22r"""Base classes for forced measurement plugins and the driver task for these.
24In forced measurement, a reference catalog is used to define restricted
25measurements (usually just fluxes) on an image. As the reference catalog may
26be deeper than the detection limit of the measurement image, we do not assume
27that we can use detection
and deblend information
from the measurement image.
28Instead, we assume this information
is present
in the reference catalog
and
29can be
"transformed" in some sense to the measurement frame. At the very
31catalog should be transformed
and installed
as Footprints
in the output
32measurement catalog. If we have a procedure that can transform
"heavy"
33Footprints (ie, including pixel data), we can then proceed
with measurement
as
34usual, but using the reference catalog
's ``id`` and ``parent`` fields to
35define deblend families. If this transformation does not preserve
36heavy Footprints (this
is currently the case, at least
for CCD forced
37photometry), then we will only be able to replace objects
with noise one
38deblend family at a time,
and hence measurements run
in single-object mode may
39be contaminated by neighbors when run on objects
with ``parent != 0``.
41Measurements are generally recorded
in the coordinate system of the image
42being measured (
and all slot-eligible fields must be), but non-slot fields may
43be recorded
in other coordinate systems
if necessary to avoid information loss
44(this should, of course, be indicated
in the field documentation). Note that
45the reference catalog may be
in a different coordinate system; it
is the
46responsibility of plugins to transform the data they need themselves, using
47the reference WCS provided. However,
for plugins that only require a position
49centroid or shape slots, which will generally be set to the transformed
50position of the reference object before any other plugins are run,
and hence
51avoid using the reference catalog at all.
53Command-line driver tasks
for forced measurement include
54`ForcedPhotCcdTask`,
and `ForcedPhotCoaddTask`.
61from .pluginRegistry import PluginRegistry
62from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
63 BaseMeasurementConfig, BaseMeasurementTask)
64from .noiseReplacer
import NoiseReplacer, DummyNoiseReplacer
66__all__ = (
"ForcedPluginConfig",
"ForcedPlugin",
67 "ForcedMeasurementConfig",
"ForcedMeasurementTask")
71 """Base class for configs of forced measurement plugins."""
77 """Base class for forced measurement plugins.
81 config : `ForcedPlugin.ConfigClass`
82 Configuration for this plugin.
84 The string
with which the plugin was registered.
86 A mapping
from reference catalog fields to output catalog fields.
87 Output fields should be added to the output schema. While most plugins
88 will
not need to map fields
from the reference schema,
if they do so,
89 those fields will be transferred before any plugins are run.
91 Plugin metadata that will be attached to the output catalog.
92 logName : `str`, optional
93 Name to use when logging errors.
97 """Subclasses of `ForcedPlugin` must be registered here (`PluginRegistry`).
100 ConfigClass = ForcedPluginConfig
102 def __init__(self, config, name, schemaMapper, metadata, logName=None):
103 BaseMeasurementPlugin.__init__(self, config, name, logName=logName)
105 def measure(self, measRecord, exposure, refRecord, refWcs):
106 """Measure the properties of a source given an image and a reference.
110 exposure : `lsst.afw.image.ExposureF`
111 The pixel data to be measured, together with the associated PSF,
112 WCS, etc. All other sources
in the image should have been replaced
113 by noise according to deblender outputs.
115 Record describing the object being measured. Previously-measured
116 quantities will be retrieved
from here,
and it will be updated
117 in-place
with the outputs of this plugin.
119 Additional parameters to define the fit,
as measured elsewhere.
121 The coordinate system
for the reference catalog values. An
123 WCS should be created
for each object using the given angle
as a
128 In the normal mode of operation, the source centroid will be set to
129 the WCS-transformed position of the reference object, so plugins that
130 only require a reference position should
not have to access the
131 reference object at all.
133 raise NotImplementedError()
135 def measureN(self, measCat, exposure, refCat, refWcs):
136 """Measure the properties of blended sources from image & reference.
138 This operates on all members of a blend family at once.
142 exposure : `lsst.afw.image.ExposureF`
143 The pixel data to be measured, together with the associated PSF,
144 WCS, etc. Sources
not in the blended hierarchy to be measured
145 should have been replaced
with noise using deblender outputs.
147 Catalog describing the objects (
and only those objects) being
148 measured. Previously-measured quantities will be retrieved
from
149 here,
and it will be updated
in-place
with the outputs of this
152 Additional parameters to define the fit,
as measured elsewhere.
153 Ordered such that ``zip(measCat, refcat)`` may be used.
155 The coordinate system
for the reference catalog values. An
157 WCS should be created
for each object using the given angle
as a
162 In the normal mode of operation, the source centroids will be set to
163 the WCS-transformed position of the reference object, so plugins that
164 only require a reference position should
not have to access the
165 reference object at all.
167 raise NotImplementedError()
171 """Config class for forced measurement driver task.
174 plugins = ForcedPlugin.registry.makeField(
176 default=[
"base_PixelFlags",
177 "base_TransformedCentroid",
179 "base_TransformedShape",
182 "base_CircularApertureFlux",
184 "base_LocalBackground",
186 doc=
"Plugins to be run and their configuration"
188 algorithms = property(
lambda self: self.
pluginsplugins, doc=
"backwards-compatibility alias for plugins")
189 undeblended = ForcedPlugin.registry.makeField(
192 doc=
"Plugins to run on undeblended image"
194 copyColumns = lsst.pex.config.DictField(
195 keytype=str, itemtype=str, doc=
"Mapping of reference columns to source columns",
196 default={
"id":
"objectId",
"parent":
"parentObjectId",
"deblend_nChild":
"deblend_nChild",
197 "coord_ra":
"coord_ra",
"coord_dec":
"coord_dec"}
199 checkUnitsParseStrict = lsst.pex.config.Field(
200 doc=
"Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
204 loggingInterval = lsst.pex.config.Field(
207 doc=
"Interval (in seconds) to log messages (at VERBOSE level) while running measurement plugins."
211 self.
slotsslots.centroid =
"base_TransformedCentroid"
212 self.
slotsslots.shape =
"base_TransformedShape"
213 self.
slotsslots.apFlux =
None
214 self.
slotsslots.modelFlux =
None
215 self.
slotsslots.psfFlux =
None
216 self.
slotsslots.gaussianFlux =
None
217 self.
slotsslots.calibFlux =
None
221 """Measure sources on an image, constrained by a reference catalog.
223 A subtask for measuring the properties of sources on a single image,
224 using an existing
"reference" catalog to constrain some aspects of the
230 Schema of the reference catalog. Must match the catalog later passed
231 to
'ForcedMeasurementTask.generateMeasCat` and/or
232 `ForcedMeasurementTask.run`.
234 Will be updated
in place to to record information about each
238 Keyword arguments are passed to the supertask constructor.
242 Note that
while `SingleFrameMeasurementTask`
is passed an initial
248 before ``Plugin`` fields are added.
251 ConfigClass = ForcedMeasurementConfig
253 def __init__(self, refSchema, algMetadata=None, **kwds):
254 super(ForcedMeasurementTask, self).
__init__(algMetadata=algMetadata, **kwds)
257 self.config.slots.setupSchema(self.
mappermapper.editOutputSchema())
258 for refName, targetName
in self.config.copyColumns.items():
259 refItem = refSchema.find(refName)
260 self.
mappermapper.addMapping(refItem.key, targetName)
261 self.config.slots.setupSchema(self.
mappermapper.editOutputSchema())
264 self.
schemaschema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
266 def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None):
267 r"""Perform forced measurement.
271 exposure : `lsst.afw.image.exposureF`
275 Source catalog for measurement results; must be initialized
with
276 empty records already corresponding to those
in ``refCat`` (via
277 e.g. `generateMeasCat`).
280 reference information
for the measurement. These will be passed
281 to each plugin
in addition to the output
284 Defines the X,Y coordinate system of ``refCat``.
285 exposureId : `int`, optional
286 Optional unique exposureId used to calculate random number
287 generator seed
in the NoiseReplacer.
288 beginOrder : `int`, optional
289 Beginning execution order (inclusive). Algorithms
with
290 ``executionOrder`` < ``beginOrder`` are
not executed. `
None`
for no limit.
291 endOrder : `int`, optional
292 Ending execution order (exclusive). Algorithms
with
293 ``executionOrder`` >= ``endOrder`` are
not executed. `
None`
for no limit.
298 measurement results. Two steps must occur before `run` can be called:
300 - `generateMeasCat` must be called to create the output ``measCat``
303 must be attached to the ``measCat`` records. The
304 `attachTransformedFootprints` method can be used to do this, but
305 this degrades
"heavy" (i.e., including pixel values)
308 measurement, so most callers should provide
310 code will have access to information that will allow them to provide
311 heavy footprints -
for instance, `ForcedPhotCoaddTask` uses the
312 heavy footprints
from deblending run
in the same band just before
313 non-forced
is run measurement
in that band.
325 refCatIdDict = {ref.getId(): ref.getParent()
for ref
in refCat}
330 if topId
not in refCatIdDict:
331 raise RuntimeError(
"Reference catalog contains a child for which at least "
332 "one parent in its parent chain is not in the catalog.")
333 topId = refCatIdDict[topId]
338 footprints = {ref.getId(): (ref.getParent(), measRecord.getFootprint())
339 for (ref, measRecord)
in zip(refCat, measCat)}
341 self.log.info(
"Performing forced measurement on %d source%s", len(refCat),
342 "" if len(refCat) == 1
else "s")
343 nextLogTime = time.time() + self.config.loggingInterval
345 if self.config.doReplaceWithNoise:
346 noiseReplacer =
NoiseReplacer(self.config.noiseReplacer, exposure,
347 footprints, log=self.log, exposureId=exposureId)
348 algMetadata = measCat.getTable().getMetadata()
349 if algMetadata
is not None:
350 algMetadata.addInt(
"NOISE_SEED_MULTIPLIER", self.config.noiseReplacer.noiseSeedMultiplier)
351 algMetadata.addString(
"NOISE_SOURCE", self.config.noiseReplacer.noiseSource)
352 algMetadata.addDouble(
"NOISE_OFFSET", self.config.noiseReplacer.noiseOffset)
353 if exposureId
is not None:
354 algMetadata.addLong(
"NOISE_EXPOSURE_ID", exposureId)
360 refParentCat, measParentCat = refCat.getChildren(0, measCat)
361 childrenIter = refCat.getChildren((refParentRecord.getId()
for refParentRecord
in refCat), measCat)
362 for parentIdx, records
in enumerate(zip(refParentCat, measParentCat, childrenIter)):
364 refParentRecord, measParentRecord, (refChildCat, measChildCat) = records
367 for refChildRecord, measChildRecord
in zip(refChildCat, measChildCat):
368 noiseReplacer.insertSource(refChildRecord.getId())
369 self.
callMeasurecallMeasure(measChildRecord, exposure, refChildRecord, refWcs,
370 beginOrder=beginOrder, endOrder=endOrder)
371 noiseReplacer.removeSource(refChildRecord.getId())
374 noiseReplacer.insertSource(refParentRecord.getId())
375 self.
callMeasurecallMeasure(measParentRecord, exposure, refParentRecord, refWcs,
376 beginOrder=beginOrder, endOrder=endOrder)
377 self.
callMeasureNcallMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
378 refParentCat[parentIdx:parentIdx+1],
379 beginOrder=beginOrder, endOrder=endOrder)
381 self.
callMeasureNcallMeasureN(measChildCat, exposure, refChildCat,
382 beginOrder=beginOrder, endOrder=endOrder)
383 noiseReplacer.removeSource(refParentRecord.getId())
385 if (currentTime := time.time()) > nextLogTime:
386 self.log.verbose(
"Forced measurement complete for %d parents (and their children) out of %d",
387 parentIdx + 1, len(refParentCat))
388 nextLogTime = currentTime + self.config.loggingInterval
393 for recordIndex, (measRecord, refRecord)
in enumerate(zip(measCat, refCat)):
395 self.
doMeasurementdoMeasurement(plugin, measRecord, exposure, refRecord, refWcs)
396 if (currentTime := time.time()) > nextLogTime:
397 self.log.verbose(
"Undeblended forced measurement complete for %d sources out of %d",
398 recordIndex + 1, len(refCat))
399 nextLogTime = currentTime + self.config.loggingInterval
402 r"""Initialize an output catalog from the reference catalog.
406 exposure : `lsst.afw.image.exposureF`
407 Image to be measured.
409 Catalog of reference sources.
411 Defines the X,Y coordinate system of ``refCat``.
413 Factory for creating IDs
for sources.
418 Source catalog ready
for measurement.
423 record
in ``refCat``. Note that this method does
not attach any
425 may call `attachedTransformedFootprints`
or define their own method -
426 see `run`
for more information).
428 if idFactory
is None:
432 table = measCat.table
434 table.preallocate(len(refCat))
436 newSource = measCat.addNew()
437 newSource.assign(ref, self.
mappermapper)
441 r"""Attach Footprints to blank sources prior to measurement, by
442 transforming Footprints attached to the reference catalog.
447 pixel coordinate system of the image being measured,
while the actual
448 detections may start out
in a different coordinate system. This
449 default implementation transforms the Footprints
from the reference
450 catalog
from the WCS to the exposure
's WCS, which downgrades
452 destroying deblend information.
454 See the documentation for `run`
for information about the
455 relationships between `run`, `generateMeasCat`,
and
456 `attachTransformedFootprints`.
458 exposureWcs = exposure.getWcs()
459 region = exposure.getBBox(lsst.afw.image.PARENT)
460 for srcRecord, refRecord
in zip(sources, refCat):
461 srcRecord.setFootprint(refRecord.getFootprint().
transform(refWcs, exposureWcs, region))
464 """Attach Footprints to blank sources prior to measurement, by
465 creating elliptical Footprints from the PSF moments.
470 Blank catalog (
with all rows
and columns, but values other than
471 ``coord_ra``, ``coord_dec`` unpopulated).
472 to which footprints should be attached.
474 Image object
from which peak values
and the PSF are obtained.
475 scaling : `int`, optional
476 Scaling factor to apply to the PSF second-moments ellipse
in order
477 to determine the footprint boundary.
481 This
is a utility function
for use by parent tasks; see
482 `attachTransformedFootprints`
for more information.
484 psf = exposure.getPsf()
486 raise RuntimeError(
"Cannot construct Footprints from PSF shape without a PSF.")
487 bbox = exposure.getBBox()
488 wcs = exposure.getWcs()
489 for record
in sources:
490 localPoint = wcs.skyToPixel(record.getCoord())
492 assert bbox.contains(localIntPoint), (
493 f
"Center for record {record.getId()} is not in exposure; this should be guaranteed by "
497 ellipse.getCore().scale(scaling)
500 footprint.addPeak(localIntPoint.getX(), localIntPoint.getY(),
501 exposure.image._get(localIntPoint, lsst.afw.image.PARENT))
502 record.setFootprint(footprint)
static std::shared_ptr< geom::SpanSet > fromShape(int r, Stencil s=Stencil::CIRCLE, lsst::geom::Point2I offset=lsst::geom::Point2I())
static std::shared_ptr< IdFactory > makeSimple()
static std::shared_ptr< SourceTable > make(Schema const &schema, std::shared_ptr< IdFactory > const &idFactory)
static Schema makeMinimalSchema()
def doMeasurement(self, plugin, measRecord, *args, **kwds)
def initializePlugins(self, **kwds)
def callMeasure(self, measRecord, *args, **kwds)
def callMeasureN(self, measCat, *args, **kwds)
def attachTransformedFootprints(self, sources, refCat, exposure, refWcs)
def __init__(self, refSchema, algMetadata=None, **kwds)
def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None)
def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None)
def attachPsfShapeFootprints(self, sources, exposure, scaling=3)
def measureN(self, measCat, exposure, refCat, refWcs)
def measure(self, measRecord, exposure, refRecord, refWcs)
def __init__(self, config, name, schemaMapper, metadata, logName=None)