Coverage for python/lsst/meas/base/sfm.py: 30%

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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 single-frame measurement plugins and the associated task. 

23 

24In single-frame measurement, we assume that detection and probably deblending 

25have already been run on the same frame, so a `~lsst.afw.table.SourceCatalog` 

26has already been created with `lsst.afw.detection.Footprint`\ s (which may be 

27"heavy" — that is, include pixel data). Measurements are generally recorded in 

28the coordinate system of the image being measured (and all slot-eligible 

29fields must be), but non-slot fields may be recorded in other coordinate 

30systems if necessary to avoid information loss (this should, of course, be 

31indicated in the field documentation). 

32""" 

33 

34from lsst.utils.logging import PeriodicLogger 

35from lsst.utils.timer import timeMethod 

36 

37from .pluginRegistry import PluginRegistry 

38from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin, 

39 BaseMeasurementConfig, BaseMeasurementTask) 

40from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer 

41 

42__all__ = ("SingleFramePluginConfig", "SingleFramePlugin", 

43 "SingleFrameMeasurementConfig", "SingleFrameMeasurementTask") 

44 

45 

46class SingleFramePluginConfig(BaseMeasurementPluginConfig): 

47 """Base class for single-frame plugin configuration classes. 

48 """ 

49 pass 

50 

51 

52class SingleFramePlugin(BaseMeasurementPlugin): 

53 """Base class for single-frame measurement plugin. 

54 

55 Parameters 

56 ---------- 

57 config : `SingleFramePlugin.ConfigClass` 

58 Configuration for this plugin. 

59 name : `str` 

60 The string with which the plugin was registered. 

61 schema : `lsst.afw.table.Schema` 

62 The schema for the source table . New fields are added here to 

63 hold measurements produced by this plugin. 

64 metadata : `lsst.daf.base.PropertySet` 

65 Plugin metadata that will be attached to the output catalog 

66 logName : `str`, optional 

67 Name to use when logging errors. 

68 

69 Notes 

70 ----- 

71 New plugins can be created in Python by inheriting directly from this 

72 class and implementing the `measure`, `fail` (from `BasePlugin`), and 

73 optionally `__init__` and `measureN` methods. Plugins can also be defined 

74 in C++ via the `WrappedSingleFramePlugin` class. 

75 """ 

76 

77 registry = PluginRegistry(SingleFramePluginConfig) 

78 """Registry of subclasses of `SingleFramePlugin` (`PluginRegistry`). 

79 """ 

80 

81 ConfigClass = SingleFramePluginConfig 

82 

83 def __init__(self, config, name, schema, metadata, logName=None, **kwds): 

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

85 

86 def measure(self, measRecord, exposure): 

87 """Measure the properties of a source on a single image. 

88 

89 The image may be from a single epoch, or it may be a coadd. 

90 

91 Parameters 

92 ---------- 

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

94 Record describing the object being measured. Previously-measured 

95 quantities may be retrieved from here, and it will be updated 

96 in-place tih the outputs of this plugin. 

97 exposure : `lsst.afw.image.ExposureF` 

98 The pixel data to be measured, together with the associated PSF, 

99 WCS, etc. All other sources in the image should have been replaced 

100 by noise according to deblender outputs. 

101 """ 

102 raise NotImplementedError() 

103 

104 def measureN(self, measCat, exposure): 

105 """Measure the properties of blended sources on a single image. 

106 

107 This operates on all members of a blend family at once. The image may 

108 be from a single epoch, or it may be a coadd. 

109 

110 Parameters 

111 ---------- 

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

113 Catalog describing the objects (and only those objects) being 

114 measured. Previously-measured quantities will be retrieved from 

115 here, and it will be updated in-place with the outputs of this 

116 plugin. 

117 exposure : `lsst.afw.image.ExposureF` 

118 The pixel data to be measured, together with the associated PSF, 

119 WCS, etc. All other sources in the image should have been replaced 

120 by noise according to deblender outputs. 

121 

122 Notes 

123 ----- 

124 Derived classes that do not implement ``measureN`` should just inherit 

125 this disabled version. Derived classes that do implement ``measureN`` 

126 should additionally add a bool doMeasureN config field to their config 

127 class to signal that measureN-mode is available. 

128 """ 

129 raise NotImplementedError() 

130 

131 

132class SingleFrameMeasurementConfig(BaseMeasurementConfig): 

133 """Config class for single frame measurement driver task. 

134 """ 

135 

136 plugins = SingleFramePlugin.registry.makeField( 

137 multi=True, 

138 default=["base_PixelFlags", 

139 "base_SdssCentroid", 

140 "base_SdssShape", 

141 "base_GaussianFlux", 

142 "base_PsfFlux", 

143 "base_CircularApertureFlux", 

144 "base_SkyCoord", 

145 "base_Variance", 

146 "base_Blendedness", 

147 "base_LocalBackground", 

148 "base_CompensatedGaussianFlux", 

149 "base_ClassificationSizeExtendedness", 

150 ], 

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

152 ) 

153 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins") 153 ↛ exitline 153 didn't run the lambda on line 153

154 undeblended = SingleFramePlugin.registry.makeField( 

155 multi=True, 

156 default=[], 

157 doc="Plugins to run on undeblended image" 

158 ) 

159 

160 

161class SingleFrameMeasurementTask(BaseMeasurementTask): 

162 """A subtask for measuring the properties of sources on a single exposure. 

163 

164 Parameters 

165 ---------- 

166 schema : `lsst.afw.table.Schema` 

167 Schema of the output resultant catalog. Will be updated to provide 

168 fields to accept the outputs of plugins which will be executed by this 

169 task. 

170 algMetadata : `lsst.daf.base.PropertyList`, optional 

171 Used to record metadaa about algorithm execution. An empty 

172 `lsst.daf.base.PropertyList` will be created if `None`. 

173 **kwds 

174 Keyword arguments forwarded to `BaseMeasurementTask`. 

175 """ 

176 

177 ConfigClass = SingleFrameMeasurementConfig 

178 

179 NOISE_SEED_MULTIPLIER = "NOISE_SEED_MULTIPLIER" 

180 """Name by which the noise seed multiplier is recorded in metadata ('str'). 

181 """ 

182 

183 NOISE_SOURCE = "NOISE_SOURCE" 

184 """Name by which the noise source is recorded in metadata ('str'). 

185 """ 

186 

187 NOISE_OFFSET = "NOISE_OFFSET" 

188 """Name by which the noise offset is recorded in metadata ('str'). 

189 """ 

190 

191 NOISE_EXPOSURE_ID = "NOISE_EXPOSURE_ID" 

192 """Name by which the noise exposire ID is recorded in metadata ('str'). 

193 """ 

194 

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

196 super(SingleFrameMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds) 

197 self.schema = schema 

198 self.config.slots.setupSchema(self.schema) 

199 self.initializePlugins(schema=self.schema) 

200 

201 # Check to see if blendedness is one of the plugins 

202 if 'base_Blendedness' in self.plugins: 

203 self.doBlendedness = True 

204 self.blendPlugin = self.plugins['base_Blendedness'] 

205 else: 

206 self.doBlendedness = False 

207 

208 @timeMethod 

209 def run( 

210 self, 

211 measCat, 

212 exposure, 

213 noiseImage=None, 

214 exposureId=None, 

215 beginOrder=None, 

216 endOrder=None, 

217 footprints=None, 

218 ): 

219 r"""Run single frame measurement over an exposure and source catalog. 

220 

221 Parameters 

222 ---------- 

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

224 Catalog to be filled with the results of measurement. Must contain 

225 all the `lsst.afw.table.SourceRecord`\ s to be measured (with 

226 `lsst.afw.detection.Footprint`\ s attached), and have a schema 

227 that is a superset of ``self.schema``. 

228 exposure : `lsst.afw.image.ExposureF` 

229 Image containing the pixel data to be measured together with 

230 associated PSF, WCS, etc. 

231 noiseImage : `lsst.afw.image.ImageF`, optional 

232 Can be used to specify the a predictable noise replacement field 

233 for testing purposes. 

234 exposureId : `int`, optional 

235 Unique exposure identifier used to calculate the random number 

236 generator seed during noise replacement. 

237 beginOrder : `float`, optional 

238 Start execution order (inclusive): measurements with 

239 ``executionOrder < beginOrder`` are not executed. `None` for no 

240 limit. 

241 endOrder : `float`, optional 

242 Final execution order (exclusive): measurements with 

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

244 limit. 

245 footprints : `dict` {`int`: `lsst.afw.detection.Footprint`}, optional 

246 List of footprints to use for noise replacement. If this is not 

247 supplied then the footprints from the measCat are used. 

248 """ 

249 assert measCat.getSchema().contains(self.schema) 

250 if footprints is None: 

251 footprints = self.getFootprintsFromCatalog(measCat) 

252 

253 # noiseReplacer is used to fill the footprints with noise and save 

254 # heavy footprints of the source pixels so that they can be restored 

255 # one at a time for measurement. After the NoiseReplacer is 

256 # constructed, all pixels in the exposure.getMaskedImage() which 

257 # belong to objects in measCat will be replaced with noise 

258 

259 if self.config.doReplaceWithNoise: 

260 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure, footprints, 

261 noiseImage=noiseImage, log=self.log, exposureId=exposureId) 

262 algMetadata = measCat.getMetadata() 

263 if algMetadata is not None: 

264 algMetadata.addInt(self.NOISE_SEED_MULTIPLIER, self.config.noiseReplacer.noiseSeedMultiplier) 

265 algMetadata.addString(self.NOISE_SOURCE, self.config.noiseReplacer.noiseSource) 

266 algMetadata.addDouble(self.NOISE_OFFSET, self.config.noiseReplacer.noiseOffset) 

267 if exposureId is not None: 

268 algMetadata.addLong(self.NOISE_EXPOSURE_ID, exposureId) 

269 else: 

270 noiseReplacer = DummyNoiseReplacer() 

271 

272 self.runPlugins(noiseReplacer, measCat, exposure, beginOrder, endOrder) 

273 

274 def runPlugins(self, noiseReplacer, measCat, exposure, beginOrder=None, endOrder=None): 

275 r"""Call the configured measument plugins on an image. 

276 

277 Parameters 

278 ---------- 

279 noiseReplacer : `NoiseReplacer` 

280 Used to fill sources not being measured with noise. 

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

282 Catalog to be filled with the results of measurement. Must contain 

283 all the `lsst.afw.table.SourceRecord`\ s to be measured (with 

284 `lsst.afw.detection.Footprint`\ s attached), and have a schema 

285 that is a superset of ``self.schema``. 

286 exposure : `lsst.afw.image.ExposureF` 

287 Image containing the pixel data to be measured together with 

288 associated PSF, WCS, etc. 

289 beginOrder : `float`, optional 

290 Start execution order (inclusive): measurements with 

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

292 limit. 

293 endOrder : `float`, optional 

294 Final execution order (exclusive): measurements with 

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

296 limit. 

297 """ 

298 # First, create a catalog of all parentless sources. Loop through all 

299 # the parent sources, first processing the children, then the parent. 

300 measParentCat = measCat.getChildren(0) 

301 

302 nMeasCat = len(measCat) 

303 nMeasParentCat = len(measParentCat) 

304 self.log.info("Measuring %d source%s (%d parent%s, %d child%s) ", 

305 nMeasCat, ("" if nMeasCat == 1 else "s"), 

306 nMeasParentCat, ("" if nMeasParentCat == 1 else "s"), 

307 nMeasCat - nMeasParentCat, ("" if nMeasCat - nMeasParentCat == 1 else "ren")) 

308 

309 # Wrap the task logger into a period logger 

310 periodicLog = PeriodicLogger(self.log) 

311 

312 childrenIter = measCat.getChildren([measParentRecord.getId() for measParentRecord in measParentCat]) 

313 for parentIdx, (measParentRecord, measChildCat) in enumerate(zip(measParentCat, childrenIter)): 

314 # first get all the children of this parent, insert footprint in 

315 # turn, and measure 

316 # TODO: skip this loop if there are no plugins configured for 

317 # single-object mode 

318 for measChildRecord in measChildCat: 

319 noiseReplacer.insertSource(measChildRecord.getId()) 

320 self.callMeasure(measChildRecord, exposure, beginOrder=beginOrder, endOrder=endOrder) 

321 

322 if self.doBlendedness: 

323 self.blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measChildRecord) 

324 

325 noiseReplacer.removeSource(measChildRecord.getId()) 

326 

327 # Then insert the parent footprint, and measure that 

328 noiseReplacer.insertSource(measParentRecord.getId()) 

329 self.callMeasure(measParentRecord, exposure, beginOrder=beginOrder, endOrder=endOrder) 

330 

331 if self.doBlendedness: 

332 self.blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measParentRecord) 

333 

334 # Finally, process both parent and child set through measureN 

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

336 beginOrder=beginOrder, endOrder=endOrder) 

337 self.callMeasureN(measChildCat, exposure, beginOrder=beginOrder, endOrder=endOrder) 

338 noiseReplacer.removeSource(measParentRecord.getId()) 

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

340 periodicLog.log("Measurement complete for %d parents (and their children) out of %d", 

341 parentIdx + 1, nMeasParentCat) 

342 

343 # When done, restore the exposure to its original state 

344 noiseReplacer.end() 

345 

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

347 if endOrder is None: 

348 for sourceIndex, source in enumerate(measCat): 

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

350 self.doMeasurement(plugin, source, exposure) 

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

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

353 sourceIndex + 1, nMeasCat) 

354 

355 # Now we loop over all of the sources one more time to compute the 

356 # blendedness metrics 

357 if self.doBlendedness: 

358 for source in measCat: 

359 self.blendPlugin.cpp.measureParentPixels(exposure.getMaskedImage(), source) 

360 

361 def measure(self, measCat, exposure): 

362 """Backwards-compatibility alias for `run`. 

363 """ 

364 self.run(measCat, exposure)