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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 

22"""Base measurement task, which subclassed by the single frame and forced 

23measurement tasks. 

24""" 

25 

26import lsst.pipe.base 

27import lsst.pex.config 

28 

29from .pluginRegistry import PluginMap 

30from .exceptions import FatalAlgorithmError, MeasurementError 

31from .pluginsBase import BasePluginConfig, BasePlugin 

32from .noiseReplacer import NoiseReplacerConfig 

33 

34__all__ = ("BaseMeasurementPluginConfig", "BaseMeasurementPlugin", 

35 "BaseMeasurementConfig", "BaseMeasurementTask") 

36 

37# Exceptions that the measurement tasks should always propagate up to their callers 

38FATAL_EXCEPTIONS = (MemoryError, FatalAlgorithmError) 

39 

40 

41class BaseMeasurementPluginConfig(BasePluginConfig): 

42 """Base config class for all measurement plugins. 

43 

44 Notes 

45 ----- 

46 Most derived classes will want to override `setDefaults` in order to 

47 customize the default `executionOrder`. 

48 

49 A derived class whose corresponding Plugin class implements a do `measureN` 

50 method should additionally add a bool `doMeasureN` field to replace the 

51 bool class attribute defined here. 

52 """ 

53 

54 doMeasure = lsst.pex.config.Field(dtype=bool, default=True, 

55 doc="whether to run this plugin in single-object mode") 

56 

57 doMeasureN = False # replace this class attribute with a Field if measureN-capable 

58 

59 

60class BaseMeasurementPlugin(BasePlugin): 

61 """Base class for all measurement plugins. 

62 

63 Notes 

64 ----- 

65 This is class is a placeholder for future behavior which will be shared 

66 only between measurement plugins and is implemented for symmetry with the 

67 measurement base plugin configuration class 

68 """ 

69 

70 pass 

71 

72 

73class SourceSlotConfig(lsst.pex.config.Config): 

74 """Assign named plugins to measurement slots. 

75 

76 Slot configuration which assigns a particular named plugin to each of a set 

77 of slots. Each slot allows a type of measurement to be fetched from the 

78 `lsst.afw.table.SourceTable` without knowing which algorithm was used to 

79 produced the data. 

80 

81 Notes 

82 ----- 

83 The default algorithm for each slot must be registered, even if the default 

84 is not used. 

85 """ 

86 

87 Field = lsst.pex.config.Field 

88 centroid = Field(dtype=str, default="base_SdssCentroid", optional=True, 

89 doc="the name of the centroiding algorithm used to set source x,y") 

90 shape = Field(dtype=str, default="base_SdssShape", optional=True, 

91 doc="the name of the algorithm used to set source moments parameters") 

92 psfShape = Field(dtype=str, default="base_SdssShape_psf", optional=True, 

93 doc="the name of the algorithm used to set PSF moments parameters") 

94 apFlux = Field(dtype=str, default="base_CircularApertureFlux_12_0", optional=True, 

95 doc="the name of the algorithm used to set the source aperture instFlux slot") 

96 modelFlux = Field(dtype=str, default="base_GaussianFlux", optional=True, 

97 doc="the name of the algorithm used to set the source model instFlux slot") 

98 psfFlux = Field(dtype=str, default="base_PsfFlux", optional=True, 

99 doc="the name of the algorithm used to set the source psf instFlux slot") 

100 gaussianFlux = Field(dtype=str, default="base_GaussianFlux", optional=True, 

101 doc="the name of the algorithm used to set the source Gaussian instFlux slot") 

102 calibFlux = Field(dtype=str, default="base_CircularApertureFlux_12_0", optional=True, 

103 doc="the name of the instFlux measurement algorithm used for calibration") 

104 

105 def setupSchema(self, schema): 

106 """Set up a slots in a schema following configuration directives. 

107 

108 Parameters 

109 ---------- 

110 schema : `lsst.afw.table.Schema` 

111 The schema in which slots will be set up. 

112 

113 Notes 

114 ----- 

115 This is defined in this configuration class to support use in unit 

116 tests without needing to construct an `lsst.pipe.base.Task` object. 

117 """ 

118 aliases = schema.getAliasMap() 

119 if self.centroid is not None: 

120 aliases.set("slot_Centroid", self.centroid) 

121 if self.shape is not None: 

122 aliases.set("slot_Shape", self.shape) 

123 if self.psfShape is not None: 

124 aliases.set("slot_PsfShape", self.psfShape) 

125 if self.apFlux is not None: 

126 aliases.set("slot_ApFlux", self.apFlux) 

127 if self.modelFlux is not None: 

128 aliases.set("slot_ModelFlux", self.modelFlux) 

129 if self.psfFlux is not None: 

130 aliases.set("slot_PsfFlux", self.psfFlux) 

131 if self.gaussianFlux is not None: 

132 aliases.set("slot_GaussianFlux", self.gaussianFlux) 

133 if self.calibFlux is not None: 

134 aliases.set("slot_CalibFlux", self.calibFlux) 

135 

136 

137class BaseMeasurementConfig(lsst.pex.config.Config): 

138 """Base configuration for all measurement driver tasks. 

139 

140 Examples 

141 -------- 

142 Subclasses should define the 'plugins' and 'undeblended' registries, e.g. 

143 

144 .. code-block:: py 

145 

146 plugins = PluginBaseClass.registry.makeField( 

147 multi=True, 

148 default=[], 

149 doc="Plugins to be run and their configuration" 

150 ) 

151 undeblended = PluginBaseClass.registry.makeField( 

152 multi=True, 

153 default=[], 

154 doc="Plugins to run on undeblended image" 

155 ) 

156 

157 where ``PluginBaseClass`` is the appropriate base class of the plugin 

158 (e.g., `SingleFramePlugin` or `ForcedPlugin`). 

159 """ 

160 

161 slots = lsst.pex.config.ConfigField( 

162 dtype=SourceSlotConfig, 

163 doc="Mapping from algorithms to special aliases in Source." 

164 ) 

165 

166 doReplaceWithNoise = lsst.pex.config.Field( 

167 dtype=bool, default=True, optional=False, 

168 doc='When measuring, replace other detected footprints with noise?') 

169 

170 noiseReplacer = lsst.pex.config.ConfigField( 

171 dtype=NoiseReplacerConfig, 

172 doc="configuration that sets how to replace neighboring sources with noise" 

173 ) 

174 undeblendedPrefix = lsst.pex.config.Field( 

175 dtype=str, default="undeblended_", 

176 doc="Prefix to give undeblended plugins" 

177 ) 

178 

179 def validate(self): 

180 lsst.pex.config.Config.validate(self) 

181 if self.slots.centroid is not None and self.slots.centroid not in self.plugins.names: 

182 raise ValueError("source centroid slot algorithm is not being run.") 

183 if self.slots.shape is not None and self.slots.shape not in self.plugins.names: 

184 raise ValueError("source shape slot algorithm '%s' is not being run." % self.slots.shape) 

185 for slot in (self.slots.psfFlux, self.slots.apFlux, self.slots.modelFlux, 

186 self.slots.gaussianFlux, self.slots.calibFlux): 

187 if slot is not None: 

188 for name in self.plugins.names: 

189 if len(name) <= len(slot) and name == slot[:len(name)]: 

190 break 

191 else: 

192 raise ValueError("source instFlux slot algorithm '%s' is not being run." % slot) 

193 

194 

195class BaseMeasurementTask(lsst.pipe.base.Task): 

196 """Ultimate base class for all measurement tasks. 

197 

198 Parameters 

199 ---------- 

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

201 Will be modified in-place to contain metadata about the plugins being 

202 run. If `None`, an empty `~lsst.daf.base.PropertyList` will be 

203 created. 

204 **kwds 

205 Additional arguments passed to `lsst.pipe.base.Task.__init__`. 

206 

207 Notes 

208 ----- 

209 This base class for `SingleFrameMeasurementTask` and 

210 `ForcedMeasurementTask` mostly exists to share code between the two, and 

211 generally should not be used directly. 

212 """ 

213 

214 ConfigClass = BaseMeasurementConfig 

215 _DefaultName = "measurement" 

216 

217 plugins = None 

218 """Plugins to be invoked (`PluginMap`). 

219 

220 Initially empty, this will be populated as plugins are initialized. It 

221 should be considered read-only. 

222 """ 

223 

224 algMetadata = None 

225 """Metadata about active plugins (`lsst.daf.base.PropertyList`). 

226 

227 Contains additional information about active plugins to be saved with 

228 the output catalog. Will be filled by subclasses. 

229 """ 

230 

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

232 super(BaseMeasurementTask, self).__init__(**kwds) 

233 self.plugins = PluginMap() 

234 self.undeblendedPlugins = PluginMap() 

235 if algMetadata is None: 

236 algMetadata = lsst.daf.base.PropertyList() 

237 self.algMetadata = algMetadata 

238 

239 def initializePlugins(self, **kwds): 

240 """Initialize plugins (and slots) according to configuration. 

241 

242 Parameters 

243 ---------- 

244 **kwds 

245 Keyword arguments forwarded directly to plugin constructors. 

246 

247 Notes 

248 ----- 

249 Derived class constructors should call this method to fill the 

250 `plugins` attribute and add corresponding output fields and slot 

251 aliases to the output schema. 

252 

253 In addition to the attributes added by `BaseMeasurementTask.__init__`, 

254 a ``schema``` attribute holding the output schema must be present 

255 before this method is called. 

256 

257 Keyword arguments are forwarded directly to plugin constructors, 

258 allowing derived classes to use plugins with different signatures. 

259 """ 

260 # Make a place at the beginning for the centroid plugin to run first (because it's an OrderedDict, 

261 # adding an empty element in advance means it will get run first when it's reassigned to the 

262 # actual Plugin). 

263 if self.config.slots.centroid is not None: 

264 self.plugins[self.config.slots.centroid] = None 

265 # Init the plugins, sorted by execution order. At the same time add to the schema 

266 for executionOrder, name, config, PluginClass in sorted(self.config.plugins.apply()): 

267 # Pass logName to the plugin if the plugin is marked as using it 

268 # The task will use this name to log plugin errors, regardless. 

269 if hasattr(PluginClass, "hasLogName") and PluginClass.hasLogName: 

270 self.plugins[name] = PluginClass(config, name, metadata=self.algMetadata, 

271 logName=self.log.getChild(name).getName(), **kwds) 

272 else: 

273 self.plugins[name] = PluginClass(config, name, metadata=self.algMetadata, **kwds) 

274 

275 # In rare circumstances (usually tests), the centroid slot not be coming from an algorithm, 

276 # which means we'll have added something we don't want to the plugins map, and we should 

277 # remove it. 

278 if self.config.slots.centroid is not None and self.plugins[self.config.slots.centroid] is None: 

279 del self.plugins[self.config.slots.centroid] 

280 # Initialize the plugins to run on the undeblended image 

281 for executionOrder, name, config, PluginClass in sorted(self.config.undeblended.apply()): 

282 undeblendedName = self.config.undeblendedPrefix + name 

283 self.undeblendedPlugins[name] = PluginClass(config, undeblendedName, metadata=self.algMetadata, 

284 **kwds) 

285 

286 def callMeasure(self, measRecord, *args, **kwds): 

287 """Call ``measure`` on all plugins and consistently handle exceptions. 

288 

289 Parameters 

290 ---------- 

291 measRecord : `lsst.afw.table.SourceRecord` 

292 The record corresponding to the object being measured. Will be 

293 updated in-place with the results of measurement. 

294 *args 

295 Positional arguments forwarded to ``plugin.measure`` 

296 **kwds 

297 Keyword arguments. Two are handled locally: 

298 

299 beginOrder : `int` 

300 Beginning execution order (inclusive). Measurements with 

301 ``executionOrder`` < ``beginOrder`` are not executed. `None` 

302 for no limit. 

303 

304 endOrder : `int` 

305 Ending execution order (exclusive). Measurements with 

306 ``executionOrder`` >= ``endOrder`` are not executed. `None` 

307 for no limit. 

308 

309 Others are forwarded to ``plugin.measure()``. 

310 

311 Notes 

312 ----- 

313 This method can be used with plugins that have different signatures; 

314 the only requirement is that ``measRecord`` be the first argument. 

315 Subsequent positional arguments and keyword arguments are forwarded 

316 directly to the plugin. 

317 

318 This method should be considered "protected": it is intended for use by 

319 derived classes, not users. 

320 """ 

321 beginOrder = kwds.pop("beginOrder", None) 

322 endOrder = kwds.pop("endOrder", None) 

323 for plugin in self.plugins.iter(): 

324 if beginOrder is not None and plugin.getExecutionOrder() < beginOrder: 

325 continue 

326 if endOrder is not None and plugin.getExecutionOrder() >= endOrder: 

327 break 

328 self.doMeasurement(plugin, measRecord, *args, **kwds) 

329 

330 def doMeasurement(self, plugin, measRecord, *args, **kwds): 

331 """Call ``measure`` on the specified plugin. 

332 

333 Exceptions are handled in a consistent way. 

334 

335 Parameters 

336 ---------- 

337 plugin : subclass of `BasePlugin` 

338 Plugin that will be executed. 

339 measRecord : `lsst.afw.table.SourceRecord` 

340 The record corresponding to the object being measured. Will be 

341 updated in-place with the results of measurement. 

342 *args 

343 Positional arguments forwarded to ``plugin.measure()``. 

344 **kwds 

345 Keyword arguments forwarded to ``plugin.measure()``. 

346 

347 Notes 

348 ----- 

349 This method can be used with plugins that have different signatures; 

350 the only requirement is that ``plugin`` and ``measRecord`` be the first 

351 two arguments. Subsequent positional arguments and keyword arguments 

352 are forwarded directly to the plugin. 

353 

354 This method should be considered "protected": it is intended for use by 

355 derived classes, not users. 

356 """ 

357 try: 

358 plugin.measure(measRecord, *args, **kwds) 

359 except FATAL_EXCEPTIONS: 

360 raise 

361 except MeasurementError as error: 

362 self.log.getChild(plugin.name).debug( 

363 "MeasurementError in %s.measure on record %s: %s", 

364 plugin.name, measRecord.getId(), error) 

365 plugin.fail(measRecord, error) 

366 except Exception as error: 

367 self.log.getChild(plugin.name).debug( 

368 "Exception in %s.measure on record %s: %s", 

369 plugin.name, measRecord.getId(), error) 

370 plugin.fail(measRecord) 

371 

372 def callMeasureN(self, measCat, *args, **kwds): 

373 """Call ``measureN`` on all plugins and consistently handle exceptions. 

374 

375 Parameters 

376 ---------- 

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

378 Catalog containing only the records for the source family to be 

379 measured, and where outputs should be written. 

380 *args 

381 Positional arguments forwarded to ``plugin.measure()`` 

382 **kwds 

383 Keyword arguments. Two are handled locally: 

384 

385 beginOrder: 

386 Beginning execution order (inclusive): Measurements with 

387 ``executionOrder`` < ``beginOrder`` are not executed. `None` 

388 for no limit. 

389 endOrder: 

390 Ending execution order (exclusive): measurements with 

391 ``executionOrder`` >= ``endOrder`` are not executed. `None` for 

392 no ``limit``. 

393 

394 Others are are forwarded to ``plugin.measure()``. 

395 

396 Notes 

397 ----- 

398 This method can be used with plugins that have different signatures; 

399 the only requirement is that ``measRecord`` be the first argument. 

400 Subsequent positional arguments and keyword arguments are forwarded 

401 directly to the plugin. 

402 

403 This method should be considered "protected": it is intended for use by 

404 derived classes, not users. 

405 """ 

406 beginOrder = kwds.pop("beginOrder", None) 

407 endOrder = kwds.pop("endOrder", None) 

408 for plugin in self.plugins.iterN(): 

409 if beginOrder is not None and plugin.getExecutionOrder() < beginOrder: 

410 continue 

411 if endOrder is not None and plugin.getExecutionOrder() >= endOrder: 

412 break 

413 self.doMeasurementN(plugin, measCat, *args, **kwds) 

414 

415 def doMeasurementN(self, plugin, measCat, *args, **kwds): 

416 """Call ``measureN`` on the specified plugin. 

417 

418 Exceptions are handled in a consistent way. 

419 

420 Parameters 

421 ---------- 

422 plugin : subclass of `BasePlugin` 

423 Plugin that will be executed. 

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

425 Catalog containing only the records for the source family to be 

426 measured, and where outputs should be written. 

427 *args 

428 Positional arguments forwarded to ``plugin.measureN()``. 

429 **kwds 

430 Keyword arguments forwarded to ``plugin.measureN()``. 

431 

432 Notes 

433 ----- 

434 This method can be used with plugins that have different signatures; 

435 the only requirement is that the ``plugin`` and ``measCat`` be the 

436 first two arguments. Subsequent positional arguments and keyword 

437 arguments are forwarded directly to the plugin. 

438 

439 This method should be considered "protected": it is intended for use by 

440 derived classes, not users. 

441 """ 

442 try: 

443 plugin.measureN(measCat, *args, **kwds) 

444 except FATAL_EXCEPTIONS: 

445 raise 

446 

447 except MeasurementError as error: 

448 for measRecord in measCat: 

449 self.log.getChild(plugin.name).debug( 

450 "MeasurementError in %s.measureN on records %s-%s: %s", 

451 plugin.name, measCat[0].getId(), measCat[-1].getId(), error) 

452 plugin.fail(measRecord, error) 

453 except Exception as error: 

454 for measRecord in measCat: 

455 plugin.fail(measRecord) 

456 self.log.getChild(plugin.name).debug( 

457 "Exception in %s.measureN on records %s-%s: %s", 

458 plugin.name, measCat[0].getId(), measCat[-1].getId(), error)