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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/>. 

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 

59import time 

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 ) 

209 

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 

218 

219 

220class ForcedMeasurementTask(BaseMeasurementTask): 

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

222 

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. 

226 

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. 

239 

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 """ 

250 

251 ConfigClass = ForcedMeasurementConfig 

252 

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) 

265 

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

267 r"""Perform forced measurement. 

268 

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. 

294 

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: 

299 

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] 

334 

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)} 

340 

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 

344 

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() 

357 

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()) 

372 

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() 

390 

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 

400 

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

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

403 

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. 

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)