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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
60from .pluginRegistry import PluginRegistry
61from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
62 BaseMeasurementConfig, BaseMeasurementTask)
63from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer
65__all__ = ("ForcedPluginConfig", "ForcedPlugin",
66 "ForcedMeasurementConfig", "ForcedMeasurementTask")
69class ForcedPluginConfig(BaseMeasurementPluginConfig):
70 """Base class for configs of forced measurement plugins."""
72 pass
75class ForcedPlugin(BaseMeasurementPlugin):
76 """Base class for forced measurement plugins.
78 Parameters
79 ----------
80 config : `ForcedPlugin.ConfigClass`
81 Configuration for this plugin.
82 name : `str`
83 The string with which the plugin was registered.
84 schemaMapper : `lsst.afw.table.SchemaMapper`
85 A mapping from reference catalog fields to output catalog fields.
86 Output fields should be added to the output schema. While most plugins
87 will not need to map fields from the reference schema, if they do so,
88 those fields will be transferred before any plugins are run.
89 metadata : `lsst.daf.base.PropertySet`
90 Plugin metadata that will be attached to the output catalog.
91 logName : `str`, optional
92 Name to use when logging errors.
93 """
95 registry = PluginRegistry(ForcedPluginConfig)
96 """Subclasses of `ForcedPlugin` must be registered here (`PluginRegistry`).
97 """
99 ConfigClass = ForcedPluginConfig
101 def __init__(self, config, name, schemaMapper, metadata, logName=None):
102 BaseMeasurementPlugin.__init__(self, config, name, logName=logName)
104 def measure(self, measRecord, exposure, refRecord, refWcs):
105 """Measure the properties of a source given an image and a reference.
107 Parameters
108 ----------
109 exposure : `lsst.afw.image.ExposureF`
110 The pixel data to be measured, together with the associated PSF,
111 WCS, etc. All other sources in the image should have been replaced
112 by noise according to deblender outputs.
113 measRecord : `lsst.afw.table.SourceRecord`
114 Record describing the object being measured. Previously-measured
115 quantities will be retrieved from here, and it will be updated
116 in-place with the outputs of this plugin.
117 refRecord : `lsst.afw.table.SimpleRecord`
118 Additional parameters to define the fit, as measured elsewhere.
119 refWcs : `lsst.afw.geom.SkyWcs` or `lsst.afw.geom.Angle`
120 The coordinate system for the reference catalog values. An
121 `~lsst.geom.Angle` may be passed, indicating that a local tangent
122 WCS should be created for each object using the given angle as a
123 pixel scale.
125 Notes
126 -----
127 In the normal mode of operation, the source centroid will be set to
128 the WCS-transformed position of the reference object, so plugins that
129 only require a reference position should not have to access the
130 reference object at all.
131 """
132 raise NotImplementedError()
134 def measureN(self, measCat, exposure, refCat, refWcs):
135 """Measure the properties of blended sources from image & reference.
137 This operates on all members of a blend family at once.
139 Parameters
140 ----------
141 exposure : `lsst.afw.image.ExposureF`
142 The pixel data to be measured, together with the associated PSF,
143 WCS, etc. Sources not in the blended hierarchy to be measured
144 should have been replaced with noise using deblender outputs.
145 measCat : `lsst.afw.table.SourceCatalog`
146 Catalog describing the objects (and only those objects) being
147 measured. Previously-measured quantities will be retrieved from
148 here, and it will be updated in-place with the outputs of this
149 plugin.
150 refCat : `lsst.afw.table.SimpleCatalog`
151 Additional parameters to define the fit, as measured elsewhere.
152 Ordered such that ``zip(measCat, refcat)`` may be used.
153 refWcs : `lsst.afw.geom.SkyWcs` or `lsst.afw.geom.Angle`
154 The coordinate system for the reference catalog values. An
155 `~lsst.geom.Angle` may be passed, indicating that a local tangent
156 WCS should be created for each object using the given angle as a
157 pixel scale.
159 Notes
160 -----
161 In the normal mode of operation, the source centroids will be set to
162 the WCS-transformed position of the reference object, so plugins that
163 only require a reference position should not have to access the
164 reference object at all.
165 """
166 raise NotImplementedError()
169class ForcedMeasurementConfig(BaseMeasurementConfig):
170 """Config class for forced measurement driver task.
171 """
173 plugins = ForcedPlugin.registry.makeField(
174 multi=True,
175 default=["base_PixelFlags",
176 "base_TransformedCentroid",
177 "base_SdssCentroid",
178 "base_TransformedShape",
179 "base_SdssShape",
180 "base_GaussianFlux",
181 "base_CircularApertureFlux",
182 "base_PsfFlux",
183 "base_LocalBackground",
184 ],
185 doc="Plugins to be run and their configuration"
186 )
187 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins") 187 ↛ exitline 187 didn't run the lambda on line 187
188 undeblended = ForcedPlugin.registry.makeField(
189 multi=True,
190 default=[],
191 doc="Plugins to run on undeblended image"
192 )
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 )
200 checkUnitsParseStrict = lsst.pex.config.Field(
201 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
202 dtype=str,
203 default="raise",
204 )
206 def setDefaults(self):
207 self.slots.centroid = "base_TransformedCentroid"
208 self.slots.shape = "base_TransformedShape"
209 self.slots.apFlux = None
210 self.slots.modelFlux = None
211 self.slots.psfFlux = None
212 self.slots.gaussianFlux = None
213 self.slots.calibFlux = None
216class ForcedMeasurementTask(BaseMeasurementTask):
217 """Measure sources on an image, constrained by a reference catalog.
219 A subtask for measuring the properties of sources on a single image,
220 using an existing "reference" catalog to constrain some aspects of the
221 measurement.
223 Parameters
224 ----------
225 refSchema : `lsst.afw.table.Schema`
226 Schema of the reference catalog. Must match the catalog later passed
227 to 'ForcedMeasurementTask.generateMeasCat` and/or
228 `ForcedMeasurementTask.run`.
229 algMetadata : `lsst.daf.base.PropertyList` or `None`
230 Will be updated in place to to record information about each
231 algorithm. An empty `~lsst.daf.base.PropertyList` will be created if
232 `None`.
233 **kwds
234 Keyword arguments are passed to the supertask constructor.
236 Notes
237 -----
238 Note that while `SingleFrameMeasurementTask` is passed an initial
239 `~lsst.afw.table.Schema` that is appended to in order to create the output
240 `~lsst.afw.table.Schema`, `ForcedMeasurementTask` is initialized with the
241 `~lsst.afw.table.Schema` of the reference catalog, from which a new
242 `~lsst.afw.table.Schema` for the output catalog is created. Fields to be
243 copied directly from the reference `~lsst.afw.table.Schema` are added
244 before ``Plugin`` fields are added.
245 """
247 ConfigClass = ForcedMeasurementConfig
249 def __init__(self, refSchema, algMetadata=None, **kwds):
250 super(ForcedMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds)
251 self.mapper = lsst.afw.table.SchemaMapper(refSchema)
252 self.mapper.addMinimalSchema(lsst.afw.table.SourceTable.makeMinimalSchema(), False)
253 self.config.slots.setupSchema(self.mapper.editOutputSchema())
254 for refName, targetName in self.config.copyColumns.items():
255 refItem = refSchema.find(refName)
256 self.mapper.addMapping(refItem.key, targetName)
257 self.config.slots.setupSchema(self.mapper.editOutputSchema())
258 self.initializePlugins(schemaMapper=self.mapper)
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 if self.config.doReplaceWithNoise:
341 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure,
342 footprints, log=self.log, exposureId=exposureId)
343 algMetadata = measCat.getTable().getMetadata()
344 if algMetadata is not None:
345 algMetadata.addInt("NOISE_SEED_MULTIPLIER", self.config.noiseReplacer.noiseSeedMultiplier)
346 algMetadata.addString("NOISE_SOURCE", self.config.noiseReplacer.noiseSource)
347 algMetadata.addDouble("NOISE_OFFSET", self.config.noiseReplacer.noiseOffset)
348 if exposureId is not None:
349 algMetadata.addLong("NOISE_EXPOSURE_ID", exposureId)
350 else:
351 noiseReplacer = DummyNoiseReplacer()
353 # Create parent cat which slices both the refCat and measCat (sources)
354 # first, get the reference and source records which have no parent
355 refParentCat, measParentCat = refCat.getChildren(0, measCat)
356 childrenIter = refCat.getChildren((refParentRecord.getId() for refParentRecord in refCat), measCat)
357 for parentIdx, records in enumerate(zip(refParentCat, measParentCat, childrenIter)):
358 # Unpack records
359 refParentRecord, measParentRecord, (refChildCat, measChildCat) = records
360 # First process the records which have the current parent as children
361 # TODO: skip this loop if there are no plugins configured for single-object mode
362 for refChildRecord, measChildRecord in zip(refChildCat, measChildCat):
363 noiseReplacer.insertSource(refChildRecord.getId())
364 self.callMeasure(measChildRecord, exposure, refChildRecord, refWcs,
365 beginOrder=beginOrder, endOrder=endOrder)
366 noiseReplacer.removeSource(refChildRecord.getId())
368 # Then process the parent record
369 noiseReplacer.insertSource(refParentRecord.getId())
370 self.callMeasure(measParentRecord, exposure, refParentRecord, refWcs,
371 beginOrder=beginOrder, endOrder=endOrder)
372 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
373 refParentCat[parentIdx:parentIdx+1],
374 beginOrder=beginOrder, endOrder=endOrder)
375 # Measure all the children simultaneously
376 self.callMeasureN(measChildCat, exposure, refChildCat,
377 beginOrder=beginOrder, endOrder=endOrder)
378 noiseReplacer.removeSource(refParentRecord.getId())
379 noiseReplacer.end()
381 # Undeblended plugins only fire if we're running everything
382 if endOrder is None:
383 for measRecord, refRecord in zip(measCat, refCat):
384 for plugin in self.undeblendedPlugins.iter():
385 self.doMeasurement(plugin, measRecord, exposure, refRecord, refWcs)
387 def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None):
388 r"""Initialize an output catalog from the reference catalog.
390 Parameters
391 ----------
392 exposure : `lsst.afw.image.exposureF`
393 Image to be measured.
394 refCat : iterable of `lsst.afw.table.SourceRecord`
395 Catalog of reference sources.
396 refWcs : `lsst.afw.geom.SkyWcs`
397 Defines the X,Y coordinate system of ``refCat``.
398 idFactory : `lsst.afw.table.IdFactory`, optional
399 Factory for creating IDs for sources.
401 Returns
402 -------
403 meascat : `lsst.afw.table.SourceCatalog`
404 Source catalog ready for measurement.
406 Notes
407 -----
408 This generates a new blank `~lsst.afw.table.SourceRecord` for each
409 record in ``refCat``. Note that this method does not attach any
410 `~lsst.afw.detection.Footprint`\ s. Doing so is up to the caller (who
411 may call `attachedTransformedFootprints` or define their own method -
412 see `run` for more information).
413 """
414 if idFactory is None:
415 idFactory = lsst.afw.table.IdFactory.makeSimple()
416 table = lsst.afw.table.SourceTable.make(self.schema, idFactory)
417 measCat = lsst.afw.table.SourceCatalog(table)
418 table = measCat.table
419 table.setMetadata(self.algMetadata)
420 table.preallocate(len(refCat))
421 for ref in refCat:
422 newSource = measCat.addNew()
423 newSource.assign(ref, self.mapper)
424 return measCat
426 def attachTransformedFootprints(self, sources, refCat, exposure, refWcs):
427 r"""Attach Footprints to blank sources prior to measurement.
429 Notes
430 -----
431 `~lsst.afw.detection.Footprint`\s for forced photometry must be in the
432 pixel coordinate system of the image being measured, while the actual
433 detections may start out in a different coordinate system. This
434 default implementation transforms the Footprints from the reference
435 catalog from the WCS to the exposure's WCS, which downgrades
436 ``HeavyFootprint``\s into regular `~lsst.afw.detection.Footprint`\s,
437 destroying deblend information.
439 See the documentation for `run` for information about the
440 relationships between `run`, `generateMeasCat`, and
441 `attachTransformedFootprints`.
442 """
443 exposureWcs = exposure.getWcs()
444 region = exposure.getBBox(lsst.afw.image.PARENT)
445 for srcRecord, refRecord in zip(sources, refCat):
446 srcRecord.setFootprint(refRecord.getFootprint().transform(refWcs, exposureWcs, region))