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lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset Class Reference
Inheritance diagram for lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset:
lsst.ip.isr.calibType.IsrCalib

Public Member Functions

 __init__ (self, ampNames=[], ptcFitType=None, covMatrixSide=1, covMatrixSideFullCovFit=None, **kwargs)
 
 setAmpValuesPartialDataset (self, ampName, inputExpIdPair=(-1, -1), inputExpPairMjdStart=np.nan, rawExpTime=np.nan, rawMean=np.nan, rawVar=np.nan, rawDelta=np.nan, rowMeanVariance=np.nan, photoCharge=np.nan, photoChargeDelta=np.nan, ampOffset=np.nan, expIdMask=False, expIdRolloffMask=False, nPixelCovariance=-1, covariance=None, covSqrtWeights=None, gain=np.nan, noise=np.nan, overscanMedianLevel=np.nan, histVar=np.nan, histChi2Dof=np.nan, kspValue=0.0)
 
 setAuxValuesPartialDataset (self, auxDict)
 
 updateMetadata (self, **kwargs)
 
 fromDict (cls, dictionary)
 
 toDict (self)
 
 fromTable (cls, tableList)
 
 toTable (self)
 
 fromDetector (self, detector)
 
 appendPartialPtc (self, partialPtc)
 
 sort (self, sortIndex)
 
 getExpIdsUsed (self, ampName)
 
 getGoodAmps (self)
 
 getGoodPoints (self, ampName)
 
 validateGainNoiseTurnoffValues (self, ampName, doWarn=False)
 
 evalPtcModel (self, mu)
 
 requiredAttributes (self)
 
 requiredAttributes (self, value)
 
 __str__ (self)
 
 __eq__ (self, other)
 
 metadata (self)
 
 getMetadata (self)
 
 setMetadata (self, metadata)
 
 updateMetadataFromExposures (self, exposures)
 
 calibInfoFromDict (self, dictionary)
 
 determineCalibClass (cls, metadata, message)
 
 readText (cls, filename, **kwargs)
 
 writeText (self, filename, format="auto")
 
 readFits (cls, filename, **kwargs)
 
 writeFits (self, filename)
 
 validate (self, other=None)
 
 apply (self, target)
 

Public Attributes

str ptcFitType = ptcFitType
 
 ampNames = ampNames
 
 covMatrixSide = covMatrixSide
 
 covMatrixSideFullCovFit = covMatrixSide
 
list badAmps = []
 
dict inputExpIdPairs = {ampName: [] for ampName in ampNames}
 
dict inputExpPairMjdStartList = {ampName: np.array([]) for ampName in ampNames}
 
dict expIdMask = {ampName: np.array([], dtype=bool) for ampName in ampNames}
 
dict expIdRolloffMask = {ampName: np.array([], dtype=bool) for ampName in ampNames}
 
dict rawExpTimes = {ampName: np.array([]) for ampName in ampNames}
 
dict rawMeans = {ampName: np.array([]) for ampName in ampNames}
 
dict rawVars = {ampName: np.array([]) for ampName in ampNames}
 
dict rawDeltas = {ampName: np.array([]) for ampName in ampNames}
 
dict rowMeanVariance = {ampName: np.array([]) for ampName in ampNames}
 
dict photoCharges = {ampName: np.array([]) for ampName in ampNames}
 
dict photoChargeDeltas = {ampName: np.array([]) for ampName in ampNames}
 
dict ampOffsets = {ampName: np.array([]) for ampName in ampNames}
 
dict gain = {ampName: np.nan for ampName in ampNames}
 
dict gainUnadjusted = {ampName: np.nan for ampName in ampNames}
 
dict gainErr = {ampName: np.nan for ampName in ampNames}
 
dict gainList = {ampName: np.array([]) for ampName in ampNames}
 
dict overscanMedianLevelList = {ampName: np.array([]) for ampName in ampNames}
 
dict overscanMedian = {ampName: np.nan for ampName in ampNames}
 
dict overscanMedianSigma = {ampName: np.nan for ampName in ampNames}
 
dict noiseList = {ampName: np.array([]) for ampName in ampNames}
 
dict noise = {ampName: np.nan for ampName in ampNames}
 
dict noiseErr = {ampName: np.nan for ampName in ampNames}
 
dict histVars = {ampName: np.array([]) for ampName in ampNames}
 
dict histChi2Dofs = {ampName: np.array([]) for ampName in ampNames}
 
dict kspValues = {ampName: np.array([]) for ampName in ampNames}
 
dict ptcFitPars = {ampName: np.array([]) for ampName in ampNames}
 
dict ptcFitParsError = {ampName: np.array([]) for ampName in ampNames}
 
dict ptcFitChiSq = {ampName: np.nan for ampName in ampNames}
 
dict ptcTurnoff = {ampName: np.nan for ampName in ampNames}
 
dict ptcTurnoffSamplingError = {ampName: np.nan for ampName in ampNames}
 
dict ptcRolloff = {ampName: np.nan for ampName in ampNames}
 
dict ptcRolloffError = {ampName: np.nan for ampName in ampNames}
 
dict ptcRolloffTau = {ampName: np.nan for ampName in ampNames}
 
dict ptcRolloffTauError = {ampName: np.nan for ampName in ampNames}
 
dict nPixelCovariances = {ampName: -1 for ampName in ampNames}
 
dict covariances = {ampName: np.array([]) for ampName in ampNames}
 
dict covariancesModel = {ampName: np.array([]) for ampName in ampNames}
 
dict covariancesSqrtWeights = {ampName: np.array([]) for ampName in ampNames}
 
dict aMatrix = {ampName: np.array([]) for ampName in ampNames}
 
dict bMatrix = {ampName: np.array([]) for ampName in ampNames}
 
dict noiseMatrix = {ampName: np.array([]) for ampName in ampNames}
 
dict finalVars = {ampName: np.array([]) for ampName in ampNames}
 
dict finalModelVars = {ampName: np.array([]) for ampName in ampNames}
 
dict finalMeans = {ampName: np.array([]) for ampName in ampNames}
 
dict auxValues = {}
 
 requiredAttributes = set(["_OBSTYPE", "_SCHEMA", "_VERSION"])
 
 log = log if log else logging.getLogger(__name__)
 

Protected Member Functions

 _validateCovarianceMatrixSizes (self)
 

Protected Attributes

 _instrument = None
 
 _raftName = None
 
 _slotName = None
 
 _detectorName = None
 
 _detectorSerial = None
 
 _detectorId = None
 
 _filter = None
 
str _calibId = None
 
 _seqfile = None
 
 _seqname = None
 
 _seqcksum = None
 
 _metadata = PropertyList()
 
 _requiredAttributes
 

Static Protected Attributes

str _OBSTYPE = "generic"
 
str _SCHEMA = "NO SCHEMA"
 
int _VERSION = 0
 

Detailed Description

A simple class to hold the output data from the PTC task.

The dataset is made up of a dictionary for each item, keyed by the
amplifiers' names, which much be supplied at construction time.
New items cannot be added to the class to save accidentally saving to the
wrong property, and the class can be frozen if desired.
inputExpIdPairs records the exposures used to produce the data.
When fitPtc() or fitCovariancesAstier() is run, a mask is built up, which
is by definition always the same length as inputExpIdPairs, rawExpTimes,
rawMeans and rawVars, and is a list of bools, which are incrementally set
to False as points are discarded from the fits.

Parameters
----------
ampNames : `list`
    List with the names of the amplifiers of the detector at hand.
ptcFitType : `str`, optional
    Type of model fitted to the PTC: "EXPAPPROXIMATION",
    or "FULLCOVARIANCE" or "FULLCOVARIANCE_NO_B".
covMatrixSide : `int`, optional
    Maximum lag of measured covariances (size of square covariance
    matrices).
covMatrixSideFullCovFit : `int`, optional
    Maximum covariances lag for FULLCOVARIANCE fit. It should be less or
    equal than covMatrixSide.
kwargs : `dict`, optional
    Other keyword arguments to pass to the parent init.

Notes
-----
The stored attributes are:

badAmps : `list` [`str`]
    List with bad amplifiers names.
inputExpIdPairs : `dict`, [`str`, `list`]
    Dictionary keyed by amp names containing the input exposures IDs.
inputExpPairMjdStartList : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the start mjd from
    the first exposure in each flat pair.
expIdMask : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the mask produced after
    outlier rejection. The mask produced by the "FULLCOVARIANCE"
    option may differ from the one produced in the other two PTC
    fit types.
expIdRolloffMask : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the mask produced after
    outlier rejection and extended to fit the PTC rolloff.
rawExpTimes : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the unmasked exposure times.
rawMeans : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the unmasked average of the
    means of the exposures in each flat pair (units: adu).
rawVars : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the variance of the
    difference image of the exposures in each flat pair (units: adu^2).
rawDeltas : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the scaled unmasked delta of
    the means of the exposures in each flat pair (mean2 - mean1)
    (units: adu).
rowMeanVariance : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the variance of the
    means of the rows of the difference image of the exposures
    in each flat pair (units: adu^2).
histVars : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the variance of the
    difference image of the exposures in each flat pair estimated
    by fitting a Gaussian model.
histChi2Dofs : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the chi-squared per degree
    of freedom fitting the difference image to a Gaussian model.
kspValues : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the KS test p-value from
    fitting the difference image to a Gaussian model.
gain : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing the fitted gains. May be
    adjusted by amp-offset gain ratios if configured in PTC solver.
gainUnadjusted : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing unadjusted (raw) fit gain
    values. May be the same as gain values if amp-offset adjustment
    is not turned on.
gainErr : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing the errors on the
    fitted gains.
gainList : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the gain estimated from
    each flat pair.
overscanMedianLevelList : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the median overscan
    level from each input flat pair (units: adu).
overscanMedian : `dict `, [`str`, `float`]
    Dictionary keyed by amp names containing the median of
    overscanMedianLevelList[expIdMask] (units: adu).
overscanMedianSigma : `dict `, [`str`, `float`]
    Dictionary keyed by amp names containing the median absolute
    deviation of overscanMedianLevelList[expIdMask] (units: adu).
noiseList : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the mean overscan
    standard deviation from each flat pair (units: adu).
noise : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing the fitted noise
    (units: electron).
noiseErr : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing the errors on the fitted
    noise (units: electron).
ampOffsets : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing amp-to-amp offsets
    (units: adu).
ptcFitPars : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the raveled array fitted
    parameters of the PTC model.
ptcFitParsError : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the raveled array errors
    on the fitted parameters of the PTC model for ptcFitType.
ptcFitChiSq : `dict`, [`str`, `float`]
    Dictionary keyed by amp names containing the reduced chi squared
    of the fit.
ptcTurnoff : `dict` [`str, `float`]
    Flux value (in adu) where the variance of the PTC curve starts
    decreasing consistently.
ptcTurnoffSamplingError : `dict` [`str`, `float`]
    ``Sampling`` error on the ptcTurnoff, based on the flux sampling
    of the input PTC (units: adu).
ptcRolloff : `dict` [`str, `float`]
    Flux value (in adu) where the variance of the PTC curve begins starts
    to move away from the PTC model by some threshold.
ptcRolloffError : `dict` [`str`, `float`]
    Covariance error from the fit to the PTC rolloff (units: adu).
ptcRolloff : `dict` [`str, `float`]
    Curvature parameter of the PTC rolloff.
ptcRolloffError : `dict` [`str`, `float`]
    Fitting error of the curvature parameter of the PTC rolloff.
nPixelCovariances : `dict`, [`str`, `int`]
    Dictionary keyed by amp names containing the number of pixels
    that were used to measure the covariances.
covariances : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing a list of measured
    covariances per mean flux (units: adu^2).
covariancesModel : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containinging covariances model
    (Eq. 20 of Astier+19) per mean flux (units: adu^2).
covariancesSqrtWeights : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containinging sqrt. of covariances
    weights (units: 1/adu).
aMatrix : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the "a" parameters from
    the model in Eq. 20 of Astier+19 (units: 1/electron).
bMatrix : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the "b" parameters from
    the model in Eq. 20 of Astier+19 (units: 1/electron).
noiseMatrix : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the "noise" parameters from
    the model in Eq. 20 of Astier+19 (units: electron^2).
covariancesModelNoB : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing covariances model
    (with 'b'=0 in Eq. 20 of Astier+19) per mean flux (units:
    adu^2). Will be removed after v29.
aMatrixNoB : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the "a" parameters from the
    model in Eq. 20 of Astier+19 (and 'b' = 0) (units: 1/electron).
    Will be removed after v29.
noiseMatrixNoB : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the "noise" parameters from
    the model in Eq. 20 of Astier+19, with 'b' = 0 (units: electron^2).
    Will be removed after v29.
finalVars : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the masked variance of the
    difference image of each flat
    pair. If needed, each array will be right-padded with
    np.nan to match the length of rawExpTimes.
finalModelVars : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the masked modeled
    variance of the difference image of each flat pair. If needed, each
    array will be right-padded with np.nan to match the length of
    rawExpTimes.
finalMeans : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the masked average of the
    means of the exposures in each flat pair. If needed, each array
    will be right-padded with np.nan to match the length of
    rawExpTimes.
photoCharges : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the integrated photocharge
    for linearity calibration.
photoChargeDeltas : `dict`, [`str`, `np.ndarray`]
    Dictionary keyed by amp names containing the delta for the integrated
    photocharge (photocharge2 - photocharge1).
auxValues : `dict`, [`str`, `np.ndarray`]
    Dictionary of per-detector auxiliary header values that can be used
    for PTC, linearity computation.

Version 1.1 adds the `ptcTurnoff` attribute.
Version 1.2 adds the `histVars`, `histChi2Dofs`, and `kspValues`
    attributes.
Version 1.3 adds the `noiseMatrix` and `noiseMatrixNoB` attributes.
Version 1.4 adds the `auxValues` attribute.
Version 1.5 adds the `covMatrixSideFullCovFit` attribute.
Version 1.6 adds the `rowMeanVariance` attribute.
Version 1.7 adds the `noiseList` attribute.
Version 1.8 adds the `ptcTurnoffSamplingError` attribute.
Version 1.9 standardizes PTC noise units to electron.
Version 2.0 adds the `ampOffsets`, `gainUnadjusted`, and
    `gainList` attributes.
Version 2.1 deprecates the `covariancesModelNoB`, `aMatrixNoB`, and
    `noiseMatrixNoB` attributes.
Version 2.2 adds the `overscanMedianLevelList` and
    `inputExpPairMjdStartList` attributes.
Version 2.3 adds the `overscanMedian` and
    `overscanMedianSigma` attrbutes.
Version 2.4 adds the `nPixelCovariances` attribute.
Version 2.5 adds the `rawDeltas` and `photoChargeDeltas` attributes.
Version 2.6 adds the `expIdRolloffMask`, `ptcRolloff`, `ptcRolloffError`,
    `ptcRolloffTau`, and `ptcRolloffTauError` attributes. Also
    deprecates the POLYNOMIAL fit type.

Definition at line 66 of file ptcDataset.py.

Constructor & Destructor Documentation

◆ __init__()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.__init__ ( self,
ampNames = [],
ptcFitType = None,
covMatrixSide = 1,
covMatrixSideFullCovFit = None,
** kwargs )

Definition at line 299 of file ptcDataset.py.

Member Function Documentation

◆ __eq__()

lsst.ip.isr.calibType.IsrCalib.__eq__ ( self,
other )
inherited
Calibration equivalence.

Running ``calib.log.setLevel(0)`` enables debug statements to
identify problematic fields.

Definition at line 105 of file calibType.py.

◆ __str__()

lsst.ip.isr.calibType.IsrCalib.__str__ ( self)
inherited

Definition at line 102 of file calibType.py.

◆ _validateCovarianceMatrixSizes()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset._validateCovarianceMatrixSizes ( self)
protected
Ensure  covMatrixSideFullCovFit <= covMatrixSide.

Definition at line 1486 of file ptcDataset.py.

◆ appendPartialPtc()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.appendPartialPtc ( self,
partialPtc )
Append a partial PTC dataset to this dataset.

Parameters
----------
partialPtc : `lsst.ip.isr.PhotonTransferCurveDataset`
    Partial PTC to append. Should only have one element.

Definition at line 1109 of file ptcDataset.py.

◆ apply()

lsst.ip.isr.calibType.IsrCalib.apply ( self,
target )
inherited
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.

Definition at line 706 of file calibType.py.

◆ calibInfoFromDict()

lsst.ip.isr.calibType.IsrCalib.calibInfoFromDict ( self,
dictionary )
inherited
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.

Definition at line 325 of file calibType.py.

◆ determineCalibClass()

lsst.ip.isr.calibType.IsrCalib.determineCalibClass ( cls,
metadata,
message )
inherited
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).

Definition at line 391 of file calibType.py.

◆ evalPtcModel()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.evalPtcModel ( self,
mu )
Computes the covariance model at specific signal levels.

Parameters
----------
mu : `numpy.array`, (N,)
    List of mean signals in ADU.

Raises
------
RuntimeError
    Raised if ptcFitType is invalid.

Returns
-------
covModel : `numpy.array`, (N, M, M)
    Covariances model at mu (in ADU^2).

Notes
-----
Computes the covModel for all mu, and it returns
cov[N, M, M], where the variance model is cov[:,0,0].
Both mu and cov are in ADUs and ADUs squared. This
routine evaluates the approximation in Eq. 16 of
Astier+19 (1905.08677)
if self.ptcFitType == EXPAPPROXIMATION, and Eq. 20 of
Astier+19 if self.ptcFitType == FULLCOVARIANCE(_NO_B).

The EXPAPPROXIMATION model (Eq. 16 of Astier+19) is
only an approximation for the variance (cov[0,0]),
so the function returns covModel of shape (N,),
representing an array of [C_{00}]
if self.ptcFitType == EXPAPPROXIMATION.

Definition at line 1377 of file ptcDataset.py.

◆ fromDetector()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.fromDetector ( self,
detector )
Read metadata parameters from a detector.

Parameters
----------
detector : `lsst.afw.cameraGeom.detector`
    Input detector with parameters to use.

Returns
-------
calib : `lsst.ip.isr.PhotonTransferCurveDataset`
    The calibration constructed from the detector.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 1093 of file ptcDataset.py.

◆ fromDict()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.fromDict ( cls,
dictionary )
Construct a calibration from a dictionary of properties.
Must be implemented by the specific calibration subclasses.

Parameters
----------
dictionary : `dict`
    Dictionary of properties.

Returns
-------
calib : `lsst.ip.isr.PhotonTransferCurveDataset`
    Constructed calibration.

Raises
------
RuntimeError
    Raised if the supplied dictionary is for a different
    calibration.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 547 of file ptcDataset.py.

◆ fromTable()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.fromTable ( cls,
tableList )
Construct calibration from a list of tables.
This method uses the `fromDict` method to create the
calibration, after constructing an appropriate dictionary from
the input tables.

Parameters
----------
tableList : `list` [`lsst.afw.table.Table`]
    List of tables to use to construct the datasetPtc.

Returns
-------
calib : `lsst.ip.isr.PhotonTransferCurveDataset`
    The calibration defined in the tables.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 755 of file ptcDataset.py.

◆ getExpIdsUsed()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.getExpIdsUsed ( self,
ampName )
Get the exposures used, i.e. not discarded, for a given amp.
If no mask has been created yet, all exposures are returned.

Parameters
----------
ampName : `str`

Returns
-------
expIdsUsed : `list` [`tuple`]
    List of pairs of exposure ids used in PTC.

Definition at line 1285 of file ptcDataset.py.

◆ getGoodAmps()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.getGoodAmps ( self)
Get the good amps from this PTC.

Definition at line 1319 of file ptcDataset.py.

◆ getGoodPoints()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.getGoodPoints ( self,
ampName )
Get the good points used for a given amp in the PTC.

Parameters
----------
ampName : `str`
    Amplifier's name.

Returns
-------
goodPoints : `np.ndarray`
    Boolean array of good points used in PTC.

Definition at line 1323 of file ptcDataset.py.

◆ getMetadata()

lsst.ip.isr.calibType.IsrCalib.getMetadata ( self)
inherited
Retrieve metadata associated with this calibration.

Returns
-------
meta : `lsst.daf.base.PropertyList`
    Metadata. The returned `~lsst.daf.base.PropertyList` can be
    modified by the caller and the changes will be written to
    external files.

Definition at line 174 of file calibType.py.

◆ metadata()

lsst.ip.isr.calibType.IsrCalib.metadata ( self)
inherited

Definition at line 171 of file calibType.py.

◆ readFits()

lsst.ip.isr.calibType.IsrCalib.readFits ( cls,
filename,
** kwargs )
inherited
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.

Definition at line 517 of file calibType.py.

◆ readText()

lsst.ip.isr.calibType.IsrCalib.readText ( cls,
filename,
** kwargs )
inherited
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 : `~lsst.ip.isr.IsrCalibType`
    Calibration class.

Raises
------
RuntimeError
    Raised if the filename does not end in ".ecsv" or ".yaml".

Definition at line 425 of file calibType.py.

◆ requiredAttributes() [1/2]

lsst.ip.isr.calibType.IsrCalib.requiredAttributes ( self)
inherited

Definition at line 162 of file calibType.py.

◆ requiredAttributes() [2/2]

lsst.ip.isr.calibType.IsrCalib.requiredAttributes ( self,
value )
inherited

Definition at line 166 of file calibType.py.

◆ setAmpValuesPartialDataset()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.setAmpValuesPartialDataset ( self,
ampName,
inputExpIdPair = (-1, -1),
inputExpPairMjdStart = np.nan,
rawExpTime = np.nan,
rawMean = np.nan,
rawVar = np.nan,
rawDelta = np.nan,
rowMeanVariance = np.nan,
photoCharge = np.nan,
photoChargeDelta = np.nan,
ampOffset = np.nan,
expIdMask = False,
expIdRolloffMask = False,
nPixelCovariance = -1,
covariance = None,
covSqrtWeights = None,
gain = np.nan,
noise = np.nan,
overscanMedianLevel = np.nan,
histVar = np.nan,
histChi2Dof = np.nan,
kspValue = 0.0 )
Set the amp values for a partial PTC Dataset (from cpExtractPtcTask).

Parameters
----------
ampName : `str`
    Name of the amp to set the values.
inputExpIdPair : `tuple` [`int`]
    Exposure IDs of input pair.
inputExpPairMjdStart : `float`, optional
    The start MJD of first exposure in the flat pair.
rawExpTime : `float`, optional
    Exposure time for this exposure pair (units: sec).
rawMean : `float`, optional
    Average of the means of the exposures in this pair
    (units: adu).
rawVar : `float`, optional
    Variance of the difference of the exposures in this pair
    (units: adu^2).
rawDelta : `float`, optional
    Delta of the means of the exposure in this pair
    (units: adu).
rowMeanVariance : `float`, optional
    Variance of the means of the rows in the difference image
    of the exposures in this pair (units: adu^2).
photoCharge : `float`, optional
    Integrated photocharge for flat pair for linearity calibration
    (arbitrary units).
photoChargeDelta : `float`, optional
    Delta between integrated photocharge for the flat pair
    (arbitrary units).
ampOffset : `float`, optional
    Amp offset for this amplifier.
expIdMask : `bool`, optional
    Flag setting if this exposure pair should be used (True)
    or not used (False).
expIdRolloffMask : `bool`, optional
    Flag setting if this exposure pair should be used (True)
    or not used for rolloff search (False).
nPixelCovariance : `int`, optional
    Number of pixels that went into the covariance measurement.
covariance : `np.ndarray` or None, optional
    Measured covariance for this exposure pair (units: adu^2).
covSqrtWeights : `np.ndarray` or None, optional
    Measured sqrt of covariance weights in this exposure pair
    (units: 1/adu).
gain : `float`, optional
    Estimated gain for this exposure pair (units: electron/adu).
noise : `float`, optional
    Estimated read noise for this exposure pair (units: electron).
overscanMedianLevel : `float`, optional
    Average of the median overscan levels for this exposure pair.
    (units: adu)
histVar : `float`, optional
    Variance estimated from fitting a histogram with a Gaussian model
    (units: adu).
histChi2Dof : `float`, optional
    Chi-squared per degree of freedom from Gaussian histogram fit.
kspValue : `float`, optional
    KS test p-value from the Gaussian histogram fit.

Definition at line 382 of file ptcDataset.py.

◆ setAuxValuesPartialDataset()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.setAuxValuesPartialDataset ( self,
auxDict )
Set a dictionary of auxiliary values for a partial dataset.

Parameters
----------
auxDict : `dict` [`str`, `float`]
    Dictionary of float values.

Definition at line 514 of file ptcDataset.py.

◆ setMetadata()

lsst.ip.isr.calibType.IsrCalib.setMetadata ( self,
metadata )
inherited
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.

Reimplemented in lsst.ip.isr.transmissionCurve.IntermediateTransmissionCurve.

Definition at line 186 of file calibType.py.

◆ sort()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.sort ( self,
sortIndex )
Sort the components of the PTC by a given sort index.

The PTC is sorted in-place.

Parameters
----------
sortIndex : `list` or `np.ndarray`
    The sorting index, which must be the same length as
    the number of elements of the PTC.

Definition at line 1222 of file ptcDataset.py.

◆ toDict()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.toDict ( self)
Return a dictionary containing the calibration properties.
The dictionary should be able to be round-tripped through
`fromDict`.

Returns
-------
dictionary : `dict`
    Dictionary of properties.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 678 of file ptcDataset.py.

◆ toTable()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.toTable ( self)
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.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 1005 of file ptcDataset.py.

◆ updateMetadata()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.updateMetadata ( self,
** kwargs )
Update calibration metadata.
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.

Reimplemented from lsst.ip.isr.calibType.IsrCalib.

Definition at line 531 of file ptcDataset.py.

◆ updateMetadataFromExposures()

lsst.ip.isr.calibType.IsrCalib.updateMetadataFromExposures ( self,
exposures )
inherited
Extract and unify metadata information.

Parameters
----------
exposures : `list`
    Exposures or other calibrations to scan.

Definition at line 294 of file calibType.py.

◆ validate()

lsst.ip.isr.calibType.IsrCalib.validate ( self,
other = None )
inherited
Validate that this calibration is defined and can be used.

Parameters
----------
other : `object`, optional
    Thing to validate against.

Returns
-------
valid : `bool`
    Returns true if the calibration is valid and appropriate.

Reimplemented in lsst.ip.isr.linearize.Linearizer, and lsst.ip.isr.photodiodeCorrection.PhotodiodeCorrection.

Definition at line 691 of file calibType.py.

◆ validateGainNoiseTurnoffValues()

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.validateGainNoiseTurnoffValues ( self,
ampName,
doWarn = False )
Ensure the gain, read noise, and PTC turnoff have
sensible values.

Parameters
----------
ampName : `str`
    Amplifier's name.

Definition at line 1338 of file ptcDataset.py.

◆ writeFits()

lsst.ip.isr.calibType.IsrCalib.writeFits ( self,
filename )
inherited
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.

Reimplemented in lsst.ip.isr.transmissionCurve.IntermediateTransmissionCurve.

Definition at line 565 of file calibType.py.

◆ writeText()

lsst.ip.isr.calibType.IsrCalib.writeText ( self,
filename,
format = "auto" )
inherited
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.

Definition at line 463 of file calibType.py.

Member Data Documentation

◆ _calibId

str lsst.ip.isr.calibType.IsrCalib._calibId = None
protectedinherited

Definition at line 76 of file calibType.py.

◆ _detectorId

lsst.ip.isr.calibType.IsrCalib._detectorId = None
protectedinherited

Definition at line 74 of file calibType.py.

◆ _detectorName

lsst.ip.isr.calibType.IsrCalib._detectorName = None
protectedinherited

Definition at line 72 of file calibType.py.

◆ _detectorSerial

lsst.ip.isr.calibType.IsrCalib._detectorSerial = None
protectedinherited

Definition at line 73 of file calibType.py.

◆ _filter

lsst.ip.isr.calibType.IsrCalib._filter = None
protectedinherited

Definition at line 75 of file calibType.py.

◆ _instrument

lsst.ip.isr.calibType.IsrCalib._instrument = None
protectedinherited

Definition at line 69 of file calibType.py.

◆ _metadata

lsst.ip.isr.calibType.IsrCalib._metadata = PropertyList()
protectedinherited

Definition at line 80 of file calibType.py.

◆ _OBSTYPE

str lsst.ip.isr.calibType.IsrCalib._OBSTYPE = "generic"
staticprotectedinherited

Definition at line 64 of file calibType.py.

◆ _raftName

lsst.ip.isr.calibType.IsrCalib._raftName = None
protectedinherited

Definition at line 70 of file calibType.py.

◆ _requiredAttributes

lsst.ip.isr.calibType.IsrCalib._requiredAttributes
protectedinherited

Definition at line 115 of file calibType.py.

◆ _SCHEMA

str lsst.ip.isr.calibType.IsrCalib._SCHEMA = "NO SCHEMA"
staticprotectedinherited

Definition at line 65 of file calibType.py.

◆ _seqcksum

lsst.ip.isr.calibType.IsrCalib._seqcksum = None
protectedinherited

Definition at line 79 of file calibType.py.

◆ _seqfile

lsst.ip.isr.calibType.IsrCalib._seqfile = None
protectedinherited

Definition at line 77 of file calibType.py.

◆ _seqname

lsst.ip.isr.calibType.IsrCalib._seqname = None
protectedinherited

Definition at line 78 of file calibType.py.

◆ _slotName

lsst.ip.isr.calibType.IsrCalib._slotName = None
protectedinherited

Definition at line 71 of file calibType.py.

◆ _VERSION

int lsst.ip.isr.calibType.IsrCalib._VERSION = 0
staticprotectedinherited

Definition at line 66 of file calibType.py.

◆ aMatrix

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.aMatrix = {ampName: np.array([]) for ampName in ampNames}

Definition at line 353 of file ptcDataset.py.

◆ ampNames

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ampNames = ampNames

Definition at line 302 of file ptcDataset.py.

◆ ampOffsets

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ampOffsets = {ampName: np.array([]) for ampName in ampNames}

Definition at line 322 of file ptcDataset.py.

◆ auxValues

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.auxValues = {}

Definition at line 362 of file ptcDataset.py.

◆ badAmps

list lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.badAmps = []

Definition at line 309 of file ptcDataset.py.

◆ bMatrix

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.bMatrix = {ampName: np.array([]) for ampName in ampNames}

Definition at line 354 of file ptcDataset.py.

◆ covariances

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.covariances = {ampName: np.array([]) for ampName in ampNames}

Definition at line 350 of file ptcDataset.py.

◆ covariancesModel

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.covariancesModel = {ampName: np.array([]) for ampName in ampNames}

Definition at line 351 of file ptcDataset.py.

◆ covariancesSqrtWeights

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.covariancesSqrtWeights = {ampName: np.array([]) for ampName in ampNames}

Definition at line 352 of file ptcDataset.py.

◆ covMatrixSide

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.covMatrixSide = covMatrixSide

Definition at line 303 of file ptcDataset.py.

◆ covMatrixSideFullCovFit

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.covMatrixSideFullCovFit = covMatrixSide

Definition at line 305 of file ptcDataset.py.

◆ expIdMask

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.expIdMask = {ampName: np.array([], dtype=bool) for ampName in ampNames}

Definition at line 313 of file ptcDataset.py.

◆ expIdRolloffMask

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.expIdRolloffMask = {ampName: np.array([], dtype=bool) for ampName in ampNames}

Definition at line 314 of file ptcDataset.py.

◆ finalMeans

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.finalMeans = {ampName: np.array([]) for ampName in ampNames}

Definition at line 359 of file ptcDataset.py.

◆ finalModelVars

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.finalModelVars = {ampName: np.array([]) for ampName in ampNames}

Definition at line 358 of file ptcDataset.py.

◆ finalVars

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.finalVars = {ampName: np.array([]) for ampName in ampNames}

Definition at line 357 of file ptcDataset.py.

◆ gain

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.gain = {ampName: np.nan for ampName in ampNames}

Definition at line 324 of file ptcDataset.py.

◆ gainErr

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.gainErr = {ampName: np.nan for ampName in ampNames}

Definition at line 326 of file ptcDataset.py.

◆ gainList

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.gainList = {ampName: np.array([]) for ampName in ampNames}

Definition at line 327 of file ptcDataset.py.

◆ gainUnadjusted

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.gainUnadjusted = {ampName: np.nan for ampName in ampNames}

Definition at line 325 of file ptcDataset.py.

◆ histChi2Dofs

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.histChi2Dofs = {ampName: np.array([]) for ampName in ampNames}

Definition at line 336 of file ptcDataset.py.

◆ histVars

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.histVars = {ampName: np.array([]) for ampName in ampNames}

Definition at line 335 of file ptcDataset.py.

◆ inputExpIdPairs

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.inputExpIdPairs = {ampName: [] for ampName in ampNames}

Definition at line 311 of file ptcDataset.py.

◆ inputExpPairMjdStartList

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.inputExpPairMjdStartList = {ampName: np.array([]) for ampName in ampNames}

Definition at line 312 of file ptcDataset.py.

◆ kspValues

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.kspValues = {ampName: np.array([]) for ampName in ampNames}

Definition at line 337 of file ptcDataset.py.

◆ log

lsst.ip.isr.calibType.IsrCalib.log = log if log else logging.getLogger(__name__)
inherited

Definition at line 96 of file calibType.py.

◆ noise

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.noise = {ampName: np.nan for ampName in ampNames}

Definition at line 332 of file ptcDataset.py.

◆ noiseErr

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.noiseErr = {ampName: np.nan for ampName in ampNames}

Definition at line 333 of file ptcDataset.py.

◆ noiseList

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.noiseList = {ampName: np.array([]) for ampName in ampNames}

Definition at line 331 of file ptcDataset.py.

◆ noiseMatrix

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.noiseMatrix = {ampName: np.array([]) for ampName in ampNames}

Definition at line 355 of file ptcDataset.py.

◆ nPixelCovariances

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.nPixelCovariances = {ampName: -1 for ampName in ampNames}

Definition at line 349 of file ptcDataset.py.

◆ overscanMedian

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.overscanMedian = {ampName: np.nan for ampName in ampNames}

Definition at line 329 of file ptcDataset.py.

◆ overscanMedianLevelList

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.overscanMedianLevelList = {ampName: np.array([]) for ampName in ampNames}

Definition at line 328 of file ptcDataset.py.

◆ overscanMedianSigma

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.overscanMedianSigma = {ampName: np.nan for ampName in ampNames}

Definition at line 330 of file ptcDataset.py.

◆ photoChargeDeltas

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.photoChargeDeltas = {ampName: np.array([]) for ampName in ampNames}

Definition at line 321 of file ptcDataset.py.

◆ photoCharges

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.photoCharges = {ampName: np.array([]) for ampName in ampNames}

Definition at line 320 of file ptcDataset.py.

◆ ptcFitChiSq

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcFitChiSq = {ampName: np.nan for ampName in ampNames}

Definition at line 341 of file ptcDataset.py.

◆ ptcFitPars

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcFitPars = {ampName: np.array([]) for ampName in ampNames}

Definition at line 339 of file ptcDataset.py.

◆ ptcFitParsError

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcFitParsError = {ampName: np.array([]) for ampName in ampNames}

Definition at line 340 of file ptcDataset.py.

◆ ptcFitType

lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcFitType = ptcFitType

Definition at line 301 of file ptcDataset.py.

◆ ptcRolloff

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcRolloff = {ampName: np.nan for ampName in ampNames}

Definition at line 344 of file ptcDataset.py.

◆ ptcRolloffError

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcRolloffError = {ampName: np.nan for ampName in ampNames}

Definition at line 345 of file ptcDataset.py.

◆ ptcRolloffTau

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcRolloffTau = {ampName: np.nan for ampName in ampNames}

Definition at line 346 of file ptcDataset.py.

◆ ptcRolloffTauError

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcRolloffTauError = {ampName: np.nan for ampName in ampNames}

Definition at line 347 of file ptcDataset.py.

◆ ptcTurnoff

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcTurnoff = {ampName: np.nan for ampName in ampNames}

Definition at line 342 of file ptcDataset.py.

◆ ptcTurnoffSamplingError

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.ptcTurnoffSamplingError = {ampName: np.nan for ampName in ampNames}

Definition at line 343 of file ptcDataset.py.

◆ rawDeltas

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.rawDeltas = {ampName: np.array([]) for ampName in ampNames}

Definition at line 318 of file ptcDataset.py.

◆ rawExpTimes

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.rawExpTimes = {ampName: np.array([]) for ampName in ampNames}

Definition at line 315 of file ptcDataset.py.

◆ rawMeans

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.rawMeans = {ampName: np.array([]) for ampName in ampNames}

Definition at line 316 of file ptcDataset.py.

◆ rawVars

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.rawVars = {ampName: np.array([]) for ampName in ampNames}

Definition at line 317 of file ptcDataset.py.

◆ requiredAttributes

lsst.ip.isr.calibType.IsrCalib.requiredAttributes = set(["_OBSTYPE", "_SCHEMA", "_VERSION"])
inherited

Definition at line 90 of file calibType.py.

◆ rowMeanVariance

dict lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset.rowMeanVariance = {ampName: np.array([]) for ampName in ampNames}

Definition at line 319 of file ptcDataset.py.


The documentation for this class was generated from the following file: