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=SourceDetectionTask, 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.background.useApprox =
False 133 self.
detection.background.undersampleStyle =
'REDUCE_INTERP_ORDER' 145 \anchor DetectCoaddSourcesTask_ 147 \brief Detect sources on a coadd 149 \section pipe_tasks_multiBand_Contents Contents 151 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose 152 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize 153 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run 154 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config 155 - \ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug 156 - \ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example 158 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description 160 Command-line task that detects sources on a coadd of exposures obtained with a single filter. 162 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise 163 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane 164 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should 165 propagate the full covariance matrix -- but it is simple and works well in practice. 167 After scaling the variance plane, we detect sources and generate footprints by delegating to the \ref 168 SourceDetectionTask_ "detection" subtask. 171 deepCoadd{tract,patch,filter}: ExposureF 173 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) 174 \n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input 176 \n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList 180 DetectCoaddSourcesTask delegates most of its work to the \ref SourceDetectionTask_ "detection" subtask. 181 You can retarget this subtask if you wish. 183 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization 185 \copydoc \_\_init\_\_ 187 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task 191 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters 193 See \ref DetectCoaddSourcesConfig_ "DetectSourcesConfig" 195 \section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables 197 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a 198 flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py 201 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to 202 \ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for 203 \ref SourceDetectionTask_ "SourceDetectionTask" for further information. 205 \section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example of using DetectCoaddSourcesTask 207 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of 208 the task is to update the background, detect all sources in a single band and generate a set of parent 209 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and, 210 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data 211 reference to the coadd to be processed. A list of the available optional arguments can be obtained by 212 calling detectCoaddSources.py with the `--help` command line argument: 214 detectCoaddSources.py --help 217 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 218 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed 219 steps 1 - 4 at \ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows: 221 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 223 that will process the HSC-I band data. The results are written to 224 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`. 226 It is also necessary to run: 228 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 230 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 231 processing procedure: \ref MergeDetectionsTask_ "MergeDetectionsTask". 233 _DefaultName =
"detectCoaddSources" 234 ConfigClass = DetectCoaddSourcesConfig
235 getSchemaCatalogs = _makeGetSchemaCatalogs(
"det")
236 makeIdFactory = _makeMakeIdFactory(
"CoaddId")
239 def _makeArgumentParser(cls):
241 parser.add_id_argument(
"--id",
"deepCoadd", help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
242 ContainerClass=ExistingCoaddDataIdContainer)
247 \brief Initialize the task. Create the \ref SourceDetectionTask_ "detection" subtask. 249 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 251 \param[in] schema: initial schema for the output catalog, modified-in place to include all 252 fields set by this task. If None, the source minimal schema will be used. 253 \param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__ 255 CmdLineTask.__init__(self, **kwargs)
257 schema = afwTable.SourceTable.makeMinimalSchema()
258 if self.config.doInsertFakes:
259 self.makeSubtask(
"insertFakes")
261 self.makeSubtask(
"detection", schema=self.
schema)
265 \brief Run detection on a coadd. 267 Invokes \ref runDetection and then uses \ref write to output the 270 \param[in] patchRef: data reference for patch 272 exposure = patchRef.get(self.config.coaddName +
"Coadd", immediate=
True)
274 self.
write(exposure, results, patchRef)
279 \brief Run detection on an exposure. 281 First scale the variance plane to match the observed variance 282 using \ref scaleVariance. Then invoke the \ref SourceDetectionTask_ "detection" subtask to 285 \param[in] exposure: Exposure on which to detect 286 \param[in] idFactory: IdFactory to set source identifiers 288 \return a pipe.base.Struct with fields 289 - sources: catalog of detections 290 - backgrounds: list of backgrounds 292 if self.config.doScaleVariance:
293 varScale =
scaleVariance(exposure.getMaskedImage(), self.config.mask, log=self.log)
294 self.metadata.add(
"variance_scale", varScale)
295 backgrounds = afwMath.BackgroundList()
296 if self.config.doInsertFakes:
297 self.insertFakes.
run(exposure, background=backgrounds)
298 table = afwTable.SourceTable.make(self.
schema, idFactory)
299 detections = self.detection.makeSourceCatalog(table, exposure)
300 sources = detections.sources
301 fpSets = detections.fpSets
302 if fpSets.background:
303 backgrounds.append(fpSets.background)
304 return Struct(sources=sources, backgrounds=backgrounds)
306 def write(self, exposure, results, patchRef):
308 \brief Write out results from runDetection. 310 \param[in] exposure: Exposure to write out 311 \param[in] results: Struct returned from runDetection 312 \param[in] patchRef: data reference for patch 314 coaddName = self.config.coaddName +
"Coadd" 315 patchRef.put(results.backgrounds, coaddName +
"_calexp_background")
316 patchRef.put(results.sources, coaddName +
"_det")
317 patchRef.put(exposure, coaddName +
"_calexp")
324 \anchor MergeSourcesRunner_ 326 \brief Task runner for the \ref MergeSourcesTask_ "MergeSourcesTask". Required because the run method 327 requires a list of dataRefs rather than a single dataRef. 332 \brief Provide a butler to the Task constructor. 334 \param[in] parsedCmd the parsed command 335 \param[in] args tuple of a list of data references and kwargs (un-used) 336 \throws RuntimeError if both parsedCmd & args are None 338 if parsedCmd
is not None:
339 butler = parsedCmd.butler
340 elif args
is not None:
341 dataRefList, kwargs = args
342 butler = dataRefList[0].getButler()
344 raise RuntimeError(
"Neither parsedCmd or args specified")
345 return self.TaskClass(config=self.config, log=self.log, butler=butler)
350 \brief Provide a list of patch references for each patch. 352 The patch references within the list will have different filters. 354 \param[in] parsedCmd the parsed command 355 \param **kwargs key word arguments (unused) 356 \throws RuntimeError if multiple references are provided for the same combination of tract, patch and 360 for ref
in parsedCmd.id.refList:
361 tract = ref.dataId[
"tract"]
362 patch = ref.dataId[
"patch"]
363 filter = ref.dataId[
"filter"]
364 if not tract
in refList:
366 if not patch
in refList[tract]:
367 refList[tract][patch] = {}
368 if filter
in refList[tract][patch]:
369 raise RuntimeError(
"Multiple versions of %s" % (ref.dataId,))
370 refList[tract][patch][filter] = ref
371 return [(list(p.values()), kwargs)
for t
in refList.values()
for p
in t.values()]
376 \anchor MergeSourcesConfig_ 378 \brief Configuration for merging sources. 380 priorityList = ListField(dtype=str, default=[],
381 doc=
"Priority-ordered list of bands for the merge.")
382 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
385 Config.validate(self)
387 raise RuntimeError(
"No priority list provided")
392 \anchor MergeSourcesTask_ 394 \brief A base class for merging source catalogs. 396 Merging detections (MergeDetectionsTask) and merging measurements (MergeMeasurementsTask) are 397 so similar that it makes sense to re-use the code, in the form of this abstract base class. 399 NB: Do not use this class directly. Instead use one of the child classes that inherit from 400 MergeSourcesTask such as \ref MergeDetectionsTask_ "MergeDetectionsTask" or \ref MergeMeasurementsTask_ 401 "MergeMeasurementsTask" 403 Sub-classes should set the following class variables: 404 * `_DefaultName`: name of Task 405 * `inputDataset`: name of dataset to read 406 * `outputDataset`: name of dataset to write 407 * `getSchemaCatalogs` to the result of `_makeGetSchemaCatalogs(outputDataset)` 409 In addition, sub-classes must implement the mergeCatalogs method. 412 ConfigClass = MergeSourcesConfig
413 RunnerClass = MergeSourcesRunner
416 getSchemaCatalogs =
None 419 def _makeArgumentParser(cls):
421 \brief Create a suitable ArgumentParser. 423 We will use the ArgumentParser to get a provide a list of data 424 references for patches; the RunnerClass will sort them into lists 425 of data references for the same patch 428 parser.add_id_argument(
"--id",
"deepCoadd_" + cls.
inputDataset,
429 ContainerClass=ExistingCoaddDataIdContainer,
430 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i")
435 \brief Obtain the input schema either directly or froma butler reference. 437 \param[in] butler butler reference to obtain the input schema from 438 \param[in] schema the input schema 441 assert butler
is not None,
"Neither butler nor schema specified" 442 schema = butler.get(self.config.coaddName +
"Coadd_" + self.
inputDataset +
"_schema",
443 immediate=
True).schema
446 def __init__(self, butler=None, schema=None, **kwargs):
448 \brief Initialize the task. 450 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 451 \param[in] schema the schema of the detection catalogs used as input to this one 452 \param[in] butler a butler used to read the input schema from disk, if schema is None 454 Derived classes should use the getInputSchema() method to handle the additional 455 arguments and retreive the actual input schema. 457 CmdLineTask.__init__(self, **kwargs)
459 def run(self, patchRefList):
461 \brief Merge coadd sources from multiple bands. Calls \ref mergeCatalogs which must be defined in 462 subclasses that inherit from MergeSourcesTask. 464 \param[in] patchRefList list of data references for each filter 466 catalogs = dict(self.
readCatalog(patchRef)
for patchRef
in patchRefList)
467 mergedCatalog = self.
mergeCatalogs(catalogs, patchRefList[0])
468 self.
write(patchRefList[0], mergedCatalog)
472 \brief Read input catalog. 474 We read the input dataset provided by the 'inputDataset' 477 \param[in] patchRef data reference for patch 478 \return tuple consisting of the filter name and the catalog 480 filterName = patchRef.dataId[
"filter"]
481 catalog = patchRef.get(self.config.coaddName +
"Coadd_" + self.
inputDataset, immediate=
True)
482 self.log.info(
"Read %d sources for filter %s: %s" % (len(catalog), filterName, patchRef.dataId))
483 return filterName, catalog
487 \brief Merge multiple catalogs. This function must be defined in all subclasses that inherit from 490 \param[in] catalogs dict mapping filter name to source catalog 492 \return merged catalog 494 raise NotImplementedError()
498 \brief Write the output. 500 \param[in] patchRef data reference for patch 501 \param[in] catalog catalog 503 We write as the dataset provided by the 'outputDataset' 506 patchRef.put(catalog, self.config.coaddName +
"Coadd_" + self.
outputDataset)
509 mergeDataId = patchRef.dataId.copy()
510 del mergeDataId[
"filter"]
511 self.log.info(
"Wrote merged catalog: %s" % (mergeDataId,))
515 \brief No metadata to write, and not sure how to write it for a list of dataRefs. 520 class CullPeaksConfig(Config):
522 \anchor CullPeaksConfig_ 524 \brief Configuration for culling garbage peaks after merging footprints. 526 Peaks may also be culled after detection or during deblending; this configuration object 527 only deals with culling after merging Footprints. 529 These cuts are based on three quantities: 530 - nBands: the number of bands in which the peak was detected 531 - peakRank: the position of the peak within its family, sorted from brightest to faintest. 532 - peakRankNormalized: the peak rank divided by the total number of peaks in the family. 534 The formula that identifie peaks to cull is: 536 nBands < nBandsSufficient 537 AND (rank >= rankSufficient) 538 AND (rank >= rankConsider OR rank >= rankNormalizedConsider) 540 To disable peak culling, simply set nBandsSufficient=1. 543 nBandsSufficient = RangeField(dtype=int, default=2, min=1,
544 doc=
"Always keep peaks detected in this many bands")
545 rankSufficient = RangeField(dtype=int, default=20, min=1,
546 doc=
"Always keep this many peaks in each family")
547 rankConsidered = RangeField(dtype=int, default=30, min=1,
548 doc=(
"Keep peaks with less than this rank that also match the " 549 "rankNormalizedConsidered condition."))
550 rankNormalizedConsidered = RangeField(dtype=float, default=0.7, min=0.0,
551 doc=(
"Keep peaks with less than this normalized rank that" 552 " also match the rankConsidered condition."))
557 \anchor MergeDetectionsConfig_ 559 \brief Configuration parameters for the MergeDetectionsTask. 561 minNewPeak = Field(dtype=float, default=1,
562 doc=
"Minimum distance from closest peak to create a new one (in arcsec).")
564 maxSamePeak = Field(dtype=float, default=0.3,
565 doc=
"When adding new catalogs to the merge, all peaks less than this distance " 566 " (in arcsec) to an existing peak will be flagged as detected in that catalog.")
567 cullPeaks = ConfigField(dtype=CullPeaksConfig, doc=
"Configuration for how to cull peaks.")
569 skyFilterName = Field(dtype=str, default=
"sky",
570 doc=
"Name of `filter' used to label sky objects (e.g. flag merge_peak_sky is set)\n" 571 "(N.b. should be in MergeMeasurementsConfig.pseudoFilterList)")
572 skySourceRadius = Field(dtype=float, default=8,
573 doc=
"Radius, in pixels, of sky objects")
574 skyGrowDetectedFootprints = Field(dtype=int, default=0,
575 doc=
"Number of pixels to grow the detected footprint mask " 576 "when adding sky objects")
577 nSkySourcesPerPatch = Field(dtype=int, default=100,
578 doc=
"Try to add this many sky objects to the mergeDet list, which will\n" 579 "then be measured along with the detected objects in sourceMeasurementTask")
580 nTrialSkySourcesPerPatch = Field(dtype=int, default=
None, optional=
True,
581 doc=
"Maximum number of trial sky object positions\n" 582 "(default: nSkySourcesPerPatch*nTrialSkySourcesPerPatchMultiplier)")
583 nTrialSkySourcesPerPatchMultiplier = Field(dtype=int, default=5,
584 doc=
"Set nTrialSkySourcesPerPatch to\n" 585 " nSkySourcesPerPatch*nTrialSkySourcesPerPatchMultiplier\n" 586 "if nTrialSkySourcesPerPatch is None")
598 \anchor MergeDetectionsTask_ 600 \brief Merge coadd detections from multiple bands. 602 \section pipe_tasks_multiBand_Contents Contents 604 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Purpose 605 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Init 606 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Run 607 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Config 608 - \ref pipe_tasks_multiBand_MergeDetectionsTask_Debug 609 - \ref pipe_tasks_multiband_MergeDetectionsTask_Example 611 \section pipe_tasks_multiBand_MergeDetectionsTask_Purpose Description 613 Command-line task that merges sources detected in coadds of exposures obtained with different filters. 615 To perform photometry consistently across coadds in multiple filter bands, we create a master catalog of 616 sources from all bands by merging the sources (peaks & footprints) detected in each coadd, while keeping 617 track of which band each source originates in. 619 The catalog merge is performed by \ref getMergedSourceCatalog. Spurious peaks detected around bright 620 objects are culled as described in \ref CullPeaksConfig_. 623 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) 625 deepCoadd_mergeDet{tract,patch}: SourceCatalog (only parent Footprints) 629 MergeDetectionsTask subclasses \ref MergeSourcesTask_ "MergeSourcesTask". 631 \section pipe_tasks_multiBand_MergeDetectionsTask_Init Task initialisation 633 \copydoc \_\_init\_\_ 635 \section pipe_tasks_multiBand_MergeDetectionsTask_Run Invoking the Task 639 \section pipe_tasks_multiBand_MergeDetectionsTask_Config Configuration parameters 641 See \ref MergeDetectionsConfig_ 643 \section pipe_tasks_multiBand_MergeDetectionsTask_Debug Debug variables 645 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a flag \c -d 646 to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py files. 648 MergeDetectionsTask has no debug variables. 650 \section pipe_tasks_multiband_MergeDetectionsTask_Example A complete example of using MergeDetectionsTask 652 MergeDetectionsTask is meant to be run after detecting sources in coadds generated for the chosen subset 653 of the available bands. 654 The purpose of the task is to merge sources (peaks & footprints) detected in the coadds generated from the 655 chosen subset of filters. 656 Subsequent tasks in the multi-band processing procedure will deblend the generated master list of sources 657 and, eventually, perform forced photometry. 658 Command-line usage of MergeDetectionsTask expects data references for all the coadds to be processed. 659 A list of the available optional arguments can be obtained by calling mergeCoaddDetections.py with the 660 `--help` command line argument: 662 mergeCoaddDetections.py --help 665 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 666 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 667 step 5 at \ref pipeTasks_multiBand, one may merge the catalogs of sources from each coadd as follows: 669 mergeCoaddDetections.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R 671 This will merge the HSC-I & -R band parent source catalogs and write the results to 672 `$CI_HSC_DIR/DATA/deepCoadd-results/merged/0/5,4/mergeDet-0-5,4.fits`. 674 The next step in the multi-band processing procedure is 675 \ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" 677 ConfigClass = MergeDetectionsConfig
678 _DefaultName =
"mergeCoaddDetections" 680 outputDataset =
"mergeDet" 681 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId")
683 def __init__(self, butler=None, schema=None, **kwargs):
685 \brief Initialize the merge detections task. 687 A \ref FootprintMergeList_ "FootprintMergeList" will be used to 688 merge the source catalogs. 690 Additional keyword arguments (forwarded to MergeSourcesTask.__init__): 691 \param[in] schema the schema of the detection catalogs used as input to this one 692 \param[in] butler a butler used to read the input schema from disk, if schema is None 693 \param[in] **kwargs keyword arguments to be passed to MergeSourcesTask.__init__ 695 The task will set its own self.schema attribute to the schema of the output merged catalog. 697 MergeSourcesTask.__init__(self, butler=butler, schema=schema, **kwargs)
701 if self.config.nSkySourcesPerPatch > 0:
702 filterNames += [self.config.skyFilterName]
707 \brief Merge multiple catalogs. 709 After ordering the catalogs and filters in priority order, 710 \ref getMergedSourceCatalog of the \ref FootprintMergeList_ "FootprintMergeList" created by 711 \ref \_\_init\_\_ is used to perform the actual merging. Finally, \ref cullPeaks is used to remove 712 garbage peaks detected around bright objects. 716 \param[out] mergedList 720 skyInfo =
getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
721 tractWcs = skyInfo.wcs
722 peakDistance = self.config.minNewPeak / tractWcs.pixelScale().asArcseconds()
723 samePeakDistance = self.config.maxSamePeak / tractWcs.pixelScale().asArcseconds()
726 orderedCatalogs = [catalogs[band]
for band
in self.config.priorityList
if band
in catalogs.keys()]
728 if band
in catalogs.keys()]
730 mergedList = self.
merged.getMergedSourceCatalog(orderedCatalogs, orderedBands, peakDistance,
738 mergedList, skyInfo, self.config.skyGrowDetectedFootprints)
739 if skySourceFootprints:
740 key = mergedList.schema.find(
"merge_footprint_%s" % self.config.skyFilterName).key
742 for foot
in skySourceFootprints:
743 s = mergedList.addNew()
747 self.log.info(
"Added %d sky sources (%.0f%% of requested)",
748 len(skySourceFootprints),
749 100*len(skySourceFootprints)/float(self.config.nSkySourcesPerPatch))
752 for record
in mergedList:
753 record.getFootprint().sortPeaks()
754 self.log.info(
"Merged to %d sources" % len(mergedList))
761 \brief Attempt to remove garbage peaks (mostly on the outskirts of large blends). 763 \param[in] catalog Source catalog 765 keys = [item.key
for item
in self.
merged.getPeakSchema().extract(
"merge_peak_*").values()]
766 assert len(keys) > 0,
"Error finding flags that associate peaks with their detection bands." 769 for parentSource
in catalog:
772 keptPeaks = parentSource.getFootprint().getPeaks()
773 oldPeaks = list(keptPeaks)
775 familySize = len(oldPeaks)
776 totalPeaks += familySize
777 for rank, peak
in enumerate(oldPeaks):
778 if ((rank < self.config.cullPeaks.rankSufficient)
or 779 (sum([peak.get(k)
for k
in keys]) >= self.config.cullPeaks.nBandsSufficient)
or 780 (rank < self.config.cullPeaks.rankConsidered
and 781 rank < self.config.cullPeaks.rankNormalizedConsidered * familySize)):
782 keptPeaks.append(peak)
785 self.log.info(
"Culled %d of %d peaks" % (culledPeaks, totalPeaks))
789 Return a dict of empty catalogs for each catalog dataset produced by this task. 791 \param[out] dictionary of empty catalogs 793 mergeDet = afwTable.SourceCatalog(self.
schema)
794 peak = afwDetect.PeakCatalog(self.
merged.getPeakSchema())
795 return {self.config.coaddName +
"Coadd_mergeDet": mergeDet,
796 self.config.coaddName +
"Coadd_peak": peak}
800 \brief Return a list of Footprints of sky objects which don't overlap with anything in mergedList 802 \param mergedList The merged Footprints from all the input bands 803 \param skyInfo A description of the patch 804 \param growDetectedFootprints The number of pixels to grow the detected footprints 807 if self.config.nSkySourcesPerPatch <= 0:
810 skySourceRadius = self.config.skySourceRadius
811 nSkySourcesPerPatch = self.config.nSkySourcesPerPatch
812 nTrialSkySourcesPerPatch = self.config.nTrialSkySourcesPerPatch
813 if nTrialSkySourcesPerPatch
is None:
814 nTrialSkySourcesPerPatch = self.config.nTrialSkySourcesPerPatchMultiplier*nSkySourcesPerPatch
820 patchBBox = skyInfo.patchInfo.getOuterBBox()
821 mask = afwImage.Mask(patchBBox)
822 detectedMask = mask.getPlaneBitMask(
"DETECTED")
824 foot = s.getFootprint()
825 if growDetectedFootprints > 0:
826 foot.dilate(growDetectedFootprints)
827 foot.spans.setMask(mask, detectedMask)
829 xmin, ymin = patchBBox.getMin()
830 xmax, ymax = patchBBox.getMax()
832 xmin += skySourceRadius + 1
833 ymin += skySourceRadius + 1
834 xmax -= skySourceRadius + 1
835 ymax -= skySourceRadius + 1
837 skySourceFootprints = []
838 maskToSpanSet = afwGeom.SpanSet.fromMask(mask)
839 for i
in range(nTrialSkySourcesPerPatch):
840 if len(skySourceFootprints) == nSkySourcesPerPatch:
843 x = int(numpy.random.uniform(xmin, xmax))
844 y = int(numpy.random.uniform(ymin, ymax))
845 spans = afwGeom.SpanSet.fromShape(int(skySourceRadius),
847 foot = afwDetect.Footprint(spans, patchBBox)
848 foot.setPeakSchema(self.
merged.getPeakSchema())
850 if not foot.spans.overlaps(maskToSpanSet):
851 foot.addPeak(x, y, 0)
852 foot.getPeaks()[0].set(
"merge_peak_%s" % self.config.skyFilterName,
True)
853 skySourceFootprints.append(foot)
855 return skySourceFootprints
860 \anchor MeasureMergedCoaddSourcesConfig_ 862 \brief Configuration parameters for the MeasureMergedCoaddSourcesTask 864 doDeblend = Field(dtype=bool, default=
True, doc=
"Deblend sources?")
865 deblend = ConfigurableField(target=SourceDeblendTask, doc=
"Deblend sources")
866 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc=
"Source measurement")
867 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc=
"Set flags for primary tract/patch")
868 doPropagateFlags = Field(
869 dtype=bool, default=
True,
870 doc=
"Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)" 872 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc=
"Propagate visit flags to coadd")
873 doMatchSources = Field(dtype=bool, default=
True, doc=
"Match sources to reference catalog?")
874 match = ConfigurableField(target=DirectMatchTask, doc=
"Matching to reference catalog")
875 doWriteMatchesDenormalized = Field(
878 doc=(
"Write reference matches in denormalized format? " 879 "This format uses more disk space, but is more convenient to read."),
881 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
882 checkUnitsParseStrict = Field(
883 doc=
"Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
890 doc=
"Apply aperture corrections" 892 applyApCorr = ConfigurableField(
893 target=ApplyApCorrTask,
894 doc=
"Subtask to apply aperture corrections" 896 doRunCatalogCalculation = Field(
899 doc=
'Run catalogCalculation task' 901 catalogCalculation = ConfigurableField(
902 target=CatalogCalculationTask,
903 doc=
"Subtask to run catalogCalculation plugins on catalog" 907 Config.setDefaults(self)
908 self.
deblend.propagateAllPeaks =
True 909 self.
measurement.plugins.names |= [
'base_InputCount']
912 self.
measurement.plugins[
'base_PixelFlags'].masksFpAnywhere = [
'CLIPPED']
924 \anchor MeasureMergedCoaddSourcesTask_ 926 \brief Deblend sources from master catalog in each coadd seperately and measure. 928 \section pipe_tasks_multiBand_Contents Contents 930 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose 931 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize 932 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run 933 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config 934 - \ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug 935 - \ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example 937 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description 939 Command-line task that uses peaks and footprints from a master catalog to perform deblending and 940 measurement in each coadd. 942 Given a master input catalog of sources (peaks and footprints), deblend and measure each source on the 943 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a 944 consistent set of child sources. 946 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source 947 properties are measured and the \c is-primary flag (indicating sources with no children) is set. Visit 948 flags are propagated to the coadd sources. 950 Optionally, we can match the coadd sources to an external reference catalog. 953 deepCoadd_mergeDet{tract,patch}: SourceCatalog 954 \n deepCoadd_calexp{tract,patch,filter}: ExposureF 956 deepCoadd_meas{tract,patch,filter}: SourceCatalog 960 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks: 963 <DT> \ref SourceDeblendTask_ "deblend" 964 <DD> Deblend all the sources from the master catalog.</DD> 965 <DT> \ref SingleFrameMeasurementTask_ "measurement" 966 <DD> Measure source properties of deblended sources.</DD> 967 <DT> \ref SetPrimaryFlagsTask_ "setPrimaryFlags" 968 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are 969 not at the edge of the field and that have either not been deblended or are the children of deblended 971 <DT> \ref PropagateVisitFlagsTask_ "propagateFlags" 972 <DD> Propagate flags set in individual visits to the coadd.</DD> 973 <DT> \ref DirectMatchTask_ "match" 974 <DD> Match input sources to a reference catalog (optional). 977 These subtasks may be retargeted as required. 979 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization 981 \copydoc \_\_init\_\_ 983 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task 987 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters 989 See \ref MeasureMergedCoaddSourcesConfig_ 991 \section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables 993 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a 994 flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py 997 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to 998 the various sub-tasks. See the documetation for individual sub-tasks for more information. 1000 \section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using MeasureMergedCoaddSourcesTask 1002 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs. 1003 The next stage in the multi-band processing procedure will merge these measurements into a suitable 1004 catalog for driving forced photometry. 1006 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds to be processed. 1007 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the 1008 `--help` command line argument: 1010 measureCoaddSources.py --help 1013 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 1014 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 1015 step 6 at \ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band 1018 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 1020 This will process the HSC-I band data. The results are written in 1021 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits 1023 It is also necessary to run 1025 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 1027 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 1028 procedure: \ref MergeMeasurementsTask_ "MergeMeasurementsTask". 1030 _DefaultName =
"measureCoaddSources" 1031 ConfigClass = MeasureMergedCoaddSourcesConfig
1032 RunnerClass = ButlerInitializedTaskRunner
1033 getSchemaCatalogs = _makeGetSchemaCatalogs(
"meas")
1034 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId")
1037 def _makeArgumentParser(cls):
1039 parser.add_id_argument(
"--id",
"deepCoadd_calexp",
1040 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
1041 ContainerClass=ExistingCoaddDataIdContainer)
1044 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, **kwargs):
1046 \brief Initialize the task. 1048 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 1049 \param[in] schema: the schema of the merged detection catalog used as input to this one 1050 \param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog 1051 \param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference 1052 catalog. May be None if the loader can be constructed from the butler argument or all steps 1053 requiring a reference catalog are disabled. 1054 \param[in] butler: a butler used to read the input schemas from disk or construct the reference 1055 catalog loader, if schema or peakSchema or refObjLoader is None 1057 The task will set its own self.schema attribute to the schema of the output measurement catalog. 1058 This will include all fields from the input schema, as well as additional fields for all the 1061 CmdLineTask.__init__(self, **kwargs)
1063 assert butler
is not None,
"Neither butler nor schema is defined" 1064 schema = butler.get(self.config.coaddName +
"Coadd_mergeDet_schema", immediate=
True).schema
1069 if self.config.doDeblend:
1070 if peakSchema
is None:
1071 assert butler
is not None,
"Neither butler nor peakSchema is defined" 1072 peakSchema = butler.get(self.config.coaddName +
"Coadd_peak_schema", immediate=
True).schema
1073 self.makeSubtask(
"deblend", schema=self.
schema, peakSchema=peakSchema)
1074 self.makeSubtask(
"measurement", schema=self.
schema, algMetadata=self.
algMetadata)
1075 self.makeSubtask(
"setPrimaryFlags", schema=self.
schema)
1076 if self.config.doMatchSources:
1077 if refObjLoader
is None:
1078 assert butler
is not None,
"Neither butler nor refObjLoader is defined" 1079 self.makeSubtask(
"match", butler=butler, refObjLoader=refObjLoader)
1080 if self.config.doPropagateFlags:
1081 self.makeSubtask(
"propagateFlags", schema=self.
schema)
1082 self.
schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
1083 if self.config.doApCorr:
1084 self.makeSubtask(
"applyApCorr", schema=self.
schema)
1085 if self.config.doRunCatalogCalculation:
1086 self.makeSubtask(
"catalogCalculation", schema=self.
schema)
1090 \brief Deblend and measure. 1092 \param[in] patchRef: Patch reference. 1094 Deblend each source in every coadd and measure. Set 'is-primary' and related flags. Propagate flags 1095 from individual visits. Optionally match the sources to a reference catalog and write the matches. 1096 Finally, write the deblended sources and measurements out. 1098 exposure = patchRef.get(self.config.coaddName +
"Coadd_calexp", immediate=
True)
1100 if self.config.doDeblend:
1101 self.deblend.
run(exposure, sources)
1103 bigKey = sources.schema[
"deblend_parentTooBig"].asKey()
1105 numBig = sum((s.get(bigKey)
for s
in sources))
1107 self.log.warn(
"Patch %s contains %d large footprints that were not deblended" %
1108 (patchRef.dataId, numBig))
1110 table = sources.getTable()
1113 self.measurement.
run(sources, exposure, exposureId=self.
getExposureId(patchRef))
1115 if self.config.doApCorr:
1116 self.applyApCorr.
run(
1118 apCorrMap=exposure.getInfo().getApCorrMap()
1121 if self.config.doRunCatalogCalculation:
1122 self.catalogCalculation.
run(sources)
1124 skyInfo =
getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1125 self.setPrimaryFlags.
run(sources, skyInfo.skyMap, skyInfo.tractInfo, skyInfo.patchInfo,
1126 includeDeblend=self.config.doDeblend)
1127 if self.config.doPropagateFlags:
1128 self.propagateFlags.
run(patchRef.getButler(), sources, self.propagateFlags.getCcdInputs(exposure),
1130 if self.config.doMatchSources:
1132 self.
write(patchRef, sources)
1136 \brief Read input sources. 1138 \param[in] dataRef: Data reference for catalog of merged detections 1139 \return List of sources in merged catalog 1141 We also need to add columns to hold the measurements we're about to make 1142 so we can measure in-place. 1144 merged = dataRef.get(self.config.coaddName +
"Coadd_mergeDet", immediate=
True)
1145 self.log.info(
"Read %d detections: %s" % (len(merged), dataRef.dataId))
1148 idFactory.notify(s.getId())
1149 table = afwTable.SourceTable.make(self.
schema, idFactory)
1150 sources = afwTable.SourceCatalog(table)
1156 \brief Write matches of the sources to the astrometric reference catalog. 1158 We use the Wcs in the exposure to match sources. 1160 \param[in] dataRef: data reference 1161 \param[in] exposure: exposure with Wcs 1162 \param[in] sources: source catalog 1164 result = self.match.
run(sources, exposure.getInfo().getFilter().getName())
1166 matches = afwTable.packMatches(result.matches)
1167 matches.table.setMetadata(result.matchMeta)
1168 dataRef.put(matches, self.config.coaddName +
"Coadd_measMatch")
1169 if self.config.doWriteMatchesDenormalized:
1170 denormMatches = denormalizeMatches(result.matches, result.matchMeta)
1171 dataRef.put(denormMatches, self.config.coaddName +
"Coadd_measMatchFull")
1176 \brief Write the source catalog. 1178 \param[in] dataRef: data reference 1179 \param[in] sources: source catalog 1181 dataRef.put(sources, self.config.coaddName +
"Coadd_meas")
1182 self.log.info(
"Wrote %d sources: %s" % (len(sources), dataRef.dataId))
1185 return int(dataRef.get(self.config.coaddName +
"CoaddId"))
1192 \anchor MergeMeasurementsConfig_ 1194 \brief Configuration parameters for the MergeMeasurementsTask 1196 pseudoFilterList = ListField(dtype=str, default=[
"sky"],
1197 doc=
"Names of filters which may have no associated detection\n" 1198 "(N.b. should include MergeDetectionsConfig.skyFilterName)")
1199 snName = Field(dtype=str, default=
"base_PsfFlux",
1200 doc=
"Name of flux measurement for calculating the S/N when choosing the reference band.")
1201 minSN = Field(dtype=float, default=10.,
1202 doc=
"If the S/N from the priority band is below this value (and the S/N " 1203 "is larger than minSNDiff compared to the priority band), use the band with " 1204 "the largest S/N as the reference band.")
1205 minSNDiff = Field(dtype=float, default=3.,
1206 doc=
"If the difference in S/N between another band and the priority band is larger " 1207 "than this value (and the S/N in the priority band is less than minSN) " 1208 "use the band with the largest S/N as the reference band")
1209 flags = ListField(dtype=str, doc=
"Require that these flags, if available, are not set",
1210 default=[
"base_PixelFlags_flag_interpolatedCenter",
"base_PsfFlux_flag",
1211 "ext_photometryKron_KronFlux_flag",
"modelfit_CModel_flag", ])
1223 \anchor MergeMeasurementsTask_ 1225 \brief Merge measurements from multiple bands 1227 \section pipe_tasks_multiBand_Contents Contents 1229 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Purpose 1230 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Initialize 1231 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Run 1232 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Config 1233 - \ref pipe_tasks_multiBand_MergeMeasurementsTask_Debug 1234 - \ref pipe_tasks_multiband_MergeMeasurementsTask_Example 1236 \section pipe_tasks_multiBand_MergeMeasurementsTask_Purpose Description 1238 Command-line task that merges measurements from multiple bands. 1240 Combines consistent (i.e. with the same peaks and footprints) catalogs of sources from multiple filter 1241 bands to construct a unified catalog that is suitable for driving forced photometry. Every source is 1242 required to have centroid, shape and flux measurements in each band. 1245 deepCoadd_meas{tract,patch,filter}: SourceCatalog 1247 deepCoadd_ref{tract,patch}: SourceCatalog 1251 MergeMeasurementsTask subclasses \ref MergeSourcesTask_ "MergeSourcesTask". 1253 \section pipe_tasks_multiBand_MergeMeasurementsTask_Initialize Task initialization 1255 \copydoc \_\_init\_\_ 1257 \section pipe_tasks_multiBand_MergeMeasurementsTask_Run Invoking the Task 1261 \section pipe_tasks_multiBand_MergeMeasurementsTask_Config Configuration parameters 1263 See \ref MergeMeasurementsConfig_ 1265 \section pipe_tasks_multiBand_MergeMeasurementsTask_Debug Debug variables 1267 The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a 1268 flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py 1271 MergeMeasurementsTask has no debug variables. 1273 \section pipe_tasks_multiband_MergeMeasurementsTask_Example A complete example of using MergeMeasurementsTask 1275 MergeMeasurementsTask is meant to be run after deblending & measuring sources in every band. 1276 The purpose of the task is to generate a catalog of sources suitable for driving forced photometry in 1277 coadds and individual exposures. 1278 Command-line usage of MergeMeasurementsTask expects a data reference to the coadds to be processed. A list 1279 of the available optional arguments can be obtained by calling mergeCoaddMeasurements.py with the `--help` 1280 command line argument: 1282 mergeCoaddMeasurements.py --help 1285 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 1286 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 1287 step 7 at \ref pipeTasks_multiBand, one may merge the catalogs generated after deblending and measuring 1290 mergeCoaddMeasurements.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R 1292 This will merge the HSC-I & HSC-R band catalogs. The results are written in 1293 `$CI_HSC_DIR/DATA/deepCoadd-results/`. 1295 _DefaultName =
"mergeCoaddMeasurements" 1296 ConfigClass = MergeMeasurementsConfig
1297 inputDataset =
"meas" 1298 outputDataset =
"ref" 1299 getSchemaCatalogs = _makeGetSchemaCatalogs(
"ref")
1301 def __init__(self, butler=None, schema=None, **kwargs):
1303 Initialize the task. 1305 Additional keyword arguments (forwarded to MergeSourcesTask.__init__): 1306 \param[in] schema: the schema of the detection catalogs used as input to this one 1307 \param[in] butler: a butler used to read the input schema from disk, if schema is None 1309 The task will set its own self.schema attribute to the schema of the output merged catalog. 1311 MergeSourcesTask.__init__(self, butler=butler, schema=schema, **kwargs)
1315 self.
fluxKey = inputSchema.find(self.config.snName +
"_flux").getKey()
1316 self.
fluxErrKey = inputSchema.find(self.config.snName +
"_fluxSigma").getKey()
1317 self.
fluxFlagKey = inputSchema.find(self.config.snName +
"_flag").getKey()
1320 for band
in self.config.priorityList:
1322 outputKey = self.
schemaMapper.editOutputSchema().addField(
1323 "merge_measurement_%s" % short,
1325 doc=
"Flag field set if the measurements here are from the %s filter" % band
1327 peakKey = inputSchema.find(
"merge_peak_%s" % short).key
1328 footprintKey = inputSchema.find(
"merge_footprint_%s" % short).key
1329 self.
flagKeys[band] = Struct(peak=peakKey, footprint=footprintKey, output=outputKey)
1333 for filt
in self.config.pseudoFilterList:
1337 self.log.warn(
"merge_peak is not set for pseudo-filter %s" % filt)
1340 for flag
in self.config.flags:
1343 except KeyError
as exc:
1344 self.log.warn(
"Can't find flag %s in schema: %s" % (flag, exc,))
1348 Merge measurement catalogs to create a single reference catalog for forced photometry 1350 \param[in] catalogs: the catalogs to be merged 1351 \param[in] patchRef: patch reference for data 1353 For parent sources, we choose the first band in config.priorityList for which the 1354 merge_footprint flag for that band is is True. 1356 For child sources, the logic is the same, except that we use the merge_peak flags. 1359 orderedCatalogs = [catalogs[band]
for band
in self.config.priorityList
if band
in catalogs.keys()]
1360 orderedKeys = [self.
flagKeys[band]
for band
in self.config.priorityList
if band
in catalogs.keys()]
1362 mergedCatalog = afwTable.SourceCatalog(self.
schema)
1363 mergedCatalog.reserve(len(orderedCatalogs[0]))
1365 idKey = orderedCatalogs[0].table.getIdKey()
1366 for catalog
in orderedCatalogs[1:]:
1367 if numpy.any(orderedCatalogs[0].get(idKey) != catalog.get(idKey)):
1368 raise ValueError(
"Error in inputs to MergeCoaddMeasurements: source IDs do not match")
1372 for orderedRecords
in zip(*orderedCatalogs):
1375 maxSNFlagKeys =
None 1377 priorityRecord =
None 1378 priorityFlagKeys =
None 1380 hasPseudoFilter =
False 1384 for inputRecord, flagKeys
in zip(orderedRecords, orderedKeys):
1385 parent = (inputRecord.getParent() == 0
and inputRecord.get(flagKeys.footprint))
1386 child = (inputRecord.getParent() != 0
and inputRecord.get(flagKeys.peak))
1388 if not (parent
or child):
1390 if inputRecord.get(pseudoFilterKey):
1391 hasPseudoFilter =
True 1392 priorityRecord = inputRecord
1393 priorityFlagKeys = flagKeys
1398 isBad = any(inputRecord.get(flag)
for flag
in self.
badFlags)
1403 if numpy.isnan(sn)
or sn < 0.:
1405 if (parent
or child)
and priorityRecord
is None:
1406 priorityRecord = inputRecord
1407 priorityFlagKeys = flagKeys
1410 maxSNRecord = inputRecord
1411 maxSNFlagKeys = flagKeys
1424 bestRecord = priorityRecord
1425 bestFlagKeys = priorityFlagKeys
1426 elif (prioritySN < self.config.minSN
and (maxSN - prioritySN) > self.config.minSNDiff
and 1427 maxSNRecord
is not None):
1428 bestRecord = maxSNRecord
1429 bestFlagKeys = maxSNFlagKeys
1430 elif priorityRecord
is not None:
1431 bestRecord = priorityRecord
1432 bestFlagKeys = priorityFlagKeys
1434 if bestRecord
is not None and bestFlagKeys
is not None:
1435 outputRecord = mergedCatalog.addNew()
1437 outputRecord.set(bestFlagKeys.output,
True)
1439 raise ValueError(
"Error in inputs to MergeCoaddMeasurements: no valid reference for %s" %
1440 inputRecord.getId())
1443 for inputCatalog
in orderedCatalogs:
1444 if len(mergedCatalog) != len(inputCatalog):
1445 raise ValueError(
"Mismatch between catalog sizes: %s != %s" %
1446 (len(mergedCatalog), len(orderedCatalogs)))
1448 return mergedCatalog
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 getSkySourceFootprints(self, mergedList, skyInfo, growDetectedFootprints=0)
Return a list of Footprints of sky objects which don't overlap with anything in mergedList.
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 runDetection(self, exposure, idFactory)
Run detection on an exposure.
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.