PhotonTransferCurveExtractTask¶

class lsst.cp.pipe.PhotonTransferCurveExtractTask(*, config: Optional[PipelineTaskConfig] = None, log: Optional[Union[logging.Logger, LsstLogAdapter]] = None, initInputs: Optional[Dict[str, Any]] = None, **kwargs)¶

Bases: lsst.pipe.base.PipelineTask, lsst.pipe.base.CmdLineTask

Task to measure covariances from flat fields.

This task receives as input a list of flat-field images (flats), and sorts these flats in pairs taken at the same time (the task will raise if there is one one flat at a given exposure time, and it will discard extra flats if there are more than two per exposure time). This task measures the mean, variance, and covariances from a region (e.g., an amplifier) of the difference image of the two flats with the same exposure time.

The variance is calculated via afwMath, and the covariance via the methods in Astier+19 (appendix A). In theory, var = covariance[0,0]. This should be validated, and in the future, we may decide to just keep one (covariance). At this moment, if the two values differ by more than the value of thresholdDiffAfwVarVsCov00 (default: 1%), a warning will be issued.

The measured covariances at a given exposure time (along with other quantities such as the mean) are stored in a PTC dataset object (PhotonTransferCurveDataset), which gets partially filled at this stage (the remainder of the attributes of the dataset will be filled after running the second task of the PTC-measurement pipeline, PhotonTransferCurveSolveTask).

The number of partially-filled PhotonTransferCurveDataset objects will be less than the number of input exposures because the task combines input flats in pairs. However, it is required at this moment that the number of input dimensions matches bijectively the number of output dimensions. Therefore, a number of “dummy” PTC datasets are inserted in the output list. This output list will then be used as input of the next task in the PTC-measurement pipeline, PhotonTransferCurveSolveTask, which will assemble the multiple PhotonTransferCurveDataset objects into a single one in order to fit the measured covariances as a function of flux to one of three models (see PhotonTransferCurveSolveTask for details).

Reference: Astier+19: “The Shape of the Photon Transfer Curve of CCD sensors”, arXiv:1905.08677.

Attributes Summary

canMultiprocess

Methods Summary

`applyOverrides`(config)	A hook to allow a task to change the values of its config after the camera-specific overrides are loaded but before any command-line overrides are applied.
`emptyMetadata`()	Empty (clear) the metadata for this Task and all sub-Tasks.
`getAllSchemaCatalogs`()	Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.
`getFullMetadata`()	Get metadata for all tasks.
`getFullName`()	Get the task name as a hierarchical name including parent task names.
`getGainFromFlatPair`(exposure1, exposure2[, …])	Estimate the gain from a single pair of flats.
`getName`()	Get the name of the task.
`getReadNoiseFromMetadata`(taskMetadata, ampName)	Gets readout noise for an amp from ISR metadata.
`getResourceConfig`()	Return resource configuration for this task.
`getSchemaCatalogs`()	Get the schemas generated by this task.
`getTaskDict`()	Get a dictionary of all tasks as a shallow copy.
`makeCovArray`(inputTuple, maxRangeFromTuple)	Make covariances array from tuple.
`makeField`(doc)	Make a `lsst.pex.config.ConfigurableField` for this task.
`makeSubtask`(name, **keyArgs)	Create a subtask as a new instance as the `name` attribute of this task.
`measureMeanVarCov`(exposure1, exposure2[, region])	Calculate the mean of each of two exposures and the variance and covariance of their difference.
`parseAndRun`([args, config, log, doReturnResults])	Parse an argument list and run the command.
`run`(inputExp, inputDims, taskMetadata)	Measure covariances from difference of flat pairs
`runQuantum`(butlerQC, inputRefs, outputRefs)	Ensure that the input and output dimensions are passed along.
`timer`(name, logLevel)	Context manager to log performance data for an arbitrary block of code.
`writeConfig`(butler[, clobber, doBackup])	Write the configuration used for processing the data, or check that an existing one is equal to the new one if present.
`writeMetadata`(dataRef)	Write the metadata produced from processing the data.
`writePackageVersions`(butler[, clobber, …])	Compare and write package versions.
`writeSchemas`(butler[, clobber, doBackup])	Write the schemas returned by `lsst.pipe.base.Task.getAllSchemaCatalogs`.

Attributes Documentation

canMultiprocess = True¶

Methods Documentation

classmethod applyOverrides(config)¶

A hook to allow a task to change the values of its config after the camera-specific overrides are loaded but before any command-line overrides are applied.

Parameters:	config : instance of task’s `ConfigClass` Task configuration.

Notes

This is necessary in some cases because the camera-specific overrides may retarget subtasks, wiping out changes made in ConfigClass.setDefaults. See LSST Trac ticket #2282 for more discussion.

Warning

This is called by CmdLineTask.parseAndRun; other ways of constructing a config will not apply these overrides.

emptyMetadata() → None¶: Empty (clear) the metadata for this Task and all sub-Tasks.

getAllSchemaCatalogs() → Dict[str, Any]¶

Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.

Returns:	schemacatalogs : `dict` Keys are butler dataset type, values are a empty catalog (an instance of the appropriate `lsst.afw.table` Catalog type) for all tasks in the hierarchy, from the top-level task down through all subtasks.

Notes

This method may be called on any task in the hierarchy; it will return the same answer, regardless.

The default implementation should always suffice. If your subtask uses schemas the override Task.getSchemaCatalogs, not this method.

getFullMetadata() → lsst.pipe.base._task_metadata.TaskMetadata¶

Get metadata for all tasks.

Returns:	metadata : `TaskMetadata` The keys are the full task name. Values are metadata for the top-level task and all subtasks, sub-subtasks, etc.

Notes

The returned metadata includes timing information (if @timer.timeMethod is used) and any metadata set by the task. The name of each item consists of the full task name with . replaced by :, followed by . and the name of the item, e.g.:

topLevelTaskName:subtaskName:subsubtaskName.itemName

using : in the full task name disambiguates the rare situation that a task has a subtask and a metadata item with the same name.

getFullName() → str¶

Get the task name as a hierarchical name including parent task names.

Returns:	fullName : `str` The full name consists of the name of the parent task and each subtask separated by periods. For example: The full name of top-level task “top” is simply “top”. The full name of subtask “sub” of top-level task “top” is “top.sub”. The full name of subtask “sub2” of subtask “sub” of top-level task “top” is “top.sub.sub2”.

getGainFromFlatPair(exposure1, exposure2, correctionType='NONE', readNoise=None, region=None)¶

Estimate the gain from a single pair of flats.

The basic premise is 1/g = <(I1 - I2)^2/(I1 + I2)> = 1/const, where I1 and I2 correspond to flats 1 and 2, respectively. Corrections for the variable QE and the read-noise are then made following the derivation in Robert Lupton’s forthcoming book, which gets

1/g = <(I1 - I2)^2/(I1 + I2)> - 1/mu(sigma^2 - 1/2g^2).

This is a quadratic equation, whose solutions are given by:

g = mu +/- sqrt(2*sigma^2 - 2*const*mu + mu^2)/(2*const*mu*2

2*sigma^2)

where ‘mu’ is the average signal level and ‘sigma’ is the amplifier’s readnoise. The positive solution will be used. The way the correction is applied depends on the value supplied for correctionType.

correctionType is one of [‘NONE’, ‘SIMPLE’ or ‘FULL’]

‘NONE’ : uses the 1/g = <(I1 - I2)^2/(I1 + I2)> formula. ‘SIMPLE’ : uses the gain from the ‘NONE’ method for the

1/2g^2 term.

‘FULL’ : solves the full equation for g, discarding the: non-physical solution to the resulting quadratic.

Parameters:	exposure1 : `lsst.afw.image.exposure.ExposureF` First exposure of flat field pair. exposure2 : `lsst.afw.image.exposure.ExposureF` Second exposure of flat field pair. correctionType : `str`, optional The correction applied, one of [‘NONE’, ‘SIMPLE’, ‘FULL’] readNoise : `float`, optional Amplifier readout noise (ADU). region : `lsst.geom.Box2I`, optional Region of each exposure where to perform the calculations (e.g, an amplifier).
Returns:	gain : `float` Gain, in e/ADU.
Raises:	RuntimeError: if `correctionType` is not one of ‘NONE’, ‘SIMPLE’, or ‘FULL’. RuntimeError: if a readout noise value is not provided when `correctionType` is different from ‘NONE’.

getName() → str¶

Get the name of the task.

Returns:	taskName : `str` Name of the task.

See also

Task.getAllSchemaCatalogs

Notes

Warning

Subclasses that use schemas must override this method. The default implementation returns an empty dict.

This method may be called at any time after the Task is constructed, which means that all task schemas should be computed at construction time, not when data is actually processed. This reflects the philosophy that the schema should not depend on the data.

Returning catalogs rather than just schemas allows us to save e.g. slots for SourceCatalog as well.

getTaskDict() → Dict[str, weakref.ReferenceType[Task]]¶

Get a dictionary of all tasks as a shallow copy.

Returns:	taskDict : `dict` Dictionary containing full task name: task object for the top-level task and all subtasks, sub-subtasks, etc.

makeCovArray(inputTuple, maxRangeFromTuple)¶

Make covariances array from tuple.

Parameters:

inputTuple : numpy.ndarray

Structured array with rows with at least (mu, afwVar, cov, var, i, j, npix), where: mu : float

0.5*(m1 + m2), where mu1 is the mean value of flat1 and mu2 is the mean value of flat2.

afwVar : float: Variance of difference flat, calculated with afw.
cov : float: Covariance value at lag(i, j)
var : float: Variance(covariance value at lag(0, 0))
i : int: Lag in dimension “x”.
j : int: Lag in dimension “y”.
npix : int: Number of pixels used for covariance calculation.

maxRangeFromTuple : int

Maximum range to select from tuple.

Returns:

cov : numpy.array: Covariance arrays, indexed by mean signal mu.
vCov : numpy.array: Variance arrays, indexed by mean signal mu.
muVals : numpy.array: List of mean signal values.

classmethod makeField(doc: str) → lsst.pex.config.configurableField.ConfigurableField¶

Make a lsst.pex.config.ConfigurableField for this task.

Parameters:	doc : `str` Help text for the field.
Returns:	configurableField : `lsst.pex.config.ConfigurableField` A `ConfigurableField` for this task.

Examples

Provides a convenient way to specify this task is a subtask of another task.

Here is an example of use:

class OtherTaskConfig(lsst.pex.config.Config):
    aSubtask = ATaskClass.makeField("brief description of task")

makeSubtask(name: str, **keyArgs) → None¶

Create a subtask as a new instance as the name attribute of this task.

Parameters:	name : `str` Brief name of the subtask. keyArgs Extra keyword arguments used to construct the task. The following arguments are automatically provided and cannot be overridden: “config”. “parentTask”.

Notes

The subtask must be defined by Task.config.name, an instance of ConfigurableField or RegistryField.

measureMeanVarCov(exposure1, exposure2, region=None)¶

Calculate the mean of each of two exposures and the variance and covariance of their difference. The variance is calculated via afwMath, and the covariance via the methods in Astier+19 (appendix A). In theory, var = covariance[0,0]. This should be validated, and in the future, we may decide to just keep one (covariance).

Parameters:

exposure1 : lsst.afw.image.exposure.ExposureF: First exposure of flat field pair.
exposure2 : lsst.afw.image.exposure.ExposureF: Second exposure of flat field pair.
region : lsst.geom.Box2I, optional: Region of each exposure where to perform the calculations (e.g, an amplifier).

Returns:

mu : float or NaN

0.5*(mu1 + mu2), where mu1, and mu2 are the clipped means of the regions in both exposures. If either mu1 or m2 are NaN’s, the returned value is NaN.

varDiff : float or NaN

Half of the clipped variance of the difference of the regions inthe two input exposures. If either mu1 or m2 are NaN’s, the returned value is NaN.

covDiffAstier : list or NaN

List with tuples of the form (dx, dy, var, cov, npix), where:

dx : int: Lag in x
dy : int: Lag in y
var : float: Variance at (dx, dy).
cov : float: Covariance at (dx, dy).
nPix : int: Number of pixel pairs used to evaluate var and cov.

If either mu1 or m2 are NaN’s, the returned value is NaN.

classmethod parseAndRun(args=None, config=None, log=None, doReturnResults=False)¶

Parse an argument list and run the command.

Parameters:

args : list, optional: List of command-line arguments; if None use sys.argv.
config : lsst.pex.config.Config-type, optional: Config for task. If None use Task.ConfigClass.
log : logging.Logger-type, optional: Log. If None use the default log.
doReturnResults : bool, optional: If True, return the results of this task. Default is False. This is only intended for unit tests and similar use. It can easily exhaust memory (if the task returns enough data and you call it enough times) and it will fail when using multiprocessing if the returned data cannot be pickled.

Returns:

struct : lsst.pipe.base.Struct

Fields are:

argumentParser: the argument parser (lsst.pipe.base.ArgumentParser).
parsedCmd: the parsed command returned by the argument parser’s parse_args method (argparse.Namespace).
taskRunner: the task runner used to run the task (an instance of Task.RunnerClass).
resultList: results returned by the task runner’s run method, one entry per invocation (list). This will typically be a list of Struct, each containing at least an exitStatus integer (0 or 1); see Task.RunnerClass (TaskRunner by default) for more details.

Notes

Calling this method with no arguments specified is the standard way to run a command-line task from the command-line. For an example see pipe_tasks bin/makeSkyMap.py or almost any other file in that directory.

If one or more of the dataIds fails then this routine will exit (with a status giving the number of failed dataIds) rather than returning this struct; this behaviour can be overridden by specifying the --noExit command-line option.

run(inputExp, inputDims, taskMetadata)¶

Measure covariances from difference of flat pairs

Parameters:	inputExp : `dict` [`float`, `list` [`DeferredDatasetRef`]] Dictionary that groups references to flat-field exposures that have the same exposure time (seconds), or that groups them sequentially by their exposure id. inputDims : `list` List of exposure IDs. taskMetadata : `list` [`lsst.pipe.base.TaskMetadata`] List of exposures metadata from ISR.
Returns:	results : `lsst.pipe.base.Struct` The resulting Struct contains: `outputCovariances` A list containing the per-pair PTC measurements (`list` [`lsst.ip.isr.PhotonTransferCurveDataset`])

runQuantum(butlerQC, inputRefs, outputRefs)¶

Ensure that the input and output dimensions are passed along.

Parameters:	butlerQC : `ButlerQuantumContext` Butler to operate on. inputRefs : `InputQuantizedConnection` Input data refs to load. ouptutRefs : `OutputQuantizedConnection` Output data refs to persist.

timer(name: str, logLevel: int = 10) → Iterator[None]¶

Context manager to log performance data for an arbitrary block of code.

Parameters:	name : `str` Name of code being timed; data will be logged using item name: `Start` and `End`. logLevel A `logging` level constant.

Parameters:	taskMetadata : `list` [`lsst.pipe.base.TaskMetadata`] List of exposures metadata from ISR. ampName : `str` Amplifier name.
Returns:	readNoise : `float` Median of the overscan readnoise in the post-ISR metadata of the input exposures (ADU). Returns ‘None’ if the median could not be calculated.

Navigation

PhotonTransferCurveExtractTask¶