Coverage for python/lsst/meas/base/sfm.py: 31%

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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 

34import lsst.pex.config 

35from lsst.utils.logging import PeriodicLogger 

36from lsst.utils.timer import timeMethod 

37 

38from .pluginRegistry import PluginRegistry 

39from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin, 

40 BaseMeasurementConfig, BaseMeasurementTask) 

41from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer 

42 

43__all__ = ("SingleFramePluginConfig", "SingleFramePlugin", 

44 "SingleFrameMeasurementConfig", "SingleFrameMeasurementTask") 

45 

46 

47class SingleFramePluginConfig(BaseMeasurementPluginConfig): 

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

49 """ 

50 pass 

51 

52 

53class SingleFramePlugin(BaseMeasurementPlugin): 

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

55 

56 Parameters 

57 ---------- 

58 config : `SingleFramePlugin.ConfigClass` 

59 Configuration for this plugin. 

60 name : `str` 

61 The string with which the plugin was registered. 

62 schema : `lsst.afw.table.Schema` 

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

64 hold measurements produced by this plugin. 

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

66 Plugin metadata that will be attached to the output catalog 

67 logName : `str`, optional 

68 Name to use when logging errors. 

69 

70 Notes 

71 ----- 

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

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

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

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

76 """ 

77 

78 registry = PluginRegistry(SingleFramePluginConfig) 

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

80 """ 

81 

82 ConfigClass = SingleFramePluginConfig 

83 

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

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

86 

87 def measure(self, measRecord, exposure): 

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

89 

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

91 

92 Parameters 

93 ---------- 

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

95 Record describing the object being measured. Previously-measured 

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

97 in-place tih the outputs of this plugin. 

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

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

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

101 by noise according to deblender outputs. 

102 """ 

103 raise NotImplementedError() 

104 

105 def measureN(self, measCat, exposure): 

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

107 

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

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

110 

111 Parameters 

112 ---------- 

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

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

115 measured. Previously-measured quantities will be retrieved from 

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

117 plugin. 

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

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

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

121 by noise according to deblender outputs. 

122 

123 Notes 

124 ----- 

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

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

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

128 class to signal that measureN-mode is available. 

129 """ 

130 raise NotImplementedError() 

131 

132 

133class SingleFrameMeasurementConfig(BaseMeasurementConfig): 

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

135 """ 

136 

137 plugins = SingleFramePlugin.registry.makeField( 

138 multi=True, 

139 default=["base_PixelFlags", 

140 "base_SdssCentroid", 

141 "base_NaiveCentroid", 

142 "base_SdssShape", 

143 "base_GaussianFlux", 

144 "base_PsfFlux", 

145 "base_CircularApertureFlux", 

146 "base_SkyCoord", 

147 "base_Variance", 

148 "base_Blendedness", 

149 "base_LocalBackground", 

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 loggingInterval = lsst.pex.config.Field( 

160 dtype=int, 

161 default=600, 

162 doc="Interval (in seconds) to log messages (at VERBOSE level) while running measurement plugins.", 

163 deprecated="This field is no longer used and will be removed in v25.", 

164 ) 

165 

166 

167class SingleFrameMeasurementTask(BaseMeasurementTask): 

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

169 

170 Parameters 

171 ---------- 

172 schema : `lsst.afw.table.Schema` 

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

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

175 task. 

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

177 Used to record metadaa about algorithm execution. An empty 

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

179 **kwds 

180 Keyword arguments forwarded to `BaseMeasurementTask`. 

181 """ 

182 

183 ConfigClass = SingleFrameMeasurementConfig 

184 

185 NOISE_SEED_MULTIPLIER = "NOISE_SEED_MULTIPLIER" 

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

187 """ 

188 

189 NOISE_SOURCE = "NOISE_SOURCE" 

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

191 """ 

192 

193 NOISE_OFFSET = "NOISE_OFFSET" 

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

195 """ 

196 

197 NOISE_EXPOSURE_ID = "NOISE_EXPOSURE_ID" 

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

199 """ 

200 

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

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

203 self.schema = schema 

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

205 self.initializePlugins(schema=self.schema) 

206 

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

208 if 'base_Blendedness' in self.plugins: 

209 self.doBlendedness = True 

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

211 else: 

212 self.doBlendedness = False 

213 

214 @timeMethod 

215 def run(self, measCat, exposure, noiseImage=None, exposureId=None, beginOrder=None, endOrder=None): 

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

217 

218 Parameters 

219 ---------- 

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

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

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

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

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

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

226 Image containing the pixel data to be measured together with 

227 associated PSF, WCS, etc. 

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

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

230 for testing purposes. 

231 exposureId : `int`, optional 

232 Unique exposure identifier used to calculate the random number 

233 generator seed during noise replacement. 

234 beginOrder : `float`, optional 

235 Start execution order (inclusive): measurements with 

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

237 limit. 

238 endOrder : `float`, optional 

239 Final execution order (exclusive): measurements with 

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

241 limit. 

242 """ 

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

244 footprints = {measRecord.getId(): (measRecord.getParent(), measRecord.getFootprint()) 

245 for measRecord in measCat} 

246 

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

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

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

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

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

252 

253 if self.config.doReplaceWithNoise: 

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

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

256 algMetadata = measCat.getMetadata() 

257 if algMetadata is not None: 

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

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

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

261 if exposureId is not None: 

262 algMetadata.addLong(self.NOISE_EXPOSURE_ID, exposureId) 

263 else: 

264 noiseReplacer = DummyNoiseReplacer() 

265 

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

267 

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

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

270 

271 Parameters 

272 ---------- 

273 noiseReplacer : `NoiseReplacer` 

274 Used to fill sources not being measured with noise. 

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

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

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

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

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

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

281 Image containing the pixel data to be measured together with 

282 associated PSF, WCS, etc. 

283 beginOrder : `float`, optional 

284 Start execution order (inclusive): measurements with 

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

286 limit. 

287 endOrder : `float`, optional 

288 Final execution order (exclusive): measurements with 

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

290 limit. 

291 """ 

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

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

294 measParentCat = measCat.getChildren(0) 

295 

296 nMeasCat = len(measCat) 

297 nMeasParentCat = len(measParentCat) 

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

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

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

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

302 

303 # Wrap the task logger into a period logger 

304 periodicLog = PeriodicLogger(self.log) 

305 

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

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

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

309 # turn, and measure 

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

311 # single-object mode 

312 for measChildRecord in measChildCat: 

313 noiseReplacer.insertSource(measChildRecord.getId()) 

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

315 

316 if self.doBlendedness: 

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

318 

319 noiseReplacer.removeSource(measChildRecord.getId()) 

320 

321 # Then insert the parent footprint, and measure that 

322 noiseReplacer.insertSource(measParentRecord.getId()) 

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

324 

325 if self.doBlendedness: 

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

327 

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

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

330 beginOrder=beginOrder, endOrder=endOrder) 

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

332 noiseReplacer.removeSource(measParentRecord.getId()) 

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

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

335 parentIdx + 1, nMeasParentCat) 

336 

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

338 noiseReplacer.end() 

339 

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

341 if endOrder is None: 

342 for sourceIndex, source in enumerate(measCat): 

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

344 self.doMeasurement(plugin, source, exposure) 

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

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

347 sourceIndex + 1, nMeasCat) 

348 

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

350 # blendedness metrics 

351 if self.doBlendedness: 

352 for source in measCat: 

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

354 

355 def measure(self, measCat, exposure): 

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

357 """ 

358 self.run(measCat, exposure)