Coverage for python/lsst/pipe/tasks/transformMeasurement.py : 52%

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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
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
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 )
46## \addtogroup LSST_task_documentation
47## \{
48## \page TransformTask
49## \ref TransformTask_ "TransformTask"
50## \copybrief TransformTask
51## \}
54class TransformTask(pipeBase.Task):
55 r"""!
56 \anchor TransformTask_
58 \brief Transform a SourceCatalog containing raw measurements to calibrated form.
60 \section pipe_tasks_transform_Contents Contents
62 - \ref pipe_tasks_transform_purpose
63 - \ref pipe_tasks_transform_initialize
64 - \ref pipe_tasks_transform_invoke
66 \section pipe_tasks_transform_purpose Description
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.
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.
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.
86 \section pipe_tasks_transform_initialize Task initialization
88 \copydoc \_\_init\_\_
90 \section pipe_tasks_transform_invoke Task invocation
92 \copydoc run
93 """
94 ConfigClass = TransformConfig
95 _DefaultName = "transform"
97 def __init__(self, measConfig, inputSchema, outputDataset, *args, **kwargs):
98 """!Initialize TransformTask.
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)
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
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)
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))
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}
131 @pipeBase.timeMethod
132 def run(self, inputCat, wcs, photoCalib):
133 """!Transform raw source measurements to calibrated quantities.
135 @param[in] inputCat SourceCatalog of sources to transform.
136 @param[in] wcs The world coordinate system under which transformations will take place.
137 @param[in] photoCalib The calibration under which transformations will take place.
139 @return A BaseCatalog containing the transformed measurements.
140 """
141 outputCat = afwTable.BaseCatalog(self.mapper.getOutputSchema())
142 outputCat.extend(inputCat, mapper=self.mapper)
144 # Transforms may use a ColumnView on the input and output catalogs,
145 # which requires that the data be contiguous in memory.
146 inputCat = makeContiguous(inputCat)
147 outputCat = makeContiguous(outputCat)
149 for transform in self.transforms:
150 transform(inputCat, outputCat, wcs, photoCalib)
151 return outputCat
154class RunTransformConfig(pexConfig.Config):
155 """!Configuration for RunTransformTaskBase derivatives."""
156 transform = pexConfig.ConfigurableField(
157 doc="Subtask which performs transformations",
158 target=TransformTask
159 )
160 inputConfigType = pexConfig.Field(
161 dtype=str,
162 doc="Dataset type of measurement operation configuration",
163 )
166class RunTransformTaskBase(pipeBase.CmdLineTask):
167 r"""!
168 \anchor RunTransformTaskBase_
170 \brief Command line interface for TransformTask.
172 \section pipe_tasks_transform_Contents Contents
174 - \ref pipe_tasks_runtransform_purpose
175 - \ref pipe_tasks_runtransform_invoke
177 \section pipe_tasks_runtransform_purpose Description
179 Provides a command-line task which can be used to run TransformTask.
181 - Loads a plugin registry based on configuration;
182 - Loads configuration for the measurement task which was applied from a repository;
183 - Loads the SourceCatalog input schema from a repository;
184 - For each input dataRef, reads the SourceCatalog, WCS and calibration from the
185 repository and executes TransformTask.
187 This is not a fully-fledged command line task: it requires specialization to a particular
188 source type by defining the variables indicated below.
190 \section pipe_tasks_runtransform_invoke Task invocation
192 \copydoc run
193 """
194 RunnerClass = pipeBase.ButlerInitializedTaskRunner
195 ConfigClass = RunTransformConfig
197 # Subclasses should provide definitions for the attributes named below.
198 # Properties can be used if appropriate.
199 #
200 # Standard CmdLineTask attributes:
201 _DefaultName = None
203 # Butler dataset type of the source type to be transformed ("src", "forced_src", etc):
204 sourceType = None
206 # Butler dataset type of the calibration exposure to use when transforming ("calexp", etc):
207 calexpType = None
209 @property
210 def inputSchemaType(self):
211 """!
212 The Butler dataset type for the schema of the input source catalog.
214 By default, we append `_schema` to the input source type. Subclasses may customize
215 if required.
216 """
217 return self.sourceType + "_schema"
219 @property
220 def outputDataset(self):
221 """!
222 The Butler dataset type for the schema of the output catalog.
224 By default, we prepend `transformed_` to the input source type. Subclasses may
225 customize if required.
226 """
227 return 'transformed_' + self.sourceType
229 @property
230 def measurementConfig(self):
231 """!
232 The configuration of the measurement operation used to generate the input catalog.
234 By default we look for `measurement` under the root configuration of the
235 generating task. Subclasses may customize this (e.g. to `calibrate.measurement`)
236 if required.
237 """
238 return self.butler.get(self.config.inputConfigType).measurement.value
240 def __init__(self, *args, **kwargs):
241 pipeBase.CmdLineTask.__init__(self, *args, config=kwargs['config'], log=kwargs['log'])
242 self.butler = kwargs['butler']
243 self.makeSubtask('transform', measConfig=self.measurementConfig,
244 inputSchema=self.butler.get(self.inputSchemaType).schema,
245 outputDataset=self.outputDataset)
247 @pipeBase.timeMethod
248 def runDataRef(self, dataRef):
249 """!Transform the source catalog referred to by dataRef.
251 The result is both returned and written as dataset type "transformed_" + the input
252 source dataset type to the provided dataRef.
254 @param[in] dataRef Data reference for source catalog & calibrated exposure.
256 @returns A BaseCatalog containing the transformed measurements.
257 """
258 inputCat = dataRef.get(self.sourceType)
259 wcs = dataRef.get(self.calexpType).getWcs()
260 photoCalib = dataRef.get(self.calexpType).getPhotoCalib()
261 outputCat = self.transform.run(inputCat, wcs, photoCalib)
262 dataRef.put(outputCat, self.outputDataset)
263 return outputCat
266## \addtogroup LSST_task_documentation
267## \{
268## \page SrcTransformTask
269## \ref SrcTransformTask_ "SrcTransformTask"
270## \copybrief SrcTransformTask
271## \}
273class SrcTransformTask(RunTransformTaskBase):
274 """!
275 \anchor SrcTransformTask_
277 \brief Transform ``src`` measuremenents to calibrated form.
279 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which
280 operates on ``src`` measurements. Refer to the parent documentation for details.
281 """
282 _DefaultName = "transformSrcMeasurement"
283 sourceType = 'src'
284 calexpType = 'calexp'
286 @property
287 def measurementConfig(self):
288 return self.butler.get(self.config.inputConfigType).calibrate.measurement.value
291## \addtogroup LSST_task_documentation
292## \{
293## \page ForcedSrcTransformTask
294## \ref ForcedSrcTransformTask_ "ForcedSrcTransformTask"
295## \copybrief ForcedSrcTransformTask
296## \}
298class ForcedSrcTransformTask(RunTransformTaskBase):
299 """!
300 \anchor ForcedSrcTransformTask_
302 \brief Transform ``forced_src`` measuremenents to calibrated form.
304 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which
305 operates on ``forced_src`` measurements. Refer to the parent documentation for details.
306 """
307 _DefaultName = "transformForcedSrcMeasurement"
308 sourceType = 'forced_src'
309 calexpType = 'calexp'
312## \addtogroup LSST_task_documentation
313## \{
314## \page CoaddSrcTransformTask
315## \ref CoaddSrcTransformTask_ "CoaddSrcTransformTask"
316## \copybrief CoaddSrcTransformTask
317## \}
319class CoaddSrcTransformTask(RunTransformTaskBase):
320 """!
321 \anchor CoaddSrcTransformTask_
323 \brief Transform measuremenents made on coadds to calibrated form.
325 This is a specialization of \ref RunTransformTaskBase_ "RunTransformTaskBase" which
326 operates on measurements made on coadds. Refer to the parent documentation for details.
327 """
328 _DefaultName = "transformCoaddSrcMeasurement"
330 @property
331 def coaddName(self):
332 return self.butler.get(self.config.inputConfigType).coaddName
334 @property
335 def sourceType(self):
336 return self.coaddName + "Coadd_meas"
338 @property
339 def calexpType(self):
340 return self.coaddName + "Coadd_calexp"
342 def _getConfigName(self):
343 return "%s_transformCoaddSrcMeasurement_config" % (self.coaddName,)
345 def _getMetaDataName(self):
346 return "%s_transformCoaddSrcMeasurement_metadata" % (self.coaddName,)