Coverage for python/lsst/meas/deblender/sourceDeblendTask.py: 18%
237 statements
« prev ^ index » next coverage.py v7.3.2, created at 2023-11-30 13:01 +0000
1# This file is part of meas_deblender.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
22__all__ = ['SourceDeblendConfig', 'SourceDeblendTask']
24import math
25import numpy as np
27import lsst.pex.config as pexConfig
28import lsst.pipe.base as pipeBase
29import lsst.afw.math as afwMath
30import lsst.geom as geom
31import lsst.afw.geom.ellipses as afwEll
32import lsst.afw.image as afwImage
33import lsst.afw.detection as afwDet
34import lsst.afw.table as afwTable
35from lsst.utils.timer import timeMethod
38class SourceDeblendConfig(pexConfig.Config):
40 edgeHandling = pexConfig.ChoiceField(
41 doc='What to do when a peak to be deblended is close to the edge of the image',
42 dtype=str, default='ramp',
43 allowed={
44 'clip': 'Clip the template at the edge AND the mirror of the edge.',
45 'ramp': 'Ramp down flux at the image edge by the PSF',
46 'noclip': 'Ignore the edge when building the symmetric template.',
47 }
48 )
50 strayFluxToPointSources = pexConfig.ChoiceField(
51 doc='When the deblender should attribute stray flux to point sources',
52 dtype=str, default='necessary',
53 allowed={
54 'necessary': 'When there is not an extended object in the footprint',
55 'always': 'Always',
56 'never': ('Never; stray flux will not be attributed to any deblended child '
57 'if the deblender thinks all peaks look like point sources'),
58 }
59 )
61 assignStrayFlux = pexConfig.Field(dtype=bool, default=True,
62 doc='Assign stray flux (not claimed by any child in the deblender) '
63 'to deblend children.')
65 strayFluxRule = pexConfig.ChoiceField(
66 doc='How to split flux among peaks',
67 dtype=str, default='trim',
68 allowed={
69 'r-to-peak': '~ 1/(1+R^2) to the peak',
70 'r-to-footprint': ('~ 1/(1+R^2) to the closest pixel in the footprint. '
71 'CAUTION: this can be computationally expensive on large footprints!'),
72 'nearest-footprint': ('Assign 100% to the nearest footprint (using L-1 norm aka '
73 'Manhattan distance)'),
74 'trim': ('Shrink the parent footprint to pixels that are not assigned to children')
75 }
76 )
78 clipStrayFluxFraction = pexConfig.Field(dtype=float, default=0.001,
79 doc=('When splitting stray flux, clip fractions below '
80 'this value to zero.'))
81 psfChisq1 = pexConfig.Field(dtype=float, default=1.5, optional=False,
82 doc=('Chi-squared per DOF cut for deciding a source is '
83 'a PSF during deblending (un-shifted PSF model)'))
84 psfChisq2 = pexConfig.Field(dtype=float, default=1.5, optional=False,
85 doc=('Chi-squared per DOF cut for deciding a source is '
86 'PSF during deblending (shifted PSF model)'))
87 psfChisq2b = pexConfig.Field(dtype=float, default=1.5, optional=False,
88 doc=('Chi-squared per DOF cut for deciding a source is '
89 'a PSF during deblending (shifted PSF model #2)'))
90 maxNumberOfPeaks = pexConfig.Field(dtype=int, default=0,
91 doc=("Only deblend the brightest maxNumberOfPeaks peaks in the parent"
92 " (<= 0: unlimited)"))
93 maxFootprintArea = pexConfig.Field(dtype=int, default=10000,
94 doc=("Maximum area for footprints before they are ignored as large; "
95 "non-positive means no threshold applied."
96 " Default value is to prevent excessive memory usage."))
97 maxFootprintSize = pexConfig.Field(dtype=int, default=0,
98 doc=("Maximum linear dimension for footprints before they are ignored "
99 "as large; non-positive means no threshold applied"))
100 minFootprintAxisRatio = pexConfig.Field(dtype=float, default=0.0,
101 doc=("Minimum axis ratio for footprints before they are ignored "
102 "as large; non-positive means no threshold applied"))
103 notDeblendedMask = pexConfig.Field(dtype=str, default="NOT_DEBLENDED", optional=True,
104 doc="Mask name for footprints not deblended, or None")
106 tinyFootprintSize = pexConfig.RangeField(dtype=int, default=2, min=2, inclusiveMin=True,
107 doc=('Footprints smaller in width or height than this value '
108 'will be ignored; minimum of 2 due to PSF gradient '
109 'calculation.'))
111 propagateAllPeaks = pexConfig.Field(dtype=bool, default=False,
112 doc=('Guarantee that all peaks produce a child source.'))
113 catchFailures = pexConfig.Field(
114 dtype=bool,
115 default=True,
116 doc=("If True, catch exceptions thrown by the deblender, log them, "
117 "and set a flag on the parent, instead of letting them propagate up."))
118 maskPlanes = pexConfig.ListField(dtype=str, default=["SAT", "INTRP", "NO_DATA"],
119 doc="Mask planes to ignore when performing statistics")
120 maskLimits = pexConfig.DictField(
121 keytype=str,
122 itemtype=float,
123 default={"NO_DATA": 0.25},
124 doc=("Mask planes with the corresponding limit on the fraction of masked pixels. "
125 "Sources violating this limit will not be deblended. "
126 "Default rejects sources in vignetted regions."),
127 )
128 weightTemplates = pexConfig.Field(
129 dtype=bool, default=False,
130 doc=("If true, a least-squares fit of the templates will be done to the "
131 "full image. The templates will be re-weighted based on this fit."))
132 removeDegenerateTemplates = pexConfig.Field(dtype=bool, default=False,
133 doc=("Try to remove similar templates?"))
134 maxTempDotProd = pexConfig.Field(
135 dtype=float, default=0.5,
136 doc=("If the dot product between two templates is larger than this value, we consider them to be "
137 "describing the same object (i.e. they are degenerate). If one of the objects has been "
138 "labeled as a PSF it will be removed, otherwise the template with the lowest value will "
139 "be removed."))
140 medianSmoothTemplate = pexConfig.Field(dtype=bool, default=True,
141 doc="Apply a smoothing filter to all of the template images")
143 # Testing options
144 # Some obs packages and ci packages run the full pipeline on a small
145 # subset of data to test that the pipeline is functioning properly.
146 # This is not meant as scientific validation, so it can be useful
147 # to only run on a small subset of the data that is large enough to
148 # test the desired pipeline features but not so long that the deblender
149 # is the tall pole in terms of execution times.
150 useCiLimits = pexConfig.Field(
151 dtype=bool, default=False,
152 doc="Limit the number of sources deblended for CI to prevent long build times")
153 ciDeblendChildRange = pexConfig.ListField(
154 dtype=int, default=[2, 10],
155 doc="Only deblend parent Footprints with a number of peaks in the (inclusive) range indicated."
156 "If `useCiLimits==False` then this parameter is ignored.")
157 ciNumParentsToDeblend = pexConfig.Field(
158 dtype=int, default=10,
159 doc="Only use the first `ciNumParentsToDeblend` parent footprints with a total peak count "
160 "within `ciDebledChildRange`. "
161 "If `useCiLimits==False` then this parameter is ignored.")
164class SourceDeblendTask(pipeBase.Task):
165 """Split blended sources into individual sources.
167 This task has no return value; it only modifies the SourceCatalog in-place.
168 """
169 ConfigClass = SourceDeblendConfig
170 _DefaultName = "sourceDeblend"
172 def __init__(self, schema, peakSchema=None, **kwargs):
173 """Create the task, adding necessary fields to the given schema.
175 Parameters
176 ----------
177 schema : `lsst.afw.table.Schema`
178 Schema object for measurement fields; will be modified in-place.
179 peakSchema : `lsst.afw.table.peakSchema`
180 Schema of Footprint Peaks that will be passed to the deblender.
181 Any fields beyond the PeakTable minimal schema will be transferred
182 to the main source Schema. If None, no fields will be transferred
183 from the Peaks
184 **kwargs
185 Additional keyword arguments passed to ~lsst.pipe.base.task
186 """
187 pipeBase.Task.__init__(self, **kwargs)
188 self.schema = schema
189 self.toCopyFromParent = [item.key for item in self.schema
190 if item.field.getName().startswith("merge_footprint")]
191 peakMinimalSchema = afwDet.PeakTable.makeMinimalSchema()
192 if peakSchema is None:
193 # In this case, the peakSchemaMapper will transfer nothing, but we'll still have one
194 # to simplify downstream code
195 self.peakSchemaMapper = afwTable.SchemaMapper(peakMinimalSchema, schema)
196 else:
197 self.peakSchemaMapper = afwTable.SchemaMapper(peakSchema, schema)
198 for item in peakSchema:
199 if item.key not in peakMinimalSchema:
200 self.peakSchemaMapper.addMapping(item.key, item.field)
201 # Because SchemaMapper makes a copy of the output schema you give its ctor, it isn't
202 # updating this Schema in place. That's probably a design flaw, but in the meantime,
203 # we'll keep that schema in sync with the peakSchemaMapper.getOutputSchema() manually,
204 # by adding the same fields to both.
205 schema.addField(item.field)
206 assert schema == self.peakSchemaMapper.getOutputSchema(), "Logic bug mapping schemas"
207 self.addSchemaKeys(schema)
209 def addSchemaKeys(self, schema):
210 self.nChildKey = schema.addField('deblend_nChild', type=np.int32,
211 doc='Number of children this object has (defaults to 0)')
212 self.psfKey = schema.addField('deblend_deblendedAsPsf', type='Flag',
213 doc='Deblender thought this source looked like a PSF')
214 self.psfCenterKey = afwTable.Point2DKey.addFields(schema, 'deblend_psfCenter',
215 'If deblended-as-psf, the PSF centroid', "pixel")
216 self.psfFluxKey = schema.addField('deblend_psf_instFlux', type='D',
217 doc='If deblended-as-psf, the instrumental PSF flux', units='count')
218 self.tooManyPeaksKey = schema.addField('deblend_tooManyPeaks', type='Flag',
219 doc='Source had too many peaks; '
220 'only the brightest were included')
221 self.tooBigKey = schema.addField('deblend_parentTooBig', type='Flag',
222 doc='Parent footprint covered too many pixels')
223 self.maskedKey = schema.addField('deblend_masked', type='Flag',
224 doc='Parent footprint was predominantly masked')
226 if self.config.catchFailures:
227 self.deblendFailedKey = schema.addField('deblend_failed', type='Flag',
228 doc="Deblending failed on source")
230 self.deblendSkippedKey = schema.addField('deblend_skipped', type='Flag',
231 doc="Deblender skipped this source")
233 self.deblendRampedTemplateKey = schema.addField(
234 'deblend_rampedTemplate', type='Flag',
235 doc=('This source was near an image edge and the deblender used '
236 '"ramp" edge-handling.'))
238 self.deblendPatchedTemplateKey = schema.addField(
239 'deblend_patchedTemplate', type='Flag',
240 doc=('This source was near an image edge and the deblender used '
241 '"patched" edge-handling.'))
243 self.hasStrayFluxKey = schema.addField(
244 'deblend_hasStrayFlux', type='Flag',
245 doc=('This source was assigned some stray flux'))
247 self.log.trace('Added keys to schema: %s', ", ".join(str(x) for x in (
248 self.nChildKey, self.psfKey, self.psfCenterKey, self.psfFluxKey,
249 self.tooManyPeaksKey, self.tooBigKey)))
250 self.peakCenter = afwTable.Point2IKey.addFields(schema, name="deblend_peak_center",
251 doc="Center used to apply constraints in scarlet",
252 unit="pixel")
253 self.peakIdKey = schema.addField("deblend_peakId", type=np.int32,
254 doc="ID of the peak in the parent footprint. "
255 "This is not unique, but the combination of 'parent'"
256 "and 'peakId' should be for all child sources. "
257 "Top level blends with no parents have 'peakId=0'")
258 self.nPeaksKey = schema.addField("deblend_nPeaks", type=np.int32,
259 doc="Number of initial peaks in the blend. "
260 "This includes peaks that may have been culled "
261 "during deblending or failed to deblend")
262 self.parentNPeaksKey = schema.addField("deblend_parentNPeaks", type=np.int32,
263 doc="Same as deblend_n_peaks, but the number of peaks "
264 "in the parent footprint")
266 @timeMethod
267 def run(self, exposure, sources):
268 """Get the PSF from the provided exposure and then run deblend.
270 Parameters
271 ----------
272 exposure : `lsst.afw.image.Exposure`
273 Exposure to be processed
274 sources : `lsst.afw.table.SourceCatalog`
275 SourceCatalog containing sources detected on this exposure.
276 """
277 psf = exposure.getPsf()
278 assert sources.getSchema() == self.schema
279 self.deblend(exposure, sources, psf)
281 def _getPsfFwhm(self, psf, position):
282 return psf.computeShape(position).getDeterminantRadius() * 2.35
284 @timeMethod
285 def deblend(self, exposure, srcs, psf):
286 """Deblend.
288 Parameters
289 ----------
290 exposure : `lsst.afw.image.Exposure`
291 Exposure to be processed
292 srcs : `lsst.afw.table.SourceCatalog`
293 SourceCatalog containing sources detected on this exposure
294 psf : `lsst.afw.detection.Psf`
295 Point source function
297 Returns
298 -------
299 None
300 """
301 # Cull footprints if required by ci
302 if self.config.useCiLimits:
303 self.log.info(f"Using CI catalog limits, "
304 f"the original number of sources to deblend was {len(srcs)}.")
305 # Select parents with a number of children in the range
306 # config.ciDeblendChildRange
307 minChildren, maxChildren = self.config.ciDeblendChildRange
308 nPeaks = np.array([len(src.getFootprint().peaks) for src in srcs])
309 childrenInRange = np.where((nPeaks >= minChildren) & (nPeaks <= maxChildren))[0]
310 if len(childrenInRange) < self.config.ciNumParentsToDeblend:
311 raise ValueError("Fewer than ciNumParentsToDeblend children were contained in the range "
312 "indicated by ciDeblendChildRange. Adjust this range to include more "
313 "parents.")
314 # Keep all of the isolated parents and the first
315 # `ciNumParentsToDeblend` children
316 parents = nPeaks == 1
317 children = np.zeros((len(srcs),), dtype=bool)
318 children[childrenInRange[:self.config.ciNumParentsToDeblend]] = True
319 srcs = srcs[parents | children]
320 # We need to update the IdFactory, otherwise the the source ids
321 # will not be sequential
322 idFactory = srcs.getIdFactory()
323 maxId = np.max(srcs["id"])
324 idFactory.notify(maxId)
326 self.log.info("Deblending %d sources", len(srcs))
328 from lsst.meas.deblender.baseline import deblend
330 # find the median stdev in the image...
331 mi = exposure.getMaskedImage()
332 statsCtrl = afwMath.StatisticsControl()
333 statsCtrl.setAndMask(mi.getMask().getPlaneBitMask(self.config.maskPlanes))
334 stats = afwMath.makeStatistics(mi.getVariance(), mi.getMask(), afwMath.MEDIAN, statsCtrl)
335 sigma1 = math.sqrt(stats.getValue(afwMath.MEDIAN))
336 self.log.trace('sigma1: %g', sigma1)
338 n0 = len(srcs)
339 nparents = 0
340 for i, src in enumerate(srcs):
341 # t0 = time.clock()
343 fp = src.getFootprint()
344 pks = fp.getPeaks()
346 # Since we use the first peak for the parent object, we should propagate its flags
347 # to the parent source.
348 src.assign(pks[0], self.peakSchemaMapper)
350 if len(pks) < 2:
351 continue
353 if self.isLargeFootprint(fp):
354 src.set(self.tooBigKey, True)
355 self.skipParent(src, mi.getMask())
356 self.log.warning('Parent %i: skipping large footprint (area: %i)',
357 int(src.getId()), int(fp.getArea()))
358 continue
359 if self.isMasked(fp, exposure.getMaskedImage().getMask()):
360 src.set(self.maskedKey, True)
361 self.skipParent(src, mi.getMask())
362 self.log.warning('Parent %i: skipping masked footprint (area: %i)',
363 int(src.getId()), int(fp.getArea()))
364 continue
366 nparents += 1
367 center = fp.getCentroid()
368 psf_fwhm = self._getPsfFwhm(psf, center)
370 if not (psf_fwhm > 0):
371 if self.config.catchFailures:
372 self.log.warning("Unable to deblend source %d: because PSF FWHM=%f is invalid.",
373 src.getId(), psf_fwhm)
374 src.set(self.deblendFailedKey, True)
375 continue
376 else:
377 raise ValueError(f"PSF at {center} has an invalid FWHM value of {psf_fwhm}")
379 self.log.trace('Parent %i: deblending %i peaks', int(src.getId()), len(pks))
381 self.preSingleDeblendHook(exposure, srcs, i, fp, psf, psf_fwhm, sigma1)
382 npre = len(srcs)
384 # This should really be set in deblend, but deblend doesn't have access to the src
385 src.set(self.tooManyPeaksKey, len(fp.getPeaks()) > self.config.maxNumberOfPeaks)
387 try:
388 res = deblend(
389 fp, mi, psf, psf_fwhm, sigma1=sigma1,
390 psfChisqCut1=self.config.psfChisq1,
391 psfChisqCut2=self.config.psfChisq2,
392 psfChisqCut2b=self.config.psfChisq2b,
393 maxNumberOfPeaks=self.config.maxNumberOfPeaks,
394 strayFluxToPointSources=self.config.strayFluxToPointSources,
395 assignStrayFlux=self.config.assignStrayFlux,
396 strayFluxAssignment=self.config.strayFluxRule,
397 rampFluxAtEdge=(self.config.edgeHandling == 'ramp'),
398 patchEdges=(self.config.edgeHandling == 'noclip'),
399 tinyFootprintSize=self.config.tinyFootprintSize,
400 clipStrayFluxFraction=self.config.clipStrayFluxFraction,
401 weightTemplates=self.config.weightTemplates,
402 removeDegenerateTemplates=self.config.removeDegenerateTemplates,
403 maxTempDotProd=self.config.maxTempDotProd,
404 medianSmoothTemplate=self.config.medianSmoothTemplate
405 )
406 if self.config.catchFailures:
407 src.set(self.deblendFailedKey, False)
408 except Exception as e:
409 if self.config.catchFailures:
410 self.log.warning("Unable to deblend source %d: %s", src.getId(), e)
411 src.set(self.deblendFailedKey, True)
412 import traceback
413 traceback.print_exc()
414 continue
415 else:
416 raise
418 kids = []
419 nchild = 0
420 for j, peak in enumerate(res.deblendedParents[0].peaks):
421 heavy = peak.getFluxPortion()
422 if heavy is None or peak.skip:
423 src.set(self.deblendSkippedKey, True)
424 if not self.config.propagateAllPeaks:
425 # Don't care
426 continue
427 # We need to preserve the peak: make sure we have enough info to create a minimal
428 # child src
429 self.log.trace("Peak at (%i,%i) failed. Using minimal default info for child.",
430 pks[j].getIx(), pks[j].getIy())
431 if heavy is None:
432 # copy the full footprint and strip out extra peaks
433 foot = afwDet.Footprint(src.getFootprint())
434 peakList = foot.getPeaks()
435 peakList.clear()
436 peakList.append(peak.peak)
437 zeroMimg = afwImage.MaskedImageF(foot.getBBox())
438 heavy = afwDet.makeHeavyFootprint(foot, zeroMimg)
439 if peak.deblendedAsPsf:
440 if peak.psfFitFlux is None:
441 peak.psfFitFlux = 0.0
442 if peak.psfFitCenter is None:
443 peak.psfFitCenter = (peak.peak.getIx(), peak.peak.getIy())
445 assert len(heavy.getPeaks()) == 1
447 src.set(self.deblendSkippedKey, False)
448 child = srcs.addNew()
449 nchild += 1
450 for key in self.toCopyFromParent:
451 child.set(key, src.get(key))
452 child.assign(heavy.getPeaks()[0], self.peakSchemaMapper)
453 child.setParent(src.getId())
454 child.setFootprint(heavy)
455 child.set(self.psfKey, peak.deblendedAsPsf)
456 child.set(self.hasStrayFluxKey, peak.strayFlux is not None)
457 if peak.deblendedAsPsf:
458 (cx, cy) = peak.psfFitCenter
459 child.set(self.psfCenterKey, geom.Point2D(cx, cy))
460 child.set(self.psfFluxKey, peak.psfFitFlux)
461 child.set(self.deblendRampedTemplateKey, peak.hasRampedTemplate)
462 child.set(self.deblendPatchedTemplateKey, peak.patched)
464 # Set the position of the peak from the parent footprint
465 # This will make it easier to match the same source across
466 # deblenders and across observations, where the peak
467 # position is unlikely to change unless enough time passes
468 # for a source to move on the sky.
469 child.set(self.peakCenter, geom.Point2I(pks[j].getIx(), pks[j].getIy()))
470 child.set(self.peakIdKey, pks[j].getId())
472 # The children have a single peak
473 child.set(self.nPeaksKey, 1)
474 # Set the number of peaks in the parent
475 child.set(self.parentNPeaksKey, len(pks))
477 kids.append(child)
479 # Child footprints may extend beyond the full extent of their parent's which
480 # results in a failure of the replace-by-noise code to reinstate these pixels
481 # to their original values. The following updates the parent footprint
482 # in-place to ensure it contains the full union of itself and all of its
483 # children's footprints.
484 spans = src.getFootprint().spans
485 for child in kids:
486 spans = spans.union(child.getFootprint().spans)
487 src.getFootprint().setSpans(spans)
489 src.set(self.nChildKey, nchild)
491 self.postSingleDeblendHook(exposure, srcs, i, npre, kids, fp, psf, psf_fwhm, sigma1, res)
492 # print('Deblending parent id', src.getId(), 'took', time.clock() - t0)
494 n1 = len(srcs)
495 self.log.info('Deblended: of %i sources, %i were deblended, creating %i children, total %i sources',
496 n0, nparents, n1-n0, n1)
498 def preSingleDeblendHook(self, exposure, srcs, i, fp, psf, psf_fwhm, sigma1):
499 pass
501 def postSingleDeblendHook(self, exposure, srcs, i, npre, kids, fp, psf, psf_fwhm, sigma1, res):
502 pass
504 def isLargeFootprint(self, footprint):
505 """Returns whether a Footprint is large
507 'Large' is defined by thresholds on the area, size and axis ratio.
508 These may be disabled independently by configuring them to be non-positive.
510 This is principally intended to get rid of satellite streaks, which the
511 deblender or other downstream processing can have trouble dealing with
512 (e.g., multiple large HeavyFootprints can chew up memory).
513 """
514 if self.config.maxFootprintArea > 0 and footprint.getArea() > self.config.maxFootprintArea:
515 return True
516 if self.config.maxFootprintSize > 0:
517 bbox = footprint.getBBox()
518 if max(bbox.getWidth(), bbox.getHeight()) > self.config.maxFootprintSize:
519 return True
520 if self.config.minFootprintAxisRatio > 0:
521 axes = afwEll.Axes(footprint.getShape())
522 if axes.getB() < self.config.minFootprintAxisRatio*axes.getA():
523 return True
524 return False
526 def isMasked(self, footprint, mask):
527 """Returns whether the footprint violates the mask limits
528 """
529 size = float(footprint.getArea())
530 for maskName, limit in self.config.maskLimits.items():
531 maskVal = mask.getPlaneBitMask(maskName)
532 unmaskedSpan = footprint.spans.intersectNot(mask, maskVal) # spanset of unmasked pixels
533 if (size - unmaskedSpan.getArea())/size > limit:
534 return True
535 return False
537 def skipParent(self, source, mask):
538 """Indicate that the parent source is not being deblended
540 We set the appropriate flags and mask.
542 Parameters
543 ----------
544 source : `lsst.afw.table.SourceRecord`
545 The source to flag as skipped
546 mask : `lsst.afw.image.Mask`
547 The mask to update
548 """
549 fp = source.getFootprint()
550 source.set(self.deblendSkippedKey, True)
551 if self.config.notDeblendedMask:
552 mask.addMaskPlane(self.config.notDeblendedMask)
553 fp.spans.setMask(mask, mask.getPlaneBitMask(self.config.notDeblendedMask))
555 # Set the center of the parent
556 bbox = fp.getBBox()
557 centerX = int(bbox.getMinX()+bbox.getWidth()/2)
558 centerY = int(bbox.getMinY()+bbox.getHeight()/2)
559 source.set(self.peakCenter, geom.Point2I(centerX, centerY))
560 # There are no deblended children, so nChild = 0
561 source.set(self.nChildKey, 0)
562 # But we also want to know how many peaks that we would have
563 # deblended if the parent wasn't skipped.
564 source.set(self.nPeaksKey, len(fp.peaks))
565 # Top level parents are not a detected peak, so they have no peakId
566 source.set(self.peakIdKey, 0)
567 # Top level parents also have no parentNPeaks
568 source.set(self.parentNPeaksKey, 0)