Coverage for python/lsst/meas/deblender/sourceDeblendTask.py: 19%

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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/>. 

21 

22__all__ = ['SourceDeblendConfig', 'SourceDeblendTask'] 

23 

24import math 

25import numpy as np 

26 

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 

36 

37 

38class SourceDeblendConfig(pexConfig.Config): 

39 

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 ) 

49 

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 ) 

60 

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.') 

64 

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 ) 

77 

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=1000000, 

94 doc=("Maximum area for footprints before they are ignored as large; " 

95 "non-positive means no threshold applied")) 

96 maxFootprintSize = pexConfig.Field(dtype=int, default=0, 

97 doc=("Maximum linear dimension for footprints before they are ignored " 

98 "as large; non-positive means no threshold applied")) 

99 minFootprintAxisRatio = pexConfig.Field(dtype=float, default=0.0, 

100 doc=("Minimum axis ratio for footprints before they are ignored " 

101 "as large; non-positive means no threshold applied")) 

102 notDeblendedMask = pexConfig.Field(dtype=str, default="NOT_DEBLENDED", optional=True, 

103 doc="Mask name for footprints not deblended, or None") 

104 

105 tinyFootprintSize = pexConfig.RangeField(dtype=int, default=2, min=2, inclusiveMin=True, 

106 doc=('Footprints smaller in width or height than this value ' 

107 'will be ignored; minimum of 2 due to PSF gradient ' 

108 'calculation.')) 

109 

110 propagateAllPeaks = pexConfig.Field(dtype=bool, default=False, 

111 doc=('Guarantee that all peaks produce a child source.')) 

112 catchFailures = pexConfig.Field( 

113 dtype=bool, default=False, 

114 doc=("If True, catch exceptions thrown by the deblender, log them, " 

115 "and set a flag on the parent, instead of letting them propagate up")) 

116 maskPlanes = pexConfig.ListField(dtype=str, default=["SAT", "INTRP", "NO_DATA"], 

117 doc="Mask planes to ignore when performing statistics") 

118 maskLimits = pexConfig.DictField( 

119 keytype=str, 

120 itemtype=float, 

121 default={}, 

122 doc=("Mask planes with the corresponding limit on the fraction of masked pixels. " 

123 "Sources violating this limit will not be deblended."), 

124 ) 

125 weightTemplates = pexConfig.Field( 

126 dtype=bool, default=False, 

127 doc=("If true, a least-squares fit of the templates will be done to the " 

128 "full image. The templates will be re-weighted based on this fit.")) 

129 removeDegenerateTemplates = pexConfig.Field(dtype=bool, default=False, 

130 doc=("Try to remove similar templates?")) 

131 maxTempDotProd = pexConfig.Field( 

132 dtype=float, default=0.5, 

133 doc=("If the dot product between two templates is larger than this value, we consider them to be " 

134 "describing the same object (i.e. they are degenerate). If one of the objects has been " 

135 "labeled as a PSF it will be removed, otherwise the template with the lowest value will " 

136 "be removed.")) 

137 medianSmoothTemplate = pexConfig.Field(dtype=bool, default=True, 

138 doc="Apply a smoothing filter to all of the template images") 

139 

140 # Testing options 

141 # Some obs packages and ci packages run the full pipeline on a small 

142 # subset of data to test that the pipeline is functioning properly. 

143 # This is not meant as scientific validation, so it can be useful 

144 # to only run on a small subset of the data that is large enough to 

145 # test the desired pipeline features but not so long that the deblender 

146 # is the tall pole in terms of execution times. 

147 useCiLimits = pexConfig.Field( 

148 dtype=bool, default=False, 

149 doc="Limit the number of sources deblended for CI to prevent long build times") 

150 ciDeblendChildRange = pexConfig.ListField( 

151 dtype=int, default=[2, 10], 

152 doc="Only deblend parent Footprints with a number of peaks in the (inclusive) range indicated." 

153 "If `useCiLimits==False` then this parameter is ignored.") 

154 ciNumParentsToDeblend = pexConfig.Field( 

155 dtype=int, default=10, 

156 doc="Only use the first `ciNumParentsToDeblend` parent footprints with a total peak count " 

157 "within `ciDebledChildRange`. " 

158 "If `useCiLimits==False` then this parameter is ignored.") 

159 

160 

161class SourceDeblendTask(pipeBase.Task): 

162 """Split blended sources into individual sources. 

163 

164 This task has no return value; it only modifies the SourceCatalog in-place. 

165 """ 

166 ConfigClass = SourceDeblendConfig 

167 _DefaultName = "sourceDeblend" 

168 

169 def __init__(self, schema, peakSchema=None, **kwargs): 

170 """Create the task, adding necessary fields to the given schema. 

171 

172 Parameters 

173 ---------- 

174 schema : `lsst.afw.table.Schema` 

175 Schema object for measurement fields; will be modified in-place. 

176 peakSchema : `lsst.afw.table.peakSchema` 

177 Schema of Footprint Peaks that will be passed to the deblender. 

178 Any fields beyond the PeakTable minimal schema will be transferred 

179 to the main source Schema. If None, no fields will be transferred 

180 from the Peaks 

181 **kwargs 

182 Additional keyword arguments passed to ~lsst.pipe.base.task 

183 """ 

184 pipeBase.Task.__init__(self, **kwargs) 

185 self.schema = schema 

186 self.toCopyFromParent = [item.key for item in self.schema 

187 if item.field.getName().startswith("merge_footprint")] 

188 peakMinimalSchema = afwDet.PeakTable.makeMinimalSchema() 

189 if peakSchema is None: 

190 # In this case, the peakSchemaMapper will transfer nothing, but we'll still have one 

191 # to simplify downstream code 

192 self.peakSchemaMapper = afwTable.SchemaMapper(peakMinimalSchema, schema) 

193 else: 

194 self.peakSchemaMapper = afwTable.SchemaMapper(peakSchema, schema) 

195 for item in peakSchema: 

196 if item.key not in peakMinimalSchema: 

197 self.peakSchemaMapper.addMapping(item.key, item.field) 

198 # Because SchemaMapper makes a copy of the output schema you give its ctor, it isn't 

199 # updating this Schema in place. That's probably a design flaw, but in the meantime, 

200 # we'll keep that schema in sync with the peakSchemaMapper.getOutputSchema() manually, 

201 # by adding the same fields to both. 

202 schema.addField(item.field) 

203 assert schema == self.peakSchemaMapper.getOutputSchema(), "Logic bug mapping schemas" 

204 self.addSchemaKeys(schema) 

205 

206 def addSchemaKeys(self, schema): 

207 self.nChildKey = schema.addField('deblend_nChild', type=np.int32, 

208 doc='Number of children this object has (defaults to 0)') 

209 self.psfKey = schema.addField('deblend_deblendedAsPsf', type='Flag', 

210 doc='Deblender thought this source looked like a PSF') 

211 self.psfCenterKey = afwTable.Point2DKey.addFields(schema, 'deblend_psfCenter', 

212 'If deblended-as-psf, the PSF centroid', "pixel") 

213 self.psfFluxKey = schema.addField('deblend_psf_instFlux', type='D', 

214 doc='If deblended-as-psf, the instrumental PSF flux', units='count') 

215 self.tooManyPeaksKey = schema.addField('deblend_tooManyPeaks', type='Flag', 

216 doc='Source had too many peaks; ' 

217 'only the brightest were included') 

218 self.tooBigKey = schema.addField('deblend_parentTooBig', type='Flag', 

219 doc='Parent footprint covered too many pixels') 

220 self.maskedKey = schema.addField('deblend_masked', type='Flag', 

221 doc='Parent footprint was predominantly masked') 

222 

223 if self.config.catchFailures: 

224 self.deblendFailedKey = schema.addField('deblend_failed', type='Flag', 

225 doc="Deblending failed on source") 

226 

227 self.deblendSkippedKey = schema.addField('deblend_skipped', type='Flag', 

228 doc="Deblender skipped this source") 

229 

230 self.deblendRampedTemplateKey = schema.addField( 

231 'deblend_rampedTemplate', type='Flag', 

232 doc=('This source was near an image edge and the deblender used ' 

233 '"ramp" edge-handling.')) 

234 

235 self.deblendPatchedTemplateKey = schema.addField( 

236 'deblend_patchedTemplate', type='Flag', 

237 doc=('This source was near an image edge and the deblender used ' 

238 '"patched" edge-handling.')) 

239 

240 self.hasStrayFluxKey = schema.addField( 

241 'deblend_hasStrayFlux', type='Flag', 

242 doc=('This source was assigned some stray flux')) 

243 

244 self.log.trace('Added keys to schema: %s', ", ".join(str(x) for x in ( 

245 self.nChildKey, self.psfKey, self.psfCenterKey, self.psfFluxKey, 

246 self.tooManyPeaksKey, self.tooBigKey))) 

247 self.peakCenter = afwTable.Point2IKey.addFields(schema, name="deblend_peak_center", 

248 doc="Center used to apply constraints in scarlet", 

249 unit="pixel") 

250 self.peakIdKey = schema.addField("deblend_peakId", type=np.int32, 

251 doc="ID of the peak in the parent footprint. " 

252 "This is not unique, but the combination of 'parent'" 

253 "and 'peakId' should be for all child sources. " 

254 "Top level blends with no parents have 'peakId=0'") 

255 self.nPeaksKey = schema.addField("deblend_nPeaks", type=np.int32, 

256 doc="Number of initial peaks in the blend. " 

257 "This includes peaks that may have been culled " 

258 "during deblending or failed to deblend") 

259 self.parentNPeaksKey = schema.addField("deblend_parentNPeaks", type=np.int32, 

260 doc="Same as deblend_n_peaks, but the number of peaks " 

261 "in the parent footprint") 

262 

263 @timeMethod 

264 def run(self, exposure, sources): 

265 """Get the PSF from the provided exposure and then run deblend. 

266 

267 Parameters 

268 ---------- 

269 exposure : `lsst.afw.image.Exposure` 

270 Exposure to be processed 

271 sources : `lsst.afw.table.SourceCatalog` 

272 SourceCatalog containing sources detected on this exposure. 

273 """ 

274 psf = exposure.getPsf() 

275 assert sources.getSchema() == self.schema 

276 self.deblend(exposure, sources, psf) 

277 

278 def _getPsfFwhm(self, psf, position): 

279 return psf.computeShape(position).getDeterminantRadius() * 2.35 

280 

281 @timeMethod 

282 def deblend(self, exposure, srcs, psf): 

283 """Deblend. 

284 

285 Parameters 

286 ---------- 

287 exposure : `lsst.afw.image.Exposure` 

288 Exposure to be processed 

289 srcs : `lsst.afw.table.SourceCatalog` 

290 SourceCatalog containing sources detected on this exposure 

291 psf : `lsst.afw.detection.Psf` 

292 Point source function 

293 

294 Returns 

295 ------- 

296 None 

297 """ 

298 # Cull footprints if required by ci 

299 if self.config.useCiLimits: 

300 self.log.info(f"Using CI catalog limits, " 

301 f"the original number of sources to deblend was {len(srcs)}.") 

302 # Select parents with a number of children in the range 

303 # config.ciDeblendChildRange 

304 minChildren, maxChildren = self.config.ciDeblendChildRange 

305 nPeaks = np.array([len(src.getFootprint().peaks) for src in srcs]) 

306 childrenInRange = np.where((nPeaks >= minChildren) & (nPeaks <= maxChildren))[0] 

307 if len(childrenInRange) < self.config.ciNumParentsToDeblend: 

308 raise ValueError("Fewer than ciNumParentsToDeblend children were contained in the range " 

309 "indicated by ciDeblendChildRange. Adjust this range to include more " 

310 "parents.") 

311 # Keep all of the isolated parents and the first 

312 # `ciNumParentsToDeblend` children 

313 parents = nPeaks == 1 

314 children = np.zeros((len(srcs),), dtype=bool) 

315 children[childrenInRange[:self.config.ciNumParentsToDeblend]] = True 

316 srcs = srcs[parents | children] 

317 # We need to update the IdFactory, otherwise the the source ids 

318 # will not be sequential 

319 idFactory = srcs.getIdFactory() 

320 maxId = np.max(srcs["id"]) 

321 idFactory.notify(maxId) 

322 

323 self.log.info("Deblending %d sources", len(srcs)) 

324 

325 from lsst.meas.deblender.baseline import deblend 

326 

327 # find the median stdev in the image... 

328 mi = exposure.getMaskedImage() 

329 statsCtrl = afwMath.StatisticsControl() 

330 statsCtrl.setAndMask(mi.getMask().getPlaneBitMask(self.config.maskPlanes)) 

331 stats = afwMath.makeStatistics(mi.getVariance(), mi.getMask(), afwMath.MEDIAN, statsCtrl) 

332 sigma1 = math.sqrt(stats.getValue(afwMath.MEDIAN)) 

333 self.log.trace('sigma1: %g', sigma1) 

334 

335 n0 = len(srcs) 

336 nparents = 0 

337 for i, src in enumerate(srcs): 

338 # t0 = time.clock() 

339 

340 fp = src.getFootprint() 

341 pks = fp.getPeaks() 

342 

343 # Since we use the first peak for the parent object, we should propagate its flags 

344 # to the parent source. 

345 src.assign(pks[0], self.peakSchemaMapper) 

346 

347 if len(pks) < 2: 

348 continue 

349 

350 if self.isLargeFootprint(fp): 

351 src.set(self.tooBigKey, True) 

352 self.skipParent(src, mi.getMask()) 

353 self.log.warning('Parent %i: skipping large footprint (area: %i)', 

354 int(src.getId()), int(fp.getArea())) 

355 continue 

356 if self.isMasked(fp, exposure.getMaskedImage().getMask()): 

357 src.set(self.maskedKey, True) 

358 self.skipParent(src, mi.getMask()) 

359 self.log.warning('Parent %i: skipping masked footprint (area: %i)', 

360 int(src.getId()), int(fp.getArea())) 

361 continue 

362 

363 nparents += 1 

364 center = fp.getCentroid() 

365 psf_fwhm = self._getPsfFwhm(psf, center) 

366 

367 self.log.trace('Parent %i: deblending %i peaks', int(src.getId()), len(pks)) 

368 

369 self.preSingleDeblendHook(exposure, srcs, i, fp, psf, psf_fwhm, sigma1) 

370 npre = len(srcs) 

371 

372 # This should really be set in deblend, but deblend doesn't have access to the src 

373 src.set(self.tooManyPeaksKey, len(fp.getPeaks()) > self.config.maxNumberOfPeaks) 

374 

375 try: 

376 res = deblend( 

377 fp, mi, psf, psf_fwhm, sigma1=sigma1, 

378 psfChisqCut1=self.config.psfChisq1, 

379 psfChisqCut2=self.config.psfChisq2, 

380 psfChisqCut2b=self.config.psfChisq2b, 

381 maxNumberOfPeaks=self.config.maxNumberOfPeaks, 

382 strayFluxToPointSources=self.config.strayFluxToPointSources, 

383 assignStrayFlux=self.config.assignStrayFlux, 

384 strayFluxAssignment=self.config.strayFluxRule, 

385 rampFluxAtEdge=(self.config.edgeHandling == 'ramp'), 

386 patchEdges=(self.config.edgeHandling == 'noclip'), 

387 tinyFootprintSize=self.config.tinyFootprintSize, 

388 clipStrayFluxFraction=self.config.clipStrayFluxFraction, 

389 weightTemplates=self.config.weightTemplates, 

390 removeDegenerateTemplates=self.config.removeDegenerateTemplates, 

391 maxTempDotProd=self.config.maxTempDotProd, 

392 medianSmoothTemplate=self.config.medianSmoothTemplate 

393 ) 

394 if self.config.catchFailures: 

395 src.set(self.deblendFailedKey, False) 

396 except Exception as e: 

397 if self.config.catchFailures: 

398 self.log.warning("Unable to deblend source %d: %s", src.getId(), e) 

399 src.set(self.deblendFailedKey, True) 

400 import traceback 

401 traceback.print_exc() 

402 continue 

403 else: 

404 raise 

405 

406 kids = [] 

407 nchild = 0 

408 for j, peak in enumerate(res.deblendedParents[0].peaks): 

409 heavy = peak.getFluxPortion() 

410 if heavy is None or peak.skip: 

411 src.set(self.deblendSkippedKey, True) 

412 if not self.config.propagateAllPeaks: 

413 # Don't care 

414 continue 

415 # We need to preserve the peak: make sure we have enough info to create a minimal 

416 # child src 

417 self.log.trace("Peak at (%i,%i) failed. Using minimal default info for child.", 

418 pks[j].getIx(), pks[j].getIy()) 

419 if heavy is None: 

420 # copy the full footprint and strip out extra peaks 

421 foot = afwDet.Footprint(src.getFootprint()) 

422 peakList = foot.getPeaks() 

423 peakList.clear() 

424 peakList.append(peak.peak) 

425 zeroMimg = afwImage.MaskedImageF(foot.getBBox()) 

426 heavy = afwDet.makeHeavyFootprint(foot, zeroMimg) 

427 if peak.deblendedAsPsf: 

428 if peak.psfFitFlux is None: 

429 peak.psfFitFlux = 0.0 

430 if peak.psfFitCenter is None: 

431 peak.psfFitCenter = (peak.peak.getIx(), peak.peak.getIy()) 

432 

433 assert(len(heavy.getPeaks()) == 1) 

434 

435 src.set(self.deblendSkippedKey, False) 

436 child = srcs.addNew() 

437 nchild += 1 

438 for key in self.toCopyFromParent: 

439 child.set(key, src.get(key)) 

440 child.assign(heavy.getPeaks()[0], self.peakSchemaMapper) 

441 child.setParent(src.getId()) 

442 child.setFootprint(heavy) 

443 child.set(self.psfKey, peak.deblendedAsPsf) 

444 child.set(self.hasStrayFluxKey, peak.strayFlux is not None) 

445 if peak.deblendedAsPsf: 

446 (cx, cy) = peak.psfFitCenter 

447 child.set(self.psfCenterKey, geom.Point2D(cx, cy)) 

448 child.set(self.psfFluxKey, peak.psfFitFlux) 

449 child.set(self.deblendRampedTemplateKey, peak.hasRampedTemplate) 

450 child.set(self.deblendPatchedTemplateKey, peak.patched) 

451 

452 # Set the position of the peak from the parent footprint 

453 # This will make it easier to match the same source across 

454 # deblenders and across observations, where the peak 

455 # position is unlikely to change unless enough time passes 

456 # for a source to move on the sky. 

457 child.set(self.peakCenter, geom.Point2I(pks[j].getIx(), pks[j].getIy())) 

458 child.set(self.peakIdKey, pks[j].getId()) 

459 

460 # The children have a single peak 

461 child.set(self.nPeaksKey, 1) 

462 # Set the number of peaks in the parent 

463 child.set(self.parentNPeaksKey, len(pks)) 

464 

465 kids.append(child) 

466 

467 # Child footprints may extend beyond the full extent of their parent's which 

468 # results in a failure of the replace-by-noise code to reinstate these pixels 

469 # to their original values. The following updates the parent footprint 

470 # in-place to ensure it contains the full union of itself and all of its 

471 # children's footprints. 

472 spans = src.getFootprint().spans 

473 for child in kids: 

474 spans = spans.union(child.getFootprint().spans) 

475 src.getFootprint().setSpans(spans) 

476 

477 src.set(self.nChildKey, nchild) 

478 

479 self.postSingleDeblendHook(exposure, srcs, i, npre, kids, fp, psf, psf_fwhm, sigma1, res) 

480 # print('Deblending parent id', src.getId(), 'took', time.clock() - t0) 

481 

482 n1 = len(srcs) 

483 self.log.info('Deblended: of %i sources, %i were deblended, creating %i children, total %i sources', 

484 n0, nparents, n1-n0, n1) 

485 

486 def preSingleDeblendHook(self, exposure, srcs, i, fp, psf, psf_fwhm, sigma1): 

487 pass 

488 

489 def postSingleDeblendHook(self, exposure, srcs, i, npre, kids, fp, psf, psf_fwhm, sigma1, res): 

490 pass 

491 

492 def isLargeFootprint(self, footprint): 

493 """Returns whether a Footprint is large 

494 

495 'Large' is defined by thresholds on the area, size and axis ratio. 

496 These may be disabled independently by configuring them to be non-positive. 

497 

498 This is principally intended to get rid of satellite streaks, which the 

499 deblender or other downstream processing can have trouble dealing with 

500 (e.g., multiple large HeavyFootprints can chew up memory). 

501 """ 

502 if self.config.maxFootprintArea > 0 and footprint.getArea() > self.config.maxFootprintArea: 

503 return True 

504 if self.config.maxFootprintSize > 0: 

505 bbox = footprint.getBBox() 

506 if max(bbox.getWidth(), bbox.getHeight()) > self.config.maxFootprintSize: 

507 return True 

508 if self.config.minFootprintAxisRatio > 0: 

509 axes = afwEll.Axes(footprint.getShape()) 

510 if axes.getB() < self.config.minFootprintAxisRatio*axes.getA(): 

511 return True 

512 return False 

513 

514 def isMasked(self, footprint, mask): 

515 """Returns whether the footprint violates the mask limits 

516 """ 

517 size = float(footprint.getArea()) 

518 for maskName, limit in self.config.maskLimits.items(): 

519 maskVal = mask.getPlaneBitMask(maskName) 

520 unmaskedSpan = footprint.spans.intersectNot(mask, maskVal) # spanset of unmasked pixels 

521 if (size - unmaskedSpan.getArea())/size > limit: 

522 return True 

523 return False 

524 

525 def skipParent(self, source, mask): 

526 """Indicate that the parent source is not being deblended 

527 

528 We set the appropriate flags and mask. 

529 

530 Parameters 

531 ---------- 

532 source : `lsst.afw.table.SourceRecord` 

533 The source to flag as skipped 

534 mask : `lsst.afw.image.Mask` 

535 The mask to update 

536 """ 

537 fp = source.getFootprint() 

538 source.set(self.deblendSkippedKey, True) 

539 if self.config.notDeblendedMask: 

540 mask.addMaskPlane(self.config.notDeblendedMask) 

541 fp.spans.setMask(mask, mask.getPlaneBitMask(self.config.notDeblendedMask)) 

542 

543 # Set the center of the parent 

544 bbox = fp.getBBox() 

545 centerX = int(bbox.getMinX()+bbox.getWidth()/2) 

546 centerY = int(bbox.getMinY()+bbox.getHeight()/2) 

547 source.set(self.peakCenter, geom.Point2I(centerX, centerY)) 

548 # There are no deblended children, so nChild = 0 

549 source.set(self.nChildKey, 0) 

550 # But we also want to know how many peaks that we would have 

551 # deblended if the parent wasn't skipped. 

552 source.set(self.nPeaksKey, len(fp.peaks)) 

553 # Top level parents are not a detected peak, so they have no peakId 

554 source.set(self.peakIdKey, 0) 

555 # Top level parents also have no parentNPeaks 

556 source.set(self.parentNPeaksKey, 0)