lsst.pipe.drivers.coaddDriver.CoaddDriverTask Class Reference

Inheritance diagram for lsst.pipe.drivers.coaddDriver.CoaddDriverTask:

Public Member Functions
def	__init__ (self, reuse=tuple(), **kwargs)
def	__reduce__ (self)
def	batchWallTime (cls, time, parsedCmd, numCores)
	Return walltime request for batch job. More...
def	runDataRef (self, tractPatchRefList, butler, selectIdList=[])
	Determine which tracts are non-empty before processing. More...
def	run (self, patchRefList, butler, selectDataList=[])
	Run stacking on a tract. More...
def	readSelection (self, cache, selectId)
	Read Wcs of selected inputs. More...
def	checkTract (self, cache, tractId, selectIdList)
	Check whether a tract has any overlapping inputs. More...
def	warp (self, cache, patchId, selectDataList)
	Warp all images for a patch. More...
def	coadd (self, cache, data)
	Construct coadd for a patch and measure. More...
def	selectExposures (self, patchRef, selectDataList)
	Select exposures to operate upon, via the SelectImagesTask. More...
def	writeMetadata (self, dataRef)
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	applyOverrides (cls, config)
def	writeConfig (self, butler, clobber=False, doBackup=True)
def	writeSchemas (self, butler, clobber=False, doBackup=True)
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)

Public Attributes
	reuse
	calexpType
	metadata
	log
	config

Static Public Attributes
	ConfigClass = CoaddDriverConfig
	RunnerClass = CoaddDriverTaskRunner
bool	canMultiprocess = True

Detailed Description

Definition at line 84 of file coaddDriver.py.

Constructor & Destructor Documentation

__init__()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.__init__	(		self,
			reuse = tuple(),
		**	kwargs
	)

Definition at line 89 of file coaddDriver.py.

    def __init__(self, reuse=tuple(), **kwargs):
        BatchPoolTask.__init__(self, **kwargs)
        self.reuse = reuse
        self.makeSubtask("select")
        self.makeSubtask("makeCoaddTempExp", reuse=("makeCoaddTempExp" in self.reuse))
        self.makeSubtask("backgroundReference")
        self.makeSubtask("assembleCoadd")
        self.makeSubtask("detectCoaddSources")
        if self.config.hasFakes:
            self.calexpType = "fakes_calexp"
        else:
            self.calexpType = "calexp"
 

Member Function Documentation

__reduce__()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.__reduce__

(

self

)

Pickler

Reimplemented from lsst.pipe.base.task.Task.

Definition at line 102 of file coaddDriver.py.

    def __reduce__(self):
        """Pickler"""
        return unpickle, (self.__class__, [], dict(config=self.config, name=self._name,
                                                   parentTask=self._parentTask, log=self.log,
                                                   reuse=self.reuse))
 

applyOverrides()

def lsst.pipe.base.cmdLineTask.CmdLineTask.applyOverrides (   cls,   config  )

inherited

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.

Reimplemented in lsst.pipe.drivers.constructCalibs.FringeTask, lsst.pipe.drivers.constructCalibs.FlatTask, lsst.pipe.drivers.constructCalibs.DarkTask, and lsst.pipe.drivers.constructCalibs.BiasTask.

Definition at line 587 of file cmdLineTask.py.

    def applyOverrides(cls, 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.
        """
        pass
 

batchCommand()

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

inherited

Return command to run CmdLineTask.

    @param cls: Class
    @param args: Parsed batch job arguments (from BatchArgumentParser)

Definition at line 476 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.coaddDriver.CoaddDriverTask.batchWallTime	(		cls,
			time,
			parsedCmd,
			numCores
	)

Return walltime request for batch job.

Parameters

time	Requested time per iteration
parsedCmd	Results of argument parsing
numCores	Number of cores

Returns

float walltime request length

Reimplemented from lsst.ctrl.pool.parallel.BatchCmdLineTask.

Definition at line 125 of file coaddDriver.py.

    def batchWallTime(cls, time, parsedCmd, numCores):
        """!
        Return walltime request for batch job
 
        @param time: Requested time per iteration
        @param parsedCmd: Results of argument parsing
        @param numCores: Number of cores
        @return float walltime request length
        """
        numTargets = len(parsedCmd.selectId.refList)
        return time*numTargets/float(numCores)
 

checkTract()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.checkTract	(		self,
			cache,
			tractId,
			selectIdList
	)

Check whether a tract has any overlapping inputs.

    This method only runs on slave nodes.

    @param cache: Pool cache
    @param tractId: Data identifier for tract
    @param selectDataList: List of selection data
    @return whether tract has any overlapping inputs

Definition at line 223 of file coaddDriver.py.

    def checkTract(self, cache, tractId, selectIdList):
        """!Check whether a tract has any overlapping inputs
 
        This method only runs on slave nodes.
 
        @param cache: Pool cache
        @param tractId: Data identifier for tract
        @param selectDataList: List of selection data
        @return whether tract has any overlapping inputs
        """
        def makePolygon(wcs, bbox):
            """Return a polygon for the image, given Wcs and bounding box"""
            boxPixelCorners = geom.Box2D(bbox).getCorners()
            boxSkyCorners = wcs.pixelToSky(boxPixelCorners)
            return lsst.sphgeom.ConvexPolygon.convexHull([coord.getVector() for coord in boxSkyCorners])
 
        skymap = cache.skymap
        tract = skymap[tractId]
        tractWcs = tract.getWcs()
        tractPoly = makePolygon(tractWcs, tract.getBBox())
 
        for selectData in selectIdList:
            if not hasattr(selectData, "poly"):
                selectData.poly = makePolygon(selectData.wcs, selectData.bbox)
            if tractPoly.intersects(selectData.poly):
                return True
        return False
 

coadd()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.coadd	(		self,
			cache,
			data
	)

Construct coadd for a patch and measure.

    Only slave nodes execute this method.

    Because only one argument may be passed, it is expected to
    contain multiple elements, which are:

    @param patchRef: data reference for patch
    @param selectDataList: List of SelectStruct for inputs

Definition at line 269 of file coaddDriver.py.

    def coadd(self, cache, data):
        """!Construct coadd for a patch and measure
 
        Only slave nodes execute this method.
 
        Because only one argument may be passed, it is expected to
        contain multiple elements, which are:
 
        @param patchRef: data reference for patch
        @param selectDataList: List of SelectStruct for inputs
        """
        patchRef = getDataRef(cache.butler, data.patchId, cache.coaddType)
        selectDataList = data.selectDataList
        coadd = None
 
        # We skip the assembleCoadd step if either the *Coadd dataset exists
        # or we aren't configured to write it, we're supposed to reuse
        # detectCoaddSources outputs too, and those outputs already exist.
        canSkipDetection = (
            "detectCoaddSources" in self.reuse and
            patchRef.datasetExists(self.detectCoaddSources.config.coaddName+"Coadd_det", write=True)
        )
        if "assembleCoadd" in self.reuse:
            if patchRef.datasetExists(cache.coaddType, write=True):
                self.log.info("%s: Skipping assembleCoadd for %s; outputs already exist." %
                              (NODE, patchRef.dataId))
                coadd = patchRef.get(cache.coaddType, immediate=True)
            elif not self.config.assembleCoadd.doWrite and self.config.doDetection and canSkipDetection:
                self.log.info(
                    "%s: Skipping assembleCoadd and detectCoaddSources for %s; outputs already exist." %
                    (NODE, patchRef.dataId)
                )
                return
        if coadd is None:
            with self.logOperation("coadding %s" % (patchRef.dataId,), catch=True):
                coaddResults = self.assembleCoadd.runDataRef(patchRef, selectDataList)
                if coaddResults is not None:
                    coadd = coaddResults.coaddExposure
                    canSkipDetection = False  # can't skip it because coadd may have changed
        if coadd is None:
            return
 
        # The section of code below determines if the detection task should be
        # run. If detection is run, then the products are written out as
        # deepCoadd_calexp. If detection is not run, then the outputs of the
        # assemble task are written out as deepCoadd.
        if self.config.doDetection:
            if canSkipDetection:
                self.log.info("%s: Skipping detectCoaddSources for %s; outputs already exist." %
                              (NODE, patchRef.dataId))
                return
            with self.logOperation("detection on {}".format(patchRef.dataId),
                                   catch=True):
                idFactory = self.detectCoaddSources.makeIdFactory(patchRef)
                expId = int(patchRef.get(self.config.coaddName + "CoaddId"))
                # This includes background subtraction, so do it before writing
                # the coadd
                detResults = self.detectCoaddSources.run(coadd, idFactory, expId=expId)
                self.detectCoaddSources.write(detResults, patchRef)
        else:
            if self.config.hasFakes:
                patchRef.put(coadd, "fakes_" + self.assembleCoadd.config.coaddName + "Coadd")
            else:
                patchRef.put(coadd, self.assembleCoadd.config.coaddName + "Coadd")
 

emptyMetadata()

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

inherited

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

Definition at line 166 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 204 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
 

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 229 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 256 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
 

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 274 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
 

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
   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.

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

Definition at line 172 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
           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.
 
        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 288 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()
 

logOperation()

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

inherited

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.

Definition at line 502 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))
 
 

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:

.. code-block:: python

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

Definition at line 359 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:
 
        .. code-block:: python
 
            class OtherTaskConfig(lsst.pex.config.Config):
                aSubtask = ATaskClass.makeField("brief description of task")
        """
        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
`~lsst.pex.config.ConfigurableField` or
`~lsst.pex.config.RegistryField`.

Definition at line 299 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
        `~lsst.pex.config.ConfigurableField` or
        `~lsst.pex.config.RegistryField`.
        """
        taskField = getattr(self.config, name, None)
        if taskField is None:
            raise KeyError(f"{self.getFullName()}'s config does not have field {name!r}")
        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 534 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 612 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 435 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:
            if batchArgs.walltime > 0:
                walltime = batchArgs.walltime
            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)
 

readSelection()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.readSelection	(		self,
			cache,
			selectId
	)

Read Wcs of selected inputs.

    This method only runs on slave nodes.
    This method is similar to SelectDataIdContainer.makeDataRefList,
    creating a Struct like a SelectStruct, except with a dataId instead
    of a dataRef (to ease MPI).

    @param cache: Pool cache
    @param selectId: Data identifier for selected input
    @return a SelectStruct with a dataId instead of dataRef

Definition at line 200 of file coaddDriver.py.

    def readSelection(self, cache, selectId):
        """!Read Wcs of selected inputs
 
        This method only runs on slave nodes.
        This method is similar to SelectDataIdContainer.makeDataRefList,
        creating a Struct like a SelectStruct, except with a dataId instead
        of a dataRef (to ease MPI).
 
        @param cache: Pool cache
        @param selectId: Data identifier for selected input
        @return a SelectStruct with a dataId instead of dataRef
        """
        try:
            ref = getDataRef(cache.butler, selectId, self.calexpType)
            self.log.info("Reading Wcs from %s" % (selectId,))
            md = ref.get("calexp_md", immediate=True)
            wcs = afwGeom.makeSkyWcs(md)
            data = Struct(dataId=selectId, wcs=wcs, bbox=afwImage.bboxFromMetadata(md))
        except FitsError:
            self.log.warn("Unable to construct Wcs from %s" % (selectId,))
            return None
        return data
 

run()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.run	(		self,
			patchRefList,
			butler,
			selectDataList = []
	)

Run stacking on a tract.

    This method only runs on the master node.

    @param patchRefList: List of patch data references for tract
    @param butler: Data butler
    @param selectDataList: List of SelectStruct for inputs

Definition at line 173 of file coaddDriver.py.

    def run(self, patchRefList, butler, selectDataList=[]):
        """!Run stacking on a tract
 
        This method only runs on the master node.
 
        @param patchRefList: List of patch data references for tract
        @param butler: Data butler
        @param selectDataList: List of SelectStruct for inputs
        """
        pool = Pool("stacker")
        pool.cacheClear()
        pool.storeSet(butler=butler, warpType=self.config.coaddName + "Coadd_directWarp",
                      coaddType=self.config.coaddName + "Coadd")
        patchIdList = [patchRef.dataId for patchRef in patchRefList]
 
        selectedData = pool.map(self.warp, patchIdList, selectDataList)
        if self.config.doBackgroundReference:
            self.backgroundReference.runDataRef(patchRefList, selectDataList)
 
        def refNamer(patchRef):
            return tuple(map(int, patchRef.dataId["patch"].split(",")))
 
        lookup = dict(zip(map(refNamer, patchRefList), selectedData))
        coaddData = [Struct(patchId=patchRef.dataId, selectDataList=lookup[refNamer(patchRef)]) for
                     patchRef in patchRefList]
        pool.map(self.coadd, coaddData)
 

runDataRef()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.runDataRef	(		self,
			tractPatchRefList,
			butler,
			selectIdList = []
	)

Determine which tracts are non-empty before processing.

    @param tractPatchRefList: List of tracts and patches to include in the coaddition
    @param butler: butler reference object
    @param selectIdList: List of data Ids (i.e. visit, ccd) to consider when making the coadd
    @return list of references to sel.runTract function evaluation for each tractPatchRefList member

Definition at line 138 of file coaddDriver.py.

    def runDataRef(self, tractPatchRefList, butler, selectIdList=[]):
        """!Determine which tracts are non-empty before processing
 
        @param tractPatchRefList: List of tracts and patches to include in the coaddition
        @param butler: butler reference object
        @param selectIdList: List of data Ids (i.e. visit, ccd) to consider when making the coadd
        @return list of references to sel.runTract function evaluation for each tractPatchRefList member
        """
        pool = Pool("tracts")
        pool.storeSet(butler=butler, skymap=butler.get(
            self.config.coaddName + "Coadd_skyMap"))
        tractIdList = []
        for patchRefList in tractPatchRefList:
            tractSet = set([patchRef.dataId["tract"]
                            for patchRef in patchRefList])
            assert len(tractSet) == 1
            tractIdList.append(tractSet.pop())
 
        selectDataList = [data for data in pool.mapNoBalance(self.readSelection, selectIdList) if
                          data is not None]
        nonEmptyList = pool.mapNoBalance(
            self.checkTract, tractIdList, selectDataList)
        tractPatchRefList = [patchRefList for patchRefList, nonEmpty in
                             zip(tractPatchRefList, nonEmptyList) if nonEmpty]
        self.log.info("Non-empty tracts (%d): %s" % (len(tractPatchRefList),
                                                     [patchRefList[0].dataId["tract"] for patchRefList in
                                                      tractPatchRefList]))
        # Install the dataRef in the selectDataList
        for data in selectDataList:
            data.dataRef = getDataRef(butler, data.dataId, self.calexpType)
 
        # Process the non-empty tracts
        return [self.run(patchRefList, butler, selectDataList) for patchRefList in tractPatchRefList]
 

selectExposures()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.selectExposures	(		self,
			patchRef,
			selectDataList
	)

Select exposures to operate upon, via the SelectImagesTask.

    This is very similar to CoaddBaseTask.selectExposures, except we return
    a list of SelectStruct (same as the input), so we can plug the results into
    future uses of SelectImagesTask.

    @param patchRef data reference to a particular patch
    @param selectDataList list of references to specific data products (i.e. visit, ccd)
    @return filtered list of SelectStruct

Definition at line 334 of file coaddDriver.py.

    def selectExposures(self, patchRef, selectDataList):
        """!Select exposures to operate upon, via the SelectImagesTask
 
        This is very similar to CoaddBaseTask.selectExposures, except we return
        a list of SelectStruct (same as the input), so we can plug the results into
        future uses of SelectImagesTask.
 
        @param patchRef data reference to a particular patch
        @param selectDataList list of references to specific data products (i.e. visit, ccd)
        @return filtered list of SelectStruct
        """
        def key(dataRef):
            return tuple(dataRef.dataId[k] for k in sorted(dataRef.dataId))
        inputs = dict((key(select.dataRef), select)
                      for select in selectDataList)
        skyMap = patchRef.get(self.config.coaddName + "Coadd_skyMap")
        tract = skyMap[patchRef.dataId["tract"]]
        patch = tract[(tuple(int(i)
                             for i in patchRef.dataId["patch"].split(",")))]
        bbox = patch.getOuterBBox()
        wcs = tract.getWcs()
        cornerPosList = geom.Box2D(bbox).getCorners()
        coordList = [wcs.pixelToSky(pos) for pos in cornerPosList]
        dataRefList = self.select.runDataRef(
            patchRef, coordList, selectDataList=selectDataList).dataRefList
        return [inputs[key(dataRef)] for dataRef in dataRefList]
 

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:

.. code-block:: python

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

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

Definition at line 327 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:
 
        .. code-block:: python
 
            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)
 

warp()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.warp	(		self,
			cache,
			patchId,
			selectDataList
	)

Warp all images for a patch.

    Only slave nodes execute this method.

    Because only one argument may be passed, it is expected to
    contain multiple elements, which are:

    @param patchRef: data reference for patch
    @param selectDataList: List of SelectStruct for inputs
    @return selectDataList with non-overlapping elements removed

Definition at line 251 of file coaddDriver.py.

    def warp(self, cache, patchId, selectDataList):
        """!Warp all images for a patch
 
        Only slave nodes execute this method.
 
        Because only one argument may be passed, it is expected to
        contain multiple elements, which are:
 
        @param patchRef: data reference for patch
        @param selectDataList: List of SelectStruct for inputs
        @return selectDataList with non-overlapping elements removed
        """
        patchRef = getDataRef(cache.butler, patchId, cache.coaddType)
        selectDataList = self.selectExposures(patchRef, selectDataList)
        with self.logOperation("warping %s" % (patchRef.dataId,), catch=True):
            self.makeCoaddTempExp.runDataRef(patchRef, selectDataList)
        return selectDataList
 

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 727 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)(f"Unable to read stored config file {configName} (exc); "
                                "consider using --clobber-config")
 
            def logConfigMismatch(msg):
                self.log.fatal("Comparing configuration: %s", msg)
 
            if not self.config.compare(oldConfig, shortcut=False, output=logConfigMismatch):
                raise TaskError(
                    f"Config does not match existing task config {configName!r} on disk; "
                    "tasks configurations must be consistent within the same output repo "
                    "(override with --clobber-config)")
        else:
            butler.put(self.config, configName)
 

writeMetadata()

def lsst.pipe.drivers.coaddDriver.CoaddDriverTask.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`.

Reimplemented from lsst.pipe.base.cmdLineTask.CmdLineTask.

Definition at line 361 of file coaddDriver.py.

    def writeMetadata(self, dataRef):
        pass

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 829 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)(f"Unable to read stored version dataset {dataset} ({exc}); "
                            "consider using --clobber-versions or --no-versions")
        # 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:
            versions_str = "; ".join(f"{pkg}: {diff[pkg][1]} vs {diff[pkg][0]}" for pkg in diff)
            raise TaskError(
                f"Version mismatch ({versions_str}); 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 771 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(
                        f"New schema does not match schema {dataset!r} on disk; "
                        "schemas must be consistent within the same output repo "
                        "(override with --clobber-config)")
            else:
                butler.put(catalog, schemaDataset)
 

Member Data Documentation

calexpType

lsst.pipe.drivers.coaddDriver.CoaddDriverTask.calexpType

Definition at line 98 of file coaddDriver.py.

canMultiprocess

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

staticinherited

Definition at line 584 of file cmdLineTask.py.

config

lsst.pipe.base.task.Task.config

inherited

Definition at line 162 of file task.py.

ConfigClass

lsst.pipe.drivers.coaddDriver.CoaddDriverTask.ConfigClass = CoaddDriverConfig

static

Definition at line 85 of file coaddDriver.py.

log

lsst.pipe.base.task.Task.log

inherited

Definition at line 161 of file task.py.

metadata

lsst.pipe.base.task.Task.metadata

inherited

Definition at line 134 of file task.py.

reuse

lsst.pipe.drivers.coaddDriver.CoaddDriverTask.reuse

Definition at line 91 of file coaddDriver.py.

RunnerClass

lsst.pipe.drivers.coaddDriver.CoaddDriverTask.RunnerClass = CoaddDriverTaskRunner

static

Definition at line 87 of file coaddDriver.py.

---

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

• /j/snowflake/release/lsstsw/stack/0.4.3/Linux64/pipe_drivers/21.0.0-5-gd00fb1e+05fce91b99/python/lsst/pipe/drivers/coaddDriver.py