lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask Class Reference

Inheritance diagram for lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask:

Public Member Functions
def	__init__ (self, **kwargs)
def	run (self, exposure, background)
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
	rng
	npRand
	galData
	bitmask
	metadata
	log
	config

Static Public Attributes
	ConfigClass

Detailed Description

Definition at line 50 of file positionGalSimFakes.py.

Constructor & Destructor Documentation

__init__()

def lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask.__init__	(		self,
		**	kwargs
	)

Initialize the Task.

Subclasses that define their own __init__ should simply forward all arguments to the base
class constructor.  They can then assume self.config is an instance of their ConfigClass.

If an external catalog is used to add sources consistently to multiple overlapping images,
that catalog should generally be loaded and attached to self here, so it can be used
multiple times by the run() method.

Reimplemented from lsst.pipe.tasks.fakes.BaseFakeSourcesTask.

Definition at line 53 of file positionGalSimFakes.py.

    def __init__(self, **kwargs):
        BaseFakeSourcesTask.__init__(self, **kwargs)
        print("RNG seed:", self.config.seed)
        self.rng = lsst.afw.math.Random(seed=self.config.seed)
        self.npRand = np.random.RandomState(self.config.seed)
        self.galData = fits.open(self.config.galList)[1].data
 

Member Function Documentation

__reduce__()

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

inherited

Pickler.

Reimplemented in lsst.obs.base.defineVisits.DefineVisitsTask, lsst.obs.base.ingest.RawIngestTask, lsst.pipe.drivers.multiBandDriver.MultiBandDriverTask, and lsst.pipe.drivers.coaddDriver.CoaddDriverTask.

Definition at line 373 of file task.py.

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

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
 

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
 

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
 

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()
 

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(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.synpipe.positionGalSimFakes.PositionGalSimFakesTask.run	(		self,
			exposure,
			background
	)

Add fake sources to the given Exposure, making use of the given BackgroundList if desired.

If pixels in the Exposure are replaced, not added to, extra care should be taken with the background,
mask, and variance planes.  The Exposure as given is background-subtracted (using the supplied
background model) and should be returned in the same state.

Reimplemented from lsst.pipe.tasks.fakes.BaseFakeSourcesTask.

Definition at line 60 of file positionGalSimFakes.py.

    def run(self, exposure, background):
        self.log.info("Adding fake galaxies at real positions")
        PARENT = lsst.afw.image.PARENT
        psf = exposure.getPsf()
        md = exposure.getMetadata()
        calib = exposure.getCalib()
        expBBox = exposure.getBBox(PARENT)
        wcs = exposure.getWcs()
 
        """Deal with the skipped ones."""
        skipLog = 'runAddFake.skipped'
        if not os.path.isfile(skipLog):
            os.system('touch ' + skipLog)
 
        if self.config.galType == 'cosmos':
            import galsim
            exLevel = self.config.exclusionLevel
            cosmosCat = galsim.COSMOSCatalog(exclusion_level=exLevel)
        else:
            cosmosCat = None
 
        for igal, gal in enumerate(self.galData):
            try:
                galident = gal["ID"]
            except KeyError:
                galident = igal + 1
 
            try:
                flux = calib.getFlux(float(gal['mag']))
            except KeyError:
                raise KeyError("No mag column in %s" % self.config.galList)
 
            try:
                galCoord = lsst.afw.geom.SpherePoint(gal['RA'], gal['DEC'], lsst.afw.geom.degrees)
            except KeyError:
                raise KeyError("No RA/DEC column in {} table".format(self.config.galList))
 
            skyToPixelMatrix = wcs.linearizeSkyToPixel(galCoord, lsst.afw.geom.degrees)
            skyToPixelMatrix = skyToPixelMatrix.getLinear().getParameterVector() / 3600.0
 
            galXY = wcs.skyToPixel(galCoord)
            bboxI = exposure.getBBox(PARENT)
            bboxI.grow(self.config.maxMargin)
            if not bboxI.contains(lsst.afw.geom.Point2I(galXY)):
                # Will just skip this object
                continue
 
            # Check the magnitude
            if gal['mag'] <= 0:
                self.log.info("Mag <= 0: Skipping %d" % galident)
                self.log.info("  mag: %7.3d" % gal['mag'])
                with open(skipLog, "a") as slog:
                    try:
                        fcntl.flock(slog, fcntl.LOCK_EX)
                        slog.write("%8d , negMag\n" % galident)
                        fcntl.flock(slog, fcntl.LOCK_UN)
                    except IOError:
                        continue
                continue
 
            # This is extrapolating for the PSF, probably not a good idea
            #  Return an Image of the PSF, in a form suitable for convolution.
            #  The returned image is normalized to sum to unity.
            try:
                psfImage = psf.computeKernelImage(galXY)
            except Exception:
                # There may not be any data at this point, and the object
                # should be skipped
                continue
            try:
                addShear = self.config.addShear
                prec = self.config.sersic_prec
                galType = self.config.galType
                if self.config.galType != 'cosmos':
                    galArray = makeFake.makeGalaxy(flux, gal,
                                                   psfImage.getArray(),
                                                   galType=galType,
                                                   cosmosCat=None,
                                                   calib=None,
                                                   addShear=addShear,
                                                   transform=skyToPixelMatrix)
                else:
                    galArray = makeFake.makeGalaxy(flux, gal,
                                                   psfImage.getArray(),
                                                   cosmosCat=cosmosCat,
                                                   calib=calib,
                                                   galType=galType,
                                                   addShear=addShear,
                                                   sersic_prec=prec,
                                                   transform=skyToPixelMatrix)
            except IndexError as ierr:
                self.log.info("GalSim Index Error: Skipping %d" % galident)
                self.log.info(ierr.message)
                with open(skipLog, "a") as slog:
                    try:
                        fcntl.flock(slog, fcntl.LOCK_EX)
                        slog.write("%8d , galsimI\n" % galident)
                        fcntl.flock(slog, fcntl.LOCK_UN)
                    except IOError:
                        continue
                continue
            except KeyError as kerr:
                self.log.info("GalSim Key Error: Skipping %d" % galident)
                self.log.info(kerr.message)
                with open(skipLog, "a") as slog:
                    try:
                        fcntl.flock(slog, fcntl.LOCK_EX)
                        slog.write("%8d , galsimK\n" % galident)
                        fcntl.flock(slog, fcntl.LOCK_UN)
                    except IOError:
                        continue
                continue
            except ValueError as verr:
                self.log.info("GalSim Value Error: Skipping %d" % galident)
                self.log.info(verr.message)
                with open(skipLog, "a") as slog:
                    try:
                        fcntl.flock(slog, fcntl.LOCK_EX)
                        slog.write("%8d , galsimV\n" % galident)
                        fcntl.flock(slog, fcntl.LOCK_UN)
                    except IOError:
                        continue
                continue
            except RuntimeError as rerr:
                self.log.info("GalSim Runtime Error: Skipping %d" % galident)
                self.log.info(rerr.message)
                with open(skipLog, "a") as slog:
                    try:
                        fcntl.flock(slog, fcntl.LOCK_EX)
                        slog.write("%8d , galsimR\n" % galident)
                        fcntl.flock(slog, fcntl.LOCK_UN)
                    except IOError:
                        continue
                continue
            except Exception as uerr:
                self.log.info("Unexpected Error: Skipping %d" % galident)
                self.log.info(uerr.message)
                with open(skipLog, "a") as slog:
                    try:
                        fcntl.flock(slog, fcntl.LOCK_EX)
                        slog.write("%8d , Unexpected\n" % galident)
                        fcntl.flock(slog, fcntl.LOCK_UN)
                    except IOError:
                        continue
                continue
 
            galImage = lsst.afw.image.ImageF(galArray.astype(np.float32))
            galBBox = galImage.getBBox(PARENT)
            galX0 = (galXY.getX() - galBBox.getWidth()/2.0 + 0.5)
            galY0 = (galXY.getY() - galBBox.getHeight()/2.0 + 0.5)
            galImage = lsst.afw.math.offsetImage(galImage,
                                                 galX0, galY0,
                                                 'lanczos3')
            galBBox = galImage.getBBox(PARENT)
 
            # Check that we're within the larger exposure, otherwise crop
            parentBox = galImage.getBBox(PARENT)
            if expBBox.contains(parentBox) is False:
                newBBox = galImage.getBBox(PARENT)
                newBBox.clip(expBBox)
                if newBBox.getArea() <= 0:
                    self.log.info("BBoxEdge Error: Skipping %d" % galident)
                    with open(skipLog, "a") as slog:
                        try:
                            fcntl.flock(slog, fcntl.LOCK_EX)
                            slog.write("%8d , bboxEdge\n" % galident)
                            fcntl.flock(slog, fcntl.LOCK_UN)
                        except IOError:
                            continue
                    continue
                self.log.info("Cropping FAKE%d from %s to %s" % (galident,
                                                                 str(galBBox), str(newBBox)))
                galImage = galImage.Factory(galImage, newBBox,
                                            PARENT)
                galBBox = newBBox
 
            galMaskedImage = lsst.afw.image.MaskedImageF(galImage)
 
            # Put information of the added fake galaxies into the header
            md.set("FAKE%s" % str(galident), "%.3f, %.3f" % (galXY.getX(),
                                                             galXY.getY()))
            self.log.info("Adding fake %s at: %.1f,%.1f" % (str(galident),
                                                            galXY.getX(),
                                                            galXY.getY()))
 
            galMaskedImage.getMask().set(self.bitmask)
            if not self.config.addMask:
                try:
                    galMaskedImage.getMask().removeAndClearMaskPlane('FAKE',
                                                                     True)
                except Exception:
                    pass
            try:
                galMaskedImage.getMask().removeAndClearMaskPlane('CROSSTALK',
                                                                 True)
            except Exception:
                pass
            try:
                galMaskedImage.getMask().removeAndClearMaskPlane('UNMASKEDNAN',
                                                                 True)
            except Exception:
                pass
 
            maskedImage = exposure.getMaskedImage()
            try:
                maskedImage.getMask().removeAndClearMaskPlane('CROSSTALK',
                                                              True)
            except Exception:
                pass
            try:
                maskedImage.getMask().removeAndClearMaskPlane('UNMASKEDNAN',
                                                              True)
            except Exception:
                pass
            if not self.config.addMask:
                try:
                    maskedImage.getMask().removeAndClearMaskPlane('FAKE', True)
                except Exception:
                    pass
 
            BBox = galMaskedImage.getBBox(PARENT)
            subMaskedImage = maskedImage.Factory(exposure.getMaskedImage(),
                                                 BBox,
                                                 PARENT)
            subMaskedImage += galMaskedImage
 
            """
            #
            galMaskedImage.getMask().set(self.bitmask)
 
            maskedImage = exposure.getMaskedImage()
            try:
                maskedImage.getMask().removeAndClearMaskPlane('CROSSTALK',
                                                              True)
            except Exception:
                pass
            try:
                maskedImage.getMask().removeAndClearMaskPlane('UNMASKEDNAN',
                                                              True)
            except Exception:
                pass
            try:
                maskedImage.getMask().removeAndClearMaskPlane('FAKE', True)
            except Exception:
                pass
            """

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)
 

Member Data Documentation

bitmask

lsst.pipe.tasks.fakes.BaseFakeSourcesTask.bitmask

inherited

Definition at line 61 of file fakes.py.

config

lsst.pipe.base.task.Task.config

inherited

Definition at line 149 of file task.py.

ConfigClass

lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask.ConfigClass

static

Definition at line 51 of file positionGalSimFakes.py.

galData

lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask.galData

Definition at line 58 of file positionGalSimFakes.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.

npRand

lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask.npRand

Definition at line 57 of file positionGalSimFakes.py.

rng

lsst.synpipe.positionGalSimFakes.PositionGalSimFakesTask.rng

Definition at line 56 of file positionGalSimFakes.py.

---

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

• /j/snowflake/release/lsstsw/stack/cb4e2dc/Linux64/synpipe/20.0.0+e69b5d60e7/python/lsst/synpipe/positionGalSimFakes.py