Coverage for python/lsst/meas/base/forcedMeasurement.py: 24%

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1# This file is part of meas_base. 

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21 

22r"""Base classes for forced measurement plugins and the driver task for these. 

23 

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``. 

40 

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. 

52 

53Command-line driver tasks for forced measurement include 

54`ForcedPhotCcdTask`, and `ForcedPhotCoaddTask`. 

55""" 

56 

57import lsst.pex.config 

58import lsst.pipe.base 

59from lsst.utils.logging import PeriodicLogger 

60 

61from .pluginRegistry import PluginRegistry 

62from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin, 

63 BaseMeasurementConfig, BaseMeasurementTask) 

64from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer 

65 

66__all__ = ("ForcedPluginConfig", "ForcedPlugin", 

67 "ForcedMeasurementConfig", "ForcedMeasurementTask") 

68 

69 

70class ForcedPluginConfig(BaseMeasurementPluginConfig): 

71 """Base class for configs of forced measurement plugins.""" 

72 

73 pass 

74 

75 

76class ForcedPlugin(BaseMeasurementPlugin): 

77 """Base class for forced measurement plugins. 

78 

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 """ 

95 

96 registry = PluginRegistry(ForcedPluginConfig) 

97 """Subclasses of `ForcedPlugin` must be registered here (`PluginRegistry`). 

98 """ 

99 

100 ConfigClass = ForcedPluginConfig 

101 

102 def __init__(self, config, name, schemaMapper, metadata, logName=None): 

103 BaseMeasurementPlugin.__init__(self, config, name, logName=logName) 

104 

105 def measure(self, measRecord, exposure, refRecord, refWcs): 

106 """Measure the properties of a source given an image and a reference. 

107 

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. 

125 

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() 

134 

135 def measureN(self, measCat, exposure, refCat, refWcs): 

136 """Measure the properties of blended sources from image & reference. 

137 

138 This operates on all members of a blend family at once. 

139 

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. 

159 

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() 

168 

169 

170class ForcedMeasurementConfig(BaseMeasurementConfig): 

171 """Config class for forced measurement driver task. 

172 """ 

173 

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 deprecated="This field is no longer used and will be removed in v25.", 

209 ) 

210 

211 def setDefaults(self): 

212 self.slots.centroid = "base_TransformedCentroid" 

213 self.slots.shape = "base_TransformedShape" 

214 self.slots.apFlux = None 

215 self.slots.modelFlux = None 

216 self.slots.psfFlux = None 

217 self.slots.gaussianFlux = None 

218 self.slots.calibFlux = None 

219 

220 

221class ForcedMeasurementTask(BaseMeasurementTask): 

222 """Measure sources on an image, constrained by a reference catalog. 

223 

224 A subtask for measuring the properties of sources on a single image, 

225 using an existing "reference" catalog to constrain some aspects of the 

226 measurement. 

227 

228 Parameters 

229 ---------- 

230 refSchema : `lsst.afw.table.Schema` 

231 Schema of the reference catalog. Must match the catalog later passed 

232 to 'ForcedMeasurementTask.generateMeasCat` and/or 

233 `ForcedMeasurementTask.run`. 

234 algMetadata : `lsst.daf.base.PropertyList` or `None` 

235 Will be updated in place to to record information about each 

236 algorithm. An empty `~lsst.daf.base.PropertyList` will be created if 

237 `None`. 

238 **kwds 

239 Keyword arguments are passed to the supertask constructor. 

240 

241 Notes 

242 ----- 

243 Note that while `SingleFrameMeasurementTask` is passed an initial 

244 `~lsst.afw.table.Schema` that is appended to in order to create the output 

245 `~lsst.afw.table.Schema`, `ForcedMeasurementTask` is initialized with the 

246 `~lsst.afw.table.Schema` of the reference catalog, from which a new 

247 `~lsst.afw.table.Schema` for the output catalog is created. Fields to be 

248 copied directly from the reference `~lsst.afw.table.Schema` are added 

249 before ``Plugin`` fields are added. 

250 """ 

251 

252 ConfigClass = ForcedMeasurementConfig 

253 

254 def __init__(self, refSchema, algMetadata=None, **kwds): 

255 super(ForcedMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds) 

256 self.mapper = lsst.afw.table.SchemaMapper(refSchema) 

257 self.mapper.addMinimalSchema(lsst.afw.table.SourceTable.makeMinimalSchema(), False) 

258 self.config.slots.setupSchema(self.mapper.editOutputSchema()) 

259 for refName, targetName in self.config.copyColumns.items(): 

260 refItem = refSchema.find(refName) 

261 self.mapper.addMapping(refItem.key, targetName) 

262 self.config.slots.setupSchema(self.mapper.editOutputSchema()) 

263 self.initializePlugins(schemaMapper=self.mapper) 

264 self.schema = self.mapper.getOutputSchema() 

265 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict) 

266 

267 def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None): 

268 r"""Perform forced measurement. 

269 

270 Parameters 

271 ---------- 

272 exposure : `lsst.afw.image.exposureF` 

273 Image to be measured. Must have at least a `lsst.afw.geom.SkyWcs` 

274 attached. 

275 measCat : `lsst.afw.table.SourceCatalog` 

276 Source catalog for measurement results; must be initialized with 

277 empty records already corresponding to those in ``refCat`` (via 

278 e.g. `generateMeasCat`). 

279 refCat : `lsst.afw.table.SourceCatalog` 

280 A sequence of `lsst.afw.table.SourceRecord` objects that provide 

281 reference information for the measurement. These will be passed 

282 to each plugin in addition to the output 

283 `~lsst.afw.table.SourceRecord`. 

284 refWcs : `lsst.afw.geom.SkyWcs` 

285 Defines the X,Y coordinate system of ``refCat``. 

286 exposureId : `int`, optional 

287 Optional unique exposureId used to calculate random number 

288 generator seed in the NoiseReplacer. 

289 beginOrder : `int`, optional 

290 Beginning execution order (inclusive). Algorithms with 

291 ``executionOrder`` < ``beginOrder`` are not executed. `None` for no limit. 

292 endOrder : `int`, optional 

293 Ending execution order (exclusive). Algorithms with 

294 ``executionOrder`` >= ``endOrder`` are not executed. `None` for no limit. 

295 

296 Notes 

297 ----- 

298 Fills the initial empty `~lsst.afw.table.SourceCatalog` with forced 

299 measurement results. Two steps must occur before `run` can be called: 

300 

301 - `generateMeasCat` must be called to create the output ``measCat`` 

302 argument. 

303 - `~lsst.afw.detection.Footprint`\ s appropriate for the forced sources 

304 must be attached to the ``measCat`` records. The 

305 `attachTransformedFootprints` method can be used to do this, but 

306 this degrades "heavy" (i.e., including pixel values) 

307 `~lsst.afw.detection.Footprint`\s to regular 

308 `~lsst.afw.detection.Footprint`\s, leading to non-deblended 

309 measurement, so most callers should provide 

310 `~lsst.afw.detection.Footprint`\s some other way. Typically, calling 

311 code will have access to information that will allow them to provide 

312 heavy footprints - for instance, `ForcedPhotCoaddTask` uses the 

313 heavy footprints from deblending run in the same band just before 

314 non-forced is run measurement in that band. 

315 """ 

316 # First check that the reference catalog does not contain any children 

317 # for which any member of their parent chain is not within the list. 

318 # This can occur at boundaries when the parent is outside and one of 

319 # the children is within. Currently, the parent chain is always only 

320 # one deep, but just in case, this code checks for any case where when 

321 # the parent chain to a child's topmost parent is broken and raises an 

322 # exception if it occurs. 

323 # 

324 # I.e. this code checks that this precondition is satisfied by 

325 # whatever reference catalog provider is being paired with it. 

326 refCatIdDict = {ref.getId(): ref.getParent() for ref in refCat} 

327 for ref in refCat: 

328 refId = ref.getId() 

329 topId = refId 

330 while(topId > 0): 

331 if topId not in refCatIdDict: 

332 raise RuntimeError("Reference catalog contains a child for which at least " 

333 "one parent in its parent chain is not in the catalog.") 

334 topId = refCatIdDict[topId] 

335 

336 # Construct a footprints dict which looks like 

337 # {ref.getId(): (ref.getParent(), source.getFootprint())} 

338 # (i.e. getting the footprint from the transformed source footprint) 

339 footprints = {ref.getId(): (ref.getParent(), measRecord.getFootprint()) 

340 for (ref, measRecord) in zip(refCat, measCat)} 

341 

342 self.log.info("Performing forced measurement on %d source%s", len(refCat), 

343 "" if len(refCat) == 1 else "s") 

344 

345 # Wrap the task logger into a periodic logger. 

346 periodicLog = PeriodicLogger(self.log) 

347 

348 if self.config.doReplaceWithNoise: 

349 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure, 

350 footprints, log=self.log, exposureId=exposureId) 

351 algMetadata = measCat.getTable().getMetadata() 

352 if algMetadata is not None: 

353 algMetadata.addInt("NOISE_SEED_MULTIPLIER", self.config.noiseReplacer.noiseSeedMultiplier) 

354 algMetadata.addString("NOISE_SOURCE", self.config.noiseReplacer.noiseSource) 

355 algMetadata.addDouble("NOISE_OFFSET", self.config.noiseReplacer.noiseOffset) 

356 if exposureId is not None: 

357 algMetadata.addLong("NOISE_EXPOSURE_ID", exposureId) 

358 else: 

359 noiseReplacer = DummyNoiseReplacer() 

360 

361 # Create parent cat which slices both the refCat and measCat (sources) 

362 # first, get the reference and source records which have no parent 

363 refParentCat, measParentCat = refCat.getChildren(0, measCat) 

364 childrenIter = refCat.getChildren((refParentRecord.getId() for refParentRecord in refCat), measCat) 

365 for parentIdx, records in enumerate(zip(refParentCat, measParentCat, childrenIter)): 

366 # Unpack records 

367 refParentRecord, measParentRecord, (refChildCat, measChildCat) = records 

368 # First process the records which have the current parent as children 

369 # TODO: skip this loop if there are no plugins configured for single-object mode 

370 for refChildRecord, measChildRecord in zip(refChildCat, measChildCat): 

371 noiseReplacer.insertSource(refChildRecord.getId()) 

372 self.callMeasure(measChildRecord, exposure, refChildRecord, refWcs, 

373 beginOrder=beginOrder, endOrder=endOrder) 

374 noiseReplacer.removeSource(refChildRecord.getId()) 

375 

376 # Then process the parent record 

377 noiseReplacer.insertSource(refParentRecord.getId()) 

378 self.callMeasure(measParentRecord, exposure, refParentRecord, refWcs, 

379 beginOrder=beginOrder, endOrder=endOrder) 

380 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure, 

381 refParentCat[parentIdx:parentIdx+1], 

382 beginOrder=beginOrder, endOrder=endOrder) 

383 # Measure all the children simultaneously 

384 self.callMeasureN(measChildCat, exposure, refChildCat, 

385 beginOrder=beginOrder, endOrder=endOrder) 

386 noiseReplacer.removeSource(refParentRecord.getId()) 

387 # Log a message if it has been a while since the last log. 

388 periodicLog.log("Forced measurement complete for %d parents (and their children) out of %d", 

389 parentIdx + 1, len(refParentCat)) 

390 noiseReplacer.end() 

391 

392 # Undeblended plugins only fire if we're running everything 

393 if endOrder is None: 

394 for recordIndex, (measRecord, refRecord) in enumerate(zip(measCat, refCat)): 

395 for plugin in self.undeblendedPlugins.iter(): 

396 self.doMeasurement(plugin, measRecord, exposure, refRecord, refWcs) 

397 periodicLog.log("Undeblended forced measurement complete for %d sources out of %d", 

398 recordIndex + 1, len(refCat)) 

399 

400 def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None): 

401 r"""Initialize an output catalog from the reference catalog. 

402 

403 Parameters 

404 ---------- 

405 exposure : `lsst.afw.image.exposureF` 

406 Image to be measured. 

407 refCat : iterable of `lsst.afw.table.SourceRecord` 

408 Catalog of reference sources. 

409 refWcs : `lsst.afw.geom.SkyWcs` 

410 Defines the X,Y coordinate system of ``refCat``. 

411 This parameter is not currently used. 

412 idFactory : `lsst.afw.table.IdFactory`, optional 

413 Factory for creating IDs for sources. 

414 

415 Returns 

416 ------- 

417 meascat : `lsst.afw.table.SourceCatalog` 

418 Source catalog ready for measurement. 

419 

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 

439 

440 def attachTransformedFootprints(self, sources, refCat, exposure, refWcs): 

441 r"""Attach Footprints to blank sources prior to measurement, by 

442 transforming Footprints attached to the reference catalog. 

443 

444 Notes 

445 ----- 

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. 

453 

454 See the documentation for `run` for information about the 

455 relationships between `run`, `generateMeasCat`, and 

456 `attachTransformedFootprints`. 

457 """ 

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)) 

462 

463 def attachPsfShapeFootprints(self, sources, exposure, scaling=3): 

464 """Attach Footprints to blank sources prior to measurement, by 

465 creating elliptical Footprints from the PSF moments. 

466 

467 Parameters 

468 ---------- 

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. 

478 

479 Notes 

480 ----- 

481 This is a utility function for use by parent tasks; see 

482 `attachTransformedFootprints` for more information. 

483 """ 

484 psf = exposure.getPsf() 

485 if psf is None: 

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()) 

491 localIntPoint = lsst.geom.Point2I(localPoint) 

492 assert bbox.contains(localIntPoint), ( 

493 f"Center for record {record.getId()} is not in exposure; this should be guaranteed by " 

494 "generateMeasCat." 

495 ) 

496 ellipse = lsst.afw.geom.ellipses.Ellipse(psf.computeShape(localPoint), localPoint) 

497 ellipse.getCore().scale(scaling) 

498 spans = lsst.afw.geom.SpanSet.fromShape(ellipse) 

499 footprint = lsst.afw.detection.Footprint(spans.clippedTo(bbox), bbox) 

500 footprint.addPeak(localIntPoint.getX(), localIntPoint.getY(), 

501 exposure.image._get(localIntPoint, lsst.afw.image.PARENT)) 

502 record.setFootprint(footprint)