lsst.pipe.tasks  15.0-7-g6bb3a066+2
transformMeasurement.py
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22 """
23 Tasks for transforming raw measurement outputs to calibrated quantities.
24 """
25 import lsst.afw.table as afwTable
26 import lsst.pex.config as pexConfig
27 import lsst.pipe.base as pipeBase
28 
29 
30 def 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 
38 class 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 
52 
53 
54 class TransformTask(pipeBase.Task):
55  """!
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, calib):
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] calib 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, calib)
150  return outputCat
151 
152 
153 class 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 
165 class RunTransformTaskBase(pipeBase.CmdLineTask):
166  """!
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 run(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  # TODO: pybind11 remove `immediate=True` once DM-9112 is resolved
258  inputCat = dataRef.get(self.sourceType, immediate=True)
259  wcs = dataRef.get(self.calexpType).getWcs()
260  calib = dataRef.get(self.calexpType).getCalib()
261  outputCat = self.transform.run(inputCat, wcs, calib)
262  dataRef.put(outputCat, self.outputDataset)
263  return outputCat
264 
265 
266 
272 
274  """!
275  \anchor SrcTransformTask_
276 
277  \brief Transform ``src`` measuremenents to calibrated form.
278 
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'
285 
286  @property
287  def measurementConfig(self):
288  return self.butler.get(self.config.inputConfigType).calibrate.measurement.value
289 
290 
291 
297 
299  """!
300  \anchor ForcedSrcTransformTask_
301 
302  \brief Transform ``forced_src`` measuremenents to calibrated form.
303 
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'
310 
311 
312 
318 
320  """!
321  \anchor CoaddSrcTransformTask_
322 
323  \brief Transform measuremenents made on coadds to calibrated form.
324 
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"
329 
330  @property
331  def coaddName(self):
332  return self.butler.get(self.config.inputConfigType).coaddName
333 
334  @property
335  def sourceType(self):
336  return self.coaddName + "Coadd_meas"
337 
338  @property
339  def calexpType(self):
340  return self.coaddName + "Coadd_calexp"
341 
342  def _getConfigName(self):
343  return "%s_transformCoaddSrcMeasurement_config" % (self.coaddName,)
344 
345  def _getMetaDataName(self):
346  return "%s_transformCoaddSrcMeasurement_metadata" % (self.coaddName,)
Transform a SourceCatalog containing raw measurements to calibrated form.
def getSchemaCatalogs(self)
Return a dict containing an empty catalog representative of this task&#39;s output.
Transform src measuremenents to calibrated form.
def run(self, inputCat, wcs, calib)
Transform raw source measurements to calibrated quantities.
def run(self, dataRef)
Transform the source catalog referred to by dataRef.
def inputSchemaType(self)
The Butler dataset type for the schema of the input source catalog.
def measurementConfig(self)
The configuration of the measurement operation used to generate the input catalog.
def __init__(self, measConfig, inputSchema, outputDataset, args, kwargs)
Initialize TransformTask.
def makeContiguous(catalog)
Return a version of the input catalog which is contiguous in memory.
Transform forced_src measuremenents to calibrated form.
Configuration for RunTransformTaskBase derivatives.
Transform measuremenents made on coadds to calibrated form.
def outputDataset(self)
The Butler dataset type for the schema of the output catalog.