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1# This file is part of meas_base.
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
17# GNU General Public License for more details.
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <>.
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`.
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")
71 """Base class for configs of forced measurement plugins."""
73 pass
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()
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 )
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
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 ``.
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)
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.schema = self.mapper.getOutputSchema()
259 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
261 def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None):
262 r"""Perform forced measurement.
264 Parameters
265 ----------
266 exposure : `lsst.afw.image.exposureF`
267 Image to be measured. Must have at least a `lsst.afw.geom.SkyWcs`
268 attached.
269 measCat : `lsst.afw.table.SourceCatalog`
270 Source catalog for measurement results; must be initialized with
271 empty records already corresponding to those in ``refCat`` (via
272 e.g. `generateMeasCat`).
273 refCat : `lsst.afw.table.SourceCatalog`
274 A sequence of `lsst.afw.table.SourceRecord` objects that provide
275 reference information for the measurement. These will be passed
276 to each plugin in addition to the output
277 `~lsst.afw.table.SourceRecord`.
278 refWcs : `lsst.afw.geom.SkyWcs`
279 Defines the X,Y coordinate system of ``refCat``.
280 exposureId : `int`, optional
281 Optional unique exposureId used to calculate random number
282 generator seed in the NoiseReplacer.
283 beginOrder : `int`, optional
284 Beginning execution order (inclusive). Algorithms with
285 ``executionOrder`` < ``beginOrder`` are not executed. `None` for no limit.
286 endOrder : `int`, optional
287 Ending execution order (exclusive). Algorithms with
288 ``executionOrder`` >= ``endOrder`` are not executed. `None` for no limit.
290 Notes
291 -----
292 Fills the initial empty `~lsst.afw.table.SourceCatalog` with forced
293 measurement results. Two steps must occur before `run` can be called:
295 - `generateMeasCat` must be called to create the output ``measCat``
296 argument.
297 - `~lsst.afw.detection.Footprint`\ s appropriate for the forced sources
298 must be attached to the ``measCat`` records. The
299 `attachTransformedFootprints` method can be used to do this, but
300 this degrades "heavy" (i.e., including pixel values)
301 `~lsst.afw.detection.Footprint`\s to regular
302 `~lsst.afw.detection.Footprint`\s, leading to non-deblended
303 measurement, so most callers should provide
304 `~lsst.afw.detection.Footprint`\s some other way. Typically, calling
305 code will have access to information that will allow them to provide
306 heavy footprints - for instance, `ForcedPhotCoaddTask` uses the
307 heavy footprints from deblending run in the same band just before
308 non-forced is run measurement in that band.
309 """
310 # First check that the reference catalog does not contain any children
311 # for which any member of their parent chain is not within the list.
312 # This can occur at boundaries when the parent is outside and one of
313 # the children is within. Currently, the parent chain is always only
314 # one deep, but just in case, this code checks for any case where when
315 # the parent chain to a child's topmost parent is broken and raises an
316 # exception if it occurs.
317 #
318 # I.e. this code checks that this precondition is satisfied by
319 # whatever reference catalog provider is being paired with it.
320 refCatIdDict = {ref.getId(): ref.getParent() for ref in refCat}
321 for ref in refCat:
322 refId = ref.getId()
323 topId = refId
324 while topId > 0:
325 if topId not in refCatIdDict:
326 raise RuntimeError("Reference catalog contains a child for which at least "
327 "one parent in its parent chain is not in the catalog.")
328 topId = refCatIdDict[topId]
330 # Construct a footprints dict which looks like
331 # {ref.getId(): (ref.getParent(), source.getFootprint())}
332 # (i.e. getting the footprint from the transformed source footprint)
333 footprints = {ref.getId(): (ref.getParent(), measRecord.getFootprint())
334 for (ref, measRecord) in zip(refCat, measCat)}
336"Performing forced measurement on %d source%s", len(refCat),
337 "" if len(refCat) == 1 else "s")
339 # Wrap the task logger into a periodic logger.
340 periodicLog = PeriodicLogger(self.log)
342 if self.config.doReplaceWithNoise:
343 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure,
344 footprints, log=self.log, exposureId=exposureId)
345 algMetadata = measCat.getTable().getMetadata()
346 if algMetadata is not None:
347 algMetadata.addInt("NOISE_SEED_MULTIPLIER", self.config.noiseReplacer.noiseSeedMultiplier)
348 algMetadata.addString("NOISE_SOURCE", self.config.noiseReplacer.noiseSource)
349 algMetadata.addDouble("NOISE_OFFSET", self.config.noiseReplacer.noiseOffset)
350 if exposureId is not None:
351 algMetadata.addLong("NOISE_EXPOSURE_ID", exposureId)
352 else:
353 noiseReplacer = DummyNoiseReplacer()
355 # Create parent cat which slices both the refCat and measCat (sources)
356 # first, get the reference and source records which have no parent
357 refParentCat, measParentCat = refCat.getChildren(0, measCat)
358 childrenIter = refCat.getChildren((refParentRecord.getId() for refParentRecord in refCat), measCat)
359 for parentIdx, records in enumerate(zip(refParentCat, measParentCat, childrenIter)):
360 # Unpack records
361 refParentRecord, measParentRecord, (refChildCat, measChildCat) = records
362 # First process the records which have the current parent as children
363 # TODO: skip this loop if there are no plugins configured for single-object mode
364 for refChildRecord, measChildRecord in zip(refChildCat, measChildCat):
365 noiseReplacer.insertSource(refChildRecord.getId())
366 self.callMeasure(measChildRecord, exposure, refChildRecord, refWcs,
367 beginOrder=beginOrder, endOrder=endOrder)
368 noiseReplacer.removeSource(refChildRecord.getId())
370 # Then process the parent record
371 noiseReplacer.insertSource(refParentRecord.getId())
372 self.callMeasure(measParentRecord, exposure, refParentRecord, refWcs,
373 beginOrder=beginOrder, endOrder=endOrder)
374 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
375 refParentCat[parentIdx:parentIdx+1],
376 beginOrder=beginOrder, endOrder=endOrder)
377 # Measure all the children simultaneously
378 self.callMeasureN(measChildCat, exposure, refChildCat,
379 beginOrder=beginOrder, endOrder=endOrder)
380 noiseReplacer.removeSource(refParentRecord.getId())
381 # Log a message if it has been a while since the last log.
382 periodicLog.log("Forced measurement complete for %d parents (and their children) out of %d",
383 parentIdx + 1, len(refParentCat))
384 noiseReplacer.end()
386 # Undeblended plugins only fire if we're running everything
387 if endOrder is None:
388 for recordIndex, (measRecord, refRecord) in enumerate(zip(measCat, refCat)):
389 for plugin in self.undeblendedPlugins.iter():
390 self.doMeasurement(plugin, measRecord, exposure, refRecord, refWcs)
391 periodicLog.log("Undeblended forced measurement complete for %d sources out of %d",
392 recordIndex + 1, len(refCat))
394 def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None):
395 r"""Initialize an output catalog from the reference catalog.
397 Parameters
398 ----------
399 exposure : `lsst.afw.image.exposureF`
400 Image to be measured.
401 refCat : iterable of `lsst.afw.table.SourceRecord`
402 Catalog of reference sources.
403 refWcs : `lsst.afw.geom.SkyWcs`
404 Defines the X,Y coordinate system of ``refCat``.
405 This parameter is not currently used.
406 idFactory : `lsst.afw.table.IdFactory`, optional
407 Factory for creating IDs for sources.
409 Returns
410 -------
411 meascat : `lsst.afw.table.SourceCatalog`
412 Source catalog ready for measurement.
414 Notes
415 -----
416 This generates a new blank `~lsst.afw.table.SourceRecord` for each
417 record in ``refCat``. Note that this method does not attach any
418 `~lsst.afw.detection.Footprint`\ s. Doing so is up to the caller (who
419 may call `attachedTransformedFootprints` or define their own method -
420 see `run` for more information).
421 """
422 if idFactory is None:
424 table = lsst.afw.table.SourceTable.make(self.schema, idFactory)
425 measCat = lsst.afw.table.SourceCatalog(table)
426 table = measCat.table
427 table.setMetadata(self.algMetadataalgMetadata)
428 table.preallocate(len(refCat))
429 for ref in refCat:
430 newSource = measCat.addNew()
431 newSource.assign(ref, self.mapper)
432 return measCat
434 def attachTransformedFootprints(self, sources, refCat, exposure, refWcs):
435 r"""Attach Footprints to blank sources prior to measurement, by
436 transforming Footprints attached to the reference catalog.
438 Notes
439 -----
440 `~lsst.afw.detection.Footprint`\s for forced photometry must be in the
441 pixel coordinate system of the image being measured, while the actual
442 detections may start out in a different coordinate system. This
443 default implementation transforms the Footprints from the reference
444 catalog from the WCS to the exposure's WCS, which downgrades
445 ``HeavyFootprint``\s into regular `~lsst.afw.detection.Footprint`\s,
446 destroying deblend information.
448 See the documentation for `run` for information about the
449 relationships between `run`, `generateMeasCat`, and
450 `attachTransformedFootprints`.
451 """
452 exposureWcs = exposure.getWcs()
453 region = exposure.getBBox(lsst.afw.image.PARENT)
454 for srcRecord, refRecord in zip(sources, refCat):
455 srcRecord.setFootprint(refRecord.getFootprint().transform(refWcs, exposureWcs, region))
457 def attachPsfShapeFootprints(self, sources, exposure, scaling=3):
458 """Attach Footprints to blank sources prior to measurement, by
459 creating elliptical Footprints from the PSF moments.
461 Parameters
462 ----------
463 sources : `lsst.afw.table.SourceCatalog`
464 Blank catalog (with all rows and columns, but values other than
465 ``coord_ra``, ``coord_dec`` unpopulated).
466 to which footprints should be attached.
467 exposure : `lsst.afw.image.Exposure`
468 Image object from which peak values and the PSF are obtained.
469 scaling : `int`, optional
470 Scaling factor to apply to the PSF second-moments ellipse in order
471 to determine the footprint boundary.
473 Notes
474 -----
475 This is a utility function for use by parent tasks; see
476 `attachTransformedFootprints` for more information.
477 """
478 psf = exposure.getPsf()
479 if psf is None:
480 raise RuntimeError("Cannot construct Footprints from PSF shape without a PSF.")
481 bbox = exposure.getBBox()
482 wcs = exposure.getWcs()
483 for record in sources:
484 localPoint = wcs.skyToPixel(record.getCoord())
485 localIntPoint = lsst.geom.Point2I(localPoint)
486 assert bbox.contains(localIntPoint), (
487 f"Center for record {record.getId()} is not in exposure; this should be guaranteed by "
488 "generateMeasCat."
489 )
490 ellipse = lsst.afw.geom.ellipses.Ellipse(psf.computeShape(localPoint), localPoint)
491 ellipse.getCore().scale(scaling)
492 spans = lsst.afw.geom.SpanSet.fromShape(ellipse)
493 footprint = lsst.afw.detection.Footprint(spans.clippedTo(bbox), bbox)
494 footprint.addPeak(localIntPoint.getX(), localIntPoint.getY(),
495 exposure.image._get(localIntPoint, lsst.afw.image.PARENT))
496 record.setFootprint(footprint)
Class to describe the properties of a detected object from an image.
Definition Footprint.h:63
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.
Definition Ellipse.h:51
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.
Definition Source.h:258
doMeasurement(self, plugin, measRecord, *args, **kwds)
__init__(self, refSchema, algMetadata=None, **kwds)
attachPsfShapeFootprints(self, sources, exposure, scaling=3)
attachTransformedFootprints(self, sources, refCat, exposure, refWcs)
run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None)
generateMeasCat(self, exposure, refCat, refWcs, idFactory=None)
__init__(self, config, name, schemaMapper, metadata, logName=None)
measureN(self, measCat, exposure, refCat, refWcs)
measure(self, measRecord, exposure, refRecord, refWcs)