Coverage for python/lsst/meas/base/forcedMeasurement.py: 19%

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1# This file is part of meas_base. 

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6# See the COPYRIGHT file at the top-level directory of this distribution 

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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 

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 

213 

214 

215class ForcedMeasurementTask(BaseMeasurementTask): 

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

217 

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. 

221 

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. 

234 

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 """ 

245 

246 ConfigClass = ForcedMeasurementConfig 

247 

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.schema = self.mapper.getOutputSchema() 

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

260 

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

262 r"""Perform forced measurement. 

263 

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. 

289 

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: 

294 

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] 

329 

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)} 

335 

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

337 "" if len(refCat) == 1 else "s") 

338 

339 # Wrap the task logger into a periodic logger. 

340 periodicLog = PeriodicLogger(self.log) 

341 

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() 

354 

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()) 

369 

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() 

385 

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)) 

393 

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

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

396 

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. 

408 

409 Returns 

410 ------- 

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

412 Source catalog ready for measurement. 

413 

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: 

423 idFactory = lsst.afw.table.IdFactory.makeSimple() 

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.algMetadata) 

428 table.preallocate(len(refCat)) 

429 for ref in refCat: 

430 newSource = measCat.addNew() 

431 newSource.assign(ref, self.mapper) 

432 return measCat 

433 

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. 

437 

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. 

447 

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)) 

456 

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. 

460 

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. 

472 

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)