Coverage for python/lsst/meas/base/forcedMeasurement.py : 20%

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1# This file is part of meas_base.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
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.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
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
59import time
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") 188 ↛ exitline 188 didn't run the lambda on line 188
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 )
204 loggingInterval = lsst.pex.config.Field(
205 dtype=int,
206 default=600,
207 doc="Interval (in seconds) to log messages (at VERBOSE level) while running measurement plugins."
208 )
210 def setDefaults(self):
211 self.slots.centroid = "base_TransformedCentroid"
212 self.slots.shape = "base_TransformedShape"
213 self.slots.apFlux = None
214 self.slots.modelFlux = None
215 self.slots.psfFlux = None
216 self.slots.gaussianFlux = None
217 self.slots.calibFlux = None
220class ForcedMeasurementTask(BaseMeasurementTask):
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
225 measurement.
227 Parameters
228 ----------
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
236 `None`.
237 **kwds
238 Keyword arguments are passed to the supertask constructor.
240 Notes
241 -----
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.
249 """
251 ConfigClass = ForcedMeasurementConfig
253 def __init__(self, refSchema, algMetadata=None, **kwds):
254 super(ForcedMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds)
255 self.mapper = lsst.afw.table.SchemaMapper(refSchema)
256 self.mapper.addMinimalSchema(lsst.afw.table.SourceTable.makeMinimalSchema(), False)
257 self.config.slots.setupSchema(self.mapper.editOutputSchema())
258 for refName, targetName in self.config.copyColumns.items():
259 refItem = refSchema.find(refName)
260 self.mapper.addMapping(refItem.key, targetName)
261 self.config.slots.setupSchema(self.mapper.editOutputSchema())
262 self.initializePlugins(schemaMapper=self.mapper)
263 self.schema = self.mapper.getOutputSchema()
264 self.schema.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.
269 Parameters
270 ----------
271 exposure : `lsst.afw.image.exposureF`
272 Image to be measured. Must have at least a `lsst.afw.geom.SkyWcs`
273 attached.
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.
295 Notes
296 -----
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``
301 argument.
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.
314 """
315 # First check that the reference catalog does not contain any children
316 # for which any member of their parent chain is not within the list.
317 # This can occur at boundaries when the parent is outside and one of
318 # the children is within. Currently, the parent chain is always only
319 # one deep, but just in case, this code checks for any case where when
320 # the parent chain to a child's topmost parent is broken and raises an
321 # exception if it occurs.
322 #
323 # I.e. this code checks that this precondition is satisfied by
324 # whatever reference catalog provider is being paired with it.
325 refCatIdDict = {ref.getId(): ref.getParent() for ref in refCat}
326 for ref in refCat:
327 refId = ref.getId()
328 topId = refId
329 while(topId > 0):
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]
335 # Construct a footprints dict which looks like
336 # {ref.getId(): (ref.getParent(), source.getFootprint())}
337 # (i.e. getting the footprint from the transformed source footprint)
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)
355 else:
356 noiseReplacer = DummyNoiseReplacer()
358 # Create parent cat which slices both the refCat and measCat (sources)
359 # first, get the reference and source records which have no parent
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)):
363 # Unpack records
364 refParentRecord, measParentRecord, (refChildCat, measChildCat) = records
365 # First process the records which have the current parent as children
366 # TODO: skip this loop if there are no plugins configured for single-object mode
367 for refChildRecord, measChildRecord in zip(refChildCat, measChildCat):
368 noiseReplacer.insertSource(refChildRecord.getId())
369 self.callMeasure(measChildRecord, exposure, refChildRecord, refWcs,
370 beginOrder=beginOrder, endOrder=endOrder)
371 noiseReplacer.removeSource(refChildRecord.getId())
373 # Then process the parent record
374 noiseReplacer.insertSource(refParentRecord.getId())
375 self.callMeasure(measParentRecord, exposure, refParentRecord, refWcs,
376 beginOrder=beginOrder, endOrder=endOrder)
377 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
378 refParentCat[parentIdx:parentIdx+1],
379 beginOrder=beginOrder, endOrder=endOrder)
380 # Measure all the children simultaneously
381 self.callMeasureN(measChildCat, exposure, refChildCat,
382 beginOrder=beginOrder, endOrder=endOrder)
383 noiseReplacer.removeSource(refParentRecord.getId())
384 # Log a message if it has been a while since the last log.
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
389 noiseReplacer.end()
391 # Undeblended plugins only fire if we're running everything
392 if endOrder is None:
393 for recordIndex, (measRecord, refRecord) in enumerate(zip(measCat, refCat)):
394 for plugin in self.undeblendedPlugins.iter():
395 self.doMeasurement(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
401 def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None):
402 r"""Initialize an output catalog from the reference catalog.
404 Parameters
405 ----------
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.
415 Returns
416 -------
417 meascat : `lsst.afw.table.SourceCatalog`
418 Source catalog ready for measurement.
420 Notes
421 -----
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).
427 """
428 if idFactory is None:
429 idFactory = lsst.afw.table.IdFactory.makeSimple()
430 table = lsst.afw.table.SourceTable.make(self.schema, idFactory)
431 measCat = lsst.afw.table.SourceCatalog(table)
432 table = measCat.table
433 table.setMetadata(self.algMetadata)
434 table.preallocate(len(refCat))
435 for ref in refCat:
436 newSource = measCat.addNew()
437 newSource.assign(ref, self.mapper)
438 return measCat
440 def attachTransformedFootprints(self, sources, refCat, exposure, refWcs):
441 r"""Attach Footprints to blank sources prior to measurement.
443 Notes
444 -----
445 `~lsst.afw.detection.Footprint`\s for forced photometry must be in the
446 pixel coordinate system of the image being measured, while the actual
447 detections may start out in a different coordinate system. This
448 default implementation transforms the Footprints from the reference
449 catalog from the WCS to the exposure's WCS, which downgrades
450 ``HeavyFootprint``\s into regular `~lsst.afw.detection.Footprint`\s,
451 destroying deblend information.
453 See the documentation for `run` for information about the
454 relationships between `run`, `generateMeasCat`, and
455 `attachTransformedFootprints`.
456 """
457 exposureWcs = exposure.getWcs()
458 region = exposure.getBBox(lsst.afw.image.PARENT)
459 for srcRecord, refRecord in zip(sources, refCat):
460 srcRecord.setFootprint(refRecord.getFootprint().transform(refWcs, exposureWcs, region))