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Deprecate setPrimaryFlags
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This Task has moved to meas_algorithms and will be removed in v27.
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@parejkoj
parejkoj committed Feb 21, 2024
1 parent 83996f0 commit 3b8aa8d
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Showing 5 changed files with 30 additions and 299 deletions.
3 changes: 1 addition & 2 deletions python/lsst/pipe/tasks/calibrate.py
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Expand Up @@ -34,15 +34,14 @@
import lsst.daf.base as dafBase
from lsst.afw.math import BackgroundList
from lsst.afw.table import SourceTable
from lsst.meas.algorithms import SourceDetectionTask, ReferenceObjectLoader
from lsst.meas.algorithms import SourceDetectionTask, ReferenceObjectLoader, SetPrimaryFlagsTask
from lsst.meas.base import (SingleFrameMeasurementTask,
ApplyApCorrTask,
CatalogCalculationTask,
IdGenerator,
DetectorVisitIdGeneratorConfig)
from lsst.meas.deblender import SourceDeblendTask
from lsst.utils.timer import timeMethod
from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
from .photoCal import PhotoCalTask
from .computeExposureSummaryStats import ComputeExposureSummaryStatsTask

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6 changes: 3 additions & 3 deletions python/lsst/pipe/tasks/calibrateImage.py
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import lsst.meas.algorithms
import lsst.meas.algorithms.installGaussianPsf
import lsst.meas.algorithms.measureApCorr
import lsst.meas.algorithms.setPrimaryFlags
import lsst.meas.base
import lsst.meas.astrom
import lsst.meas.deblender
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from lsst.pipe.base import connectionTypes
from lsst.utils.timer import timeMethod

from . import measurePsf, repair, setPrimaryFlags, photoCal, \
computeExposureSummaryStats, maskStreaks, snapCombine
from . import measurePsf, repair, photoCal, computeExposureSummaryStats, maskStreaks, snapCombine


class CalibrateImageConnections(pipeBase.PipelineTaskConnections,
Expand Down Expand Up @@ -221,7 +221,7 @@ class CalibrateImageConfig(pipeBase.PipelineTaskConfig, pipelineConnections=Cali
"for the star selector to remove extended sources."
)
star_set_primary_flags = pexConfig.ConfigurableField(
target=setPrimaryFlags.SetPrimaryFlagsTask,
target=lsst.meas.algorithms.setPrimaryFlags.SetPrimaryFlagsTask,
doc="Task to add isPrimary to the catalog."
)
star_selector = lsst.meas.algorithms.sourceSelectorRegistry.makeField(
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4 changes: 2 additions & 2 deletions python/lsst/pipe/tasks/multiBand.py
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from lsst.pipe.base import (Struct, PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
import lsst.pipe.base.connectionTypes as cT
from lsst.pex.config import Field, ConfigurableField, ChoiceField
from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader, ScaleVarianceTask
from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader, ScaleVarianceTask, \
SetPrimaryFlagsTask
from lsst.meas.base import (
SingleFrameMeasurementTask,
ApplyApCorrTask,
Expand All @@ -33,7 +34,6 @@
)
from lsst.meas.extensions.scarlet.io import updateCatalogFootprints
from lsst.meas.astrom import DirectMatchTask, denormalizeMatches
from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
from lsst.pipe.tasks.propagateSourceFlags import PropagateSourceFlagsTask
import lsst.afw.table as afwTable
import lsst.afw.math as afwMath
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307 changes: 21 additions & 286 deletions python/lsst/pipe/tasks/setPrimaryFlags.py
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Expand Up @@ -21,293 +21,28 @@

__all__ = ["SetPrimaryFlagsConfig", "SetPrimaryFlagsTask"]

import numpy as np
from lsst.pex.config import Config, Field, ListField
from lsst.pipe.base import Task
from lsst.geom import Box2D
from deprecated.sphinx import deprecated

from lsst.meas.algorithms import setPrimaryFlags
from lsst.pex.config import Field, ListField

def getPatchInner(sources, patchInfo):
"""Set a flag for each source if it is in the innerBBox of a patch.

Parameters
----------
sources : `lsst.afw.table.SourceCatalog`
A sourceCatalog with pre-calculated centroids.
patchInfo : `lsst.skymap.PatchInfo`
Information about a `SkyMap` `Patch`.
Returns
-------
isPatchInner : array-like of `bool`
`True` for each source that has a centroid
in the inner region of a patch.
"""
# Extract the centroid position for all the sources
x = sources["slot_Centroid_x"]
y = sources["slot_Centroid_y"]
centroidFlag = sources["slot_Centroid_flag"]

# set inner flags for each source and set primary flags for
# sources with no children (or all sources if deblend info not available)
innerFloatBBox = Box2D(patchInfo.getInnerBBox())
inInner = innerFloatBBox.contains(x, y)

# When the centroider fails, we can still fall back to the peak,
# but we don't trust that quite as much -
# so we use a slightly smaller box for the patch comparison.
shrunkInnerFloatBBox = Box2D(innerFloatBBox)
shrunkInnerFloatBBox.grow(-1)
inShrunkInner = shrunkInnerFloatBBox.contains(x, y)

# Flag sources contained in the inner region of a patch
isPatchInner = (centroidFlag & inShrunkInner) | (~centroidFlag & inInner)
return isPatchInner


def getTractInner(sources, tractInfo, skyMap):
"""Set a flag for each source that the skyMap includes in tractInfo.
Parameters
----------
sources : `lsst.afw.table.SourceCatalog`
A sourceCatalog with pre-calculated centroids.
tractInfo : `lsst.skymap.TractInfo`
Tract object
skyMap : `lsst.skymap.BaseSkyMap`
Sky tessellation object
Returns
-------
isTractInner : array-like of `bool`
True if the skyMap.findTract method returns
the same tract as tractInfo.
"""
tractId = tractInfo.getId()
isTractInner = np.array([skyMap.findTract(s.getCoord()).getId() == tractId for s in sources])
return isTractInner


def getPseudoSources(sources, pseudoFilterList, schema, log):
"""Get a flag that marks pseudo sources.
Some categories of sources, for example sky objects,
are not really detected sources and should not be considered primary
sources.
Parameters
----------
sources : `lsst.afw.table.SourceCatalog`
The catalog of sources for which to identify "pseudo"
(e.g. sky) objects.
pseudoFilterList : `list` of `str`
Names of filters which should never be primary
Returns
-------
isPseudo : array-like of `bool`
True for each source that is a pseudo source.
Note: to remove pseudo sources use `~isPseudo`.
"""
# Filter out sources that should never be primary
isPseudo = np.zeros(len(sources), dtype=bool)
for filt in pseudoFilterList:
try:
pseudoFilterKey = schema.find("merge_peak_%s" % filt).getKey()
isPseudo |= sources[pseudoFilterKey]
except KeyError:
log.warning("merge_peak is not set for pseudo-filter %s", filt)
return isPseudo


def getDeblendPrimaryFlags(sources):
"""Get flags generated by the deblender
scarlet is different than meas_deblender in that it is not
(necessarily) flux conserving. For consistency in scarlet,
all of the parents with only a single child (isolated sources)
need to be deblended. This creates a question: which type
of isolated source should we make measurements on, the
undeblended "parent" or the deblended child?
For that reason we distinguish between a DeblendedSource,
which is a source that has no children and uses the
isolated parents, and a DeblendedModelSource, which uses
the scarlet models for both isolated and blended sources.
In the case of meas_deblender, DeblendedModelSource is
`None` because it is not contained in the output catalog.
Parameters
----------
sources : `lsst.afw.table.SourceCatalog`
A sourceCatalog that has already been deblended using
either meas_extensions_scarlet or meas_deblender.
Returns
-------
fromBlend : array-like of `bool`
True for each source modeled by the deblender from a `Peak`
in a parent footprint that contained at least one other `Peak`.
While these models can be approximated as isolated,
and measurements are made on them as if that's the case,
we know deblending to introduce biases in the shape and centroid
of objects and it is important to know that the sources that these
models are based on are all bleneded in the true image.
isIsolated : array-like of `bool`
True for isolated sources, regardless of whether or not they
were modeled by the deblender.
isDeblendedSource : array-like of `bool`
True for each source that is a "DeblendedSource" as defined above.
isDeblendedModelSource : array-like of `bool`
True for each source that is a "DeblendedSourceModel"
as defined above.
"""
nChildKey = "deblend_nChild"
nChild = sources[nChildKey]
parent = sources["parent"]

if "deblend_scarletFlux" in sources.schema:
# The number of peaks in the sources footprint.
# This (may be) different than nChild,
# the number of deblended sources in the catalog,
# because some peaks might have been culled during deblending.
nPeaks = sources["deblend_nPeaks"]
parentNChild = sources["deblend_parentNChild"]
# It is possible for a catalog to contain a hierarchy of sources,
# so we mark the leaves (end nodes of the hierarchy tree with no
# children).
isLeaf = nPeaks == 1
fromBlend = parentNChild > 1
isIsolated = isLeaf & ((parent == 0) | parentNChild == 1)
isDeblendedSource = (fromBlend & isLeaf) | (isIsolated & (parent == 0))
isDeblendedModelSource = (parent != 0) & isLeaf
else:
# Set the flags for meas_deblender
fromBlend = parent != 0
isIsolated = (nChild == 0) & (parent == 0)
isDeblendedSource = nChild == 0
isDeblendedModelSource = None
return fromBlend, isIsolated, isDeblendedSource, isDeblendedModelSource


class SetPrimaryFlagsConfig(Config):
# Remove this entire file on DM-42962.
@deprecated(reason="This class has been moved to meas_algorithms. Will be removed after v27.",
version="v27.0", category=FutureWarning)
class SetPrimaryFlagsConfig(setPrimaryFlags.SetPrimaryFlagsConfig):
nChildKeyName = Field(dtype=str, default="deprecated",
doc="Deprecated. This parameter is not used.")
pseudoFilterList = ListField(dtype=str, default=['sky'],
doc="Names of filters which should never be primary")


class SetPrimaryFlagsTask(Task):
"""Add isPrimaryKey to a given schema.
Parameters
----------
schema : `lsst.afw.table.Schema`
The input schema.
isSingleFrame : `bool`
Flag specifying if task is operating with single frame imaging.
includeDeblend : `bool`
Include deblend information in isPrimary and
add isDeblendedSource field?
kwargs :
Keyword arguments passed to the task.
"""

ConfigClass = SetPrimaryFlagsConfig

def __init__(self, schema, isSingleFrame=False, **kwargs):
Task.__init__(self, **kwargs)
self.schema = schema
self.isSingleFrame = isSingleFrame
self.includeDeblend = False
if not self.isSingleFrame:
primaryDoc = ("true if source has no children and is in the inner region of a coadd patch "
"and is in the inner region of a coadd tract "
"and is not \"detected\" in a pseudo-filter (see config.pseudoFilterList)")
self.isPatchInnerKey = self.schema.addField(
"detect_isPatchInner", type="Flag",
doc="true if source is in the inner region of a coadd patch",
)
self.isTractInnerKey = self.schema.addField(
"detect_isTractInner", type="Flag",
doc="true if source is in the inner region of a coadd tract",
)
else:
primaryDoc = "true if source has no children and is not a sky source"
self.isPrimaryKey = self.schema.addField(
"detect_isPrimary", type="Flag",
doc=primaryDoc,
)

if "deblend_nChild" in schema.getNames():
self.includeDeblend = True
self.isDeblendedSourceKey = self.schema.addField(
"detect_isDeblendedSource", type="Flag",
doc=primaryDoc + " and is either an unblended isolated source or a "
"deblended child from a parent with 'deblend_nChild' > 1")
self.fromBlendKey = self.schema.addField(
"detect_fromBlend", type="Flag",
doc="This source is deblended from a parent with more than one child."
)
self.isIsolatedKey = self.schema.addField(
"detect_isIsolated", type="Flag",
doc="This source is not a part of a blend."
)
if "deblend_scarletFlux" in schema.getNames():
self.isDeblendedModelKey = self.schema.addField(
"detect_isDeblendedModelSource", type="Flag",
doc=primaryDoc + " and is a deblended child")
else:
self.isDeblendedModelKey = None

def run(self, sources, skyMap=None, tractInfo=None, patchInfo=None):
"""Set isPrimary and related flags on sources.
For coadded imaging, the `isPrimary` flag returns True when an object
has no children, is in the inner region of a coadd patch, is in the
inner region of a coadd trach, and is not detected in a pseudo-filter
(e.g., a sky_object).
For single frame imaging, the isPrimary flag returns True when a
source has no children and is not a sky source.
Parameters
----------
sources : `lsst.afw.table.SourceCatalog`
A sourceTable. Reads in centroid fields and an nChild field.
Writes is-patch-inner, is-tract-inner, and is-primary flags.
skyMap : `lsst.skymap.BaseSkyMap`
Sky tessellation object
tractInfo : `lsst.skymap.TractInfo`
Tract object
patchInfo : `lsst.skymap.PatchInfo`
Patch object
"""
# Mark whether sources are contained within the inner regions of the
# given tract/patch and are not "pseudo" (e.g. sky) sources.
if not self.isSingleFrame:
isPatchInner = getPatchInner(sources, patchInfo)
isTractInner = getTractInner(sources, tractInfo, skyMap)
isPseudo = getPseudoSources(sources, self.config.pseudoFilterList, self.schema, self.log)
isPrimary = isTractInner & isPatchInner & ~isPseudo

sources[self.isPatchInnerKey] = isPatchInner
sources[self.isTractInnerKey] = isTractInner
else:
# Mark all of the sky sources in SingleFrame images
# (if they were added)
if "sky_source" in sources.schema:
isSky = sources["sky_source"]
else:
isSky = np.zeros(len(sources), dtype=bool)
isPrimary = ~isSky

if self.includeDeblend:
result = getDeblendPrimaryFlags(sources)
fromBlend, isIsolated, isDeblendedSource, isDeblendedModelSource = result
sources[self.fromBlendKey] = fromBlend
sources[self.isIsolatedKey] = isIsolated
sources[self.isDeblendedSourceKey] = isDeblendedSource
if self.isDeblendedModelKey is not None:
sources[self.isDeblendedModelKey] = isDeblendedModelSource
isPrimary = isPrimary & isDeblendedSource

sources[self.isPrimaryKey] = isPrimary
doc="Deprecated. This parameter is not used.",
deprecated="This parameter is not used. Will be removed after v27.")
pseudoFilterList = ListField(
dtype=str,
default=['sky'],
doc="Names of filters which should never be primary",
deprecated="This class has been moved to meas_algorithms. Will be removed after v27."
)


@deprecated(reason="This class has been moved to meas_algorithms. Will be removed after v27.",
version="v27.0", category=FutureWarning)
class SetPrimaryFlagsTask(setPrimaryFlags.SetPrimaryFlagsTask):
pass
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