Coverage for python/lsst/meas/base/forcedMeasurement.py: 19%
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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
30least, this means that `~lsst.afw.detection.Footprint`\ s from the reference
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
48or shape, they may simply use output `~lsst.afw.table.SourceCatalog`\'s
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`.
55"""
57import lsst.pex.config
58import lsst.pipe.base
59from lsst.utils.logging import PeriodicLogger
61from .pluginRegistry import PluginRegistry
62from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
63 BaseMeasurementConfig, BaseMeasurementTask)
64from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer
66__all__ = ("ForcedPluginConfig", "ForcedPlugin",
67 "ForcedMeasurementConfig", "ForcedMeasurementTask")
70class ForcedPluginConfig(BaseMeasurementPluginConfig):
71 """Base class for configs of forced measurement plugins."""
73 pass
76class ForcedPlugin(BaseMeasurementPlugin):
77 """Base class for forced measurement plugins.
79 Parameters
80 ----------
81 config : `ForcedPlugin.ConfigClass`
82 Configuration for this plugin.
83 name : `str`
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.
94 """
96 registry = PluginRegistry(ForcedPluginConfig)
97 """Subclasses of `ForcedPlugin` must be registered here (`PluginRegistry`).
98 """
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.
108 Parameters
109 ----------
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
124 pixel scale.
126 Notes
127 -----
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.
132 """
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.
140 Parameters
141 ----------
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
150 plugin.
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
158 pixel scale.
160 Notes
161 -----
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.
166 """
167 raise NotImplementedError()
170class ForcedMeasurementConfig(BaseMeasurementConfig):
171 """Config class for forced measurement driver task.
172 """
174 plugins = ForcedPlugin.registry.makeField(
175 multi=True,
176 default=["base_PixelFlags",
177 "base_TransformedCentroid",
178 "base_SdssCentroid",
179 "base_TransformedShape",
180 "base_SdssShape",
181 "base_GaussianFlux",
182 "base_CircularApertureFlux",
183 "base_PsfFlux",
184 "base_LocalBackground",
185 ],
186 doc="Plugins to be run and their configuration"
187 )
188 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins")
189 undeblended = ForcedPlugin.registry.makeField(
190 multi=True,
191 default=[],
192 doc="Plugins to run on undeblended image"
193 )
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"}
198 )
199 checkUnitsParseStrict = lsst.pex.config.Field(
200 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
201 dtype=str,
202 default="raise",
203 )
205 def setDefaults(self):
206 self.slots.centroid = "base_TransformedCentroid"
207 self.slots.shape = "base_TransformedShape"
208 self.slots.apFlux = None
209 self.slots.modelFlux = None
210 self.slots.psfFlux = None
211 self.slots.gaussianFlux = None
212 self.slots.calibFlux = None
215class ForcedMeasurementTask(BaseMeasurementTask):
216 """Measure sources on an image, constrained by a reference catalog.
218 A subtask for measuring the properties of sources on a single image,
219 using an existing "reference" catalog to constrain some aspects of the
220 measurement.
222 Parameters
223 ----------
224 refSchema : `lsst.afw.table.Schema`
225 Schema of the reference catalog. Must match the catalog later passed
226 to 'ForcedMeasurementTask.generateMeasCat` and/or
227 `ForcedMeasurementTask.run`.
228 algMetadata : `lsst.daf.base.PropertyList` or `None`
229 Will be updated in place to to record information about each
230 algorithm. An empty `~lsst.daf.base.PropertyList` will be created if
231 `None`.
232 **kwds
233 Keyword arguments are passed to the supertask constructor.
235 Notes
236 -----
237 Note that while `SingleFrameMeasurementTask` is passed an initial
238 `~lsst.afw.table.Schema` that is appended to in order to create the output
239 `~lsst.afw.table.Schema`, `ForcedMeasurementTask` is initialized with the
240 `~lsst.afw.table.Schema` of the reference catalog, from which a new
241 `~lsst.afw.table.Schema` for the output catalog is created. Fields to be
242 copied directly from the reference `~lsst.afw.table.Schema` are added
243 before ``Plugin`` fields are added.
244 """
246 ConfigClass = ForcedMeasurementConfig
248 def __init__(self, refSchema, algMetadata=None, **kwds):
249 super(ForcedMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds)
250 self.mapper = lsst.afw.table.SchemaMapper(refSchema)
251 self.mapper.addMinimalSchema(lsst.afw.table.SourceTable.makeMinimalSchema(), False)
252 self.config.slots.setupSchema(self.mapper.editOutputSchema())
253 for refName, targetName in self.config.copyColumns.items():
254 refItem = refSchema.find(refName)
255 self.mapper.addMapping(refItem.key, targetName)
256 self.config.slots.setupSchema(self.mapper.editOutputSchema())
257 self.initializePlugins(schemaMapper=self.mapper)
258 self.addInvalidPsfFlag(self.mapper.editOutputSchema())
259 self.schema = self.mapper.getOutputSchema()
260 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
262 def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None):
263 r"""Perform forced measurement.
265 Parameters
266 ----------
267 exposure : `lsst.afw.image.exposureF`
268 Image to be measured. Must have at least a `lsst.afw.geom.SkyWcs`
269 attached.
270 measCat : `lsst.afw.table.SourceCatalog`
271 Source catalog for measurement results; must be initialized with
272 empty records already corresponding to those in ``refCat`` (via
273 e.g. `generateMeasCat`).
274 refCat : `lsst.afw.table.SourceCatalog`
275 A sequence of `lsst.afw.table.SourceRecord` objects that provide
276 reference information for the measurement. These will be passed
277 to each plugin in addition to the output
278 `~lsst.afw.table.SourceRecord`.
279 refWcs : `lsst.afw.geom.SkyWcs`
280 Defines the X,Y coordinate system of ``refCat``.
281 exposureId : `int`, optional
282 Optional unique exposureId used to calculate random number
283 generator seed in the NoiseReplacer.
284 beginOrder : `int`, optional
285 Beginning execution order (inclusive). Algorithms with
286 ``executionOrder`` < ``beginOrder`` are not executed. `None` for no limit.
287 endOrder : `int`, optional
288 Ending execution order (exclusive). Algorithms with
289 ``executionOrder`` >= ``endOrder`` are not executed. `None` for no limit.
291 Notes
292 -----
293 Fills the initial empty `~lsst.afw.table.SourceCatalog` with forced
294 measurement results. Two steps must occur before `run` can be called:
296 - `generateMeasCat` must be called to create the output ``measCat``
297 argument.
298 - `~lsst.afw.detection.Footprint`\ s appropriate for the forced sources
299 must be attached to the ``measCat`` records. The
300 `attachTransformedFootprints` method can be used to do this, but
301 this degrades "heavy" (i.e., including pixel values)
302 `~lsst.afw.detection.Footprint`\s to regular
303 `~lsst.afw.detection.Footprint`\s, leading to non-deblended
304 measurement, so most callers should provide
305 `~lsst.afw.detection.Footprint`\s some other way. Typically, calling
306 code will have access to information that will allow them to provide
307 heavy footprints - for instance, `ForcedPhotCoaddTask` uses the
308 heavy footprints from deblending run in the same band just before
309 non-forced is run measurement in that band.
310 """
311 # First check that the reference catalog does not contain any children
312 # for which any member of their parent chain is not within the list.
313 # This can occur at boundaries when the parent is outside and one of
314 # the children is within. Currently, the parent chain is always only
315 # one deep, but just in case, this code checks for any case where when
316 # the parent chain to a child's topmost parent is broken and raises an
317 # exception if it occurs.
318 #
319 # I.e. this code checks that this precondition is satisfied by
320 # whatever reference catalog provider is being paired with it.
321 refCatIdDict = {ref.getId(): ref.getParent() for ref in refCat}
322 for ref in refCat:
323 refId = ref.getId()
324 topId = refId
325 while topId > 0:
326 if topId not in refCatIdDict:
327 raise RuntimeError("Reference catalog contains a child for which at least "
328 "one parent in its parent chain is not in the catalog.")
329 topId = refCatIdDict[topId]
331 # Construct a footprints dict which looks like
332 # {ref.getId(): (ref.getParent(), source.getFootprint())}
333 # (i.e. getting the footprint from the transformed source footprint)
334 footprints = {ref.getId(): (ref.getParent(), measRecord.getFootprint())
335 for (ref, measRecord) in zip(refCat, measCat)}
337 self.log.info("Performing forced measurement on %d source%s", len(refCat),
338 "" if len(refCat) == 1 else "s")
340 # Wrap the task logger into a periodic logger.
341 periodicLog = PeriodicLogger(self.log)
343 if self.config.doReplaceWithNoise:
344 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure,
345 footprints, log=self.log, exposureId=exposureId)
346 algMetadata = measCat.getTable().getMetadata()
347 if algMetadata is not None:
348 algMetadata.addInt("NOISE_SEED_MULTIPLIER", self.config.noiseReplacer.noiseSeedMultiplier)
349 algMetadata.addString("NOISE_SOURCE", self.config.noiseReplacer.noiseSource)
350 algMetadata.addDouble("NOISE_OFFSET", self.config.noiseReplacer.noiseOffset)
351 if exposureId is not None:
352 algMetadata.addLong("NOISE_EXPOSURE_ID", exposureId)
353 else:
354 noiseReplacer = DummyNoiseReplacer()
356 # Create parent cat which slices both the refCat and measCat (sources)
357 # first, get the reference and source records which have no parent
358 refParentCat, measParentCat = refCat.getChildren(0, measCat)
359 childrenIter = refCat.getChildren((refParentRecord.getId() for refParentRecord in refCat), measCat)
360 for parentIdx, records in enumerate(zip(refParentCat, measParentCat, childrenIter)):
361 # Unpack records
362 refParentRecord, measParentRecord, (refChildCat, measChildCat) = records
363 # First process the records which have the current parent as children
364 # TODO: skip this loop if there are no plugins configured for single-object mode
365 for refChildRecord, measChildRecord in zip(refChildCat, measChildCat):
366 noiseReplacer.insertSource(refChildRecord.getId())
367 self.callMeasure(measChildRecord, exposure, refChildRecord, refWcs,
368 beginOrder=beginOrder, endOrder=endOrder)
369 noiseReplacer.removeSource(refChildRecord.getId())
371 # Then process the parent record
372 noiseReplacer.insertSource(refParentRecord.getId())
373 self.callMeasure(measParentRecord, exposure, refParentRecord, refWcs,
374 beginOrder=beginOrder, endOrder=endOrder)
375 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
376 refParentCat[parentIdx:parentIdx+1],
377 beginOrder=beginOrder, endOrder=endOrder)
378 # Measure all the children simultaneously
379 self.callMeasureN(measChildCat, exposure, refChildCat,
380 beginOrder=beginOrder, endOrder=endOrder)
381 noiseReplacer.removeSource(refParentRecord.getId())
382 # Log a message if it has been a while since the last log.
383 periodicLog.log("Forced measurement complete for %d parents (and their children) out of %d",
384 parentIdx + 1, len(refParentCat))
385 noiseReplacer.end()
387 # Undeblended plugins only fire if we're running everything
388 if endOrder is None:
389 for recordIndex, (measRecord, refRecord) in enumerate(zip(measCat, refCat)):
390 for plugin in self.undeblendedPlugins.iter():
391 self.doMeasurement(plugin, measRecord, exposure, refRecord, refWcs)
392 periodicLog.log("Undeblended forced measurement complete for %d sources out of %d",
393 recordIndex + 1, len(refCat))
395 def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None):
396 r"""Initialize an output catalog from the reference catalog.
398 Parameters
399 ----------
400 exposure : `lsst.afw.image.exposureF`
401 Image to be measured.
402 refCat : iterable of `lsst.afw.table.SourceRecord`
403 Catalog of reference sources.
404 refWcs : `lsst.afw.geom.SkyWcs`
405 Defines the X,Y coordinate system of ``refCat``.
406 This parameter is not currently used.
407 idFactory : `lsst.afw.table.IdFactory`, optional
408 Factory for creating IDs for sources.
410 Returns
411 -------
412 meascat : `lsst.afw.table.SourceCatalog`
413 Source catalog ready for measurement.
415 Notes
416 -----
417 This generates a new blank `~lsst.afw.table.SourceRecord` for each
418 record in ``refCat``. Note that this method does not attach any
419 `~lsst.afw.detection.Footprint`\ s. Doing so is up to the caller (who
420 may call `attachedTransformedFootprints` or define their own method -
421 see `run` for more information).
422 """
423 if idFactory is None:
424 idFactory = lsst.afw.table.IdFactory.makeSimple()
425 table = lsst.afw.table.SourceTable.make(self.schema, idFactory)
426 measCat = lsst.afw.table.SourceCatalog(table)
427 table = measCat.table
428 table.setMetadata(self.algMetadata)
429 table.preallocate(len(refCat))
430 for ref in refCat:
431 newSource = measCat.addNew()
432 newSource.assign(ref, self.mapper)
433 return measCat
435 def attachTransformedFootprints(self, sources, refCat, exposure, refWcs):
436 r"""Attach Footprints to blank sources prior to measurement, by
437 transforming Footprints attached to the reference catalog.
439 Notes
440 -----
441 `~lsst.afw.detection.Footprint`\s for forced photometry must be in the
442 pixel coordinate system of the image being measured, while the actual
443 detections may start out in a different coordinate system. This
444 default implementation transforms the Footprints from the reference
445 catalog from the WCS to the exposure's WCS, which downgrades
446 ``HeavyFootprint``\s into regular `~lsst.afw.detection.Footprint`\s,
447 destroying deblend information.
449 See the documentation for `run` for information about the
450 relationships between `run`, `generateMeasCat`, and
451 `attachTransformedFootprints`.
452 """
453 exposureWcs = exposure.getWcs()
454 region = exposure.getBBox(lsst.afw.image.PARENT)
455 for srcRecord, refRecord in zip(sources, refCat):
456 srcRecord.setFootprint(refRecord.getFootprint().transform(refWcs, exposureWcs, region))
458 def attachPsfShapeFootprints(self, sources, exposure, scaling=3):
459 """Attach Footprints to blank sources prior to measurement, by
460 creating elliptical Footprints from the PSF moments.
462 Parameters
463 ----------
464 sources : `lsst.afw.table.SourceCatalog`
465 Blank catalog (with all rows and columns, but values other than
466 ``coord_ra``, ``coord_dec`` unpopulated).
467 to which footprints should be attached.
468 exposure : `lsst.afw.image.Exposure`
469 Image object from which peak values and the PSF are obtained.
470 scaling : `int`, optional
471 Scaling factor to apply to the PSF second-moments ellipse in order
472 to determine the footprint boundary.
474 Notes
475 -----
476 This is a utility function for use by parent tasks; see
477 `attachTransformedFootprints` for more information.
478 """
479 psf = exposure.getPsf()
480 if psf is None:
481 raise RuntimeError("Cannot construct Footprints from PSF shape without a PSF.")
482 bbox = exposure.getBBox()
483 wcs = exposure.getWcs()
484 for record in sources:
485 localPoint = wcs.skyToPixel(record.getCoord())
486 localIntPoint = lsst.geom.Point2I(localPoint)
487 assert bbox.contains(localIntPoint), (
488 f"Center for record {record.getId()} is not in exposure; this should be guaranteed by "
489 "generateMeasCat."
490 )
491 ellipse = lsst.afw.geom.ellipses.Ellipse(psf.computeShape(localPoint), localPoint)
492 ellipse.getCore().scale(scaling)
493 spans = lsst.afw.geom.SpanSet.fromShape(ellipse)
494 footprint = lsst.afw.detection.Footprint(spans.clippedTo(bbox), bbox)
495 footprint.addPeak(localIntPoint.getX(), localIntPoint.getY(),
496 exposure.image._get(localIntPoint, lsst.afw.image.PARENT))
497 record.setFootprint(footprint)