lsst.meas.base.applyApCorr.ApplyApCorrTask Class Reference

Inheritance diagram for lsst.meas.base.applyApCorr.ApplyApCorrTask:

Public Member Functions
def	__init__ (self, schema, **kwds)
def	run (self, catalog, apCorrMap)
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
	apCorrInfoDict
	metadata
	log
	config

Static Public Attributes
	ConfigClass = ApplyApCorrConfig

Detailed Description

Apply aperture corrections.

Parameters
----------
schema : `lsst.afw.table.Schema`

Definition at line 188 of file applyApCorr.py.

Constructor & Destructor Documentation

__init__()

def lsst.meas.base.applyApCorr.ApplyApCorrTask.__init__	(		self,
			schema,
		**	kwds
	)

Definition at line 198 of file applyApCorr.py.

    def __init__(self, schema, **kwds):
        lsst.pipe.base.Task.__init__(self, **kwds)
 
        self.apCorrInfoDict = dict()
        apCorrNameSet = getApCorrNameSet()
        ignoreSet = set(self.config.ignoreList)
        missingNameSet = ignoreSet - set(apCorrNameSet)
        if missingNameSet:
            self.log.warn("Fields in ignoreList that are not in fluxCorrectList: %s",
                          sorted(missingNameSet))
        for name in sorted(apCorrNameSet - ignoreSet):
            if name + "_instFlux" not in schema:
                # if a field in the registry is missing from the schema, silently ignore it.
                continue
            self.apCorrInfoDict[name] = ApCorrInfo(schema=schema, model=name)
 
        for name, model in self.config.proxies.items():
            if name in apCorrNameSet:
                # Already done or ignored
                continue
            if name + "_instFlux" not in schema:
                # Silently ignore
                continue
            self.apCorrInfoDict[name] = ApCorrInfo(schema=schema, model=model, name=name)
 

Member Function Documentation

__reduce__()

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

inherited

Pickler.

Reimplemented in lsst.pipe.drivers.multiBandDriver.MultiBandDriverTask, and lsst.pipe.drivers.coaddDriver.CoaddDriverTask.

Definition at line 432 of file task.py.

    def __reduce__(self):
        """Pickler.
        """
        return self._unpickle_via_factory, (self.__class__, [], self._reduce_kwargs())

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()
 

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)
 

run()

def lsst.meas.base.applyApCorr.ApplyApCorrTask.run	(		self,
			catalog,
			apCorrMap
	)

Apply aperture corrections to a catalog of sources.

Parameters
----------
catalog : `lsst.afw.table.SourceCatalog`
    Catalog of sources. Will be updated in place.
apCorrMap : `lsst.afw.image.ApCorrMap`
    Aperture correction map

Notes
-----
If you show debug-level log messages then you will see statistics for
the effects of aperture correction.

Definition at line 223 of file applyApCorr.py.

    def run(self, catalog, apCorrMap):
        """Apply aperture corrections to a catalog of sources.
 
        Parameters
        ----------
        catalog : `lsst.afw.table.SourceCatalog`
            Catalog of sources. Will be updated in place.
        apCorrMap : `lsst.afw.image.ApCorrMap`
            Aperture correction map
 
        Notes
        -----
        If you show debug-level log messages then you will see statistics for
        the effects of aperture correction.
        """
        self.log.info("Applying aperture corrections to %d instFlux fields", len(self.apCorrInfoDict))
        if UseNaiveFluxErr:
            self.log.debug("Use naive instFlux sigma computation")
        else:
            self.log.debug("Use complex instFlux sigma computation that double-counts photon noise "
                           "and thus over-estimates instFlux uncertainty")
        for apCorrInfo in self.apCorrInfoDict.values():
            apCorrModel = apCorrMap.get(apCorrInfo.modelName)
            apCorrErrModel = apCorrMap.get(apCorrInfo.modelSigmaName)
            if None in (apCorrModel, apCorrErrModel):
                missingNames = [(apCorrInfo.modelName, apCorrInfo.modelSigmaName)[i]
                                for i, model in enumerate((apCorrModel, apCorrErrModel)) if model is None]
                self.log.warn("Cannot aperture correct %s because could not find %s in apCorrMap" %
                              (apCorrInfo.name, " or ".join(missingNames),))
                for source in catalog:
                    source.set(apCorrInfo.apCorrFlagKey, True)
                continue
 
            for source in catalog:
                center = source.getCentroid()
                # say we've failed when we start; we'll unset these flags when we succeed
                source.set(apCorrInfo.apCorrFlagKey, True)
                oldFluxFlagState = False
                if self.config.doFlagApCorrFailures:
                    oldFluxFlagState = source.get(apCorrInfo.fluxFlagKey)
                    source.set(apCorrInfo.fluxFlagKey, True)
 
                apCorr = 1.0
                apCorrErr = 0.0
                try:
                    apCorr = apCorrModel.evaluate(center)
                    if not UseNaiveFluxErr:
                        apCorrErr = apCorrErrModel.evaluate(center)
                except lsst.pex.exceptions.DomainError:
                    continue
 
                if apCorrInfo.doApCorrColumn:
                    source.set(apCorrInfo.apCorrKey, apCorr)
                    source.set(apCorrInfo.apCorrErrKey, apCorrErr)
 
                if apCorr <= 0.0 or apCorrErr < 0.0:
                    continue
 
                instFlux = source.get(apCorrInfo.instFluxKey)
                instFluxErr = source.get(apCorrInfo.instFluxErrKey)
                source.set(apCorrInfo.instFluxKey, instFlux*apCorr)
                if UseNaiveFluxErr:
                    source.set(apCorrInfo.instFluxErrKey, instFluxErr*apCorr)
                else:
                    a = instFluxErr/instFlux
                    b = apCorrErr/apCorr
                    source.set(apCorrInfo.instFluxErrKey, abs(instFlux*apCorr)*math.sqrt(a*a + b*b))
                source.set(apCorrInfo.apCorrFlagKey, False)
                if self.config.doFlagApCorrFailures:
                    source.set(apCorrInfo.fluxFlagKey, oldFluxFlagState)
 
            if self.log.getLevel() <= self.log.DEBUG:
                # log statistics on the effects of aperture correction
                apCorrArr = np.array([s.get(apCorrInfo.apCorrKey) for s in catalog])
                apCorrErrArr = np.array([s.get(apCorrInfo.apCorrErrKey) for s in catalog])
                self.log.debug("For instFlux field %r: mean apCorr=%s, stdDev apCorr=%s, "
                               "mean apCorrErr=%s, stdDev apCorrErr=%s for %s sources",
                               apCorrInfo.name, apCorrArr.mean(), apCorrArr.std(),
                               apCorrErrArr.mean(), apCorrErrArr.std(), len(catalog))

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)
 

Member Data Documentation

apCorrInfoDict

lsst.meas.base.applyApCorr.ApplyApCorrTask.apCorrInfoDict

Definition at line 201 of file applyApCorr.py.

config

lsst.pipe.base.task.Task.config

inherited

Definition at line 162 of file task.py.

ConfigClass

lsst.meas.base.applyApCorr.ApplyApCorrTask.ConfigClass = ApplyApCorrConfig

static

Definition at line 195 of file applyApCorr.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.

---

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

• /j/snowflake/release/lsstsw/stack/0.4.3/Linux64/meas_base/21.0.0-7-g04766d7+cd19d05db2/python/lsst/meas/base/applyApCorr.py