Coverage for python/lsst/pipe/tasks/mergeDetections.py : 26%

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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#
24from .multiBandUtils import (CullPeaksConfig, MergeSourcesRunner, _makeMakeIdFactory, makeMergeArgumentParser,
25 getInputSchema, readCatalog)
28import lsst.afw.detection as afwDetect
29import lsst.afw.image as afwImage
30import lsst.afw.table as afwTable
32from lsst.meas.algorithms import SkyObjectsTask
33from lsst.skymap import BaseSkyMap
34from lsst.pex.config import Config, Field, ListField, ConfigurableField, ConfigField
35from lsst.pipe.base import (CmdLineTask, PipelineTask, PipelineTaskConfig, Struct,
36 PipelineTaskConnections)
37import lsst.pipe.base.connectionTypes as cT
38from lsst.pipe.tasks.coaddBase import getSkyInfo
41class MergeDetectionsConnections(PipelineTaskConnections,
42 dimensions=("tract", "patch", "skymap"),
43 defaultTemplates={"inputCoaddName": 'deep', "outputCoaddName": "deep"}):
44 schema = cT.InitInput(
45 doc="Schema of the input detection catalog",
46 name="{inputCoaddName}Coadd_det_schema",
47 storageClass="SourceCatalog"
48 )
50 outputSchema = cT.InitOutput(
51 doc="Schema of the merged detection catalog",
52 name="{outputCoaddName}Coadd_mergeDet_schema",
53 storageClass="SourceCatalog"
54 )
56 outputPeakSchema = cT.InitOutput(
57 doc="Output schema of the Footprint peak catalog",
58 name="{outputCoaddName}Coadd_peak_schema",
59 storageClass="PeakCatalog"
60 )
62 catalogs = cT.Input(
63 doc="Detection Catalogs to be merged",
64 name="{inputCoaddName}Coadd_det",
65 storageClass="SourceCatalog",
66 dimensions=("tract", "patch", "skymap", "band"),
67 multiple=True
68 )
70 skyMap = cT.Input(
71 doc="SkyMap to be used in merging",
72 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
73 storageClass="SkyMap",
74 dimensions=("skymap",),
75 )
77 outputCatalog = cT.Output(
78 doc="Merged Detection catalog",
79 name="{outputCoaddName}Coadd_mergeDet",
80 storageClass="SourceCatalog",
81 dimensions=("tract", "patch", "skymap"),
82 )
85class MergeDetectionsConfig(PipelineTaskConfig, pipelineConnections=MergeDetectionsConnections):
86 """!
87 @anchor MergeDetectionsConfig_
89 @brief Configuration parameters for the MergeDetectionsTask.
90 """
91 minNewPeak = Field(dtype=float, default=1,
92 doc="Minimum distance from closest peak to create a new one (in arcsec).")
94 maxSamePeak = Field(dtype=float, default=0.3,
95 doc="When adding new catalogs to the merge, all peaks less than this distance "
96 " (in arcsec) to an existing peak will be flagged as detected in that catalog.")
97 cullPeaks = ConfigField(dtype=CullPeaksConfig, doc="Configuration for how to cull peaks.")
99 skyFilterName = Field(dtype=str, default="sky",
100 doc="Name of `filter' used to label sky objects (e.g. flag merge_peak_sky is set)\n"
101 "(N.b. should be in MergeMeasurementsConfig.pseudoFilterList)")
102 skyObjects = ConfigurableField(target=SkyObjectsTask, doc="Generate sky objects")
103 priorityList = ListField(dtype=str, default=[],
104 doc="Priority-ordered list of filter bands for the merge.")
105 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
107 def setDefaults(self):
108 Config.setDefaults(self)
109 self.skyObjects.avoidMask = ["DETECTED"] # Nothing else is available in our custom mask
111 def validate(self):
112 super().validate()
113 if len(self.priorityList) == 0:
114 raise RuntimeError("No priority list provided")
117class MergeDetectionsTask(PipelineTask, CmdLineTask):
118 r"""!
119 @anchor MergeDetectionsTask_
121 @brief Merge coadd detections from multiple bands.
123 @section pipe_tasks_multiBand_Contents Contents
125 - @ref pipe_tasks_multiBand_MergeDetectionsTask_Purpose
126 - @ref pipe_tasks_multiBand_MergeDetectionsTask_Init
127 - @ref pipe_tasks_multiBand_MergeDetectionsTask_Run
128 - @ref pipe_tasks_multiBand_MergeDetectionsTask_Config
129 - @ref pipe_tasks_multiBand_MergeDetectionsTask_Debug
130 - @ref pipe_tasks_multiband_MergeDetectionsTask_Example
132 @section pipe_tasks_multiBand_MergeDetectionsTask_Purpose Description
134 Command-line task that merges sources detected in coadds of exposures obtained with different filters.
136 To perform photometry consistently across coadds in multiple filter bands, we create a master catalog of
137 sources from all bands by merging the sources (peaks & footprints) detected in each coadd, while keeping
138 track of which band each source originates in.
140 The catalog merge is performed by @ref getMergedSourceCatalog. Spurious peaks detected around bright
141 objects are culled as described in @ref CullPeaksConfig_.
143 @par Inputs:
144 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
145 @par Outputs:
146 deepCoadd_mergeDet{tract,patch}: SourceCatalog (only parent Footprints)
147 @par Data Unit:
148 tract, patch
150 @section pipe_tasks_multiBand_MergeDetectionsTask_Init Task initialisation
152 @copydoc \_\_init\_\_
154 @section pipe_tasks_multiBand_MergeDetectionsTask_Run Invoking the Task
156 @copydoc run
158 @section pipe_tasks_multiBand_MergeDetectionsTask_Config Configuration parameters
160 See @ref MergeDetectionsConfig_
162 @section pipe_tasks_multiBand_MergeDetectionsTask_Debug Debug variables
164 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a flag @c -d
165 to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py files.
167 MergeDetectionsTask has no debug variables.
169 @section pipe_tasks_multiband_MergeDetectionsTask_Example A complete example of using MergeDetectionsTask
171 MergeDetectionsTask is meant to be run after detecting sources in coadds generated for the chosen subset
172 of the available bands.
173 The purpose of the task is to merge sources (peaks & footprints) detected in the coadds generated from the
174 chosen subset of filters.
175 Subsequent tasks in the multi-band processing procedure will deblend the generated master list of sources
176 and, eventually, perform forced photometry.
177 Command-line usage of MergeDetectionsTask expects data references for all the coadds to be processed.
178 A list of the available optional arguments can be obtained by calling mergeCoaddDetections.py with the
179 `--help` command line argument:
180 @code
181 mergeCoaddDetections.py --help
182 @endcode
184 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
185 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
186 step 5 at @ref pipeTasks_multiBand, one may merge the catalogs of sources from each coadd as follows:
187 @code
188 mergeCoaddDetections.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R
189 @endcode
190 This will merge the HSC-I & -R band parent source catalogs and write the results to
191 `$CI_HSC_DIR/DATA/deepCoadd-results/merged/0/5,4/mergeDet-0-5,4.fits`.
193 The next step in the multi-band processing procedure is
194 @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask"
195 """
196 ConfigClass = MergeDetectionsConfig
197 RunnerClass = MergeSourcesRunner
198 _DefaultName = "mergeCoaddDetections"
199 inputDataset = "det"
200 outputDataset = "mergeDet"
201 makeIdFactory = _makeMakeIdFactory("MergedCoaddId")
203 @classmethod
204 def _makeArgumentParser(cls):
205 return makeMergeArgumentParser(cls._DefaultName, cls.inputDataset)
207 def getInputSchema(self, butler=None, schema=None):
208 return getInputSchema(self, butler, schema)
210 def __init__(self, butler=None, schema=None, initInputs=None, **kwargs):
211 # Make PipelineTask-only wording less transitional after cmdlineTask is removed
212 """!
213 @brief Initialize the merge detections task.
215 A @ref FootprintMergeList_ "FootprintMergeList" will be used to
216 merge the source catalogs.
218 @param[in] schema the schema of the detection catalogs used as input to this one
219 @param[in] butler a butler used to read the input schema from disk, if schema is None
220 @param[in] initInputs This a PipelineTask-only argument that holds all inputs passed in
221 through the PipelineTask middleware
222 @param[in] **kwargs keyword arguments to be passed to CmdLineTask.__init__
224 The task will set its own self.schema attribute to the schema of the output merged catalog.
225 """
226 super().__init__(**kwargs)
227 if initInputs is not None:
228 schema = initInputs['schema'].schema
230 self.makeSubtask("skyObjects")
231 self.schema = self.getInputSchema(butler=butler, schema=schema)
233 filterNames = list(self.config.priorityList)
234 filterNames.append(self.config.skyFilterName)
235 self.merged = afwDetect.FootprintMergeList(self.schema, filterNames)
236 self.outputSchema = afwTable.SourceCatalog(self.schema)
237 self.outputPeakSchema = afwDetect.PeakCatalog(self.merged.getPeakSchema())
239 def runDataRef(self, patchRefList):
240 catalogs = dict(readCatalog(self, patchRef) for patchRef in patchRefList)
241 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRefList[0])
242 idFactory = self.makeIdFactory(patchRefList[0])
243 skySeed = patchRefList[0].get(self.config.coaddName + "MergedCoaddId")
244 mergeCatalogStruct = self.run(catalogs, skyInfo, idFactory, skySeed)
245 self.write(patchRefList[0], mergeCatalogStruct.outputCatalog)
247 def runQuantum(self, butlerQC, inputRefs, outputRefs):
248 inputs = butlerQC.get(inputRefs)
249 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch", returnMaxBits=True)
250 inputs["skySeed"] = packedId
251 inputs["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
252 catalogDict = {ref.dataId['band']: cat for ref, cat in zip(inputRefs.catalogs,
253 inputs['catalogs'])}
254 inputs['catalogs'] = catalogDict
255 skyMap = inputs.pop('skyMap')
256 # Can use the first dataId to find the tract and patch being worked on
257 tractNumber = inputRefs.catalogs[0].dataId['tract']
258 tractInfo = skyMap[tractNumber]
259 patchInfo = tractInfo.getPatchInfo(inputRefs.catalogs[0].dataId['patch'])
260 skyInfo = Struct(
261 skyMap=skyMap,
262 tractInfo=tractInfo,
263 patchInfo=patchInfo,
264 wcs=tractInfo.getWcs(),
265 bbox=patchInfo.getOuterBBox()
266 )
267 inputs['skyInfo'] = skyInfo
269 outputs = self.run(**inputs)
270 butlerQC.put(outputs, outputRefs)
272 def run(self, catalogs, skyInfo, idFactory, skySeed):
273 r"""!
274 @brief Merge multiple catalogs.
276 After ordering the catalogs and filters in priority order,
277 @ref getMergedSourceCatalog of the @ref FootprintMergeList_ "FootprintMergeList" created by
278 @ref \_\_init\_\_ is used to perform the actual merging. Finally, @ref cullPeaks is used to remove
279 garbage peaks detected around bright objects.
281 @param[in] catalogs
282 @param[in] patchRef
283 @param[out] mergedList
284 """
286 # Convert distance to tract coordinate
287 tractWcs = skyInfo.wcs
288 peakDistance = self.config.minNewPeak / tractWcs.getPixelScale().asArcseconds()
289 samePeakDistance = self.config.maxSamePeak / tractWcs.getPixelScale().asArcseconds()
291 # Put catalogs, filters in priority order
292 orderedCatalogs = [catalogs[band] for band in self.config.priorityList if band in catalogs.keys()]
293 orderedBands = [band for band in self.config.priorityList if band in catalogs.keys()]
295 mergedList = self.merged.getMergedSourceCatalog(orderedCatalogs, orderedBands, peakDistance,
296 self.schema, idFactory,
297 samePeakDistance)
299 #
300 # Add extra sources that correspond to blank sky
301 #
302 skySourceFootprints = self.getSkySourceFootprints(mergedList, skyInfo, skySeed)
303 if skySourceFootprints:
304 key = mergedList.schema.find("merge_footprint_%s" % self.config.skyFilterName).key
305 for foot in skySourceFootprints:
306 s = mergedList.addNew()
307 s.setFootprint(foot)
308 s.set(key, True)
310 # Sort Peaks from brightest to faintest
311 for record in mergedList:
312 record.getFootprint().sortPeaks()
313 self.log.info("Merged to %d sources" % len(mergedList))
314 # Attempt to remove garbage peaks
315 self.cullPeaks(mergedList)
316 return Struct(outputCatalog=mergedList)
318 def cullPeaks(self, catalog):
319 """!
320 @brief Attempt to remove garbage peaks (mostly on the outskirts of large blends).
322 @param[in] catalog Source catalog
323 """
324 keys = [item.key for item in self.merged.getPeakSchema().extract("merge_peak_*").values()]
325 assert len(keys) > 0, "Error finding flags that associate peaks with their detection bands."
326 totalPeaks = 0
327 culledPeaks = 0
328 for parentSource in catalog:
329 # Make a list copy so we can clear the attached PeakCatalog and append the ones we're keeping
330 # to it (which is easier than deleting as we iterate).
331 keptPeaks = parentSource.getFootprint().getPeaks()
332 oldPeaks = list(keptPeaks)
333 keptPeaks.clear()
334 familySize = len(oldPeaks)
335 totalPeaks += familySize
336 for rank, peak in enumerate(oldPeaks):
337 if ((rank < self.config.cullPeaks.rankSufficient)
338 or (sum([peak.get(k) for k in keys]) >= self.config.cullPeaks.nBandsSufficient)
339 or (rank < self.config.cullPeaks.rankConsidered
340 and rank < self.config.cullPeaks.rankNormalizedConsidered * familySize)):
341 keptPeaks.append(peak)
342 else:
343 culledPeaks += 1
344 self.log.info("Culled %d of %d peaks" % (culledPeaks, totalPeaks))
346 def getSchemaCatalogs(self):
347 """!
348 Return a dict of empty catalogs for each catalog dataset produced by this task.
350 @param[out] dictionary of empty catalogs
351 """
352 mergeDet = afwTable.SourceCatalog(self.schema)
353 peak = afwDetect.PeakCatalog(self.merged.getPeakSchema())
354 return {self.config.coaddName + "Coadd_mergeDet": mergeDet,
355 self.config.coaddName + "Coadd_peak": peak}
357 def getSkySourceFootprints(self, mergedList, skyInfo, seed):
358 """!
359 @brief Return a list of Footprints of sky objects which don't overlap with anything in mergedList
361 @param mergedList The merged Footprints from all the input bands
362 @param skyInfo A description of the patch
363 @param seed Seed for the random number generator
364 """
365 mask = afwImage.Mask(skyInfo.patchInfo.getOuterBBox())
366 detected = mask.getPlaneBitMask("DETECTED")
367 for s in mergedList:
368 s.getFootprint().spans.setMask(mask, detected)
370 footprints = self.skyObjects.run(mask, seed)
371 if not footprints:
372 return footprints
374 # Need to convert the peak catalog's schema so we can set the "merge_peak_<skyFilterName>" flags
375 schema = self.merged.getPeakSchema()
376 mergeKey = schema.find("merge_peak_%s" % self.config.skyFilterName).key
377 converted = []
378 for oldFoot in footprints:
379 assert len(oldFoot.getPeaks()) == 1, "Should be a single peak only"
380 peak = oldFoot.getPeaks()[0]
381 newFoot = afwDetect.Footprint(oldFoot.spans, schema)
382 newFoot.addPeak(peak.getFx(), peak.getFy(), peak.getPeakValue())
383 newFoot.getPeaks()[0].set(mergeKey, True)
384 converted.append(newFoot)
386 return converted
388 def write(self, patchRef, catalog):
389 """!
390 @brief Write the output.
392 @param[in] patchRef data reference for patch
393 @param[in] catalog catalog
395 We write as the dataset provided by the 'outputDataset'
396 class variable.
397 """
398 patchRef.put(catalog, self.config.coaddName + "Coadd_" + self.outputDataset)
399 # since the filter isn't actually part of the data ID for the dataset we're saving,
400 # it's confusing to see it in the log message, even if the butler simply ignores it.
401 mergeDataId = patchRef.dataId.copy()
402 del mergeDataId["filter"]
403 self.log.info("Wrote merged catalog: %s" % (mergeDataId,))
405 def writeMetadata(self, dataRefList):
406 """!
407 @brief No metadata to write, and not sure how to write it for a list of dataRefs.
408 """
409 pass