doSetBadRegions

Should we set the level of all BAD patches of the chip to the chip’s average value? (bool, default True)

doStrayLight

Subtract stray light in the y-band (due to encoder LEDs)? (bool, default False)

doSuspect

Mask suspect pixels? (bool, default True)

doTrimToMatchCalib

Trim raw data to match calibration bounding boxes? (bool, default False)

doTweakFlat

Tweak flats to match observed amplifier ratios? (bool, default False)

doUseAtmosphereTransmission

Load and use transmission_atmosphere (if doAttachTransmissionCurve is True)? (bool, default True)

doUseFilterTransmission

Load and use transmission_filter (if doAttachTransmissionCurve is True)? (bool, default True)

doUseOpticsTransmission

Load and use transmission_optics (if doAttachTransmissionCurve is True)? (bool, default True)

doUseSensorTransmission

Load and use transmission_sensor (if doAttachTransmissionCurve is True)? (bool, default True)

doVariance

Calculate variance? (bool, default True)

doVignette

Apply vignetting parameters? (bool, default False)

doWidenSaturationTrails

Widen bleed trails based on their width? (bool, default True)

doWrite

Persist postISRCCD? (bool, default True)

expectWcs

Expect input science images to have a WCS (set False for e.g. spectrographs). (bool, default True)

fallbackFilterName

Fallback default filter name for calibrations. (str, default None)

flatDataProductName

Name of the flat data product (str, default 'flat')

flatScalingType

The method for scaling the flat on the fly. (str, default 'USER')

Allowed values:

'USER'

Scale by flatUserScale

'MEAN'

Scale by the inverse of the mean

'MEDIAN'

Scale by the inverse of the median

'None'

Field is optional

flatUserScale

If flatScalingType is ‘USER’ then scale flat by this amount; ignored otherwise (float, default 1.0)

fluxMag0T1

The approximate flux of a zero-magnitude object in a one-second exposure, per filter. (Dict, default {'Unknown': 158489319246.11172})

fringe

Fringe subtraction task (ConfigurableInstance, default <class 'lsst.ip.isr.fringe.FringeConfig'>)

fringeAfterFlat

Do fringe subtraction after flat-fielding? (bool, default True)

fwhm

FWHM of PSF in arcseconds. (float, default 1.0)

gain

The gain to use if no Detector is present in the Exposure (ignored if NaN) (float, default nan)

growSaturationFootprintSize

Number of pixels by which to grow the saturation footprints (int, default 1)

history

masking

Masking task. (ConfigurableInstance, default <class 'lsst.ip.isr.masking.MaskingConfig'>)

normalizeGains

Normalize all the amplifiers in each CCD to have the same median value. (bool, default False)

numEdgeSuspect

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

overscanBiasJump

Fit the overscan in a piecewise-fashion to correct for bias jumps? (bool, default False)

overscanBiasJumpDevices

List of devices that need piecewise overscan correction. (List, default ())

overscanBiasJumpKeyword

Header keyword containing information about devices. (str, default 'NO_SUCH_KEY')

overscanBiasJumpLocation

Location of bias jump along y-axis. (int, default 0)

overscanFitType

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

'None'

Field is optional

overscanIsInt

Treat overscan as an integer image for purposes of overscan.FitType=MEDIAN (bool, default True)

overscanMaxDev

Maximum deviation from the median for overscan (float, default 1000.0)

overscanNumLeadingColumnsToSkip

Number of columns to skip in overscan, i.e. those closest to amplifier (int, default 0)

overscanNumSigmaClip

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

overscanNumTrailingColumnsToSkip

Number of columns to skip in overscan, i.e. those farthest from amplifier (int, default 0)

overscanOrder

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

qa

QA related configuration options. (IsrQaConfig, default <class 'lsst.ip.isr.isrQa.IsrQaConfig'>)

readNoise

The read noise to use if no Detector is present in the Exposure (float, default 0.0)

safe

Safety margin for CFHT sensors gain determination (float, default 0.95)

saturatedMaskName

Name of mask plane to use in saturation detection and interpolation (str, default 'SAT')

saturation

The saturation level to use if no Detector is present in the Exposure (ignored if NaN) (float, default nan)

strayLight

y-band stray light correction (ConfigurableInstance, default <class 'lsst.ip.isr.straylight.StrayLightConfig'>)

suspectMaskName

Name of mask plane to use for suspect pixels (str, default 'SUSPECT')

vignette

Vignetting task. (ConfigurableInstance, default <class 'lsst.ip.isr.vignette.VignetteConfig'>)

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:

0. Field name.
1. Field value.

See also

lsst.pex.config.Config.iteritems

iteritems()

Iterate over (field name, field value) pairs.

Yields:

item : tuple

Tuple items are:

0. Field name.
1. 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.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).

See also

lsst.pex.config.Config.saveToStream, lsst.pex.config.Config.load, lsst.pex.config.Config.loadFromStream

saveToStream(outfile, root='config')

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).

See also

lsst.pex.config.Config.save, lsst.pex.config.Config.load, lsst.pex.config.Config.loadFromStream

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