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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 

59 

60from .pluginRegistry import PluginRegistry 

61from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin, 

62 BaseMeasurementConfig, BaseMeasurementTask) 

63from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer 

64 

65__all__ = ("ForcedPluginConfig", "ForcedPlugin", 

66 "ForcedMeasurementConfig", "ForcedMeasurementTask") 

67 

68 

69class ForcedPluginConfig(BaseMeasurementPluginConfig): 

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

71 

72 pass 

73 

74 

75class ForcedPlugin(BaseMeasurementPlugin): 

76 """Base class for forced measurement plugins. 

77 

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 """ 

94 

95 registry = PluginRegistry(ForcedPluginConfig) 

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

97 """ 

98 

99 ConfigClass = ForcedPluginConfig 

100 

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

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

103 

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

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

106 

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. 

124 

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() 

133 

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

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

136 

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

138 

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. 

158 

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() 

167 

168 

169class ForcedMeasurementConfig(BaseMeasurementConfig): 

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

171 """ 

172 

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 ) 

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 

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 ) 

205 

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 

214 

215 

216class ForcedMeasurementTask(BaseMeasurementTask): 

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

218 

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. 

222 

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. 

235 

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 """ 

246 

247 ConfigClass = ForcedMeasurementConfig 

248 

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) 

261 

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

263 r"""Perform forced measurement. 

264 

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. 

290 

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: 

295 

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] 

330 

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)} 

336 

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

338 "" if len(refCat) == 1 else "s") 

339 

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() 

352 

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()) 

367 

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() 

380 

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) 

386 

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

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

389 

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. 

400 

401 Returns 

402 ------- 

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

404 Source catalog ready for measurement. 

405 

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 

425 

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

427 r"""Attach Footprints to blank sources prior to measurement. 

428 

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. 

438 

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))