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 

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_NaiveCentroid", 

141 "base_SdssShape", 

142 "base_GaussianFlux", 

143 "base_PsfFlux", 

144 "base_CircularApertureFlux", 

145 "base_SkyCoord", 

146 "base_Variance", 

147 "base_Blendedness", 

148 "base_LocalBackground", 

149 "base_CompensatedGaussianFlux", 

150 "base_ClassificationSizeExtendedness", 

151 ], 

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

153 ) 

154 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins") 154 ↛ exitline 154 didn't run the lambda on line 154

155 undeblended = SingleFramePlugin.registry.makeField( 

156 multi=True, 

157 default=[], 

158 doc="Plugins to run on undeblended image" 

159 ) 

160 

161 

162class SingleFrameMeasurementTask(BaseMeasurementTask): 

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

164 

165 Parameters 

166 ---------- 

167 schema : `lsst.afw.table.Schema` 

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

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

170 task. 

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

172 Used to record metadaa about algorithm execution. An empty 

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

174 **kwds 

175 Keyword arguments forwarded to `BaseMeasurementTask`. 

176 """ 

177 

178 ConfigClass = SingleFrameMeasurementConfig 

179 

180 NOISE_SEED_MULTIPLIER = "NOISE_SEED_MULTIPLIER" 

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

182 """ 

183 

184 NOISE_SOURCE = "NOISE_SOURCE" 

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

186 """ 

187 

188 NOISE_OFFSET = "NOISE_OFFSET" 

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

190 """ 

191 

192 NOISE_EXPOSURE_ID = "NOISE_EXPOSURE_ID" 

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

194 """ 

195 

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

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

198 self.schema = schema 

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

200 self.initializePlugins(schema=self.schema) 

201 

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

203 if 'base_Blendedness' in self.plugins: 

204 self.doBlendedness = True 

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

206 else: 

207 self.doBlendedness = False 

208 

209 @timeMethod 

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

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

212 

213 Parameters 

214 ---------- 

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

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

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

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

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

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

221 Image containing the pixel data to be measured together with 

222 associated PSF, WCS, etc. 

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

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

225 for testing purposes. 

226 exposureId : `int`, optional 

227 Unique exposure identifier used to calculate the random number 

228 generator seed during noise replacement. 

229 beginOrder : `float`, optional 

230 Start execution order (inclusive): measurements with 

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

232 limit. 

233 endOrder : `float`, optional 

234 Final execution order (exclusive): measurements with 

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

236 limit. 

237 """ 

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

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

240 for measRecord in measCat} 

241 

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

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

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

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

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

247 

248 if self.config.doReplaceWithNoise: 

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

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

251 algMetadata = measCat.getMetadata() 

252 if algMetadata is not None: 

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

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

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

256 if exposureId is not None: 

257 algMetadata.addLong(self.NOISE_EXPOSURE_ID, exposureId) 

258 else: 

259 noiseReplacer = DummyNoiseReplacer() 

260 

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

262 

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

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

265 

266 Parameters 

267 ---------- 

268 noiseReplacer : `NoiseReplacer` 

269 Used to fill sources not being measured with noise. 

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

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

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

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

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

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

276 Image containing the pixel data to be measured together with 

277 associated PSF, WCS, etc. 

278 beginOrder : `float`, optional 

279 Start execution order (inclusive): measurements with 

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

281 limit. 

282 endOrder : `float`, optional 

283 Final execution order (exclusive): measurements with 

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

285 limit. 

286 """ 

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

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

289 measParentCat = measCat.getChildren(0) 

290 

291 nMeasCat = len(measCat) 

292 nMeasParentCat = len(measParentCat) 

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

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

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

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

297 

298 # Wrap the task logger into a period logger 

299 periodicLog = PeriodicLogger(self.log) 

300 

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

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

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

304 # turn, and measure 

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

306 # single-object mode 

307 for measChildRecord in measChildCat: 

308 noiseReplacer.insertSource(measChildRecord.getId()) 

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

310 

311 if self.doBlendedness: 

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

313 

314 noiseReplacer.removeSource(measChildRecord.getId()) 

315 

316 # Then insert the parent footprint, and measure that 

317 noiseReplacer.insertSource(measParentRecord.getId()) 

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

319 

320 if self.doBlendedness: 

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

322 

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

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

325 beginOrder=beginOrder, endOrder=endOrder) 

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

327 noiseReplacer.removeSource(measParentRecord.getId()) 

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

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

330 parentIdx + 1, nMeasParentCat) 

331 

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

333 noiseReplacer.end() 

334 

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

336 if endOrder is None: 

337 for sourceIndex, source in enumerate(measCat): 

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

339 self.doMeasurement(plugin, source, exposure) 

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

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

342 sourceIndex + 1, nMeasCat) 

343 

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

345 # blendedness metrics 

346 if self.doBlendedness: 

347 for source in measCat: 

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

349 

350 def measure(self, measCat, exposure): 

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

352 """ 

353 self.run(measCat, exposure)