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, getShortFilterName, 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 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 = [getShortFilterName(name) for name in self.config.priorityList]
234 filterNames += [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 = [getShortFilterName(band) for band in self.config.priorityList
294 if band in catalogs.keys()]
296 mergedList = self.merged.getMergedSourceCatalog(orderedCatalogs, orderedBands, peakDistance,
297 self.schema, idFactory,
298 samePeakDistance)
300 #
301 # Add extra sources that correspond to blank sky
302 #
303 skySourceFootprints = self.getSkySourceFootprints(mergedList, skyInfo, skySeed)
304 if skySourceFootprints:
305 key = mergedList.schema.find("merge_footprint_%s" % self.config.skyFilterName).key
306 for foot in skySourceFootprints:
307 s = mergedList.addNew()
308 s.setFootprint(foot)
309 s.set(key, True)
311 # Sort Peaks from brightest to faintest
312 for record in mergedList:
313 record.getFootprint().sortPeaks()
314 self.log.info("Merged to %d sources" % len(mergedList))
315 # Attempt to remove garbage peaks
316 self.cullPeaks(mergedList)
317 return Struct(outputCatalog=mergedList)
319 def cullPeaks(self, catalog):
320 """!
321 @brief Attempt to remove garbage peaks (mostly on the outskirts of large blends).
323 @param[in] catalog Source catalog
324 """
325 keys = [item.key for item in self.merged.getPeakSchema().extract("merge_peak_*").values()]
326 assert len(keys) > 0, "Error finding flags that associate peaks with their detection bands."
327 totalPeaks = 0
328 culledPeaks = 0
329 for parentSource in catalog:
330 # Make a list copy so we can clear the attached PeakCatalog and append the ones we're keeping
331 # to it (which is easier than deleting as we iterate).
332 keptPeaks = parentSource.getFootprint().getPeaks()
333 oldPeaks = list(keptPeaks)
334 keptPeaks.clear()
335 familySize = len(oldPeaks)
336 totalPeaks += familySize
337 for rank, peak in enumerate(oldPeaks):
338 if ((rank < self.config.cullPeaks.rankSufficient)
339 or (sum([peak.get(k) for k in keys]) >= self.config.cullPeaks.nBandsSufficient)
340 or (rank < self.config.cullPeaks.rankConsidered
341 and rank < self.config.cullPeaks.rankNormalizedConsidered * familySize)):
342 keptPeaks.append(peak)
343 else:
344 culledPeaks += 1
345 self.log.info("Culled %d of %d peaks" % (culledPeaks, totalPeaks))
347 def getSchemaCatalogs(self):
348 """!
349 Return a dict of empty catalogs for each catalog dataset produced by this task.
351 @param[out] dictionary of empty catalogs
352 """
353 mergeDet = afwTable.SourceCatalog(self.schema)
354 peak = afwDetect.PeakCatalog(self.merged.getPeakSchema())
355 return {self.config.coaddName + "Coadd_mergeDet": mergeDet,
356 self.config.coaddName + "Coadd_peak": peak}
358 def getSkySourceFootprints(self, mergedList, skyInfo, seed):
359 """!
360 @brief Return a list of Footprints of sky objects which don't overlap with anything in mergedList
362 @param mergedList The merged Footprints from all the input bands
363 @param skyInfo A description of the patch
364 @param seed Seed for the random number generator
365 """
366 mask = afwImage.Mask(skyInfo.patchInfo.getOuterBBox())
367 detected = mask.getPlaneBitMask("DETECTED")
368 for s in mergedList:
369 s.getFootprint().spans.setMask(mask, detected)
371 footprints = self.skyObjects.run(mask, seed)
372 if not footprints:
373 return footprints
375 # Need to convert the peak catalog's schema so we can set the "merge_peak_<skyFilterName>" flags
376 schema = self.merged.getPeakSchema()
377 mergeKey = schema.find("merge_peak_%s" % self.config.skyFilterName).key
378 converted = []
379 for oldFoot in footprints:
380 assert len(oldFoot.getPeaks()) == 1, "Should be a single peak only"
381 peak = oldFoot.getPeaks()[0]
382 newFoot = afwDetect.Footprint(oldFoot.spans, schema)
383 newFoot.addPeak(peak.getFx(), peak.getFy(), peak.getPeakValue())
384 newFoot.getPeaks()[0].set(mergeKey, True)
385 converted.append(newFoot)
387 return converted
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