Coverage for python/lsst/pipe/tasks/transformMeasurement.py: 58%
93 statements
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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/).
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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
28from lsst.utils.timer import timeMethod
31def makeContiguous(catalog):
32 """!Return a version of the input catalog which is contiguous in memory."""
33 if not catalog.isContiguous():
34 return catalog.copy(deep=True)
35 else:
36 return catalog
39class TransformConfig(pexConfig.Config):
40 """!Configuration for TransformTask."""
41 copyFields = pexConfig.ListField(
42 dtype=str,
43 doc="Fields to copy from input to output catalog without transformation",
44 default=('id', 'coord_ra', 'coord_dec')
45 )
47## \addtogroup LSST_task_documentation
48## \{
49## \page page_TransformTask TransformTask
50## \ref TransformTask_ "TransformTask"
51## \copybrief TransformTask
52## \}
55class TransformTask(pipeBase.Task):
56 r"""!
57 \anchor TransformTask_
59 \brief Transform a SourceCatalog containing raw measurements to calibrated form.
61 \section pipe_tasks_transform_Contents Contents
63 - \ref pipe_tasks_transform_purpose
64 - \ref pipe_tasks_transform_initialize
65 - \ref pipe_tasks_transform_invoke
67 \section pipe_tasks_transform_purpose Description
69 Given a set of measurement algorithms with their associated configuration,
70 the table of source measurements they have produced, and information about
71 an associated WCS and calibration, transform the raw measurement output to
72 a calibrated form.
74 Transformations are defined on a per-measurement-plugin basis. In
75 addition, a configurable set of fields may be simply copied from the input
76 to the output catalog.
78 This task operates on an input SourceCatalog and returns a BaseCatalog
79 containing the transformed results. It requires that the caller supply
80 information on the configuration of the measurement task which produced
81 the input data as well as the world coordinate system and calibration
82 under which the transformation will take place. It provides no
83 functionality for reading or writing data from a Butler: rather,
84 per-dataset-type command line tasks are provided to obtain the appropriate
85 information from a Butler (or elsewhere) and then delegate to this task.
87 \section pipe_tasks_transform_initialize Task initialization
89 \copydoc \_\_init\_\_
91 \section pipe_tasks_transform_invoke Task invocation
93 \copydoc run
94 """
95 ConfigClass = TransformConfig
96 _DefaultName = "transform"
98 def __init__(self, measConfig, inputSchema, outputDataset, *args, **kwargs):
99 """!Initialize TransformTask.
101 @param[in] measConfig Configuration for the measurement task which
102 produced the measurments being transformed.
103 @param[in] inputSchema The schema of the input catalog.
104 @param[in] outputDataset The butler dataset type of the output catalog.
105 @param[in] *args Passed through to pipeBase.Task.__init__()
106 @param[in] *kwargs Passed through to pipeBase.Task.__init__()
107 """
108 pipeBase.Task.__init__(self, *args, **kwargs)
110 # This task can be used to generate multiple different output dataset types. We
111 # need to be able to specify the output type together with its schema.
112 self.outputDataset = outputDataset
114 # Define a mapper and add the basic fields to be copied.
115 self.mapper = afwTable.SchemaMapper(inputSchema)
116 for field in self.config.copyFields:
117 self.mapper.addMapping(inputSchema.find(field).key)
119 # Build a list of all transforms that will be applied to the input. We
120 # will iterate over this in run().
121 self.transforms = []
122 for name in measConfig.plugins.names:
123 config = measConfig.plugins.get(name)
124 transformClass = measConfig.plugins.registry.get(name).PluginClass.getTransformClass()
125 self.transforms.append(transformClass(config, name, self.mapper))
127 def getSchemaCatalogs(self):
128 """!Return a dict containing an empty catalog representative of this task's output."""
129 transformedSrc = afwTable.BaseCatalog(self.mapper.getOutputSchema())
130 return {self.outputDataset: transformedSrc}
132 @timeMethod
133 def run(self, inputCat, wcs, photoCalib):
134 """!Transform raw source measurements to calibrated quantities.
136 @param[in] inputCat SourceCatalog of sources to transform.
137 @param[in] wcs The world coordinate system under which transformations will take place.
138 @param[in] photoCalib The calibration under which transformations will take place.
140 @return A BaseCatalog containing the transformed measurements.
141 """
142 outputCat = afwTable.BaseCatalog(self.mapper.getOutputSchema())
143 outputCat.extend(inputCat, mapper=self.mapper)
145 # Transforms may use a ColumnView on the input and output catalogs,
146 # which requires that the data be contiguous in memory.
147 inputCat = makeContiguous(inputCat)
148 outputCat = makeContiguous(outputCat)
150 for transform in self.transforms:
151 transform(inputCat, outputCat, wcs, photoCalib)
152 return outputCat
155class RunTransformConfig(pexConfig.Config):
156 """!Configuration for RunTransformTaskBase derivatives."""
157 transform = pexConfig.ConfigurableField(
158 doc="Subtask which performs transformations",
159 target=TransformTask
160 )
161 inputConfigType = pexConfig.Field(
162 dtype=str,
163 doc="Dataset type of measurement operation configuration",
164 )
167class RunTransformTaskBase(pipeBase.CmdLineTask):
168 r"""!
169 \anchor RunTransformTaskBase_
171 \brief Command line interface for TransformTask.
173 \section pipe_tasks_runtransform_Contents Contents
175 - \ref pipe_tasks_runtransform_purpose
176 - \ref pipe_tasks_runtransform_invoke
178 \section pipe_tasks_runtransform_purpose Description
180 Provides a command-line task which can be used to run TransformTask.
182 - Loads a plugin registry based on configuration;
183 - Loads configuration for the measurement task which was applied from a repository;
184 - Loads the SourceCatalog input schema from a repository;
185 - For each input dataRef, reads the SourceCatalog, WCS and calibration from the
186 repository and executes TransformTask.
188 This is not a fully-fledged command line task: it requires specialization to a particular
189 source type by defining the variables indicated below.
191 \section pipe_tasks_runtransform_invoke Task invocation
193 \copydoc run
194 """
195 RunnerClass = pipeBase.ButlerInitializedTaskRunner
196 ConfigClass = RunTransformConfig
198 # Subclasses should provide definitions for the attributes named below.
199 # Properties can be used if appropriate.
200 #
201 # Standard CmdLineTask attributes:
202 _DefaultName = None
204 # Butler dataset type of the source type to be transformed ("src", "forced_src", etc):
205 sourceType = None
207 # Butler dataset type of the calibration exposure to use when transforming ("calexp", etc):
208 calexpType = None
210 @property
211 def inputSchemaType(self):
212 """!
213 The Butler dataset type for the schema of the input source catalog.
215 By default, we append `_schema` to the input source type. Subclasses may customize
216 if required.
217 """
218 return self.sourceType + "_schema"
220 @property
221 def outputDataset(self):
222 """!
223 The Butler dataset type for the schema of the output catalog.
225 By default, we prepend `transformed_` to the input source type. Subclasses may
226 customize if required.
227 """
228 return 'transformed_' + self.sourceType
230 @property
231 def measurementConfig(self):
232 """!
233 The configuration of the measurement operation used to generate the input catalog.
235 By default we look for `measurement` under the root configuration of the
236 generating task. Subclasses may customize this (e.g. to `calibrate.measurement`)
237 if required.
238 """
239 return self.butler.get(self.config.inputConfigType).measurement.value
241 def __init__(self, *args, **kwargs):
242 pipeBase.CmdLineTask.__init__(self, *args, config=kwargs['config'], log=kwargs['log'])
243 self.butler = kwargs['butler']
244 self.makeSubtask('transform', measConfig=self.measurementConfig,
245 inputSchema=self.butler.get(self.inputSchemaType).schema,
246 outputDataset=self.outputDataset)
248 @timeMethod
249 def runDataRef(self, dataRef):
250 """!Transform the source catalog referred to by dataRef.
252 The result is both returned and written as dataset type "transformed_" + the input
253 source dataset type to the provided dataRef.
255 @param[in] dataRef Data reference for source catalog & calibrated exposure.
257 @returns A BaseCatalog containing the transformed measurements.
258 """
259 inputCat = dataRef.get(self.sourceType)
260 wcs = dataRef.get(self.calexpType).getWcs()
261 photoCalib = dataRef.get(self.calexpType).getPhotoCalib()
262 outputCat = self.transform.run(inputCat, wcs, photoCalib)
263 dataRef.put(outputCat, self.outputDataset)
264 return outputCat
267## \addtogroup LSST_task_documentation
268## \{
269## \page page_SrcTransformTask SrcTransformTask
270## \ref SrcTransformTask_ "SrcTransformTask"
271## \copybrief SrcTransformTask
272## \}
274class SrcTransformTask(RunTransformTaskBase):
275 """!
276 \anchor SrcTransformTask_
278 \brief Transform ``src`` measuremenents to calibrated form.
280 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which
281 operates on ``src`` measurements. Refer to the parent documentation for details.
282 """
283 _DefaultName = "transformSrcMeasurement"
284 sourceType = 'src'
285 calexpType = 'calexp'
287 @property
288 def measurementConfig(self):
289 return self.butler.get(self.config.inputConfigType).calibrate.measurement.value
292## \addtogroup LSST_task_documentation
293## \{
294## \page page_ForcedSrcTransformTask ForcedSrcTransformTask
295## \ref ForcedSrcTransformTask_ "ForcedSrcTransformTask"
296## \copybrief ForcedSrcTransformTask
297## \}
299class ForcedSrcTransformTask(RunTransformTaskBase):
300 """!
301 \anchor ForcedSrcTransformTask_
303 \brief Transform ``forced_src`` measuremenents to calibrated form.
305 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which
306 operates on ``forced_src`` measurements. Refer to the parent documentation for details.
307 """
308 _DefaultName = "transformForcedSrcMeasurement"
309 sourceType = 'forced_src'
310 calexpType = 'calexp'
313## \addtogroup LSST_task_documentation
314## \{
315## \page page_CoaddSrcTransformTask CoaddSrcTransformTask
316## \ref CoaddSrcTransformTask_ "CoaddSrcTransformTask"
317## \copybrief CoaddSrcTransformTask
318## \}
320class CoaddSrcTransformTask(RunTransformTaskBase):
321 """!
322 \anchor CoaddSrcTransformTask_
324 \brief Transform measuremenents made on coadds to calibrated form.
326 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which
327 operates on measurements made on coadds. Refer to the parent documentation for details.
328 """
329 _DefaultName = "transformCoaddSrcMeasurement"
331 @property
332 def coaddName(self):
333 return self.butler.get(self.config.inputConfigType).coaddName
335 @property
336 def sourceType(self):
337 return self.coaddName + "Coadd_meas"
339 @property
340 def calexpType(self):
341 return self.coaddName + "Coadd_calexp"
343 def _getConfigName(self):
344 return "%s_transformCoaddSrcMeasurement_config" % (self.coaddName,)
346 def _getMetaDataName(self):
347 return "%s_transformCoaddSrcMeasurement_metadata" % (self.coaddName,)