lsst.pipe.drivers.constructCalibs.FringeTask Class Reference

Inheritance diagram for lsst.pipe.drivers.constructCalibs.FringeTask:

Public Member Functions
def	applyOverrides (cls, config)
def	__init__ (self, args, kwargs)
def	processSingle (self, sensorRef)
def	batchWallTime (cls, time, parsedCmd, numCores)
def	runDataRef (self, expRefList, butler, calibId)
	Construct a calib from a list of exposure references. More...
def	getOutputId (self, expRefList, calibId)
	Generate the data identifier for the output calib. More...
def	getMjd (self, butler, dataId, timescale=dafBase.DateTime.UTC)
def	getFilter (self, butler, dataId)
def	addMissingKeys (self, dataId, butler, missingKeys=None, calibName=None)
def	updateMetadata (self, calibImage, exposureTime, darkTime=None, kwargs)
	Update the metadata from the VisitInfo. More...
def	scatterProcess (self, pool, ccdIdLists)
	Scatter the processing among the nodes. More...
def	process (self, cache, ccdId, outputName="postISRCCD", kwargs)
	Process a CCD, specified by a data identifier. More...
def	processWrite (self, dataRef, exposure, outputName="postISRCCD")
	Write the processed CCD. More...
def	processResult (self, exposure)
def	scale (self, ccdIdLists, data)
	Determine scaling across CCDs and exposures. More...
def	scatterCombine (self, pool, outputId, ccdIdLists, scales)
	Scatter the combination of exposures across multiple nodes. More...
def	getFullyQualifiedOutputId (self, ccdName, butler, outputId)
def	combine (self, cache, struct, outputId)
	Combine multiple exposures of a particular CCD and write the output. More...
def	calculateOutputHeaderFromRaws (self, butler, calib, dataIdList, outputId)
	Calculate the output header from the raw headers. More...
def	recordCalibInputs (self, butler, calib, dataIdList, outputId)
	Record metadata including the inputs and creation details. More...
def	interpolateNans (self, image)
def	write (self, butler, exposure, dataId)
	Write the final combined calib. More...
def	makeCameraImage (self, camera, dataId, calibs)
	Create and write an image of the entire camera. More...
def	checkCcdIdLists (self, ccdIdLists)
def	parseAndRun (cls, args, kwargs)
def	parseAndRun (cls, args=None, config=None, log=None, doReturnResults=False)
def	parseAndSubmit (cls, args=None, kwargs)
def	batchCommand (cls, args)
	Return command to run CmdLineTask. More...
def	logOperation (self, operation, catch=False, trace=True)
	Provide a context manager for logging an operation. More...
def	writeConfig (self, butler, clobber=False, doBackup=True)
def	writeSchemas (self, butler, clobber=False, doBackup=True)
def	writeMetadata (self, dataRef)
def	writePackageVersions (self, butler, clobber=False, doBackup=True, dataset="packages")
def	emptyMetadata (self)
def	getSchemaCatalogs (self)
def	getAllSchemaCatalogs (self)
def	getFullMetadata (self)
def	getFullName (self)
def	getName (self)
def	getTaskDict (self)
def	makeSubtask (self, name, keyArgs)
def	timer (self, name, logLevel=Log.DEBUG)
def	makeField (cls, doc)
def	__reduce__ (self)

Public Attributes
	metadata
	log
	config

Static Public Attributes
	ConfigClass = FringeConfig
string	calibName = "fringe"
	RunnerClass = CalibTaskRunner
	filterName = None
float	exposureTime = 1.0
bool	canMultiprocess = True

Detailed Description

Fringe construction task

The principal change from the base class is that the images are
background-subtracted and rescaled by the background.

XXX This is probably not right for a straight-up combination, as we
are currently doing, since the fringe amplitudes need not scale with
the continuum.

XXX Would like to have this do PCA and generate multiple images, but
that will take a bit of work with the persistence code.

Definition at line 1123 of file constructCalibs.py.

Constructor & Destructor Documentation

__init__()

def lsst.pipe.drivers.constructCalibs.FringeTask.__init__	(		self,
			args,
			kwargs
	)

Definition at line 1145 of file constructCalibs.py.

    def __init__(self, *args, **kwargs):
        CalibTask.__init__(self, *args, **kwargs)
        self.makeSubtask("detection")
        self.makeSubtask("stats")
        self.makeSubtask("subtractBackground")

Member Function Documentation

__reduce__()

def lsst.pipe.base.task.Task.__reduce__ (   self )

inherited

Pickler.

Definition at line 373 of file task.py.

    def __reduce__(self):
        """Pickler.
        """
        return self.__class__, (self.config, self._name, self._parentTask, None)

addMissingKeys()

def lsst.pipe.drivers.constructCalibs.CalibTask.addMissingKeys (   self,   dataId,   butler,   missingKeys = None,   calibName = None  )

inherited

Definition at line 549 of file constructCalibs.py.

    def addMissingKeys(self, dataId, butler, missingKeys=None, calibName=None):
        if calibName is None:
            calibName = self.calibName

        if missingKeys is None:
            missingKeys = set(butler.getKeys(calibName).keys()) - set(dataId.keys())

        for k in missingKeys:
            try:
                v = butler.queryMetadata('raw', [k], dataId)  # n.b. --id refers to 'raw'
            except Exception:
                continue

            if len(v) == 0:         # failed to lookup value
                continue

            if len(v) == 1:
                dataId[k] = v[0]
            else:
                raise RuntimeError("No unique lookup for %s: %s" % (k, v))

applyOverrides()

def lsst.pipe.drivers.constructCalibs.FringeTask.applyOverrides	(		cls,
			config
	)

Overrides for fringe construction

Definition at line 1141 of file constructCalibs.py.

    def applyOverrides(cls, config):
        """Overrides for fringe construction"""
        config.isr.doFringe = False

batchCommand()

def lsst.ctrl.pool.parallel.BatchCmdLineTask.batchCommand (   cls,   args  )

inherited

Return command to run CmdLineTask.

Parameters

cls	Class
args	Parsed batch job arguments (from BatchArgumentParser)

Definition at line 471 of file parallel.py.

    def batchCommand(cls, args):
        """!Return command to run CmdLineTask

        @param cls: Class
        @param args: Parsed batch job arguments (from BatchArgumentParser)
        """
        job = args.job if args.job is not None else "job"
        module = cls.__module__
        script = ("import os; os.umask(%#05o); " +
                  "import lsst.base; lsst.base.disableImplicitThreading(); " +
                  "import lsst.ctrl.pool.log; lsst.ctrl.pool.log.jobLog(\"%s\"); ") % (UMASK, job)

        if args.batchStats:
            script += ("import lsst.ctrl.pool.parallel; import atexit; " +
                       "atexit.register(lsst.ctrl.pool.parallel.printProcessStats); ")

        script += "import %s; %s.%s.parseAndRun();" % (module, module, cls.__name__)

        profilePre = "import cProfile; import os; cProfile.run(\"\"\""
        profilePost = "\"\"\", filename=\"profile-" + job + "-%s-%d.dat\" % (os.uname()[1], os.getpid()))"

        return ("python -c '" + (profilePre if args.batchProfile else "") + script +
                (profilePost if args.batchProfile else "") + "' " + shCommandFromArgs(args.leftover) +
                " --noExit")

batchWallTime()

def lsst.pipe.drivers.constructCalibs.CalibTask.batchWallTime (   cls,   time,   parsedCmd,   numCores  )

inherited

Definition at line 410 of file constructCalibs.py.

    def batchWallTime(cls, time, parsedCmd, numCores):
        numCcds = len(parsedCmd.butler.get("camera"))
        numExps = len(cls.RunnerClass.getTargetList(
            parsedCmd)[0]['expRefList'])
        numCycles = int(numCcds/float(numCores) + 0.5)
        return time*numExps*numCycles

calculateOutputHeaderFromRaws()

def lsst.pipe.drivers.constructCalibs.CalibTask.calculateOutputHeaderFromRaws (   self,   butler,   calib,   dataIdList,   outputId  )

inherited

Calculate the output header from the raw headers.

This metadata will go into the output FITS header. It will include all headers that are identical in all inputs.

Parameters

butler	Data butler
calib	Combined calib exposure.
dataIdList	List of data identifiers for calibration inputs
outputId	Data identifier for output

Definition at line 766 of file constructCalibs.py.

    def calculateOutputHeaderFromRaws(self, butler, calib, dataIdList, outputId):
        """!Calculate the output header from the raw headers.

        This metadata will go into the output FITS header. It will include all
        headers that are identical in all inputs.

        @param butler  Data butler
        @param calib  Combined calib exposure.
        @param dataIdList  List of data identifiers for calibration inputs
        @param outputId  Data identifier for output
        """
        header = calib.getMetadata()

        rawmd = [butler.get("raw_md", dataId) for dataId in dataIdList if
                 dataId is not None]

        merged = merge_headers(rawmd, mode="drop")

        # Place merged set into the PropertyList if a value is not
        # present already
        # Comments are not present in the merged version so copy them across
        for k, v in merged.items():
            if k not in header:
                comment = rawmd[0].getComment(k) if k in rawmd[0] else None
                header.set(k, v, comment=comment)

        # Create an observation group so we can add some standard headers
        # independent of the form in the input files.
        # Use try block in case we are dealing with unexpected data headers
        try:
            group = ObservationGroup(rawmd, pedantic=False)
        except Exception:
            group = None

        comments = {"TIMESYS": "Time scale for all dates",
                    "DATE-OBS": "Start date of earliest input observation",
                    "MJD-OBS": "[d] Start MJD of earliest input observation",
                    "DATE-END": "End date of oldest input observation",
                    "MJD-END": "[d] End MJD of oldest input observation",
                    "MJD-AVG": "[d] MJD midpoint of all input observations",
                    "DATE-AVG": "Midpoint date of all input observations"}

        if group is not None:
            oldest, newest = group.extremes()
            dateCards = dates_to_fits(oldest.datetime_begin, newest.datetime_end)
        else:
            # Fall back to setting a DATE-OBS from the calibDate
            dateCards = {"DATE-OBS": "{}T00:00:00.00".format(outputId[self.config.dateCalib])}
            comments["DATE-OBS"] = "Date of start of day of calibration midpoint"

        for k, v in dateCards.items():
            header.set(k, v, comment=comments.get(k, None))

checkCcdIdLists()

def lsst.pipe.drivers.constructCalibs.CalibTask.checkCcdIdLists (   self,   ccdIdLists  )

inherited

Check that the list of CCD dataIds is consistent

@param ccdIdLists  Dict of data identifier lists for each CCD name
@return Number of exposures, number of CCDs

Definition at line 886 of file constructCalibs.py.

    def checkCcdIdLists(self, ccdIdLists):
        """Check that the list of CCD dataIds is consistent

        @param ccdIdLists  Dict of data identifier lists for each CCD name
        @return Number of exposures, number of CCDs
        """
        visitIdLists = collections.defaultdict(list)
        for ccdName in ccdIdLists:
            for dataId in ccdIdLists[ccdName]:
                visitName = dictToTuple(dataId, self.config.visitKeys)
                visitIdLists[visitName].append(dataId)

        numExps = set(len(expList) for expList in ccdIdLists.values())
        numCcds = set(len(ccdList) for ccdList in visitIdLists.values())

        if len(numExps) != 1 or len(numCcds) != 1:
            # Presumably a visit somewhere doesn't have the full complement available.
            # Dump the information so the user can figure it out.
            self.log.warn("Number of visits for each CCD: %s",
                          {ccdName: len(ccdIdLists[ccdName]) for ccdName in ccdIdLists})
            self.log.warn("Number of CCDs for each visit: %s",
                          {vv: len(visitIdLists[vv]) for vv in visitIdLists})
            raise RuntimeError("Inconsistent number of exposures/CCDs")

        return numExps.pop(), numCcds.pop()

combine()

def lsst.pipe.drivers.constructCalibs.CalibTask.combine (   self,   cache,   struct,   outputId  )

inherited

Combine multiple exposures of a particular CCD and write the output.

Only the slave nodes execute this method.

Parameters

cache	Process pool cache
struct	Parameters for the combination, which has the following components: ccdName Name tuple for CCD ccdIdList List of data identifiers for combination scales Scales to apply (expScales are scalings for each exposure, ccdScale is final scale for combined image)
outputId	Data identifier for combined image (exposure part only)

Returns

binned calib image

Definition at line 726 of file constructCalibs.py.

    def combine(self, cache, struct, outputId):
        """!Combine multiple exposures of a particular CCD and write the output

        Only the slave nodes execute this method.

        @param cache  Process pool cache
        @param struct  Parameters for the combination, which has the following components:
            * ccdName     Name tuple for CCD
            * ccdIdList   List of data identifiers for combination
            * scales      Scales to apply (expScales are scalings for each exposure,
                               ccdScale is final scale for combined image)
        @param outputId    Data identifier for combined image (exposure part only)
        @return binned calib image
        """
        outputId = self.getFullyQualifiedOutputId(struct.ccdName, cache.butler, outputId)
        dataRefList = [getDataRef(cache.butler, dataId) if dataId is not None else None for
                       dataId in struct.ccdIdList]
        self.log.info("Combining %s on %s" % (outputId, NODE))
        calib = self.combination.run(dataRefList, expScales=struct.scales.expScales,
                                     finalScale=struct.scales.ccdScale)

        if not hasattr(calib, "getMetadata"):
            if hasattr(calib, "getVariance"):
                calib = afwImage.makeExposure(calib)
            else:
                calib = afwImage.DecoratedImageF(calib.getImage())  # n.b. hardwires "F" for the output type

        self.calculateOutputHeaderFromRaws(cache.butler, calib, struct.ccdIdList, outputId)

        self.updateMetadata(calib, self.exposureTime)

        self.recordCalibInputs(cache.butler, calib,
                               struct.ccdIdList, outputId)

        self.interpolateNans(calib)

        self.write(cache.butler, calib, outputId)

        return afwMath.binImage(calib.getImage(), self.config.binning)

emptyMetadata()

def lsst.pipe.base.task.Task.emptyMetadata (   self )

inherited

Empty (clear) the metadata for this Task and all sub-Tasks.

Definition at line 153 of file task.py.

    def emptyMetadata(self):
        """Empty (clear) the metadata for this Task and all sub-Tasks.
        """
        for subtask in self._taskDict.values():
            subtask.metadata = dafBase.PropertyList()

getAllSchemaCatalogs()

def lsst.pipe.base.task.Task.getAllSchemaCatalogs (   self )

inherited

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.

Definition at line 188 of file task.py.

    def getAllSchemaCatalogs(self):
        """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.
        """
        schemaDict = self.getSchemaCatalogs()
        for subtask in self._taskDict.values():
            schemaDict.update(subtask.getSchemaCatalogs())
        return schemaDict

getFilter()

def lsst.pipe.drivers.constructCalibs.CalibTask.getFilter (   self,   butler,   dataId  )

inherited

Determine the filter from a data identifier

Definition at line 544 of file constructCalibs.py.

    def getFilter(self, butler, dataId):
        """Determine the filter from a data identifier"""
        filt = butler.queryMetadata('raw', [self.config.filter], dataId)[0]
        return filt

getFullMetadata()

def lsst.pipe.base.task.Task.getFullMetadata (   self )

inherited

Get metadata for all tasks.

Returns
-------
metadata : `lsst.daf.base.PropertySet`
    The `~lsst.daf.base.PropertySet` 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.

Definition at line 210 of file task.py.

    def getFullMetadata(self):
        """Get metadata for all tasks.

        Returns
        -------
        metadata : `lsst.daf.base.PropertySet`
            The `~lsst.daf.base.PropertySet` 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.
        """
        fullMetadata = dafBase.PropertySet()
        for fullName, task in self.getTaskDict().items():
            fullMetadata.set(fullName.replace(".", ":"), task.metadata)
        return fullMetadata

getFullName()

def lsst.pipe.base.task.Task.getFullName (   self )

inherited

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".

Definition at line 235 of file task.py.

    def getFullName(self):
        """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".
        """
        return self._fullName

getFullyQualifiedOutputId()

def lsst.pipe.drivers.constructCalibs.CalibTask.getFullyQualifiedOutputId (   self,   ccdName,   butler,   outputId  )

inherited

Get fully-qualified output data identifier

We may need to look up keys that aren't in the output dataId.

@param ccdName  Name tuple for CCD
@param butler  Data butler
@param outputId  Data identifier for combined image (exposure part only)
@return fully-qualified output dataId

Definition at line 710 of file constructCalibs.py.

    def getFullyQualifiedOutputId(self, ccdName, butler, outputId):
        """Get fully-qualified output data identifier

        We may need to look up keys that aren't in the output dataId.

        @param ccdName  Name tuple for CCD
        @param butler  Data butler
        @param outputId  Data identifier for combined image (exposure part only)
        @return fully-qualified output dataId
        """
        fullOutputId = {k: ccdName[i] for i, k in enumerate(self.config.ccdKeys)}
        fullOutputId.update(outputId)
        self.addMissingKeys(fullOutputId, butler)
        fullOutputId.update(outputId)  # must be after the call to queryMetadata in 'addMissingKeys'
        return fullOutputId

getMjd()

def lsst.pipe.drivers.constructCalibs.CalibTask.getMjd (   self,   butler,   dataId,   timescale = dafBase.DateTime.UTC  )

inherited

Determine the Modified Julian Date (MJD; in TAI) from a data identifier

Definition at line 531 of file constructCalibs.py.

    def getMjd(self, butler, dataId, timescale=dafBase.DateTime.UTC):
        """Determine the Modified Julian Date (MJD; in TAI) from a data identifier"""
        if self.config.dateObs in dataId:
            dateObs = dataId[self.config.dateObs]
        else:
            dateObs = butler.queryMetadata('raw', [self.config.dateObs], dataId)[0]
        if "T" not in dateObs:
            dateObs = dateObs + "T12:00:00.0Z"
        elif not dateObs.endswith("Z"):
            dateObs += "Z"

        return dafBase.DateTime(dateObs, timescale).get(dafBase.DateTime.MJD)

getName()

def lsst.pipe.base.task.Task.getName (   self )

inherited

Get the name of the task.

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

See also
--------
getFullName

Definition at line 250 of file task.py.

    def getName(self):
        """Get the name of the task.

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

        See also
        --------
        getFullName
        """
        return self._name

getOutputId()

def lsst.pipe.drivers.constructCalibs.CalibTask.getOutputId (   self,   expRefList,   calibId  )

inherited

Generate the data identifier for the output calib.

The mean date and the common filter are included, using keywords from the configuration. The CCD-specific part is not included in the data identifier.

Parameters

expRefList	List of data references at exposure level
calibId	Data identifier elements for the calib provided by the user

Returns

data identifier

Definition at line 496 of file constructCalibs.py.

    def getOutputId(self, expRefList, calibId):
        """!Generate the data identifier for the output calib

        The mean date and the common filter are included, using keywords
        from the configuration.  The CCD-specific part is not included
        in the data identifier.

        @param expRefList  List of data references at exposure level
        @param calibId  Data identifier elements for the calib provided by the user
        @return data identifier
        """
        midTime = 0
        filterName = None
        for expRef in expRefList:
            butler = expRef.getButler()
            dataId = expRef.dataId

            midTime += self.getMjd(butler, dataId)
            thisFilter = self.getFilter(
                butler, dataId) if self.filterName is None else self.filterName
            if filterName is None:
                filterName = thisFilter
            elif filterName != thisFilter:
                raise RuntimeError("Filter mismatch for %s: %s vs %s" % (
                    dataId, thisFilter, filterName))

        midTime /= len(expRefList)
        date = str(dafBase.DateTime(
            midTime, dafBase.DateTime.MJD).toPython().date())

        outputId = {self.config.filter: filterName,
                    self.config.dateCalib: date}
        outputId.update(calibId)
        return outputId

getSchemaCatalogs()

def lsst.pipe.base.task.Task.getSchemaCatalogs (   self )

inherited

Get the schemas generated by this task.

Returns
-------
schemaCatalogs : `dict`
    Keys are butler dataset type, values are an empty catalog (an instance of the appropriate
    `lsst.afw.table` Catalog type) for this task.

Notes
-----

.. warning::

   Subclasses that use schemas must override this method. The default implemenation 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.

See also
--------
Task.getAllSchemaCatalogs

Definition at line 159 of file task.py.

    def getSchemaCatalogs(self):
        """Get the schemas generated by this task.

        Returns
        -------
        schemaCatalogs : `dict`
            Keys are butler dataset type, values are an empty catalog (an instance of the appropriate
            `lsst.afw.table` Catalog type) for this task.

        Notes
        -----

        .. warning::

           Subclasses that use schemas must override this method. The default implemenation 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.

        See also
        --------
        Task.getAllSchemaCatalogs
        """
        return {}

getTaskDict()

def lsst.pipe.base.task.Task.getTaskDict (   self )

inherited

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..

Definition at line 264 of file task.py.

    def getTaskDict(self):
        """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..
        """
        return self._taskDict.copy()

interpolateNans()

def lsst.pipe.drivers.constructCalibs.CalibTask.interpolateNans (   self,   image  )

inherited

Interpolate over NANs in the combined image

NANs can result from masked areas on the CCD.  We don't want them getting
into our science images, so we replace them with the median of the image.

Definition at line 847 of file constructCalibs.py.

    def interpolateNans(self, image):
        """Interpolate over NANs in the combined image

        NANs can result from masked areas on the CCD.  We don't want them getting
        into our science images, so we replace them with the median of the image.
        """
        if hasattr(image, "getMaskedImage"):  # Deal with Exposure vs Image
            self.interpolateNans(image.getMaskedImage().getVariance())
            image = image.getMaskedImage().getImage()
        if hasattr(image, "getImage"):  # Deal with DecoratedImage or MaskedImage vs Image
            image = image.getImage()
        array = image.getArray()
        bad = np.isnan(array)
        array[bad] = np.median(array[np.logical_not(bad)])

logOperation()

def lsst.ctrl.pool.parallel.BatchCmdLineTask.logOperation (   self,   operation,   catch = False,   trace = True  )

inherited

Provide a context manager for logging an operation.

Parameters

operation	description of operation (string)
catch	Catch all exceptions?
trace	Log a traceback of caught exception?

Note that if 'catch' is True, all exceptions are swallowed, but there may be other side-effects such as undefined variables.

Definition at line 497 of file parallel.py.

    def logOperation(self, operation, catch=False, trace=True):
        """!Provide a context manager for logging an operation

        @param operation: description of operation (string)
        @param catch: Catch all exceptions?
        @param trace: Log a traceback of caught exception?

        Note that if 'catch' is True, all exceptions are swallowed, but there may
        be other side-effects such as undefined variables.
        """
        self.log.info("%s: Start %s" % (NODE, operation))
        try:
            yield
        except Exception:
            if catch:
                cls, e, _ = sys.exc_info()
                self.log.warn("%s: Caught %s while %s: %s" % (NODE, cls.__name__, operation, e))
                if trace:
                    self.log.info("%s: Traceback:\n%s" % (NODE, traceback.format_exc()))
                return
            raise
        finally:
            self.log.info("%s: Finished %s" % (NODE, operation))

makeCameraImage()

def lsst.pipe.drivers.constructCalibs.CalibTask.makeCameraImage (   self,   camera,   dataId,   calibs  )

inherited

Create and write an image of the entire camera.

This is useful for judging the quality or getting an overview of the features of the calib.

Parameters

camera	Camera object
dataId	Data identifier for output
calibs	Dict mapping CCD detector ID to calib image

Definition at line 874 of file constructCalibs.py.

    def makeCameraImage(self, camera, dataId, calibs):
        """!Create and write an image of the entire camera

        This is useful for judging the quality or getting an overview of
        the features of the calib.

        @param camera  Camera object
        @param dataId  Data identifier for output
        @param calibs  Dict mapping CCD detector ID to calib image
        """
        return makeCameraImage(camera, calibs, self.config.binning)

makeField()

def lsst.pipe.base.task.Task.makeField (   cls,   doc  )

inherited

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("a brief description of what this task does")

Definition at line 329 of file task.py.

    def makeField(cls, doc):
        """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("a brief description of what this task does")
        """
        return ConfigurableField(doc=doc, target=cls)

makeSubtask()

def lsst.pipe.base.task.Task.makeSubtask (   self,   name,   keyArgs  )

inherited

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 pex_config ConfigurableField
or RegistryField.

Definition at line 275 of file task.py.

    def makeSubtask(self, name, **keyArgs):
        """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 pex_config ConfigurableField
        or RegistryField.
        """
        taskField = getattr(self.config, name, None)
        if taskField is None:
            raise KeyError("%s's config does not have field %r" % (self.getFullName(), name))
        subtask = taskField.apply(name=name, parentTask=self, **keyArgs)
        setattr(self, name, subtask)

parseAndRun() [1/2]

def lsst.ctrl.pool.parallel.BatchPoolTask.parseAndRun (   cls,   args,   kwargs  )

inherited

Run with a MPI process pool

Definition at line 529 of file parallel.py.

    def parseAndRun(cls, *args, **kwargs):
        """Run with a MPI process pool"""
        pool = startPool()
        super(BatchPoolTask, cls).parseAndRun(*args, **kwargs)
        pool.exit()

parseAndRun() [2/2]

def lsst.pipe.base.cmdLineTask.CmdLineTask.parseAndRun (   cls,   args = None,   config = None,   log = None,   doReturnResults = False  )

inherited

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 : `lsst.log.Log`-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
`~lsst.pipe.base.ArgumentParser.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.

Definition at line 549 of file cmdLineTask.py.

    def parseAndRun(cls, 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 : `lsst.log.Log`-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
                `~lsst.pipe.base.ArgumentParser.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.
        """
        if args is None:
            commandAsStr = " ".join(sys.argv)
            args = sys.argv[1:]
        else:
            commandAsStr = "{}{}".format(lsst.utils.get_caller_name(skip=1), tuple(args))

        argumentParser = cls._makeArgumentParser()
        if config is None:
            config = cls.ConfigClass()
        parsedCmd = argumentParser.parse_args(config=config, args=args, log=log, override=cls.applyOverrides)
        # print this message after parsing the command so the log is fully configured
        parsedCmd.log.info("Running: %s", commandAsStr)

        taskRunner = cls.RunnerClass(TaskClass=cls, parsedCmd=parsedCmd, doReturnResults=doReturnResults)
        resultList = taskRunner.run(parsedCmd)

        try:
            nFailed = sum(((res.exitStatus != 0) for res in resultList))
        except (TypeError, AttributeError) as e:
            # NOTE: TypeError if resultList is None, AttributeError if it doesn't have exitStatus.
            parsedCmd.log.warn("Unable to retrieve exit status (%s); assuming success", e)
            nFailed = 0

        if nFailed > 0:
            if parsedCmd.noExit:
                parsedCmd.log.error("%d dataRefs failed; not exiting as --noExit was set", nFailed)
            else:
                sys.exit(nFailed)

        return Struct(
            argumentParser=argumentParser,
            parsedCmd=parsedCmd,
            taskRunner=taskRunner,
            resultList=resultList,
        )

parseAndSubmit()

def lsst.ctrl.pool.parallel.BatchCmdLineTask.parseAndSubmit (   cls,   args = None,   kwargs  )

inherited

Definition at line 433 of file parallel.py.

    def parseAndSubmit(cls, args=None, **kwargs):
        taskParser = cls._makeArgumentParser(doBatch=True, add_help=False)
        batchParser = BatchArgumentParser(parent=taskParser)
        batchArgs = batchParser.parse_args(config=cls.ConfigClass(), args=args, override=cls.applyOverrides,
                                           **kwargs)

        if not cls.RunnerClass(cls, batchArgs.parent).precall(batchArgs.parent):  # Write config, schema
            taskParser.error("Error in task preparation")

        setBatchType(batchArgs.batch)

        if batchArgs.batch is None:     # don't use a batch system
            sys.argv = [sys.argv[0]] + batchArgs.leftover  # Remove all batch arguments

            return cls.parseAndRun()
        else:
            numCores = batchArgs.cores if batchArgs.cores > 0 else batchArgs.nodes*batchArgs.procs
            walltime = cls.batchWallTime(batchArgs.time, batchArgs.parent, numCores)

            command = cls.batchCommand(batchArgs)
            batchArgs.batch.run(command, walltime=walltime)

process()

def lsst.pipe.drivers.constructCalibs.CalibTask.process (   self,   cache,   ccdId,   outputName = "postISRCCD",   kwargs  )

inherited

Process a CCD, specified by a data identifier.

After processing, optionally returns a result (produced by the 'processResult' method) calculated from the processed exposure. These results will be gathered by the master node, and is a means for coordinated scaling of all CCDs for flats, etc.

Only slave nodes execute this method.

Parameters

cache	Process pool cache
ccdId	Data identifier for CCD
outputName	Output dataset name for butler

Returns

result from 'processResult'

Definition at line 602 of file constructCalibs.py.

    def process(self, cache, ccdId, outputName="postISRCCD", **kwargs):
        """!Process a CCD, specified by a data identifier

        After processing, optionally returns a result (produced by
        the 'processResult' method) calculated from the processed
        exposure.  These results will be gathered by the master node,
        and is a means for coordinated scaling of all CCDs for flats,
        etc.

        Only slave nodes execute this method.

        @param cache  Process pool cache
        @param ccdId  Data identifier for CCD
        @param outputName  Output dataset name for butler
        @return result from 'processResult'
        """
        if ccdId is None:
            self.log.warn("Null identifier received on %s" % NODE)
            return None
        sensorRef = getDataRef(cache.butler, ccdId)
        if self.config.clobber or not sensorRef.datasetExists(outputName):
            self.log.info("Processing %s on %s" % (ccdId, NODE))
            try:
                exposure = self.processSingle(sensorRef, **kwargs)
            except Exception as e:
                self.log.warn("Unable to process %s: %s" % (ccdId, e))
                raise
                return None
            self.processWrite(sensorRef, exposure)
        else:
            self.log.info(
                "Using previously persisted processed exposure for %s" % (sensorRef.dataId,))
            exposure = sensorRef.get(outputName)
        return self.processResult(exposure)

processResult()

def lsst.pipe.drivers.constructCalibs.CalibTask.processResult (   self,   exposure  )

inherited

Extract processing results from a processed exposure

This method generates what is gathered by the master node.
This can be a background measurement or similar for scaling
flat-fields.  It must be picklable!

Only slave nodes execute this method.

Definition at line 660 of file constructCalibs.py.

    def processResult(self, exposure):
        """Extract processing results from a processed exposure

        This method generates what is gathered by the master node.
        This can be a background measurement or similar for scaling
        flat-fields.  It must be picklable!

        Only slave nodes execute this method.
        """
        return None

processSingle()

def lsst.pipe.drivers.constructCalibs.FringeTask.processSingle	(		self,
			sensorRef
	)

Subtract the background and normalise by the background level

Definition at line 1151 of file constructCalibs.py.

    def processSingle(self, sensorRef):
        """Subtract the background and normalise by the background level"""
        exposure = CalibTask.processSingle(self, sensorRef)
        bgLevel = self.stats.run(exposure)
        self.subtractBackground.run(exposure)
        mi = exposure.getMaskedImage()
        mi /= bgLevel
        footprintSets = self.detection.detectFootprints(
            exposure, sigma=self.config.detectSigma)
        mask = exposure.getMaskedImage().getMask()
        detected = 1 << mask.addMaskPlane("DETECTED")
        for fpSet in (footprintSets.positive, footprintSets.negative):
            if fpSet is not None:
                afwDet.setMaskFromFootprintList(
                    mask, fpSet.getFootprints(), detected)
        return exposure

processWrite()

def lsst.pipe.drivers.constructCalibs.CalibTask.processWrite (   self,   dataRef,   exposure,   outputName = "postISRCCD"  )

inherited

Write the processed CCD.

We need to write these out because we can't hold them all in memory at once.

Only slave nodes execute this method.

Parameters

dataRef	Data reference
exposure	CCD exposure to write
outputName	Output dataset name for butler.

Definition at line 646 of file constructCalibs.py.

    def processWrite(self, dataRef, exposure, outputName="postISRCCD"):
        """!Write the processed CCD

        We need to write these out because we can't hold them all in
        memory at once.

        Only slave nodes execute this method.

        @param dataRef     Data reference
        @param exposure    CCD exposure to write
        @param outputName  Output dataset name for butler.
        """
        dataRef.put(exposure, outputName)

recordCalibInputs()

def lsst.pipe.drivers.constructCalibs.CalibTask.recordCalibInputs (   self,   butler,   calib,   dataIdList,   outputId  )

inherited

Record metadata including the inputs and creation details.

This metadata will go into the FITS header.

Parameters

butler	Data butler
calib	Combined calib exposure.
dataIdList	List of data identifiers for calibration inputs
outputId	Data identifier for output

Definition at line 819 of file constructCalibs.py.

    def recordCalibInputs(self, butler, calib, dataIdList, outputId):
        """!Record metadata including the inputs and creation details

        This metadata will go into the FITS header.

        @param butler  Data butler
        @param calib  Combined calib exposure.
        @param dataIdList  List of data identifiers for calibration inputs
        @param outputId  Data identifier for output
        """
        header = calib.getMetadata()
        header.set("OBSTYPE", self.calibName)  # Used by ingestCalibs.py

        # date, time, host, and root
        now = time.localtime()
        header.set("CALIB_CREATION_DATE", time.strftime("%Y-%m-%d", now))
        header.set("CALIB_CREATION_TIME", time.strftime("%X %Z", now))

        # Inputs
        visits = [str(dictToTuple(dataId, self.config.visitKeys)) for dataId in dataIdList if
                  dataId is not None]
        for i, v in enumerate(sorted(set(visits))):
            header.set("CALIB_INPUT_%d" % (i,), v)

        header.set("CALIB_ID", " ".join("%s=%s" % (key, value)
                                        for key, value in outputId.items()))
        checksum(calib, header)

runDataRef()

def lsst.pipe.drivers.constructCalibs.CalibTask.runDataRef (   self,   expRefList,   butler,   calibId  )

inherited

Construct a calib from a list of exposure references.

This is the entry point, called by the TaskRunner.__call__

Only the master node executes this method.

Parameters

expRefList	List of data references at the exposure level
butler	Data butler
calibId	Identifier dict for calib

Definition at line 422 of file constructCalibs.py.

    def runDataRef(self, expRefList, butler, calibId):
        """!Construct a calib from a list of exposure references

        This is the entry point, called by the TaskRunner.__call__

        Only the master node executes this method.

        @param expRefList  List of data references at the exposure level
        @param butler      Data butler
        @param calibId   Identifier dict for calib
        """
        if len(expRefList) < 1:
            raise RuntimeError("No valid input data")

        for expRef in expRefList:
            self.addMissingKeys(expRef.dataId, butler, self.config.ccdKeys, 'raw')

        outputId = self.getOutputId(expRefList, calibId)
        ccdIdLists = getCcdIdListFromExposures(
            expRefList, level="sensor", ccdKeys=self.config.ccdKeys)
        self.checkCcdIdLists(ccdIdLists)

        # Ensure we can generate filenames for each output
        outputIdItemList = list(outputId.items())
        for ccdName in ccdIdLists:
            dataId = dict([(k, ccdName[i]) for i, k in enumerate(self.config.ccdKeys)])
            dataId.update(outputIdItemList)
            self.addMissingKeys(dataId, butler)
            dataId.update(outputIdItemList)

            try:
                butler.get(self.calibName + "_filename", dataId)
            except Exception as e:
                raise RuntimeError(
                    "Unable to determine output filename \"%s_filename\" from %s: %s" %
                    (self.calibName, dataId, e))

        processPool = Pool("process")
        processPool.storeSet(butler=butler)

        # Scatter: process CCDs independently
        data = self.scatterProcess(processPool, ccdIdLists)

        # Gather: determine scalings
        scales = self.scale(ccdIdLists, data)

        combinePool = Pool("combine")
        combinePool.storeSet(butler=butler)

        # Scatter: combine
        calibs = self.scatterCombine(combinePool, outputId, ccdIdLists, scales)

        if self.config.doCameraImage:
            camera = butler.get("camera")
            # Convert indexing of calibs from "ccdName" to detector ID (as used by makeImageFromCamera)
            calibs = {butler.get("postISRCCD_detector",
                                 dict(zip(self.config.ccdKeys, ccdName))).getId(): calibs[ccdName]
                      for ccdName in ccdIdLists}

            try:
                cameraImage = self.makeCameraImage(camera, outputId, calibs)
                butler.put(cameraImage, self.calibName + "_camera", dataId)
            except Exception as exc:
                self.log.warn("Unable to create camera image: %s" % (exc,))

        return Struct(
            outputId=outputId,
            ccdIdLists=ccdIdLists,
            scales=scales,
            calibs=calibs,
            processPool=processPool,
            combinePool=combinePool,
        )

scale()

def lsst.pipe.drivers.constructCalibs.CalibTask.scale (   self,   ccdIdLists,   data  )

inherited

Determine scaling across CCDs and exposures.

This is necessary mainly for flats, so as to determine a consistent scaling across the entire focal plane. This implementation is simply a placeholder.

Only the master node executes this method.

Parameters

ccdIdLists	Dict of data identifier lists for each CCD tuple
data	Dict of lists of returned data for each CCD tuple

Returns

dict of Struct(ccdScale: scaling for CCD, expScales: scaling for each exposure ) for each CCD tuple

Definition at line 671 of file constructCalibs.py.

    def scale(self, ccdIdLists, data):
        """!Determine scaling across CCDs and exposures

        This is necessary mainly for flats, so as to determine a
        consistent scaling across the entire focal plane.  This
        implementation is simply a placeholder.

        Only the master node executes this method.

        @param ccdIdLists  Dict of data identifier lists for each CCD tuple
        @param data        Dict of lists of returned data for each CCD tuple
        @return dict of Struct(ccdScale: scaling for CCD,
                               expScales: scaling for each exposure
                               ) for each CCD tuple
        """
        self.log.info("Scale on %s" % NODE)
        return dict((name, Struct(ccdScale=None, expScales=[None] * len(ccdIdLists[name])))
                    for name in ccdIdLists)

scatterCombine()

def lsst.pipe.drivers.constructCalibs.CalibTask.scatterCombine (   self,   pool,   outputId,   ccdIdLists,   scales  )

inherited

Scatter the combination of exposures across multiple nodes.

In this case, we can only scatter across as many nodes as there are CCDs.

Only the master node executes this method.

Parameters

pool	Process pool
outputId	Output identifier (exposure part only)
ccdIdLists	Dict of data identifier lists for each CCD name
scales	Dict of structs with scales, for each CCD name
dict	of binned images

Definition at line 690 of file constructCalibs.py.

    def scatterCombine(self, pool, outputId, ccdIdLists, scales):
        """!Scatter the combination of exposures across multiple nodes

        In this case, we can only scatter across as many nodes as
        there are CCDs.

        Only the master node executes this method.

        @param pool  Process pool
        @param outputId  Output identifier (exposure part only)
        @param ccdIdLists  Dict of data identifier lists for each CCD name
        @param scales  Dict of structs with scales, for each CCD name
        @param dict of binned images
        """
        self.log.info("Scatter combination")
        data = [Struct(ccdName=ccdName, ccdIdList=ccdIdLists[ccdName], scales=scales[ccdName]) for
                ccdName in ccdIdLists]
        images = pool.map(self.combine, data, outputId)
        return dict(zip(ccdIdLists.keys(), images))

scatterProcess()

def lsst.pipe.drivers.constructCalibs.CalibTask.scatterProcess (   self,   pool,   ccdIdLists  )

inherited

Scatter the processing among the nodes.

We scatter each CCD independently (exposures aren't grouped together), to make full use of all available processors. This necessitates piecing everything back together in the same format as ccdIdLists afterwards.

Only the master node executes this method.

Parameters

pool	Process pool
ccdIdLists	Dict of data identifier lists for each CCD name

Returns

Dict of lists of returned data for each CCD name

Definition at line 586 of file constructCalibs.py.

    def scatterProcess(self, pool, ccdIdLists):
        """!Scatter the processing among the nodes

        We scatter each CCD independently (exposures aren't grouped together),
        to make full use of all available processors. This necessitates piecing
        everything back together in the same format as ccdIdLists afterwards.

        Only the master node executes this method.

        @param pool  Process pool
        @param ccdIdLists  Dict of data identifier lists for each CCD name
        @return Dict of lists of returned data for each CCD name
        """
        self.log.info("Scatter processing")
        return mapToMatrix(pool, self.process, ccdIdLists)

timer()

def lsst.pipe.base.task.Task.timer (   self,   name,   logLevel = Log.DEBUG  )

inherited

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 `lsst.log` level constant.

Examples
--------
Creating a timer context::

    with self.timer("someCodeToTime"):
pass  # code to time

See also
--------
timer.logInfo

Definition at line 301 of file task.py.

    def timer(self, name, logLevel=Log.DEBUG):
        """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 `lsst.log` level constant.

        Examples
        --------
        Creating a timer context::

            with self.timer("someCodeToTime"):
                pass  # code to time

        See also
        --------
        timer.logInfo
        """
        logInfo(obj=self, prefix=name + "Start", logLevel=logLevel)
        try:
            yield
        finally:
            logInfo(obj=self, prefix=name + "End", logLevel=logLevel)

updateMetadata()

def lsst.pipe.drivers.constructCalibs.CalibTask.updateMetadata (   self,   calibImage,   exposureTime,   darkTime = None,   kwargs  )

inherited

Update the metadata from the VisitInfo.

Parameters

calibImage	The image whose metadata is to be set
exposureTime	The exposure time for the image
darkTime	The time since the last read (default: exposureTime)

Definition at line 570 of file constructCalibs.py.

    def updateMetadata(self, calibImage, exposureTime, darkTime=None, **kwargs):
        """!Update the metadata from the VisitInfo

        @param calibImage       The image whose metadata is to be set
        @param exposureTime     The exposure time for the image
        @param darkTime         The time since the last read (default: exposureTime)
        """

        if darkTime is None:
            darkTime = exposureTime     # avoid warning messages when using calibration products

        visitInfo = afwImage.VisitInfo(exposureTime=exposureTime, darkTime=darkTime, **kwargs)
        md = calibImage.getMetadata()

        afwImage.setVisitInfoMetadata(md, visitInfo)

write()

def lsst.pipe.drivers.constructCalibs.CalibTask.write (   self,   butler,   exposure,   dataId  )

inherited

Write the final combined calib.

Only the slave nodes execute this method

Parameters

butler	Data butler
exposure	CCD exposure to write
dataId	Data identifier for output

Definition at line 862 of file constructCalibs.py.

    def write(self, butler, exposure, dataId):
        """!Write the final combined calib

        Only the slave nodes execute this method

        @param butler  Data butler
        @param exposure  CCD exposure to write
        @param dataId  Data identifier for output
        """
        self.log.info("Writing %s on %s" % (dataId, NODE))
        butler.put(exposure, self.calibName, dataId)

writeConfig()

def lsst.pipe.base.cmdLineTask.CmdLineTask.writeConfig (   self,   butler,   clobber = False,   doBackup = True  )

inherited

Write the configuration used for processing the data, or check that an existing
one is equal to the new one if present.

Parameters
----------
butler : `lsst.daf.persistence.Butler`
    Data butler used to write the config. The config is written to dataset type
    `CmdLineTask._getConfigName`.
clobber : `bool`, optional
    A boolean flag that controls what happens if a config already has been saved:
    - `True`: overwrite or rename the existing config, depending on ``doBackup``.
    - `False`: raise `TaskError` if this config does not match the existing config.
doBackup : bool, optional
    Set to `True` to backup the config files if clobbering.

Definition at line 656 of file cmdLineTask.py.

    def writeConfig(self, butler, clobber=False, doBackup=True):
        """Write the configuration used for processing the data, or check that an existing
        one is equal to the new one if present.

        Parameters
        ----------
        butler : `lsst.daf.persistence.Butler`
            Data butler used to write the config. The config is written to dataset type
            `CmdLineTask._getConfigName`.
        clobber : `bool`, optional
            A boolean flag that controls what happens if a config already has been saved:
            - `True`: overwrite or rename the existing config, depending on ``doBackup``.
            - `False`: raise `TaskError` if this config does not match the existing config.
        doBackup : bool, optional
            Set to `True` to backup the config files if clobbering.
        """
        configName = self._getConfigName()
        if configName is None:
            return
        if clobber:
            butler.put(self.config, configName, doBackup=doBackup)
        elif butler.datasetExists(configName, write=True):
            # this may be subject to a race condition; see #2789
            try:
                oldConfig = butler.get(configName, immediate=True)
            except Exception as exc:
                raise type(exc)("Unable to read stored config file %s (%s); consider using --clobber-config" %
                                (configName, exc))

            def logConfigMismatch(msg):
                self.log.fatal("Comparing configuration: %s", msg)

            if not self.config.compare(oldConfig, shortcut=False, output=logConfigMismatch):
                raise TaskError(
                    ("Config does not match existing task config %r on disk; tasks configurations " +
                     "must be consistent within the same output repo (override with --clobber-config)") %
                    (configName,))
        else:
            butler.put(self.config, configName)

writeMetadata()

def lsst.pipe.base.cmdLineTask.CmdLineTask.writeMetadata (   self,   dataRef  )

inherited

Write the metadata produced from processing the data.

Parameters
----------
dataRef
    Butler data reference used to write the metadata.
    The metadata is written to dataset type `CmdLineTask._getMetadataName`.

Definition at line 731 of file cmdLineTask.py.

    def writeMetadata(self, dataRef):
        """Write the metadata produced from processing the data.

        Parameters
        ----------
        dataRef
            Butler data reference used to write the metadata.
            The metadata is written to dataset type `CmdLineTask._getMetadataName`.
        """
        try:
            metadataName = self._getMetadataName()
            if metadataName is not None:
                dataRef.put(self.getFullMetadata(), metadataName)
        except Exception as e:
            self.log.warn("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)

writePackageVersions()

def lsst.pipe.base.cmdLineTask.CmdLineTask.writePackageVersions (   self,   butler,   clobber = False,   doBackup = True,   dataset = "packages"  )

inherited

Compare and write package versions.

Parameters
----------
butler : `lsst.daf.persistence.Butler`
    Data butler used to read/write the package versions.
clobber : `bool`, optional
    A boolean flag that controls what happens if versions already have been saved:
    - `True`: overwrite or rename the existing version info, depending on ``doBackup``.
    - `False`: raise `TaskError` if this version info does not match the existing.
doBackup : `bool`, optional
    If `True` and clobbering, old package version files are backed up.
dataset : `str`, optional
    Name of dataset to read/write.

Raises
------
TaskError
    Raised if there is a version mismatch with current and persisted lists of package versions.

Notes
-----
Note that this operation is subject to a race condition.

Definition at line 747 of file cmdLineTask.py.

    def writePackageVersions(self, butler, clobber=False, doBackup=True, dataset="packages"):
        """Compare and write package versions.

        Parameters
        ----------
        butler : `lsst.daf.persistence.Butler`
            Data butler used to read/write the package versions.
        clobber : `bool`, optional
            A boolean flag that controls what happens if versions already have been saved:
            - `True`: overwrite or rename the existing version info, depending on ``doBackup``.
            - `False`: raise `TaskError` if this version info does not match the existing.
        doBackup : `bool`, optional
            If `True` and clobbering, old package version files are backed up.
        dataset : `str`, optional
            Name of dataset to read/write.

        Raises
        ------
        TaskError
            Raised if there is a version mismatch with current and persisted lists of package versions.

        Notes
        -----
        Note that this operation is subject to a race condition.
        """
        packages = Packages.fromSystem()

        if clobber:
            return butler.put(packages, dataset, doBackup=doBackup)
        if not butler.datasetExists(dataset, write=True):
            return butler.put(packages, dataset)

        try:
            old = butler.get(dataset, immediate=True)
        except Exception as exc:
            raise type(exc)("Unable to read stored version dataset %s (%s); "
                            "consider using --clobber-versions or --no-versions" %
                            (dataset, exc))
        # Note that because we can only detect python modules that have been imported, the stored
        # list of products may be more or less complete than what we have now.  What's important is
        # that the products that are in common have the same version.
        diff = packages.difference(old)
        if diff:
            raise TaskError(
                "Version mismatch (" +
                "; ".join("%s: %s vs %s" % (pkg, diff[pkg][1], diff[pkg][0]) for pkg in diff) +
                "); consider using --clobber-versions or --no-versions")
        # Update the old set of packages in case we have more packages that haven't been persisted.
        extra = packages.extra(old)
        if extra:
            old.update(packages)
            butler.put(old, dataset, doBackup=doBackup)

writeSchemas()

def lsst.pipe.base.cmdLineTask.CmdLineTask.writeSchemas (   self,   butler,   clobber = False,   doBackup = True  )

inherited

Write the schemas returned by `lsst.pipe.base.Task.getAllSchemaCatalogs`.

Parameters
----------
butler : `lsst.daf.persistence.Butler`
    Data butler used to write the schema. Each schema is written to the dataset type specified as the
    key in the dict returned by `~lsst.pipe.base.Task.getAllSchemaCatalogs`.
clobber : `bool`, optional
    A boolean flag that controls what happens if a schema already has been saved:
    - `True`: overwrite or rename the existing schema, depending on ``doBackup``.
    - `False`: raise `TaskError` if this schema does not match the existing schema.
doBackup : `bool`, optional
    Set to `True` to backup the schema files if clobbering.

Notes
-----
If ``clobber`` is `False` and an existing schema does not match a current schema,
then some schemas may have been saved successfully and others may not, and there is no easy way to
tell which is which.

Definition at line 696 of file cmdLineTask.py.

    def writeSchemas(self, butler, clobber=False, doBackup=True):
        """Write the schemas returned by `lsst.pipe.base.Task.getAllSchemaCatalogs`.

        Parameters
        ----------
        butler : `lsst.daf.persistence.Butler`
            Data butler used to write the schema. Each schema is written to the dataset type specified as the
            key in the dict returned by `~lsst.pipe.base.Task.getAllSchemaCatalogs`.
        clobber : `bool`, optional
            A boolean flag that controls what happens if a schema already has been saved:
            - `True`: overwrite or rename the existing schema, depending on ``doBackup``.
            - `False`: raise `TaskError` if this schema does not match the existing schema.
        doBackup : `bool`, optional
            Set to `True` to backup the schema files if clobbering.

        Notes
        -----
        If ``clobber`` is `False` and an existing schema does not match a current schema,
        then some schemas may have been saved successfully and others may not, and there is no easy way to
        tell which is which.
        """
        for dataset, catalog in self.getAllSchemaCatalogs().items():
            schemaDataset = dataset + "_schema"
            if clobber:
                butler.put(catalog, schemaDataset, doBackup=doBackup)
            elif butler.datasetExists(schemaDataset, write=True):
                oldSchema = butler.get(schemaDataset, immediate=True).getSchema()
                if not oldSchema.compare(catalog.getSchema(), afwTable.Schema.IDENTICAL):
                    raise TaskError(
                        ("New schema does not match schema %r on disk; schemas must be " +
                         " consistent within the same output repo (override with --clobber-config)") %
                        (dataset,))
            else:
                butler.put(catalog, schemaDataset)

Member Data Documentation

calibName

string lsst.pipe.drivers.constructCalibs.FringeTask.calibName = "fringe"

static

Definition at line 1138 of file constructCalibs.py.

canMultiprocess

bool lsst.pipe.base.cmdLineTask.CmdLineTask.canMultiprocess = True

staticinherited

Definition at line 524 of file cmdLineTask.py.

config

lsst.pipe.base.task.Task.config

inherited

Definition at line 149 of file task.py.

ConfigClass

lsst.pipe.drivers.constructCalibs.FringeTask.ConfigClass = FringeConfig

static

Definition at line 1136 of file constructCalibs.py.

exposureTime

float lsst.pipe.drivers.constructCalibs.CalibTask.exposureTime = 1.0

staticinherited

Definition at line 401 of file constructCalibs.py.

filterName

lsst.pipe.drivers.constructCalibs.CalibTask.filterName = None

staticinherited

Definition at line 399 of file constructCalibs.py.

log

lsst.pipe.base.task.Task.log

inherited

Definition at line 148 of file task.py.

metadata

lsst.pipe.base.task.Task.metadata

inherited

Definition at line 121 of file task.py.

RunnerClass

lsst.pipe.drivers.constructCalibs.CalibTask.RunnerClass = CalibTaskRunner

staticinherited

Definition at line 398 of file constructCalibs.py.

---

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

• /j/snowflake/release/lsstsw/stack/Linux64/pipe_drivers/19.0.0-2-gd955cfd+15/python/lsst/pipe/drivers/constructCalibs.py

---

Generated on Wed Jan 8 2020 09:12:40 for LSSTApplications by   1.8.13