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1# 

2# LSST Data Management System 

3# Copyright 2008-2015 AURA/LSST. 

4# 

5# This product includes software developed by the 

6# LSST Project (http://www.lsst.org/). 

7# 

8# This program is free software: you can redistribute it and/or modify 

9# it under the terms of the GNU General Public License as published by 

10# the Free Software Foundation, either version 3 of the License, or 

11# (at your option) any later version. 

12# 

13# This program is distributed in the hope that it will be useful, 

14# but WITHOUT ANY WARRANTY; without even the implied warranty of 

15# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

16# GNU General Public License for more details. 

17# 

18# You should have received a copy of the LSST License Statement and 

19# the GNU General Public License along with this program. If not, 

20# see <http://www.lsstcorp.org/LegalNotices/>. 

21# 

22""" 

23Tasks for transforming raw measurement outputs to calibrated quantities. 

24""" 

25import lsst.afw.table as afwTable 

26import lsst.pex.config as pexConfig 

27import lsst.pipe.base as pipeBase 

28 

29 

30def makeContiguous(catalog): 

31 """!Return a version of the input catalog which is contiguous in memory.""" 

32 if not catalog.isContiguous(): 

33 return catalog.copy(deep=True) 

34 else: 

35 return catalog 

36 

37 

38class TransformConfig(pexConfig.Config): 

39 """!Configuration for TransformTask.""" 

40 copyFields = pexConfig.ListField( 

41 dtype=str, 

42 doc="Fields to copy from input to output catalog without transformation", 

43 default=('id', 'coord_ra', 'coord_dec') 

44 ) 

45 

46## \addtogroup LSST_task_documentation 

47## \{ 

48## \page TransformTask 

49## \ref TransformTask_ "TransformTask" 

50## \copybrief TransformTask 

51## \} 

52 

53 

54class TransformTask(pipeBase.Task): 

55 r"""! 

56 \anchor TransformTask_ 

57 

58 \brief Transform a SourceCatalog containing raw measurements to calibrated form. 

59 

60 \section pipe_tasks_transform_Contents Contents 

61 

62 - \ref pipe_tasks_transform_purpose 

63 - \ref pipe_tasks_transform_initialize 

64 - \ref pipe_tasks_transform_invoke 

65 

66 \section pipe_tasks_transform_purpose Description 

67 

68 Given a set of measurement algorithms with their associated configuration, 

69 the table of source measurements they have produced, and information about 

70 an associated WCS and calibration, transform the raw measurement output to 

71 a calibrated form. 

72 

73 Transformations are defined on a per-measurement-plugin basis. In 

74 addition, a configurable set of fields may be simply copied from the input 

75 to the output catalog. 

76 

77 This task operates on an input SourceCatalog and returns a BaseCatalog 

78 containing the transformed results. It requires that the caller supply 

79 information on the configuration of the measurement task which produced 

80 the input data as well as the world coordinate system and calibration 

81 under which the transformation will take place. It provides no 

82 functionality for reading or writing data from a Butler: rather, 

83 per-dataset-type command line tasks are provided to obtain the appropriate 

84 information from a Butler (or elsewhere) and then delegate to this task. 

85 

86 \section pipe_tasks_transform_initialize Task initialization 

87 

88 \copydoc \_\_init\_\_ 

89 

90 \section pipe_tasks_transform_invoke Task invocation 

91 

92 \copydoc run 

93 """ 

94 ConfigClass = TransformConfig 

95 _DefaultName = "transform" 

96 

97 def __init__(self, measConfig, inputSchema, outputDataset, *args, **kwargs): 

98 """!Initialize TransformTask. 

99 

100 @param[in] measConfig Configuration for the measurement task which 

101 produced the measurments being transformed. 

102 @param[in] inputSchema The schema of the input catalog. 

103 @param[in] outputDataset The butler dataset type of the output catalog. 

104 @param[in] *args Passed through to pipeBase.Task.__init__() 

105 @param[in] *kwargs Passed through to pipeBase.Task.__init__() 

106 """ 

107 pipeBase.Task.__init__(self, *args, **kwargs) 

108 

109 # This task can be used to generate multiple different output dataset types. We 

110 # need to be able to specify the output type together with its schema. 

111 self.outputDataset = outputDataset 

112 

113 # Define a mapper and add the basic fields to be copied. 

114 self.mapper = afwTable.SchemaMapper(inputSchema) 

115 for field in self.config.copyFields: 

116 self.mapper.addMapping(inputSchema.find(field).key) 

117 

118 # Build a list of all transforms that will be applied to the input. We 

119 # will iterate over this in run(). 

120 self.transforms = [] 

121 for name in measConfig.plugins.names: 

122 config = measConfig.plugins.get(name) 

123 transformClass = measConfig.plugins.registry.get(name).PluginClass.getTransformClass() 

124 self.transforms.append(transformClass(config, name, self.mapper)) 

125 

126 def getSchemaCatalogs(self): 

127 """!Return a dict containing an empty catalog representative of this task's output.""" 

128 transformedSrc = afwTable.BaseCatalog(self.mapper.getOutputSchema()) 

129 return {self.outputDataset: transformedSrc} 

130 

131 def run(self, inputCat, wcs, photoCalib): 

132 """!Transform raw source measurements to calibrated quantities. 

133 

134 @param[in] inputCat SourceCatalog of sources to transform. 

135 @param[in] wcs The world coordinate system under which transformations will take place. 

136 @param[in] photoCalib The calibration under which transformations will take place. 

137 

138 @return A BaseCatalog containing the transformed measurements. 

139 """ 

140 outputCat = afwTable.BaseCatalog(self.mapper.getOutputSchema()) 

141 outputCat.extend(inputCat, mapper=self.mapper) 

142 

143 # Transforms may use a ColumnView on the input and output catalogs, 

144 # which requires that the data be contiguous in memory. 

145 inputCat = makeContiguous(inputCat) 

146 outputCat = makeContiguous(outputCat) 

147 

148 for transform in self.transforms: 

149 transform(inputCat, outputCat, wcs, photoCalib) 

150 return outputCat 

151 

152 

153class RunTransformConfig(pexConfig.Config): 

154 """!Configuration for RunTransformTaskBase derivatives.""" 

155 transform = pexConfig.ConfigurableField( 

156 doc="Subtask which performs transformations", 

157 target=TransformTask 

158 ) 

159 inputConfigType = pexConfig.Field( 

160 dtype=str, 

161 doc="Dataset type of measurement operation configuration", 

162 ) 

163 

164 

165class RunTransformTaskBase(pipeBase.CmdLineTask): 

166 r"""! 

167 \anchor RunTransformTaskBase_ 

168 

169 \brief Command line interface for TransformTask. 

170 

171 \section pipe_tasks_transform_Contents Contents 

172 

173 - \ref pipe_tasks_runtransform_purpose 

174 - \ref pipe_tasks_runtransform_invoke 

175 

176 \section pipe_tasks_runtransform_purpose Description 

177 

178 Provides a command-line task which can be used to run TransformTask. 

179 

180 - Loads a plugin registry based on configuration; 

181 - Loads configuration for the measurement task which was applied from a repository; 

182 - Loads the SourceCatalog input schema from a repository; 

183 - For each input dataRef, reads the SourceCatalog, WCS and calibration from the 

184 repository and executes TransformTask. 

185 

186 This is not a fully-fledged command line task: it requires specialization to a particular 

187 source type by defining the variables indicated below. 

188 

189 \section pipe_tasks_runtransform_invoke Task invocation 

190 

191 \copydoc run 

192 """ 

193 RunnerClass = pipeBase.ButlerInitializedTaskRunner 

194 ConfigClass = RunTransformConfig 

195 

196 # Subclasses should provide definitions for the attributes named below. 

197 # Properties can be used if appropriate. 

198 # 

199 # Standard CmdLineTask attributes: 

200 _DefaultName = None 

201 

202 # Butler dataset type of the source type to be transformed ("src", "forced_src", etc): 

203 sourceType = None 

204 

205 # Butler dataset type of the calibration exposure to use when transforming ("calexp", etc): 

206 calexpType = None 

207 

208 @property 

209 def inputSchemaType(self): 

210 """! 

211 The Butler dataset type for the schema of the input source catalog. 

212 

213 By default, we append `_schema` to the input source type. Subclasses may customize 

214 if required. 

215 """ 

216 return self.sourceType + "_schema" 

217 

218 @property 

219 def outputDataset(self): 

220 """! 

221 The Butler dataset type for the schema of the output catalog. 

222 

223 By default, we prepend `transformed_` to the input source type. Subclasses may 

224 customize if required. 

225 """ 

226 return 'transformed_' + self.sourceType 

227 

228 @property 

229 def measurementConfig(self): 

230 """! 

231 The configuration of the measurement operation used to generate the input catalog. 

232 

233 By default we look for `measurement` under the root configuration of the 

234 generating task. Subclasses may customize this (e.g. to `calibrate.measurement`) 

235 if required. 

236 """ 

237 return self.butler.get(self.config.inputConfigType).measurement.value 

238 

239 def __init__(self, *args, **kwargs): 

240 pipeBase.CmdLineTask.__init__(self, *args, config=kwargs['config'], log=kwargs['log']) 

241 self.butler = kwargs['butler'] 

242 self.makeSubtask('transform', measConfig=self.measurementConfig, 

243 inputSchema=self.butler.get(self.inputSchemaType).schema, 

244 outputDataset=self.outputDataset) 

245 

246 @pipeBase.timeMethod 

247 def runDataRef(self, dataRef): 

248 """!Transform the source catalog referred to by dataRef. 

249 

250 The result is both returned and written as dataset type "transformed_" + the input 

251 source dataset type to the provided dataRef. 

252 

253 @param[in] dataRef Data reference for source catalog & calibrated exposure. 

254 

255 @returns A BaseCatalog containing the transformed measurements. 

256 """ 

257 inputCat = dataRef.get(self.sourceType) 

258 wcs = dataRef.get(self.calexpType).getWcs() 

259 photoCalib = dataRef.get(self.calexpType).getPhotoCalib() 

260 outputCat = self.transform.run(inputCat, wcs, photoCalib) 

261 dataRef.put(outputCat, self.outputDataset) 

262 return outputCat 

263 

264 

265## \addtogroup LSST_task_documentation 

266## \{ 

267## \page SrcTransformTask 

268## \ref SrcTransformTask_ "SrcTransformTask" 

269## \copybrief SrcTransformTask 

270## \} 

271 

272class SrcTransformTask(RunTransformTaskBase): 

273 """! 

274 \anchor SrcTransformTask_ 

275 

276 \brief Transform ``src`` measuremenents to calibrated form. 

277 

278 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which 

279 operates on ``src`` measurements. Refer to the parent documentation for details. 

280 """ 

281 _DefaultName = "transformSrcMeasurement" 

282 sourceType = 'src' 

283 calexpType = 'calexp' 

284 

285 @property 

286 def measurementConfig(self): 

287 return self.butler.get(self.config.inputConfigType).calibrate.measurement.value 

288 

289 

290## \addtogroup LSST_task_documentation 

291## \{ 

292## \page ForcedSrcTransformTask 

293## \ref ForcedSrcTransformTask_ "ForcedSrcTransformTask" 

294## \copybrief ForcedSrcTransformTask 

295## \} 

296 

297class ForcedSrcTransformTask(RunTransformTaskBase): 

298 """! 

299 \anchor ForcedSrcTransformTask_ 

300 

301 \brief Transform ``forced_src`` measuremenents to calibrated form. 

302 

303 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which 

304 operates on ``forced_src`` measurements. Refer to the parent documentation for details. 

305 """ 

306 _DefaultName = "transformForcedSrcMeasurement" 

307 sourceType = 'forced_src' 

308 calexpType = 'calexp' 

309 

310 

311## \addtogroup LSST_task_documentation 

312## \{ 

313## \page CoaddSrcTransformTask 

314## \ref CoaddSrcTransformTask_ "CoaddSrcTransformTask" 

315## \copybrief CoaddSrcTransformTask 

316## \} 

317 

318class CoaddSrcTransformTask(RunTransformTaskBase): 

319 """! 

320 \anchor CoaddSrcTransformTask_ 

321 

322 \brief Transform measuremenents made on coadds to calibrated form. 

323 

324 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which 

325 operates on measurements made on coadds. Refer to the parent documentation for details. 

326 """ 

327 _DefaultName = "transformCoaddSrcMeasurement" 

328 

329 @property 

330 def coaddName(self): 

331 return self.butler.get(self.config.inputConfigType).coaddName 

332 

333 @property 

334 def sourceType(self): 

335 return self.coaddName + "Coadd_meas" 

336 

337 @property 

338 def calexpType(self): 

339 return self.coaddName + "Coadd_calexp" 

340 

341 def _getConfigName(self): 

342 return "%s_transformCoaddSrcMeasurement_config" % (self.coaddName,) 

343 

344 def _getMetaDataName(self): 

345 return "%s_transformCoaddSrcMeasurement_metadata" % (self.coaddName,)