22 r"""Base classes for forced measurement plugins and the driver task for these.
24 In forced measurement, a reference catalog is used to define restricted
25 measurements (usually just fluxes) on an image. As the reference catalog may
26 be deeper than the detection limit of the measurement image, we do not assume
27 that we can use detection and deblend information from the measurement image.
28 Instead, we assume this information is present in the reference catalog and
29 can be "transformed" in some sense to the measurement frame. At the very
30 least, this means that `~lsst.afw.detection.Footprint`\ s from the reference
31 catalog should be transformed and installed as Footprints in the output
32 measurement catalog. If we have a procedure that can transform "heavy"
33 Footprints (ie, including pixel data), we can then proceed with measurement as
34 usual, but using the reference catalog's ``id`` and ``parent`` fields to
35 define deblend families. If this transformation does not preserve
36 heavy Footprints (this is currently the case, at least for CCD forced
37 photometry), then we will only be able to replace objects with noise one
38 deblend family at a time, and hence measurements run in single-object mode may
39 be contaminated by neighbors when run on objects with ``parent != 0``.
41 Measurements are generally recorded in the coordinate system of the image
42 being measured (and all slot-eligible fields must be), but non-slot fields may
43 be recorded in other coordinate systems if necessary to avoid information loss
44 (this should, of course, be indicated in the field documentation). Note that
45 the reference catalog may be in a different coordinate system; it is the
46 responsibility of plugins to transform the data they need themselves, using
47 the reference WCS provided. However, for plugins that only require a position
48 or shape, they may simply use output `~lsst.afw.table.SourceCatalog`\'s
49 centroid or shape slots, which will generally be set to the transformed
50 position of the reference object before any other plugins are run, and hence
51 avoid using the reference catalog at all.
53 Command-line driver tasks for forced measurement include
54 `ForcedPhotCcdTask`, and `ForcedPhotCoaddTask`.
61 from .pluginRegistry
import PluginRegistry
62 from .baseMeasurement
import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
63 BaseMeasurementConfig, BaseMeasurementTask)
64 from .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.
85 schemaMapper : `lsst.afw.table.SchemaMapper`
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.
90 metadata : `lsst.daf.base.PropertySet`
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.
114 measRecord : `lsst.afw.table.SourceRecord`
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.
118 refRecord : `lsst.afw.table.SimpleRecord`
119 Additional parameters to define the fit, as measured elsewhere.
120 refWcs : `lsst.afw.geom.SkyWcs` or `lsst.afw.geom.Angle`
121 The coordinate system for the reference catalog values. An
122 `~lsst.geom.Angle` may be passed, indicating that a local tangent
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.
146 measCat : `lsst.afw.table.SourceCatalog`
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
151 refCat : `lsst.afw.table.SimpleCatalog`
152 Additional parameters to define the fit, as measured elsewhere.
153 Ordered such that ``zip(measCat, refcat)`` may be used.
154 refWcs : `lsst.afw.geom.SkyWcs` or `lsst.afw.geom.Angle`
155 The coordinate system for the reference catalog values. An
156 `~lsst.geom.Angle` may be passed, indicating that a local tangent
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"
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"}
200 doc=
"Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
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
229 refSchema : `lsst.afw.table.Schema`
230 Schema of the reference catalog. Must match the catalog later passed
231 to 'ForcedMeasurementTask.generateMeasCat` and/or
232 `ForcedMeasurementTask.run`.
233 algMetadata : `lsst.daf.base.PropertyList` or `None`
234 Will be updated in place to to record information about each
235 algorithm. An empty `~lsst.daf.base.PropertyList` will be created if
238 Keyword arguments are passed to the supertask constructor.
242 Note that while `SingleFrameMeasurementTask` is passed an initial
243 `~lsst.afw.table.Schema` that is appended to in order to create the output
244 `~lsst.afw.table.Schema`, `ForcedMeasurementTask` is initialized with the
245 `~lsst.afw.table.Schema` of the reference catalog, from which a new
246 `~lsst.afw.table.Schema` for the output catalog is created. Fields to be
247 copied directly from the reference `~lsst.afw.table.Schema` are added
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`
272 Image to be measured. Must have at least a `lsst.afw.geom.SkyWcs`
274 measCat : `lsst.afw.table.SourceCatalog`
275 Source catalog for measurement results; must be initialized with
276 empty records already corresponding to those in ``refCat`` (via
277 e.g. `generateMeasCat`).
278 refCat : `lsst.afw.table.SourceCatalog`
279 A sequence of `lsst.afw.table.SourceRecord` objects that provide
280 reference information for the measurement. These will be passed
281 to each plugin in addition to the output
282 `~lsst.afw.table.SourceRecord`.
283 refWcs : `lsst.afw.geom.SkyWcs`
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.
297 Fills the initial empty `~lsst.afw.table.SourceCatalog` with forced
298 measurement results. Two steps must occur before `run` can be called:
300 - `generateMeasCat` must be called to create the output ``measCat``
302 - `~lsst.afw.detection.Footprint`\ s appropriate for the forced sources
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)
306 `~lsst.afw.detection.Footprint`\s to regular
307 `~lsst.afw.detection.Footprint`\s, leading to non-deblended
308 measurement, so most callers should provide
309 `~lsst.afw.detection.Footprint`\s some other way. Typically, calling
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.
408 refCat : iterable of `lsst.afw.table.SourceRecord`
409 Catalog of reference sources.
410 refWcs : `lsst.afw.geom.SkyWcs`
411 Defines the X,Y coordinate system of ``refCat``.
412 idFactory : `lsst.afw.table.IdFactory`, optional
413 Factory for creating IDs for sources.
417 meascat : `lsst.afw.table.SourceCatalog`
418 Source catalog ready for measurement.
422 This generates a new blank `~lsst.afw.table.SourceRecord` for each
423 record in ``refCat``. Note that this method does not attach any
424 `~lsst.afw.detection.Footprint`\ s. Doing so is up to the caller (who
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.
446 `~lsst.afw.detection.Footprint`\s for forced photometry must be in the
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
451 ``HeavyFootprint``\s into regular `~lsst.afw.detection.Footprint`\s,
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.
469 sources : `lsst.afw.table.SourceCatalog`
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.
473 exposure : `lsst.afw.image.Exposure`
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())
Factory function for creating SpanSets from a Stencil.
An ellipse defined by an arbitrary BaseCore and a center point.
static std::shared_ptr< IdFactory > makeSimple()
Return a simple IdFactory that simply counts from 1.
A mapping between the keys of two Schemas, used to copy data between them.
static std::shared_ptr< SourceTable > make(Schema const &schema, std::shared_ptr< IdFactory > const &idFactory)
Construct a new table.
static Schema makeMinimalSchema()
Return a minimal schema for Source tables and records.
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)
def scale(algorithm, min, max=None, frame=None)