Coverage for python/lsst/pipe/tasks/mergeMeasurements.py : 18%

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1#!/usr/bin/env python
2#
3# LSST Data Management System
4# Copyright 2008-2015 AURA/LSST.
5#
6# This product includes software developed by the
7# LSST Project (http://www.lsst.org/).
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 LSST License Statement and
20# the GNU General Public License along with this program. If not,
21# see <https://www.lsstcorp.org/LegalNotices/>.
22#
23import numpy
25from .multiBandUtils import (MergeSourcesRunner, _makeGetSchemaCatalogs, makeMergeArgumentParser,
26 getInputSchema, getShortFilterName, readCatalog)
29import lsst.afw.table as afwTable
30import lsst.pex.config as pexConfig
31import lsst.pipe.base as pipeBase
33from lsst.pipe.base import PipelineTaskConnections, PipelineTaskConfig
34import lsst.pipe.base.connectionTypes as cT
37class MergeMeasurementsConnections(PipelineTaskConnections,
38 dimensions=("skymap", "tract", "patch"),
39 defaultTemplates={"inputCoaddName": "deep",
40 "outputCoaddName": "deep"}):
41 inputSchema = cT.InitInput(
42 doc="Schema for the output merged measurement catalog.",
43 name="{inputCoaddName}Coadd_meas_schema",
44 storageClass="SourceCatalog",
45 )
46 outputSchema = cT.InitOutput(
47 doc="Schema for the output merged measurement catalog.",
48 name="{outputCoaddName}Coadd_ref_schema",
49 storageClass="SourceCatalog",
50 )
51 catalogs = cT.Input(
52 doc="Input catalogs to merge.",
53 name="{inputCoaddName}Coadd_meas",
54 multiple=True,
55 storageClass="SourceCatalog",
56 dimensions=["abstract_filter", "skymap", "tract", "patch"],
57 )
58 mergedCatalog = cT.Output(
59 doc="Output merged catalog.",
60 name="{outputCoaddName}Coadd_ref",
61 storageClass="SourceCatalog",
62 dimensions=["skymap", "tract", "patch"],
63 )
66class MergeMeasurementsConfig(PipelineTaskConfig, pipelineConnections=MergeMeasurementsConnections):
67 """!
68 @anchor MergeMeasurementsConfig_
70 @brief Configuration parameters for the MergeMeasurementsTask
71 """
72 pseudoFilterList = pexConfig.ListField(
73 dtype=str,
74 default=["sky"],
75 doc="Names of filters which may have no associated detection\n"
76 "(N.b. should include MergeDetectionsConfig.skyFilterName)"
77 )
78 snName = pexConfig.Field(
79 dtype=str,
80 default="base_PsfFlux",
81 doc="Name of flux measurement for calculating the S/N when choosing the reference band."
82 )
83 minSN = pexConfig.Field(
84 dtype=float,
85 default=10.,
86 doc="If the S/N from the priority band is below this value (and the S/N "
87 "is larger than minSNDiff compared to the priority band), use the band with "
88 "the largest S/N as the reference band."
89 )
90 minSNDiff = pexConfig.Field(
91 dtype=float,
92 default=3.,
93 doc="If the difference in S/N between another band and the priority band is larger "
94 "than this value (and the S/N in the priority band is less than minSN) "
95 "use the band with the largest S/N as the reference band"
96 )
97 flags = pexConfig.ListField(
98 dtype=str,
99 doc="Require that these flags, if available, are not set",
100 default=["base_PixelFlags_flag_interpolatedCenter", "base_PsfFlux_flag",
101 "ext_photometryKron_KronFlux_flag", "modelfit_CModel_flag", ]
102 )
103 priorityList = pexConfig.ListField(
104 dtype=str,
105 default=[],
106 doc="Priority-ordered list of bands for the merge."
107 )
108 coaddName = pexConfig.Field(
109 dtype=str,
110 default="deep",
111 doc="Name of coadd"
112 )
114 def validate(self):
115 super().validate()
116 if len(self.priorityList) == 0:
117 raise RuntimeError("No priority list provided")
120## @addtogroup LSST_task_documentation
121## @{
122## @page MergeMeasurementsTask
123## @ref MergeMeasurementsTask_ "MergeMeasurementsTask"
124## @copybrief MergeMeasurementsTask
125## @}
128class MergeMeasurementsTask(pipeBase.PipelineTask, pipeBase.CmdLineTask):
129 r"""!
130 @anchor MergeMeasurementsTask_
132 @brief Merge measurements from multiple bands
134 @section pipe_tasks_multiBand_Contents Contents
136 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Purpose
137 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Initialize
138 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Run
139 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Config
140 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Debug
141 - @ref pipe_tasks_multiband_MergeMeasurementsTask_Example
143 @section pipe_tasks_multiBand_MergeMeasurementsTask_Purpose Description
145 Command-line task that merges measurements from multiple bands.
147 Combines consistent (i.e. with the same peaks and footprints) catalogs of sources from multiple filter
148 bands to construct a unified catalog that is suitable for driving forced photometry. Every source is
149 required to have centroid, shape and flux measurements in each band.
151 @par Inputs:
152 deepCoadd_meas{tract,patch,filter}: SourceCatalog
153 @par Outputs:
154 deepCoadd_ref{tract,patch}: SourceCatalog
155 @par Data Unit:
156 tract, patch
158 MergeMeasurementsTask subclasses @ref CmdLineTask_ "CmdLineTask".
160 @section pipe_tasks_multiBand_MergeMeasurementsTask_Initialize Task initialization
162 @copydoc \_\_init\_\_
164 @section pipe_tasks_multiBand_MergeMeasurementsTask_Run Invoking the Task
166 @copydoc run
168 @section pipe_tasks_multiBand_MergeMeasurementsTask_Config Configuration parameters
170 See @ref MergeMeasurementsConfig_
172 @section pipe_tasks_multiBand_MergeMeasurementsTask_Debug Debug variables
174 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
175 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
176 files.
178 MergeMeasurementsTask has no debug variables.
180 @section pipe_tasks_multiband_MergeMeasurementsTask_Example A complete example
181 of using MergeMeasurementsTask
183 MergeMeasurementsTask is meant to be run after deblending & measuring sources in every band.
184 The purpose of the task is to generate a catalog of sources suitable for driving forced photometry in
185 coadds and individual exposures.
186 Command-line usage of MergeMeasurementsTask expects a data reference to the coadds to be processed. A list
187 of the available optional arguments can be obtained by calling mergeCoaddMeasurements.py with the `--help`
188 command line argument:
189 @code
190 mergeCoaddMeasurements.py --help
191 @endcode
193 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
194 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
195 step 7 at @ref pipeTasks_multiBand, one may merge the catalogs generated after deblending and measuring
196 as follows:
197 @code
198 mergeCoaddMeasurements.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R
199 @endcode
200 This will merge the HSC-I & HSC-R band catalogs. The results are written in
201 `$CI_HSC_DIR/DATA/deepCoadd-results/`.
202 """
203 _DefaultName = "mergeCoaddMeasurements"
204 ConfigClass = MergeMeasurementsConfig
205 RunnerClass = MergeSourcesRunner
206 inputDataset = "meas"
207 outputDataset = "ref"
208 getSchemaCatalogs = _makeGetSchemaCatalogs("ref")
210 @classmethod
211 def _makeArgumentParser(cls):
212 return makeMergeArgumentParser(cls._DefaultName, cls.inputDataset)
214 def getInputSchema(self, butler=None, schema=None):
215 return getInputSchema(self, butler, schema)
217 def runQuantum(self, butlerQC, inputRefs, outputRefs):
218 inputs = butlerQC.get(inputRefs)
219 dataIds = (ref.dataId for ref in inputRefs.catalogs)
220 catalogDict = {dataId['abstract_filter']: cat for dataId, cat in zip(dataIds,
221 inputs['catalogs'])}
222 inputs['catalogs'] = catalogDict
223 outputs = self.run(**inputs)
224 butlerQC.put(outputs, outputRefs)
226 def __init__(self, butler=None, schema=None, initInputs=None, **kwargs):
227 """!
228 Initialize the task.
230 @param[in] schema: the schema of the detection catalogs used as input to this one
231 @param[in] butler: a butler used to read the input schema from disk, if schema is None
233 The task will set its own self.schema attribute to the schema of the output merged catalog.
234 """
235 super().__init__(**kwargs)
237 if initInputs is not None:
238 inputSchema = initInputs['inputSchema'].schema
239 else:
240 inputSchema = self.getInputSchema(butler=butler, schema=schema)
241 self.schemaMapper = afwTable.SchemaMapper(inputSchema, True)
242 self.schemaMapper.addMinimalSchema(inputSchema, True)
243 self.instFluxKey = inputSchema.find(self.config.snName + "_instFlux").getKey()
244 self.instFluxErrKey = inputSchema.find(self.config.snName + "_instFluxErr").getKey()
245 self.fluxFlagKey = inputSchema.find(self.config.snName + "_flag").getKey()
247 self.flagKeys = {}
248 for band in self.config.priorityList:
249 short = getShortFilterName(band)
250 outputKey = self.schemaMapper.editOutputSchema().addField(
251 "merge_measurement_%s" % short,
252 type="Flag",
253 doc="Flag field set if the measurements here are from the %s filter" % band
254 )
255 peakKey = inputSchema.find("merge_peak_%s" % short).key
256 footprintKey = inputSchema.find("merge_footprint_%s" % short).key
257 self.flagKeys[band] = pipeBase.Struct(peak=peakKey, footprint=footprintKey, output=outputKey)
258 self.schema = self.schemaMapper.getOutputSchema()
260 self.pseudoFilterKeys = []
261 for filt in self.config.pseudoFilterList:
262 try:
263 self.pseudoFilterKeys.append(self.schema.find("merge_peak_%s" % filt).getKey())
264 except Exception as e:
265 self.log.warn("merge_peak is not set for pseudo-filter %s: %s" % (filt, e))
267 self.badFlags = {}
268 for flag in self.config.flags:
269 try:
270 self.badFlags[flag] = self.schema.find(flag).getKey()
271 except KeyError as exc:
272 self.log.warn("Can't find flag %s in schema: %s" % (flag, exc,))
273 self.outputSchema = afwTable.SourceCatalog(self.schema)
275 def runDataRef(self, patchRefList):
276 """!
277 @brief Merge coadd sources from multiple bands. Calls @ref `run`.
278 @param[in] patchRefList list of data references for each filter
279 """
280 catalogs = dict(readCatalog(self, patchRef) for patchRef in patchRefList)
281 mergedCatalog = self.run(catalogs).mergedCatalog
282 self.write(patchRefList[0], mergedCatalog)
284 def run(self, catalogs):
285 """!
286 Merge measurement catalogs to create a single reference catalog for forced photometry
288 @param[in] catalogs: the catalogs to be merged
290 For parent sources, we choose the first band in config.priorityList for which the
291 merge_footprint flag for that band is is True.
293 For child sources, the logic is the same, except that we use the merge_peak flags.
294 """
295 # Put catalogs, filters in priority order
296 orderedCatalogs = [catalogs[band] for band in self.config.priorityList if band in catalogs.keys()]
297 orderedKeys = [self.flagKeys[band] for band in self.config.priorityList if band in catalogs.keys()]
299 mergedCatalog = afwTable.SourceCatalog(self.schema)
300 mergedCatalog.reserve(len(orderedCatalogs[0]))
302 idKey = orderedCatalogs[0].table.getIdKey()
303 for catalog in orderedCatalogs[1:]:
304 if numpy.any(orderedCatalogs[0].get(idKey) != catalog.get(idKey)):
305 raise ValueError("Error in inputs to MergeCoaddMeasurements: source IDs do not match")
307 # This first zip iterates over all the catalogs simultaneously, yielding a sequence of one
308 # record for each band, in priority order.
309 for orderedRecords in zip(*orderedCatalogs):
311 maxSNRecord = None
312 maxSNFlagKeys = None
313 maxSN = 0.
314 priorityRecord = None
315 priorityFlagKeys = None
316 prioritySN = 0.
317 hasPseudoFilter = False
319 # Now we iterate over those record-band pairs, keeping track of the priority and the
320 # largest S/N band.
321 for inputRecord, flagKeys in zip(orderedRecords, orderedKeys):
322 parent = (inputRecord.getParent() == 0 and inputRecord.get(flagKeys.footprint))
323 child = (inputRecord.getParent() != 0 and inputRecord.get(flagKeys.peak))
325 if not (parent or child):
326 for pseudoFilterKey in self.pseudoFilterKeys:
327 if inputRecord.get(pseudoFilterKey):
328 hasPseudoFilter = True
329 priorityRecord = inputRecord
330 priorityFlagKeys = flagKeys
331 break
332 if hasPseudoFilter:
333 break
335 isBad = any(inputRecord.get(flag) for flag in self.badFlags)
336 if isBad or inputRecord.get(self.fluxFlagKey) or inputRecord.get(self.instFluxErrKey) == 0:
337 sn = 0.
338 else:
339 sn = inputRecord.get(self.instFluxKey)/inputRecord.get(self.instFluxErrKey)
340 if numpy.isnan(sn) or sn < 0.:
341 sn = 0.
342 if (parent or child) and priorityRecord is None:
343 priorityRecord = inputRecord
344 priorityFlagKeys = flagKeys
345 prioritySN = sn
346 if sn > maxSN:
347 maxSNRecord = inputRecord
348 maxSNFlagKeys = flagKeys
349 maxSN = sn
351 # If the priority band has a low S/N we would like to choose the band with the highest S/N as
352 # the reference band instead. However, we only want to choose the highest S/N band if it is
353 # significantly better than the priority band. Therefore, to choose a band other than the
354 # priority, we require that the priority S/N is below the minimum threshold and that the
355 # difference between the priority and highest S/N is larger than the difference threshold.
356 #
357 # For pseudo code objects we always choose the first band in the priority list.
358 bestRecord = None
359 bestFlagKeys = None
360 if hasPseudoFilter:
361 bestRecord = priorityRecord
362 bestFlagKeys = priorityFlagKeys
363 elif (prioritySN < self.config.minSN and (maxSN - prioritySN) > self.config.minSNDiff
364 and maxSNRecord is not None):
365 bestRecord = maxSNRecord
366 bestFlagKeys = maxSNFlagKeys
367 elif priorityRecord is not None:
368 bestRecord = priorityRecord
369 bestFlagKeys = priorityFlagKeys
371 if bestRecord is not None and bestFlagKeys is not None:
372 outputRecord = mergedCatalog.addNew()
373 outputRecord.assign(bestRecord, self.schemaMapper)
374 outputRecord.set(bestFlagKeys.output, True)
375 else: # if we didn't find any records
376 raise ValueError("Error in inputs to MergeCoaddMeasurements: no valid reference for %s" %
377 inputRecord.getId())
379 # more checking for sane inputs, since zip silently iterates over the smallest sequence
380 for inputCatalog in orderedCatalogs:
381 if len(mergedCatalog) != len(inputCatalog):
382 raise ValueError("Mismatch between catalog sizes: %s != %s" %
383 (len(mergedCatalog), len(orderedCatalogs)))
385 return pipeBase.Struct(
386 mergedCatalog=mergedCatalog
387 )
389 def write(self, patchRef, catalog):
390 """!
391 @brief Write the output.
393 @param[in] patchRef data reference for patch
394 @param[in] catalog catalog
396 We write as the dataset provided by the 'outputDataset'
397 class variable.
398 """
399 patchRef.put(catalog, self.config.coaddName + "Coadd_" + self.outputDataset)
400 # since the filter isn't actually part of the data ID for the dataset we're saving,
401 # it's confusing to see it in the log message, even if the butler simply ignores it.
402 mergeDataId = patchRef.dataId.copy()
403 del mergeDataId["filter"]
404 self.log.info("Wrote merged catalog: %s" % (mergeDataId,))
406 def writeMetadata(self, dataRefList):
407 """!
408 @brief No metadata to write, and not sure how to write it for a list of dataRefs.
409 """
410 pass