23 from __future__
import absolute_import, division, print_function
24 from builtins
import zip
25 from builtins
import range
29 from lsst.pipe.base import CmdLineTask, Struct, TaskRunner, ArgumentParser, ButlerInitializedTaskRunner
30 from lsst.pex.config import Config, Field, ListField, ConfigurableField, RangeField, ConfigField
32 from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
48 * deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter) 49 * deepCoadd_mergeDet: merged detections (tract, patch) 50 * deepCoadd_meas: measurements of merged detections (tract, patch, filter) 51 * deepCoadd_ref: reference sources (tract, patch) 52 All of these have associated *_schema catalogs that require no data ID and hold no records. 54 In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in 55 the mergeDet, meas, and ref dataset Footprints: 56 * deepCoadd_peak_schema 60 def _makeGetSchemaCatalogs(datasetSuffix):
61 """Construct a getSchemaCatalogs instance method 63 These are identical for most of the classes here, so we'll consolidate 66 datasetSuffix: Suffix of dataset name, e.g., "src" for "deepCoadd_src" 69 def getSchemaCatalogs(self):
70 """Return a dict of empty catalogs for each catalog dataset produced by this task.""" 71 src = afwTable.SourceCatalog(self.schema)
72 if hasattr(self,
"algMetadata"):
73 src.getTable().setMetadata(self.algMetadata)
74 return {self.config.coaddName +
"Coadd_" + datasetSuffix: src}
75 return getSchemaCatalogs
78 def _makeMakeIdFactory(datasetName):
79 """Construct a makeIdFactory instance method 81 These are identical for all the classes here, so this consolidates 84 datasetName: Dataset name without the coadd name prefix, e.g., "CoaddId" for "deepCoaddId" 87 def makeIdFactory(self, dataRef):
88 """Return an IdFactory for setting the detection identifiers 90 The actual parameters used in the IdFactory are provided by 91 the butler (through the provided data reference. 93 expBits = dataRef.get(self.config.coaddName + datasetName +
"_bits")
94 expId = int(dataRef.get(self.config.coaddName + datasetName))
95 return afwTable.IdFactory.makeSource(expId, 64 - expBits)
100 """Given a longer, camera-specific filter name (e.g. "HSC-I") return its shorthand name ("i"). 104 return afwImage.Filter(name).getFilterProperty().getName()
111 \anchor DetectCoaddSourcesConfig_ 113 \brief Configuration parameters for the DetectCoaddSourcesTask 115 doScaleVariance = Field(dtype=bool, default=
True, doc=
"Scale variance plane using empirical noise?")
116 detection = ConfigurableField(target=DynamicDetectionTask, doc=
"Source detection")
117 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
118 mask = ListField(dtype=str, default=[
"DETECTED",
"BAD",
"SAT",
"NO_DATA",
"INTRP"],
119 doc=
"Mask planes for pixels to ignore when scaling variance")
120 doInsertFakes = Field(dtype=bool, default=
False,
121 doc=
"Run fake sources injection task")
122 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
123 doc=
"Injection of fake sources for testing " 124 "purposes (must be retargeted)")
127 Config.setDefaults(self)
128 self.
detection.thresholdType =
"pixel_stdev" 131 self.
detection.reEstimateBackground =
False 132 self.
detection.background.useApprox =
False 134 self.
detection.background.undersampleStyle =
'REDUCE_INTERP_ORDER' 146 \anchor DetectCoaddSourcesTask_ 148 \brief Detect sources on a coadd 150 \section pipe_tasks_multiBand_Contents Contents 152 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose 153 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize 154 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run 155 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config 156 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug 157 - \ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example 159 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description 161 Command-line task that detects sources on a coadd of exposures obtained with a single filter. 163 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise 164 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane 165 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should 166 propagate the full covariance matrix -- but it is simple and works well in practice. 168 After scaling the variance plane, we detect sources and generate footprints by delegating to the \ref 169 SourceDetectionTask_ "detection" subtask. 172 deepCoadd{tract,patch,filter}: ExposureF 174 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) 175 \n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input 177 \n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList 181 DetectCoaddSourcesTask delegates most of its work to the \ref SourceDetectionTask_ "detection" subtask. 182 You can retarget this subtask if you wish. 184 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization 186 \copydoc \_\_init\_\_ 188 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task 192 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters 194 See \ref DetectCoaddSourcesConfig_ "DetectSourcesConfig" 196 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables 198 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a 199 flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py 202 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to 203 \ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for 204 \ref SourceDetectionTask_ "SourceDetectionTask" for further information. 206 \section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example 207 of using DetectCoaddSourcesTask 209 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of 210 the task is to update the background, detect all sources in a single band and generate a set of parent 211 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and, 212 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data 213 reference to the coadd to be processed. A list of the available optional arguments can be obtained by 214 calling detectCoaddSources.py with the `--help` command line argument: 216 detectCoaddSources.py --help 219 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 220 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed 221 steps 1 - 4 at \ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows: 223 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 225 that will process the HSC-I band data. The results are written to 226 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`. 228 It is also necessary to run: 230 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 232 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 233 processing procedure: \ref MergeDetectionsTask_ "MergeDetectionsTask". 235 _DefaultName =
"detectCoaddSources" 236 ConfigClass = DetectCoaddSourcesConfig
237 getSchemaCatalogs = _makeGetSchemaCatalogs(
"det")
238 makeIdFactory = _makeMakeIdFactory(
"CoaddId")
241 def _makeArgumentParser(cls):
243 parser.add_id_argument(
"--id",
"deepCoadd", help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
244 ContainerClass=ExistingCoaddDataIdContainer)
249 \brief Initialize the task. Create the \ref SourceDetectionTask_ "detection" subtask. 251 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 253 \param[in] schema: initial schema for the output catalog, modified-in place to include all 254 fields set by this task. If None, the source minimal schema will be used. 255 \param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__ 257 CmdLineTask.__init__(self, **kwargs)
259 schema = afwTable.SourceTable.makeMinimalSchema()
260 if self.config.doInsertFakes:
261 self.makeSubtask(
"insertFakes")
263 self.makeSubtask(
"detection", schema=self.
schema)
267 \brief Run detection on a coadd. 269 Invokes \ref runDetection and then uses \ref write to output the 272 \param[in] patchRef: data reference for patch 274 exposure = patchRef.get(self.config.coaddName +
"Coadd", immediate=
True)
275 expId = int(patchRef.get(self.config.coaddName +
"CoaddId"))
277 self.
write(exposure, results, patchRef)
282 \brief Run detection on an exposure. 284 First scale the variance plane to match the observed variance 285 using \ref scaleVariance. Then invoke the \ref SourceDetectionTask_ "detection" subtask to 288 \param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled, 289 depending on configuration). 290 \param[in] idFactory: IdFactory to set source identifiers 291 \param[in] expId: Exposure identifier (integer) for RNG seed 293 \return a pipe.base.Struct with fields 294 - sources: catalog of detections 295 - backgrounds: list of backgrounds 297 if self.config.doScaleVariance:
298 varScale =
scaleVariance(exposure.getMaskedImage(), self.config.mask, log=self.log)
299 exposure.getMetadata().add(
"variance_scale", varScale)
300 backgrounds = afwMath.BackgroundList()
301 if self.config.doInsertFakes:
302 self.insertFakes.
run(exposure, background=backgrounds)
303 table = afwTable.SourceTable.make(self.
schema, idFactory)
304 detections = self.detection.makeSourceCatalog(table, exposure, expId=expId)
305 sources = detections.sources
306 fpSets = detections.fpSets
307 if hasattr(fpSets,
"background")
and fpSets.background:
308 backgrounds.append(fpSets.background)
309 return Struct(sources=sources, backgrounds=backgrounds)
311 def write(self, exposure, results, patchRef):
313 \brief Write out results from runDetection. 315 \param[in] exposure: Exposure to write out 316 \param[in] results: Struct returned from runDetection 317 \param[in] patchRef: data reference for patch 319 coaddName = self.config.coaddName +
"Coadd" 320 patchRef.put(results.backgrounds, coaddName +
"_calexp_background")
321 patchRef.put(results.sources, coaddName +
"_det")
322 patchRef.put(exposure, coaddName +
"_calexp")
329 \anchor MergeSourcesRunner_ 331 \brief Task runner for the \ref MergeSourcesTask_ "MergeSourcesTask". Required because the run method 332 requires a list of dataRefs rather than a single dataRef. 337 \brief Provide a butler to the Task constructor. 339 \param[in] parsedCmd the parsed command 340 \param[in] args tuple of a list of data references and kwargs (un-used) 341 \throws RuntimeError if both parsedCmd & args are None 343 if parsedCmd
is not None:
344 butler = parsedCmd.butler
345 elif args
is not None:
346 dataRefList, kwargs = args
347 butler = dataRefList[0].getButler()
349 raise RuntimeError(
"Neither parsedCmd or args specified")
350 return self.TaskClass(config=self.config, log=self.log, butler=butler)
355 \brief Provide a list of patch references for each patch. 357 The patch references within the list will have different filters. 359 \param[in] parsedCmd the parsed command 360 \param **kwargs key word arguments (unused) 361 \throws RuntimeError if multiple references are provided for the same combination of tract, patch and 365 for ref
in parsedCmd.id.refList:
366 tract = ref.dataId[
"tract"]
367 patch = ref.dataId[
"patch"]
368 filter = ref.dataId[
"filter"]
369 if tract
not in refList:
371 if patch
not in refList[tract]:
372 refList[tract][patch] = {}
373 if filter
in refList[tract][patch]:
374 raise RuntimeError(
"Multiple versions of %s" % (ref.dataId,))
375 refList[tract][patch][filter] = ref
376 return [(list(p.values()), kwargs)
for t
in refList.values()
for p
in t.values()]
381 \anchor MergeSourcesConfig_ 383 \brief Configuration for merging sources. 385 priorityList = ListField(dtype=str, default=[],
386 doc=
"Priority-ordered list of bands for the merge.")
387 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
390 Config.validate(self)
392 raise RuntimeError(
"No priority list provided")
397 \anchor MergeSourcesTask_ 399 \brief A base class for merging source catalogs. 401 Merging detections (MergeDetectionsTask) and merging measurements (MergeMeasurementsTask) are 402 so similar that it makes sense to re-use the code, in the form of this abstract base class. 404 NB: Do not use this class directly. Instead use one of the child classes that inherit from 405 MergeSourcesTask such as \ref MergeDetectionsTask_ "MergeDetectionsTask" or \ref MergeMeasurementsTask_ 406 "MergeMeasurementsTask" 408 Sub-classes should set the following class variables: 409 * `_DefaultName`: name of Task 410 * `inputDataset`: name of dataset to read 411 * `outputDataset`: name of dataset to write 412 * `getSchemaCatalogs` to the result of `_makeGetSchemaCatalogs(outputDataset)` 414 In addition, sub-classes must implement the mergeCatalogs method. 417 ConfigClass = MergeSourcesConfig
418 RunnerClass = MergeSourcesRunner
421 getSchemaCatalogs =
None 424 def _makeArgumentParser(cls):
426 \brief Create a suitable ArgumentParser. 428 We will use the ArgumentParser to get a provide a list of data 429 references for patches; the RunnerClass will sort them into lists 430 of data references for the same patch 433 parser.add_id_argument(
"--id",
"deepCoadd_" + cls.
inputDataset,
434 ContainerClass=ExistingCoaddDataIdContainer,
435 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i")
440 \brief Obtain the input schema either directly or froma butler reference. 442 \param[in] butler butler reference to obtain the input schema from 443 \param[in] schema the input schema 446 assert butler
is not None,
"Neither butler nor schema specified" 447 schema = butler.get(self.config.coaddName +
"Coadd_" + self.
inputDataset +
"_schema",
448 immediate=
True).schema
451 def __init__(self, butler=None, schema=None, **kwargs):
453 \brief Initialize the task. 455 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 456 \param[in] schema the schema of the detection catalogs used as input to this one 457 \param[in] butler a butler used to read the input schema from disk, if schema is None 459 Derived classes should use the getInputSchema() method to handle the additional 460 arguments and retreive the actual input schema. 462 CmdLineTask.__init__(self, **kwargs)
464 def run(self, patchRefList):
466 \brief Merge coadd sources from multiple bands. Calls \ref mergeCatalogs which must be defined in 467 subclasses that inherit from MergeSourcesTask. 469 \param[in] patchRefList list of data references for each filter 471 catalogs = dict(self.
readCatalog(patchRef)
for patchRef
in patchRefList)
472 mergedCatalog = self.
mergeCatalogs(catalogs, patchRefList[0])
473 self.
write(patchRefList[0], mergedCatalog)
477 \brief Read input catalog. 479 We read the input dataset provided by the 'inputDataset' 482 \param[in] patchRef data reference for patch 483 \return tuple consisting of the filter name and the catalog 485 filterName = patchRef.dataId[
"filter"]
486 catalog = patchRef.get(self.config.coaddName +
"Coadd_" + self.
inputDataset, immediate=
True)
487 self.log.info(
"Read %d sources for filter %s: %s" % (len(catalog), filterName, patchRef.dataId))
488 return filterName, catalog
492 \brief Merge multiple catalogs. This function must be defined in all subclasses that inherit from 495 \param[in] catalogs dict mapping filter name to source catalog 497 \return merged catalog 499 raise NotImplementedError()
503 \brief Write the output. 505 \param[in] patchRef data reference for patch 506 \param[in] catalog catalog 508 We write as the dataset provided by the 'outputDataset' 511 patchRef.put(catalog, self.config.coaddName +
"Coadd_" + self.
outputDataset)
514 mergeDataId = patchRef.dataId.copy()
515 del mergeDataId[
"filter"]
516 self.log.info(
"Wrote merged catalog: %s" % (mergeDataId,))
520 \brief No metadata to write, and not sure how to write it for a list of dataRefs. 525 class CullPeaksConfig(Config):
527 \anchor CullPeaksConfig_ 529 \brief Configuration for culling garbage peaks after merging footprints. 531 Peaks may also be culled after detection or during deblending; this configuration object 532 only deals with culling after merging Footprints. 534 These cuts are based on three quantities: 535 - nBands: the number of bands in which the peak was detected 536 - peakRank: the position of the peak within its family, sorted from brightest to faintest. 537 - peakRankNormalized: the peak rank divided by the total number of peaks in the family. 539 The formula that identifie peaks to cull is: 541 nBands < nBandsSufficient 542 AND (rank >= rankSufficient) 543 AND (rank >= rankConsider OR rank >= rankNormalizedConsider) 545 To disable peak culling, simply set nBandsSufficient=1. 548 nBandsSufficient = RangeField(dtype=int, default=2, min=1,
549 doc=
"Always keep peaks detected in this many bands")
550 rankSufficient = RangeField(dtype=int, default=20, min=1,
551 doc=
"Always keep this many peaks in each family")
552 rankConsidered = RangeField(dtype=int, default=30, min=1,
553 doc=(
"Keep peaks with less than this rank that also match the " 554 "rankNormalizedConsidered condition."))
555 rankNormalizedConsidered = RangeField(dtype=float, default=0.7, min=0.0,
556 doc=(
"Keep peaks with less than this normalized rank that" 557 " also match the rankConsidered condition."))
562 \anchor MergeDetectionsConfig_ 564 \brief Configuration parameters for the MergeDetectionsTask. 566 minNewPeak = Field(dtype=float, default=1,
567 doc=
"Minimum distance from closest peak to create a new one (in arcsec).")
569 maxSamePeak = Field(dtype=float, default=0.3,
570 doc=
"When adding new catalogs to the merge, all peaks less than this distance " 571 " (in arcsec) to an existing peak will be flagged as detected in that catalog.")
572 cullPeaks = ConfigField(dtype=CullPeaksConfig, doc=
"Configuration for how to cull peaks.")
574 skyFilterName = Field(dtype=str, default=
"sky",
575 doc=
"Name of `filter' used to label sky objects (e.g. flag merge_peak_sky is set)\n" 576 "(N.b. should be in MergeMeasurementsConfig.pseudoFilterList)")
577 skyObjects = ConfigurableField(target=SkyObjectsTask, doc=
"Generate sky objects")
580 MergeSourcesConfig.setDefaults(self)
594 \anchor MergeDetectionsTask_ 596 \brief Merge coadd detections from multiple bands. 598 \section pipe_tasks_multiBand_Contents Contents 600 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Purpose 601 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Init 602 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Run 603 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Config 604 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Debug 605 - \ref pipe_tasks_multiband_MergeDetectionsTask_Example 607 \section pipe_tasks_multiBand_MergeDetectionsTask_Purpose Description 609 Command-line task that merges sources detected in coadds of exposures obtained with different filters. 611 To perform photometry consistently across coadds in multiple filter bands, we create a master catalog of 612 sources from all bands by merging the sources (peaks & footprints) detected in each coadd, while keeping 613 track of which band each source originates in. 615 The catalog merge is performed by \ref getMergedSourceCatalog. Spurious peaks detected around bright 616 objects are culled as described in \ref CullPeaksConfig_. 619 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) 621 deepCoadd_mergeDet{tract,patch}: SourceCatalog (only parent Footprints) 625 MergeDetectionsTask subclasses \ref MergeSourcesTask_ "MergeSourcesTask". 627 \section pipe_tasks_multiBand_MergeDetectionsTask_Init Task initialisation 629 \copydoc \_\_init\_\_ 631 \section pipe_tasks_multiBand_MergeDetectionsTask_Run Invoking the Task 635 \section pipe_tasks_multiBand_MergeDetectionsTask_Config Configuration parameters 637 See \ref MergeDetectionsConfig_ 639 \section pipe_tasks_multiBand_MergeDetectionsTask_Debug Debug variables 641 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a flag \c -d 642 to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py files. 644 MergeDetectionsTask has no debug variables. 646 \section pipe_tasks_multiband_MergeDetectionsTask_Example A complete example of using MergeDetectionsTask 648 MergeDetectionsTask is meant to be run after detecting sources in coadds generated for the chosen subset 649 of the available bands. 650 The purpose of the task is to merge sources (peaks & footprints) detected in the coadds generated from the 651 chosen subset of filters. 652 Subsequent tasks in the multi-band processing procedure will deblend the generated master list of sources 653 and, eventually, perform forced photometry. 654 Command-line usage of MergeDetectionsTask expects data references for all the coadds to be processed. 655 A list of the available optional arguments can be obtained by calling mergeCoaddDetections.py with the 656 `--help` command line argument: 658 mergeCoaddDetections.py --help 661 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 662 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 663 step 5 at \ref pipeTasks_multiBand, one may merge the catalogs of sources from each coadd as follows: 665 mergeCoaddDetections.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R 667 This will merge the HSC-I & -R band parent source catalogs and write the results to 668 `$CI_HSC_DIR/DATA/deepCoadd-results/merged/0/5,4/mergeDet-0-5,4.fits`. 670 The next step in the multi-band processing procedure is 671 \ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" 673 ConfigClass = MergeDetectionsConfig
674 _DefaultName =
"mergeCoaddDetections" 676 outputDataset =
"mergeDet" 677 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId")
679 def __init__(self, butler=None, schema=None, **kwargs):
681 \brief Initialize the merge detections task. 683 A \ref FootprintMergeList_ "FootprintMergeList" will be used to 684 merge the source catalogs. 686 Additional keyword arguments (forwarded to MergeSourcesTask.__init__): 687 \param[in] schema the schema of the detection catalogs used as input to this one 688 \param[in] butler a butler used to read the input schema from disk, if schema is None 689 \param[in] **kwargs keyword arguments to be passed to MergeSourcesTask.__init__ 691 The task will set its own self.schema attribute to the schema of the output merged catalog. 693 MergeSourcesTask.__init__(self, butler=butler, schema=schema, **kwargs)
694 self.makeSubtask(
"skyObjects")
698 filterNames += [self.config.skyFilterName]
703 \brief Merge multiple catalogs. 705 After ordering the catalogs and filters in priority order, 706 \ref getMergedSourceCatalog of the \ref FootprintMergeList_ "FootprintMergeList" created by 707 \ref \_\_init\_\_ is used to perform the actual merging. Finally, \ref cullPeaks is used to remove 708 garbage peaks detected around bright objects. 712 \param[out] mergedList 716 skyInfo =
getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
717 tractWcs = skyInfo.wcs
718 peakDistance = self.config.minNewPeak / tractWcs.getPixelScale().asArcseconds()
719 samePeakDistance = self.config.maxSamePeak / tractWcs.getPixelScale().asArcseconds()
722 orderedCatalogs = [catalogs[band]
for band
in self.config.priorityList
if band
in catalogs.keys()]
724 if band
in catalogs.keys()]
726 mergedList = self.
merged.getMergedSourceCatalog(orderedCatalogs, orderedBands, peakDistance,
733 skySeed = patchRef.get(self.config.coaddName +
"MergedCoaddId")
735 if skySourceFootprints:
736 key = mergedList.schema.find(
"merge_footprint_%s" % self.config.skyFilterName).key
737 for foot
in skySourceFootprints:
738 s = mergedList.addNew()
743 for record
in mergedList:
744 record.getFootprint().sortPeaks()
745 self.log.info(
"Merged to %d sources" % len(mergedList))
752 \brief Attempt to remove garbage peaks (mostly on the outskirts of large blends). 754 \param[in] catalog Source catalog 756 keys = [item.key
for item
in self.
merged.getPeakSchema().extract(
"merge_peak_*").values()]
757 assert len(keys) > 0,
"Error finding flags that associate peaks with their detection bands." 760 for parentSource
in catalog:
763 keptPeaks = parentSource.getFootprint().getPeaks()
764 oldPeaks = list(keptPeaks)
766 familySize = len(oldPeaks)
767 totalPeaks += familySize
768 for rank, peak
in enumerate(oldPeaks):
769 if ((rank < self.config.cullPeaks.rankSufficient)
or 770 (sum([peak.get(k)
for k
in keys]) >= self.config.cullPeaks.nBandsSufficient)
or 771 (rank < self.config.cullPeaks.rankConsidered
and 772 rank < self.config.cullPeaks.rankNormalizedConsidered * familySize)):
773 keptPeaks.append(peak)
776 self.log.info(
"Culled %d of %d peaks" % (culledPeaks, totalPeaks))
780 Return a dict of empty catalogs for each catalog dataset produced by this task. 782 \param[out] dictionary of empty catalogs 784 mergeDet = afwTable.SourceCatalog(self.
schema)
785 peak = afwDetect.PeakCatalog(self.
merged.getPeakSchema())
786 return {self.config.coaddName +
"Coadd_mergeDet": mergeDet,
787 self.config.coaddName +
"Coadd_peak": peak}
791 \brief Return a list of Footprints of sky objects which don't overlap with anything in mergedList 793 \param mergedList The merged Footprints from all the input bands 794 \param skyInfo A description of the patch 795 \param seed Seed for the random number generator 797 mask = afwImage.Mask(skyInfo.patchInfo.getOuterBBox())
798 detected = mask.getPlaneBitMask(
"DETECTED")
800 s.getFootprint().spans.setMask(mask, detected)
802 footprints = self.skyObjects.
run(mask, seed)
807 schema = self.
merged.getPeakSchema()
808 mergeKey = schema.find(
"merge_peak_%s" % self.config.skyFilterName).key
810 for oldFoot
in footprints:
811 assert len(oldFoot.getPeaks()) == 1,
"Should be a single peak only" 812 peak = oldFoot.getPeaks()[0]
813 newFoot = afwDetect.Footprint(oldFoot.spans, schema)
814 newFoot.addPeak(peak.getFx(), peak.getFy(), peak.getPeakValue())
815 newFoot.getPeaks()[0].set(mergeKey,
True)
816 converted.append(newFoot)
823 \anchor MeasureMergedCoaddSourcesConfig_ 825 \brief Configuration parameters for the MeasureMergedCoaddSourcesTask 827 doDeblend = Field(dtype=bool, default=
True, doc=
"Deblend sources?")
828 deblend = ConfigurableField(target=SourceDeblendTask, doc=
"Deblend sources")
829 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc=
"Source measurement")
830 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc=
"Set flags for primary tract/patch")
831 doPropagateFlags = Field(
832 dtype=bool, default=
True,
833 doc=
"Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)" 835 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc=
"Propagate visit flags to coadd")
836 doMatchSources = Field(dtype=bool, default=
True, doc=
"Match sources to reference catalog?")
837 match = ConfigurableField(target=DirectMatchTask, doc=
"Matching to reference catalog")
838 doWriteMatchesDenormalized = Field(
841 doc=(
"Write reference matches in denormalized format? " 842 "This format uses more disk space, but is more convenient to read."),
844 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
845 checkUnitsParseStrict = Field(
846 doc=
"Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
853 doc=
"Apply aperture corrections" 855 applyApCorr = ConfigurableField(
856 target=ApplyApCorrTask,
857 doc=
"Subtask to apply aperture corrections" 859 doRunCatalogCalculation = Field(
862 doc=
'Run catalogCalculation task' 864 catalogCalculation = ConfigurableField(
865 target=CatalogCalculationTask,
866 doc=
"Subtask to run catalogCalculation plugins on catalog" 870 Config.setDefaults(self)
871 self.
deblend.propagateAllPeaks =
True 872 self.
measurement.plugins.names |= [
'base_InputCount',
'base_Variance']
873 self.
measurement.plugins[
'base_PixelFlags'].masksFpAnywhere = [
'CLIPPED',
'SENSOR_EDGE',
875 self.
measurement.plugins[
'base_PixelFlags'].masksFpCenter = [
'CLIPPED',
'SENSOR_EDGE',
888 \anchor MeasureMergedCoaddSourcesTask_ 890 \brief Deblend sources from master catalog in each coadd seperately and measure. 892 \section pipe_tasks_multiBand_Contents Contents 894 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose 895 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize 896 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run 897 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config 898 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug 899 - \ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example 901 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description 903 Command-line task that uses peaks and footprints from a master catalog to perform deblending and 904 measurement in each coadd. 906 Given a master input catalog of sources (peaks and footprints), deblend and measure each source on the 907 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a 908 consistent set of child sources. 910 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source 911 properties are measured and the \c is-primary flag (indicating sources with no children) is set. Visit 912 flags are propagated to the coadd sources. 914 Optionally, we can match the coadd sources to an external reference catalog. 917 deepCoadd_mergeDet{tract,patch}: SourceCatalog 918 \n deepCoadd_calexp{tract,patch,filter}: ExposureF 920 deepCoadd_meas{tract,patch,filter}: SourceCatalog 924 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks: 927 <DT> \ref SourceDeblendTask_ "deblend" 928 <DD> Deblend all the sources from the master catalog.</DD> 929 <DT> \ref SingleFrameMeasurementTask_ "measurement" 930 <DD> Measure source properties of deblended sources.</DD> 931 <DT> \ref SetPrimaryFlagsTask_ "setPrimaryFlags" 932 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are 933 not at the edge of the field and that have either not been deblended or are the children of deblended 935 <DT> \ref PropagateVisitFlagsTask_ "propagateFlags" 936 <DD> Propagate flags set in individual visits to the coadd.</DD> 937 <DT> \ref DirectMatchTask_ "match" 938 <DD> Match input sources to a reference catalog (optional). 941 These subtasks may be retargeted as required. 943 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization 945 \copydoc \_\_init\_\_ 947 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task 951 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters 953 See \ref MeasureMergedCoaddSourcesConfig_ 955 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables 957 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a 958 flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py 961 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to 962 the various sub-tasks. See the documetation for individual sub-tasks for more information. 964 \section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using 965 MeasureMergedCoaddSourcesTask 967 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs. 968 The next stage in the multi-band processing procedure will merge these measurements into a suitable 969 catalog for driving forced photometry. 971 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds 973 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the 974 `--help` command line argument: 976 measureCoaddSources.py --help 979 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 980 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 981 step 6 at \ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band 984 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 986 This will process the HSC-I band data. The results are written in 987 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits 989 It is also necessary to run 991 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 993 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 994 procedure: \ref MergeMeasurementsTask_ "MergeMeasurementsTask". 996 _DefaultName =
"measureCoaddSources" 997 ConfigClass = MeasureMergedCoaddSourcesConfig
998 RunnerClass = ButlerInitializedTaskRunner
999 getSchemaCatalogs = _makeGetSchemaCatalogs(
"meas")
1000 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId")
1003 def _makeArgumentParser(cls):
1005 parser.add_id_argument(
"--id",
"deepCoadd_calexp",
1006 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
1007 ContainerClass=ExistingCoaddDataIdContainer)
1010 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, **kwargs):
1012 \brief Initialize the task. 1014 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 1015 \param[in] schema: the schema of the merged detection catalog used as input to this one 1016 \param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog 1017 \param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference 1018 catalog. May be None if the loader can be constructed from the butler argument or all steps 1019 requiring a reference catalog are disabled. 1020 \param[in] butler: a butler used to read the input schemas from disk or construct the reference 1021 catalog loader, if schema or peakSchema or refObjLoader is None 1023 The task will set its own self.schema attribute to the schema of the output measurement catalog. 1024 This will include all fields from the input schema, as well as additional fields for all the 1027 CmdLineTask.__init__(self, **kwargs)
1029 assert butler
is not None,
"Neither butler nor schema is defined" 1030 schema = butler.get(self.config.coaddName +
"Coadd_mergeDet_schema", immediate=
True).schema
1035 if self.config.doDeblend:
1036 if peakSchema
is None:
1037 assert butler
is not None,
"Neither butler nor peakSchema is defined" 1038 peakSchema = butler.get(self.config.coaddName +
"Coadd_peak_schema", immediate=
True).schema
1039 self.makeSubtask(
"deblend", schema=self.
schema, peakSchema=peakSchema)
1040 self.makeSubtask(
"measurement", schema=self.
schema, algMetadata=self.
algMetadata)
1041 self.makeSubtask(
"setPrimaryFlags", schema=self.
schema)
1042 if self.config.doMatchSources:
1043 if refObjLoader
is None:
1044 assert butler
is not None,
"Neither butler nor refObjLoader is defined" 1045 self.makeSubtask(
"match", butler=butler, refObjLoader=refObjLoader)
1046 if self.config.doPropagateFlags:
1047 self.makeSubtask(
"propagateFlags", schema=self.
schema)
1048 self.
schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
1049 if self.config.doApCorr:
1050 self.makeSubtask(
"applyApCorr", schema=self.
schema)
1051 if self.config.doRunCatalogCalculation:
1052 self.makeSubtask(
"catalogCalculation", schema=self.
schema)
1056 \brief Deblend and measure. 1058 \param[in] patchRef: Patch reference. 1060 Deblend each source in every coadd and measure. Set 'is-primary' and related flags. Propagate flags 1061 from individual visits. Optionally match the sources to a reference catalog and write the matches. 1062 Finally, write the deblended sources and measurements out. 1064 exposure = patchRef.get(self.config.coaddName +
"Coadd_calexp", immediate=
True)
1066 if self.config.doDeblend:
1067 self.deblend.
run(exposure, sources)
1069 bigKey = sources.schema[
"deblend_parentTooBig"].asKey()
1071 numBig = sum((s.get(bigKey)
for s
in sources))
1073 self.log.warn(
"Patch %s contains %d large footprints that were not deblended" %
1074 (patchRef.dataId, numBig))
1076 table = sources.getTable()
1079 self.measurement.
run(sources, exposure, exposureId=self.
getExposureId(patchRef))
1081 if self.config.doApCorr:
1082 self.applyApCorr.
run(
1084 apCorrMap=exposure.getInfo().getApCorrMap()
1087 if self.config.doRunCatalogCalculation:
1088 self.catalogCalculation.
run(sources)
1090 skyInfo =
getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1091 self.setPrimaryFlags.
run(sources, skyInfo.skyMap, skyInfo.tractInfo, skyInfo.patchInfo,
1092 includeDeblend=self.config.doDeblend)
1093 if self.config.doPropagateFlags:
1094 self.propagateFlags.
run(patchRef.getButler(), sources, self.propagateFlags.getCcdInputs(exposure),
1096 if self.config.doMatchSources:
1098 self.
write(patchRef, sources)
1102 \brief Read input sources. 1104 \param[in] dataRef: Data reference for catalog of merged detections 1105 \return List of sources in merged catalog 1107 We also need to add columns to hold the measurements we're about to make 1108 so we can measure in-place. 1110 merged = dataRef.get(self.config.coaddName +
"Coadd_mergeDet", immediate=
True)
1111 self.log.info(
"Read %d detections: %s" % (len(merged), dataRef.dataId))
1114 idFactory.notify(s.getId())
1115 table = afwTable.SourceTable.make(self.
schema, idFactory)
1116 sources = afwTable.SourceCatalog(table)
1122 \brief Write matches of the sources to the astrometric reference catalog. 1124 We use the Wcs in the exposure to match sources. 1126 \param[in] dataRef: data reference 1127 \param[in] exposure: exposure with Wcs 1128 \param[in] sources: source catalog 1130 result = self.match.
run(sources, exposure.getInfo().getFilter().getName())
1132 matches = afwTable.packMatches(result.matches)
1133 matches.table.setMetadata(result.matchMeta)
1134 dataRef.put(matches, self.config.coaddName +
"Coadd_measMatch")
1135 if self.config.doWriteMatchesDenormalized:
1136 denormMatches = denormalizeMatches(result.matches, result.matchMeta)
1137 dataRef.put(denormMatches, self.config.coaddName +
"Coadd_measMatchFull")
1141 \brief Write the source catalog. 1143 \param[in] dataRef: data reference 1144 \param[in] sources: source catalog 1146 dataRef.put(sources, self.config.coaddName +
"Coadd_meas")
1147 self.log.info(
"Wrote %d sources: %s" % (len(sources), dataRef.dataId))
1150 return int(dataRef.get(self.config.coaddName +
"CoaddId"))
1155 \anchor MergeMeasurementsConfig_ 1157 \brief Configuration parameters for the MergeMeasurementsTask 1159 pseudoFilterList = ListField(dtype=str, default=[
"sky"],
1160 doc=
"Names of filters which may have no associated detection\n" 1161 "(N.b. should include MergeDetectionsConfig.skyFilterName)")
1162 snName = Field(dtype=str, default=
"base_PsfFlux",
1163 doc=
"Name of flux measurement for calculating the S/N when choosing the reference band.")
1164 minSN = Field(dtype=float, default=10.,
1165 doc=
"If the S/N from the priority band is below this value (and the S/N " 1166 "is larger than minSNDiff compared to the priority band), use the band with " 1167 "the largest S/N as the reference band.")
1168 minSNDiff = Field(dtype=float, default=3.,
1169 doc=
"If the difference in S/N between another band and the priority band is larger " 1170 "than this value (and the S/N in the priority band is less than minSN) " 1171 "use the band with the largest S/N as the reference band")
1172 flags = ListField(dtype=str, doc=
"Require that these flags, if available, are not set",
1173 default=[
"base_PixelFlags_flag_interpolatedCenter",
"base_PsfFlux_flag",
1174 "ext_photometryKron_KronFlux_flag",
"modelfit_CModel_flag", ])
1186 \anchor MergeMeasurementsTask_ 1188 \brief Merge measurements from multiple bands 1190 \section pipe_tasks_multiBand_Contents Contents 1192 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Purpose 1193 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Initialize 1194 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Run 1195 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Config 1196 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Debug 1197 - \ref pipe_tasks_multiband_MergeMeasurementsTask_Example 1199 \section pipe_tasks_multiBand_MergeMeasurementsTask_Purpose Description 1201 Command-line task that merges measurements from multiple bands. 1203 Combines consistent (i.e. with the same peaks and footprints) catalogs of sources from multiple filter 1204 bands to construct a unified catalog that is suitable for driving forced photometry. Every source is 1205 required to have centroid, shape and flux measurements in each band. 1208 deepCoadd_meas{tract,patch,filter}: SourceCatalog 1210 deepCoadd_ref{tract,patch}: SourceCatalog 1214 MergeMeasurementsTask subclasses \ref MergeSourcesTask_ "MergeSourcesTask". 1216 \section pipe_tasks_multiBand_MergeMeasurementsTask_Initialize Task initialization 1218 \copydoc \_\_init\_\_ 1220 \section pipe_tasks_multiBand_MergeMeasurementsTask_Run Invoking the Task 1224 \section pipe_tasks_multiBand_MergeMeasurementsTask_Config Configuration parameters 1226 See \ref MergeMeasurementsConfig_ 1228 \section pipe_tasks_multiBand_MergeMeasurementsTask_Debug Debug variables 1230 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a 1231 flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py 1234 MergeMeasurementsTask has no debug variables. 1236 \section pipe_tasks_multiband_MergeMeasurementsTask_Example A complete example 1237 of using MergeMeasurementsTask 1239 MergeMeasurementsTask is meant to be run after deblending & measuring sources in every band. 1240 The purpose of the task is to generate a catalog of sources suitable for driving forced photometry in 1241 coadds and individual exposures. 1242 Command-line usage of MergeMeasurementsTask expects a data reference to the coadds to be processed. A list 1243 of the available optional arguments can be obtained by calling mergeCoaddMeasurements.py with the `--help` 1244 command line argument: 1246 mergeCoaddMeasurements.py --help 1249 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 1250 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 1251 step 7 at \ref pipeTasks_multiBand, one may merge the catalogs generated after deblending and measuring 1254 mergeCoaddMeasurements.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R 1256 This will merge the HSC-I & HSC-R band catalogs. The results are written in 1257 `$CI_HSC_DIR/DATA/deepCoadd-results/`. 1259 _DefaultName =
"mergeCoaddMeasurements" 1260 ConfigClass = MergeMeasurementsConfig
1261 inputDataset =
"meas" 1262 outputDataset =
"ref" 1263 getSchemaCatalogs = _makeGetSchemaCatalogs(
"ref")
1265 def __init__(self, butler=None, schema=None, **kwargs):
1267 Initialize the task. 1269 Additional keyword arguments (forwarded to MergeSourcesTask.__init__): 1270 \param[in] schema: the schema of the detection catalogs used as input to this one 1271 \param[in] butler: a butler used to read the input schema from disk, if schema is None 1273 The task will set its own self.schema attribute to the schema of the output merged catalog. 1275 MergeSourcesTask.__init__(self, butler=butler, schema=schema, **kwargs)
1279 self.
fluxKey = inputSchema.find(self.config.snName +
"_flux").getKey()
1280 self.
fluxErrKey = inputSchema.find(self.config.snName +
"_fluxSigma").getKey()
1281 self.
fluxFlagKey = inputSchema.find(self.config.snName +
"_flag").getKey()
1284 for band
in self.config.priorityList:
1286 outputKey = self.
schemaMapper.editOutputSchema().addField(
1287 "merge_measurement_%s" % short,
1289 doc=
"Flag field set if the measurements here are from the %s filter" % band
1291 peakKey = inputSchema.find(
"merge_peak_%s" % short).key
1292 footprintKey = inputSchema.find(
"merge_footprint_%s" % short).key
1293 self.
flagKeys[band] = Struct(peak=peakKey, footprint=footprintKey, output=outputKey)
1297 for filt
in self.config.pseudoFilterList:
1301 self.log.warn(
"merge_peak is not set for pseudo-filter %s" % filt)
1304 for flag
in self.config.flags:
1307 except KeyError
as exc:
1308 self.log.warn(
"Can't find flag %s in schema: %s" % (flag, exc,))
1312 Merge measurement catalogs to create a single reference catalog for forced photometry 1314 \param[in] catalogs: the catalogs to be merged 1315 \param[in] patchRef: patch reference for data 1317 For parent sources, we choose the first band in config.priorityList for which the 1318 merge_footprint flag for that band is is True. 1320 For child sources, the logic is the same, except that we use the merge_peak flags. 1323 orderedCatalogs = [catalogs[band]
for band
in self.config.priorityList
if band
in catalogs.keys()]
1324 orderedKeys = [self.
flagKeys[band]
for band
in self.config.priorityList
if band
in catalogs.keys()]
1326 mergedCatalog = afwTable.SourceCatalog(self.
schema)
1327 mergedCatalog.reserve(len(orderedCatalogs[0]))
1329 idKey = orderedCatalogs[0].table.getIdKey()
1330 for catalog
in orderedCatalogs[1:]:
1331 if numpy.any(orderedCatalogs[0].get(idKey) != catalog.get(idKey)):
1332 raise ValueError(
"Error in inputs to MergeCoaddMeasurements: source IDs do not match")
1336 for orderedRecords
in zip(*orderedCatalogs):
1339 maxSNFlagKeys =
None 1341 priorityRecord =
None 1342 priorityFlagKeys =
None 1344 hasPseudoFilter =
False 1348 for inputRecord, flagKeys
in zip(orderedRecords, orderedKeys):
1349 parent = (inputRecord.getParent() == 0
and inputRecord.get(flagKeys.footprint))
1350 child = (inputRecord.getParent() != 0
and inputRecord.get(flagKeys.peak))
1352 if not (parent
or child):
1354 if inputRecord.get(pseudoFilterKey):
1355 hasPseudoFilter =
True 1356 priorityRecord = inputRecord
1357 priorityFlagKeys = flagKeys
1362 isBad = any(inputRecord.get(flag)
for flag
in self.
badFlags)
1367 if numpy.isnan(sn)
or sn < 0.:
1369 if (parent
or child)
and priorityRecord
is None:
1370 priorityRecord = inputRecord
1371 priorityFlagKeys = flagKeys
1374 maxSNRecord = inputRecord
1375 maxSNFlagKeys = flagKeys
1388 bestRecord = priorityRecord
1389 bestFlagKeys = priorityFlagKeys
1390 elif (prioritySN < self.config.minSN
and (maxSN - prioritySN) > self.config.minSNDiff
and 1391 maxSNRecord
is not None):
1392 bestRecord = maxSNRecord
1393 bestFlagKeys = maxSNFlagKeys
1394 elif priorityRecord
is not None:
1395 bestRecord = priorityRecord
1396 bestFlagKeys = priorityFlagKeys
1398 if bestRecord
is not None and bestFlagKeys
is not None:
1399 outputRecord = mergedCatalog.addNew()
1401 outputRecord.set(bestFlagKeys.output,
True)
1403 raise ValueError(
"Error in inputs to MergeCoaddMeasurements: no valid reference for %s" %
1404 inputRecord.getId())
1407 for inputCatalog
in orderedCatalogs:
1408 if len(mergedCatalog) != len(inputCatalog):
1409 raise ValueError(
"Mismatch between catalog sizes: %s != %s" %
1410 (len(mergedCatalog), len(orderedCatalogs)))
1412 return mergedCatalog
def getSkySourceFootprints(self, mergedList, skyInfo, seed)
Return a list of Footprints of sky objects which don't overlap with anything in mergedList.
Merge coadd detections from multiple bands.
def makeTask(self, parsedCmd=None, args=None)
Provide a butler to the Task constructor.
def getInputSchema(self, butler=None, schema=None)
Obtain the input schema either directly or froma butler reference.
def getSchemaCatalogs(self)
Return a dict of empty catalogs for each catalog dataset produced by this task.
def runDetection(self, exposure, idFactory, expId)
Run detection on an exposure.
def cullPeaks(self, catalog)
Attempt to remove garbage peaks (mostly on the outskirts of large blends).
def run(self, patchRef)
Deblend and measure.
Task runner for the MergeSourcesTask. Required because the run method requires a list of dataRefs rat...
def write(self, exposure, results, patchRef)
Write out results from runDetection.
def __init__(self, butler=None, schema=None, kwargs)
Initialize the task.
def __init__(self, butler=None, schema=None, kwargs)
Initialize the task.
Configuration parameters for the DetectCoaddSourcesTask.
def __init__(self, schema=None, kwargs)
Initialize the task.
Merge measurements from multiple bands.
def run(self, patchRefList)
Merge coadd sources from multiple bands.
Deblend sources from master catalog in each coadd seperately and measure.
def writeMatches(self, dataRef, exposure, sources)
Write matches of the sources to the astrometric reference catalog.
def getShortFilterName(name)
def run(self, patchRef)
Run detection on a coadd.
def mergeCatalogs(self, catalogs, patchRef)
Merge measurement catalogs to create a single reference catalog for forced photometry.
def mergeCatalogs(self, catalogs, patchRef)
Merge multiple catalogs.
Configuration parameters for the MergeMeasurementsTask.
def readSources(self, dataRef)
Read input sources.
def getExposureId(self, dataRef)
Configuration parameters for the MergeDetectionsTask.
Configuration for merging sources.
def write(self, patchRef, catalog)
Write the output.
def mergeCatalogs(self, catalogs, patchRef)
Merge multiple catalogs.
A base class for merging source catalogs.
def write(self, dataRef, sources)
Write the source catalog.
def readCatalog(self, patchRef)
Read input catalog.
def scaleVariance(maskedImage, maskPlanes, log=None)
Scale the variance in a maskedImage.
Configuration parameters for the MeasureMergedCoaddSourcesTask.
def getSkyInfo(coaddName, patchRef)
Return the SkyMap, tract and patch information, wcs, and outer bbox of the patch to be coadded...
def writeMetadata(self, dataRefList)
No metadata to write, and not sure how to write it for a list of dataRefs.
def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, kwargs)
Initialize the task.
Detect sources on a coadd.
def __init__(self, butler=None, schema=None, kwargs)
Initialize the merge detections task.
def getTargetList(parsedCmd, kwargs)
Provide a list of patch references for each patch.