Linearizer

class lsst.ip.isr.Linearizer(table=None, **kwargs)

Bases: lsst.ip.isr.IsrCalib

Parameter set for linearization.

These parameters are included in lsst.afw.cameraGeom.Amplifier, but should be accessible externally to allow for testing.

Parameters:

table : numpy.array, optional

Lookup table; a 2-dimensional array of floats:

• one row for each row index (value of coef[0] in the amplifier)
• one column for each image value

To avoid copying the table the last index should vary fastest (numpy default “C” order)

detector : lsst.afw.cameraGeom.Detector, optional

Detector object. Passed to self.fromDetector() on init.

log : logging.Logger, optional

Logger to handle messages.

kwargs : dict, optional

Other keyword arguments to pass to the parent init.

Raises:

RuntimeError

Raised if the supplied table is not 2D, or if the table has fewer columns than rows (indicating that the indices are swapped).

Notes

The linearizer attributes stored are:

hasLinearity : bool

Whether a linearity correction is defined for this detector.

override : bool

Whether the detector parameters should be overridden.

ampNames : list [str]

List of amplifier names to correct.

linearityCoeffs : dict [str, numpy.array]

Coefficients to use in correction. Indexed by amplifier names. The format of the array depends on the type of correction to apply.

linearityType : dict [str, str]

Type of correction to use, indexed by amplifier names.

linearityBBox : dict [str, lsst.geom.Box2I]

Bounding box the correction is valid over, indexed by amplifier names.

fitParams : dict [str, numpy.array], optional

Linearity fit parameters used to construct the correction coefficients, indexed as above.

fitParamsErr : dict [str, numpy.array], optional

Uncertainty values of the linearity fit parameters used to construct the correction coefficients, indexed as above.

fitChiSq : dict [str, float], optional

Chi-squared value of the linearity fit, indexed as above.

fitResiduals : dict [str, numpy.array], optional

Residuals of the fit, indexed as above. Used for calculating photdiode corrections

linearFit : The linear fit to the low flux region of the curve.

[intercept, slope].

tableData : numpy.array, optional

Lookup table data for the linearity correction.

Attributes Summary

requiredAttributes

Methods Summary

apply(target)	Method to apply the calibration to the target object.
applyLinearity(image[, detector, log])	Apply the linearity to an image.
calibInfoFromDict(dictionary)	Handle common keywords.
determineCalibClass(metadata, message)	Attempt to find calibration class in metadata.
fromDetector(detector)	Read linearity parameters from a detector.
fromDict(dictionary)	Construct a calibration from a dictionary of properties
fromTable(tableList)	Read linearity from a FITS file.
getLinearityTypeByName(linearityTypeName)	Determine the linearity class to use from the type name.
getMetadata()	Retrieve metadata associated with this calibration.
readFits(filename, **kwargs)	Read calibration data from a FITS file.
readText(filename, **kwargs)	Read calibration representation from a yaml/ecsv file.
setMetadata(metadata)	Store a copy of the supplied metadata with this calibration.
toDict()	Return linearity parameters as a dict.
toTable()	Construct a list of tables containing the information in this calibration.
updateMetadata([setDate])	Update metadata keywords with new values.
validate([detector, amplifier])	Validate linearity for a detector/amplifier.
writeFits(filename)	Write calibration data to a FITS file.
writeText(filename[, format])	Write the calibration data to a text file.

Attributes Documentation

requiredAttributes

Methods Documentation

apply(target)

Method to apply the calibration to the target object.

Parameters:

target : object

Thing to validate against.

Returns:

valid : bool

Returns true if the calibration was applied correctly.

Raises:

NotImplementedError

Raised if not implemented.

applyLinearity(image, detector=None, log=None)

Apply the linearity to an image.

If the linearity parameters are populated, use those, otherwise use the values from the detector.

Parameters:

image : image

Image to correct.

detector : detector

Detector to use for linearity parameters if not already populated.

log : Logger, optional

Log object to use for logging.

calibInfoFromDict(dictionary)

Handle common keywords.

This isn’t an ideal solution, but until all calibrations expect to find everything in the metadata, they still need to search through dictionaries.

Parameters:

dictionary : dict or lsst.daf.base.PropertyList

Source for the common keywords.

Raises:

RuntimeError

Raised if the dictionary does not match the expected OBSTYPE.

classmethod determineCalibClass(metadata, message)

Attempt to find calibration class in metadata.

Parameters:

metadata : dict or lsst.daf.base.PropertyList

Metadata possibly containing a calibration class entry.

message : str

Message to include in any errors.

Returns:

calibClass : object

The class to use to read the file contents. Should be an lsst.ip.isr.IsrCalib subclass.

Raises:

ValueError

Raised if the resulting calibClass is the base lsst.ip.isr.IsrClass (which does not implement the content methods).

fromDetector(detector)

Read linearity parameters from a detector.

Parameters:

detector : lsst.afw.cameraGeom.detector

Input detector with parameters to use.

Returns:

calib : lsst.ip.isr.Linearizer

The calibration constructed from the detector.

classmethod fromDict(dictionary)

Construct a calibration from a dictionary of properties

Parameters:

dictionary : dict

Dictionary of properties

Returns:

calib : lsst.ip.isr.Linearity

Constructed calibration.

Raises:

RuntimeError

Raised if the supplied dictionary is for a different calibration.

classmethod fromTable(tableList)

Read linearity from a FITS file.

This method uses the fromDict method to create the calibration, after constructing an appropriate dictionary from the input tables.

Parameters:

tableList : list [astropy.table.Table]

afwTable read from input file name.

Returns:

linearity : Linearizer`

Linearity parameters.

Notes

The method reads a FITS file with 1 or 2 extensions. The metadata is read from the header of extension 1, which must exist. Then the table is loaded, and the [‘AMPLIFIER_NAME’, ‘TYPE’, ‘COEFFS’, ‘BBOX_X0’, ‘BBOX_Y0’, ‘BBOX_DX’, ‘BBOX_DY’] columns are read and used to set each dictionary by looping over rows. Extension 2 is then attempted to read in the try block (which only exists for lookup tables). It has a column named ‘LOOKUP_VALUES’ that contains a vector of the lookup entries in each row.

getLinearityTypeByName(linearityTypeName)

Determine the linearity class to use from the type name.

Parameters:

linearityTypeName : str

String name of the linearity type that is needed.

Returns:

linearityType : LinearizeBase

The appropriate linearity class to use. If no matching class is found, None is returned.

getMetadata()

Retrieve metadata associated with this calibration.

Returns:

meta : lsst.daf.base.PropertyList

Metadata. The returned PropertyList can be modified by the caller and the changes will be written to external files.

classmethod readFits(filename, **kwargs)

Read calibration data from a FITS file.

Parameters:

filename : str

Filename to read data from.

kwargs : dict or collections.abc.Mapping`, optional

Set of key=value pairs to pass to the fromTable method.

Returns:

calib : lsst.ip.isr.IsrCalib

Calibration contained within the file.

classmethod readText(filename, **kwargs)

Read calibration representation from a yaml/ecsv file.

Parameters:

filename : str

Name of the file containing the calibration definition.

kwargs : dict or collections.abc.Mapping`, optional

Set of key=value pairs to pass to the fromDict or fromTable methods.

Returns:

calib : IsrCalibType

Calibration class.

Raises:

RuntimeError

Raised if the filename does not end in “.ecsv” or “.yaml”.

setMetadata(metadata)

Store a copy of the supplied metadata with this calibration.

Parameters:

metadata : lsst.daf.base.PropertyList

Metadata to associate with the calibration. Will be copied and overwrite existing metadata.

toDict()

Return linearity parameters as a dict.

Returns:

outDict : dict:

toTable()

Construct a list of tables containing the information in this calibration.

The list of tables should create an identical calibration after being passed to this class’s fromTable method.

Returns:

tableList : list [astropy.table.Table]

List of tables containing the linearity calibration information.

updateMetadata(setDate=False, **kwargs)

Update metadata keywords with new values.

This calls the base class’s method after ensuring the required calibration keywords will be saved.

Parameters:

setDate : bool, optional

Update the CALIBDATE fields in the metadata to the current time. Defaults to False.

kwargs

Other keyword parameters to set in the metadata.

validate(detector=None, amplifier=None)

Validate linearity for a detector/amplifier.

Parameters:

detector : lsst.afw.cameraGeom.Detector, optional

Detector to validate, along with its amplifiers.

amplifier : lsst.afw.cameraGeom.Amplifier, optional

Single amplifier to validate.

Raises:

RuntimeError

Raised if there is a mismatch in linearity parameters, and the cameraGeom parameters are not being overridden.

writeFits(filename)

Write calibration data to a FITS file.

Parameters:

filename : str

Filename to write data to.

Returns:

used : str

The name of the file used to write the data.

writeText(filename, format='auto')

Write the calibration data to a text file.

Parameters:

filename : str

Name of the file to write.

format : str

Format to write the file as. Supported values are:

"auto" : Determine filetype from filename. "yaml" : Write as yaml. "ecsv" : Write as ecsv.

Returns:

used : str

The name of the file used to write the data. This may differ from the input if the format is explicitly chosen.

Raises:

RuntimeError

Raised if filename does not end in a known extension, or if all information cannot be written.

Notes

The file is written to YAML/ECSV format and will include any associated metadata.