Coverage for python/lsst/meas/deblender/sourceDeblendTask.py: 18%

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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, 

114 default=True, 

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

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

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

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

119 maskLimits = pexConfig.DictField( 

120 keytype=str, 

121 itemtype=float, 

122 default={}, 

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

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

125 ) 

126 weightTemplates = pexConfig.Field( 

127 dtype=bool, default=False, 

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

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

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

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

132 maxTempDotProd = pexConfig.Field( 

133 dtype=float, default=0.5, 

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

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

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

137 "be removed.")) 

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

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

140 

141 # Testing options 

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

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

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

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

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

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

148 useCiLimits = pexConfig.Field( 

149 dtype=bool, default=False, 

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

151 ciDeblendChildRange = pexConfig.ListField( 

152 dtype=int, default=[2, 10], 

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

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

155 ciNumParentsToDeblend = pexConfig.Field( 

156 dtype=int, default=10, 

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

158 "within `ciDebledChildRange`. " 

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

160 

161 

162class SourceDeblendTask(pipeBase.Task): 

163 """Split blended sources into individual sources. 

164 

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

166 """ 

167 ConfigClass = SourceDeblendConfig 

168 _DefaultName = "sourceDeblend" 

169 

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

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

172 

173 Parameters 

174 ---------- 

175 schema : `lsst.afw.table.Schema` 

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

177 peakSchema : `lsst.afw.table.peakSchema` 

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

179 Any fields beyond the PeakTable minimal schema will be transferred 

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

181 from the Peaks 

182 **kwargs 

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

184 """ 

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

186 self.schema = schema 

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

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

189 peakMinimalSchema = afwDet.PeakTable.makeMinimalSchema() 

190 if peakSchema is None: 

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

192 # to simplify downstream code 

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

194 else: 

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

196 for item in peakSchema: 

197 if item.key not in peakMinimalSchema: 

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

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

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

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

202 # by adding the same fields to both. 

203 schema.addField(item.field) 

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

205 self.addSchemaKeys(schema) 

206 

207 def addSchemaKeys(self, schema): 

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

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

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

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

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

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

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

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

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

217 doc='Source had too many peaks; ' 

218 'only the brightest were included') 

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

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

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

222 doc='Parent footprint was predominantly masked') 

223 

224 if self.config.catchFailures: 

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

226 doc="Deblending failed on source") 

227 

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

229 doc="Deblender skipped this source") 

230 

231 self.deblendRampedTemplateKey = schema.addField( 

232 'deblend_rampedTemplate', type='Flag', 

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

234 '"ramp" edge-handling.')) 

235 

236 self.deblendPatchedTemplateKey = schema.addField( 

237 'deblend_patchedTemplate', type='Flag', 

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

239 '"patched" edge-handling.')) 

240 

241 self.hasStrayFluxKey = schema.addField( 

242 'deblend_hasStrayFlux', type='Flag', 

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

244 

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

246 self.nChildKey, self.psfKey, self.psfCenterKey, self.psfFluxKey, 

247 self.tooManyPeaksKey, self.tooBigKey))) 

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

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

250 unit="pixel") 

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

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

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

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

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

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

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

258 "This includes peaks that may have been culled " 

259 "during deblending or failed to deblend") 

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

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

262 "in the parent footprint") 

263 

264 @timeMethod 

265 def run(self, exposure, sources): 

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

267 

268 Parameters 

269 ---------- 

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

271 Exposure to be processed 

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

273 SourceCatalog containing sources detected on this exposure. 

274 """ 

275 psf = exposure.getPsf() 

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

277 self.deblend(exposure, sources, psf) 

278 

279 def _getPsfFwhm(self, psf, position): 

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

281 

282 @timeMethod 

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

284 """Deblend. 

285 

286 Parameters 

287 ---------- 

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

289 Exposure to be processed 

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

291 SourceCatalog containing sources detected on this exposure 

292 psf : `lsst.afw.detection.Psf` 

293 Point source function 

294 

295 Returns 

296 ------- 

297 None 

298 """ 

299 # Cull footprints if required by ci 

300 if self.config.useCiLimits: 

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

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

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

304 # config.ciDeblendChildRange 

305 minChildren, maxChildren = self.config.ciDeblendChildRange 

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

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

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

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

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

311 "parents.") 

312 # Keep all of the isolated parents and the first 

313 # `ciNumParentsToDeblend` children 

314 parents = nPeaks == 1 

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

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

317 srcs = srcs[parents | children] 

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

319 # will not be sequential 

320 idFactory = srcs.getIdFactory() 

321 maxId = np.max(srcs["id"]) 

322 idFactory.notify(maxId) 

323 

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

325 

326 from lsst.meas.deblender.baseline import deblend 

327 

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

329 mi = exposure.getMaskedImage() 

330 statsCtrl = afwMath.StatisticsControl() 

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

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

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

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

335 

336 n0 = len(srcs) 

337 nparents = 0 

338 for i, src in enumerate(srcs): 

339 # t0 = time.clock() 

340 

341 fp = src.getFootprint() 

342 pks = fp.getPeaks() 

343 

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

345 # to the parent source. 

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

347 

348 if len(pks) < 2: 

349 continue 

350 

351 if self.isLargeFootprint(fp): 

352 src.set(self.tooBigKey, True) 

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

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

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

356 continue 

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

358 src.set(self.maskedKey, True) 

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

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

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

362 continue 

363 

364 nparents += 1 

365 center = fp.getCentroid() 

366 psf_fwhm = self._getPsfFwhm(psf, center) 

367 

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

369 

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

371 npre = len(srcs) 

372 

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

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

375 

376 try: 

377 res = deblend( 

378 fp, mi, psf, psf_fwhm, sigma1=sigma1, 

379 psfChisqCut1=self.config.psfChisq1, 

380 psfChisqCut2=self.config.psfChisq2, 

381 psfChisqCut2b=self.config.psfChisq2b, 

382 maxNumberOfPeaks=self.config.maxNumberOfPeaks, 

383 strayFluxToPointSources=self.config.strayFluxToPointSources, 

384 assignStrayFlux=self.config.assignStrayFlux, 

385 strayFluxAssignment=self.config.strayFluxRule, 

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

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

388 tinyFootprintSize=self.config.tinyFootprintSize, 

389 clipStrayFluxFraction=self.config.clipStrayFluxFraction, 

390 weightTemplates=self.config.weightTemplates, 

391 removeDegenerateTemplates=self.config.removeDegenerateTemplates, 

392 maxTempDotProd=self.config.maxTempDotProd, 

393 medianSmoothTemplate=self.config.medianSmoothTemplate 

394 ) 

395 if self.config.catchFailures: 

396 src.set(self.deblendFailedKey, False) 

397 except Exception as e: 

398 if self.config.catchFailures: 

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

400 src.set(self.deblendFailedKey, True) 

401 import traceback 

402 traceback.print_exc() 

403 continue 

404 else: 

405 raise 

406 

407 kids = [] 

408 nchild = 0 

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

410 heavy = peak.getFluxPortion() 

411 if heavy is None or peak.skip: 

412 src.set(self.deblendSkippedKey, True) 

413 if not self.config.propagateAllPeaks: 

414 # Don't care 

415 continue 

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

417 # child src 

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

419 pks[j].getIx(), pks[j].getIy()) 

420 if heavy is None: 

421 # copy the full footprint and strip out extra peaks 

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

423 peakList = foot.getPeaks() 

424 peakList.clear() 

425 peakList.append(peak.peak) 

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

427 heavy = afwDet.makeHeavyFootprint(foot, zeroMimg) 

428 if peak.deblendedAsPsf: 

429 if peak.psfFitFlux is None: 

430 peak.psfFitFlux = 0.0 

431 if peak.psfFitCenter is None: 

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

433 

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

435 

436 src.set(self.deblendSkippedKey, False) 

437 child = srcs.addNew() 

438 nchild += 1 

439 for key in self.toCopyFromParent: 

440 child.set(key, src.get(key)) 

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

442 child.setParent(src.getId()) 

443 child.setFootprint(heavy) 

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

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

446 if peak.deblendedAsPsf: 

447 (cx, cy) = peak.psfFitCenter 

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

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

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

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

452 

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

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

455 # deblenders and across observations, where the peak 

456 # position is unlikely to change unless enough time passes 

457 # for a source to move on the sky. 

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

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

460 

461 # The children have a single peak 

462 child.set(self.nPeaksKey, 1) 

463 # Set the number of peaks in the parent 

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

465 

466 kids.append(child) 

467 

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

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

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

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

472 # children's footprints. 

473 spans = src.getFootprint().spans 

474 for child in kids: 

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

476 src.getFootprint().setSpans(spans) 

477 

478 src.set(self.nChildKey, nchild) 

479 

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

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

482 

483 n1 = len(srcs) 

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

485 n0, nparents, n1-n0, n1) 

486 

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

488 pass 

489 

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

491 pass 

492 

493 def isLargeFootprint(self, footprint): 

494 """Returns whether a Footprint is large 

495 

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

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

498 

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

500 deblender or other downstream processing can have trouble dealing with 

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

502 """ 

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

504 return True 

505 if self.config.maxFootprintSize > 0: 

506 bbox = footprint.getBBox() 

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

508 return True 

509 if self.config.minFootprintAxisRatio > 0: 

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

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

512 return True 

513 return False 

514 

515 def isMasked(self, footprint, mask): 

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

517 """ 

518 size = float(footprint.getArea()) 

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

520 maskVal = mask.getPlaneBitMask(maskName) 

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

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

523 return True 

524 return False 

525 

526 def skipParent(self, source, mask): 

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

528 

529 We set the appropriate flags and mask. 

530 

531 Parameters 

532 ---------- 

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

534 The source to flag as skipped 

535 mask : `lsst.afw.image.Mask` 

536 The mask to update 

537 """ 

538 fp = source.getFootprint() 

539 source.set(self.deblendSkippedKey, True) 

540 if self.config.notDeblendedMask: 

541 mask.addMaskPlane(self.config.notDeblendedMask) 

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

543 

544 # Set the center of the parent 

545 bbox = fp.getBBox() 

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

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

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

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

550 source.set(self.nChildKey, 0) 

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

552 # deblended if the parent wasn't skipped. 

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

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

555 source.set(self.peakIdKey, 0) 

556 # Top level parents also have no parentNPeaks 

557 source.set(self.parentNPeaksKey, 0)