Coverage for python/lsst/meas/extensions/scarlet/scarletDeblendTask.py : 14%

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1# This file is part of meas_extensions_scarlet.
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/>.
22import numpy as np
23import scarlet
24from scarlet.psf import ImagePSF, GaussianPSF
25from scarlet import Blend, Frame, Observation
26from scarlet.initialization import initAllSources
28import lsst.log
29import lsst.pex.config as pexConfig
30from lsst.pex.exceptions import InvalidParameterError
31import lsst.pipe.base as pipeBase
32from lsst.geom import Point2I, Box2I, Point2D
33import lsst.afw.geom.ellipses as afwEll
34import lsst.afw.image.utils
35import lsst.afw.image as afwImage
36import lsst.afw.detection as afwDet
37import lsst.afw.table as afwTable
39from .source import modelToHeavy
41__all__ = ["deblend", "ScarletDeblendConfig", "ScarletDeblendTask"]
43logger = lsst.log.Log.getLogger("meas.deblender.deblend")
46class IncompleteDataError(Exception):
47 """The PSF could not be computed due to incomplete data
48 """
49 pass
52class ScarletGradientError(Exception):
53 """An error occurred during optimization
55 This error occurs when the optimizer encounters
56 a NaN value while calculating the gradient.
57 """
58 def __init__(self, iterations, sources):
59 self.iterations = iterations
60 self.sources = sources
61 msg = ("ScalarGradientError in iteration {0}. "
62 "NaN values introduced in sources {1}")
63 self.message = msg.format(iterations, sources)
65 def __str__(self):
66 return self.message
69def _checkBlendConvergence(blend, f_rel):
70 """Check whether or not a blend has converged
71 """
72 deltaLoss = np.abs(blend.loss[-2] - blend.loss[-1])
73 convergence = f_rel * np.abs(blend.loss[-1])
74 return deltaLoss < convergence
77def _getPsfFwhm(psf):
78 """Calculate the FWHM of the `psf`
79 """
80 return psf.computeShape().getDeterminantRadius() * 2.35
83def _computePsfImage(self, position=None):
84 """Get a multiband PSF image
85 The PSF Kernel Image is computed for each band
86 and combined into a (filter, y, x) array and stored
87 as `self._psfImage`.
88 The result is not cached, so if the same PSF is expected
89 to be used multiple times it is a good idea to store the
90 result in another variable.
91 Note: this is a temporary fix during the deblender sprint.
92 In the future this function will replace the current method
93 in `afw.MultibandExposure.computePsfImage` (DM-19789).
94 Parameters
95 ----------
96 position : `Point2D` or `tuple`
97 Coordinates to evaluate the PSF. If `position` is `None`
98 then `Psf.getAveragePosition()` is used.
99 Returns
100 -------
101 self._psfImage: array
102 The multiband PSF image.
103 """
104 psfs = []
105 # Make the coordinates into a Point2D (if necessary)
106 if not isinstance(position, Point2D) and position is not None:
107 position = Point2D(position[0], position[1])
109 for bidx, single in enumerate(self.singles):
110 try:
111 if position is None:
112 psf = single.getPsf().computeImage()
113 psfs.append(psf)
114 else:
115 psf = single.getPsf().computeKernelImage(position)
116 psfs.append(psf)
117 except InvalidParameterError:
118 # This band failed to compute the PSF due to incomplete data
119 # at that location. This is unlikely to be a problem for Rubin,
120 # however the edges of some HSC COSMOS fields contain incomplete
121 # data in some bands, so we track this error to distinguish it
122 # from unknown errors.
123 msg = "Failed to compute PSF at {} in band {}"
124 raise IncompleteDataError(msg.format(position, self.filters[bidx]))
126 left = np.min([psf.getBBox().getMinX() for psf in psfs])
127 bottom = np.min([psf.getBBox().getMinY() for psf in psfs])
128 right = np.max([psf.getBBox().getMaxX() for psf in psfs])
129 top = np.max([psf.getBBox().getMaxY() for psf in psfs])
130 bbox = Box2I(Point2I(left, bottom), Point2I(right, top))
131 psfs = [afwImage.utils.projectImage(psf, bbox) for psf in psfs]
132 psfImage = afwImage.MultibandImage.fromImages(self.filters, psfs)
133 return psfImage
136def getFootprintMask(footprint, mExposure):
137 """Mask pixels outside the footprint
139 Parameters
140 ----------
141 mExposure : `lsst.image.MultibandExposure`
142 - The multiband exposure containing the image,
143 mask, and variance data
144 footprint : `lsst.detection.Footprint`
145 - The footprint of the parent to deblend
147 Returns
148 -------
149 footprintMask : array
150 Boolean array with pixels not in the footprint set to one.
151 """
152 bbox = footprint.getBBox()
153 fpMask = afwImage.Mask(bbox)
154 footprint.spans.setMask(fpMask, 1)
155 fpMask = ~fpMask.getArray().astype(bool)
156 return fpMask
159def deblend(mExposure, footprint, config):
160 """Deblend a parent footprint
162 Parameters
163 ----------
164 mExposure : `lsst.image.MultibandExposure`
165 - The multiband exposure containing the image,
166 mask, and variance data
167 footprint : `lsst.detection.Footprint`
168 - The footprint of the parent to deblend
169 config : `ScarletDeblendConfig`
170 - Configuration of the deblending task
171 """
172 # Extract coordinates from each MultiColorPeak
173 bbox = footprint.getBBox()
175 # Create the data array from the masked images
176 images = mExposure.image[:, bbox].array
178 # Use the inverse variance as the weights
179 if config.useWeights:
180 weights = 1/mExposure.variance[:, bbox].array
181 else:
182 weights = np.ones_like(images)
183 badPixels = mExposure.mask.getPlaneBitMask(config.badMask)
184 mask = mExposure.mask[:, bbox].array & badPixels
185 weights[mask > 0] = 0
187 # Mask out the pixels outside the footprint
188 mask = getFootprintMask(footprint, mExposure)
189 weights *= ~mask
191 psfs = _computePsfImage(mExposure, footprint.getCentroid()).array.astype(np.float32)
192 psfs = ImagePSF(psfs)
193 model_psf = GaussianPSF(sigma=(config.modelPsfSigma,)*len(mExposure.filters))
195 frame = Frame(images.shape, psfs=model_psf, channels=mExposure.filters)
196 observation = Observation(images, psfs=psfs, weights=weights, channels=mExposure.filters)
197 observation.match(frame)
199 assert(config.sourceModel in ["single", "double", "point", "fit"])
201 # Set the appropriate number of components
202 if config.sourceModel == "single":
203 maxComponents = 1
204 elif config.sourceModel == "double":
205 maxComponents = 2
206 elif config.sourceModel == "compact":
207 raise NotImplementedError("CompactSource initialization has not yet been ported"
208 "to the stack version of scarlet")
209 elif config.sourceModel == "point":
210 maxComponents = 0
211 elif config.sourceModel == "fit":
212 # It is likely in the future that there will be some heuristic
213 # used to determine what type of model to use for each source,
214 # but that has not yet been implemented (see DM-22551)
215 raise NotImplementedError("sourceModel 'fit' has not been implemented yet")
217 # Convert the centers to pixel coordinates
218 xmin = bbox.getMinX()
219 ymin = bbox.getMinY()
220 centers = [np.array([peak.getIy()-ymin, peak.getIx()-xmin], dtype=int) for peak in footprint.peaks]
222 # Only deblend sources that can be initialized
223 sources, skipped = initAllSources(
224 frame=frame,
225 centers=centers,
226 observation=observation,
227 symmetric=config.symmetric,
228 monotonic=config.monotonic,
229 thresh=config.morphThresh,
230 maxComponents=maxComponents,
231 edgeDistance=config.edgeDistance,
232 shifting=False,
233 downgrade=config.downgrade,
234 fallback=config.fallback,
235 )
237 # Attach the peak to all of the initialized sources
238 srcIndex = 0
239 for k, center in enumerate(centers):
240 if k not in skipped:
241 # This is just to make sure that there isn't a coding bug
242 assert np.all(sources[srcIndex].center == center)
243 # Store the record for the peak with the appropriate source
244 sources[srcIndex].detectedPeak = footprint.peaks[k]
245 srcIndex += 1
247 # Create the blend and attempt to optimize it
248 blend = Blend(sources, observation)
249 try:
250 blend.fit(max_iter=config.maxIter, e_rel=config.relativeError)
251 except ArithmeticError:
252 # This occurs when a gradient update produces a NaN value
253 # This is usually due to a source initialized with a
254 # negative SED or no flux, often because the peak
255 # is a noise fluctuation in one band and not a real source.
256 iterations = len(blend.loss)
257 failedSources = []
258 for k, src in enumerate(sources):
259 if np.any(~np.isfinite(src.get_model())):
260 failedSources.append(k)
261 raise ScarletGradientError(iterations, failedSources)
263 return blend, skipped
266class ScarletDeblendConfig(pexConfig.Config):
267 """MultibandDeblendConfig
269 Configuration for the multiband deblender.
270 The parameters are organized by the parameter types, which are
271 - Stopping Criteria: Used to determine if the fit has converged
272 - Position Fitting Criteria: Used to fit the positions of the peaks
273 - Constraints: Used to apply constraints to the peaks and their components
274 - Other: Parameters that don't fit into the above categories
275 """
276 # Stopping Criteria
277 maxIter = pexConfig.Field(dtype=int, default=300,
278 doc=("Maximum number of iterations to deblend a single parent"))
279 relativeError = pexConfig.Field(dtype=float, default=1e-4,
280 doc=("Change in the loss function between"
281 "iterations to exit fitter"))
283 # Blend Configuration options
284 edgeDistance = pexConfig.Field(dtype=int, default=1,
285 doc="All sources with flux within `edgeDistance` from the edge "
286 "will be considered edge sources.")
288 # Constraints
289 morphThresh = pexConfig.Field(dtype=float, default=1,
290 doc="Fraction of background RMS a pixel must have"
291 "to be included in the initial morphology")
292 monotonic = pexConfig.Field(dtype=bool, default=True, doc="Make models monotonic")
293 symmetric = pexConfig.Field(dtype=bool, default=False, doc="Make models symmetric")
295 # Other scarlet paremeters
296 useWeights = pexConfig.Field(
297 dtype=bool, default=True,
298 doc=("Whether or not use use inverse variance weighting."
299 "If `useWeights` is `False` then flat weights are used"))
300 modelPsfSize = pexConfig.Field(
301 dtype=int, default=11,
302 doc="Model PSF side length in pixels")
303 modelPsfSigma = pexConfig.Field(
304 dtype=float, default=0.8,
305 doc="Define sigma for the model frame PSF")
306 saveTemplates = pexConfig.Field(
307 dtype=bool, default=True,
308 doc="Whether or not to save the SEDs and templates")
309 processSingles = pexConfig.Field(
310 dtype=bool, default=True,
311 doc="Whether or not to process isolated sources in the deblender")
312 sourceModel = pexConfig.Field(
313 dtype=str, default="single",
314 doc=("How to determine which model to use for sources, from\n"
315 "- 'single': use a single component for all sources\n"
316 "- 'double': use a bulge disk model for all sources\n"
317 "- 'compact': use a single component model, initialzed with a point source morphology, "
318 " for all sources\n"
319 "- 'point': use a point-source model for all sources\n"
320 "- 'fit: use a PSF fitting model to determine the number of components (not yet implemented)")
321 )
322 downgrade = pexConfig.Field(
323 dtype=bool, default=False,
324 doc="Whether or not to downgrade the number of components for sources in small bounding boxes"
325 )
327 # Mask-plane restrictions
328 badMask = pexConfig.ListField(
329 dtype=str, default=["BAD", "CR", "NO_DATA", "SAT", "SUSPECT"],
330 doc="Whether or not to process isolated sources in the deblender")
331 statsMask = pexConfig.ListField(dtype=str, default=["SAT", "INTRP", "NO_DATA"],
332 doc="Mask planes to ignore when performing statistics")
333 maskLimits = pexConfig.DictField(
334 keytype=str,
335 itemtype=float,
336 default={},
337 doc=("Mask planes with the corresponding limit on the fraction of masked pixels. "
338 "Sources violating this limit will not be deblended."),
339 )
341 # Size restrictions
342 maxNumberOfPeaks = pexConfig.Field(
343 dtype=int, default=0,
344 doc=("Only deblend the brightest maxNumberOfPeaks peaks in the parent"
345 " (<= 0: unlimited)"))
346 maxFootprintArea = pexConfig.Field(
347 dtype=int, default=1000000,
348 doc=("Maximum area for footprints before they are ignored as large; "
349 "non-positive means no threshold applied"))
350 maxFootprintSize = pexConfig.Field(
351 dtype=int, default=0,
352 doc=("Maximum linear dimension for footprints before they are ignored "
353 "as large; non-positive means no threshold applied"))
354 minFootprintAxisRatio = pexConfig.Field(
355 dtype=float, default=0.0,
356 doc=("Minimum axis ratio for footprints before they are ignored "
357 "as large; non-positive means no threshold applied"))
359 # Failure modes
360 fallback = pexConfig.Field(
361 dtype=bool, default=True,
362 doc="Whether or not to fallback to a smaller number of components if a source does not initialize"
363 )
364 notDeblendedMask = pexConfig.Field(
365 dtype=str, default="NOT_DEBLENDED", optional=True,
366 doc="Mask name for footprints not deblended, or None")
367 catchFailures = pexConfig.Field(
368 dtype=bool, default=True,
369 doc=("If True, catch exceptions thrown by the deblender, log them, "
370 "and set a flag on the parent, instead of letting them propagate up"))
373class ScarletDeblendTask(pipeBase.Task):
374 """ScarletDeblendTask
376 Split blended sources into individual sources.
378 This task has no return value; it only modifies the SourceCatalog in-place.
379 """
380 ConfigClass = ScarletDeblendConfig
381 _DefaultName = "scarletDeblend"
383 def __init__(self, schema, peakSchema=None, **kwargs):
384 """Create the task, adding necessary fields to the given schema.
386 Parameters
387 ----------
388 schema : `lsst.afw.table.schema.schema.Schema`
389 Schema object for measurement fields; will be modified in-place.
390 peakSchema : `lsst.afw.table.schema.schema.Schema`
391 Schema of Footprint Peaks that will be passed to the deblender.
392 Any fields beyond the PeakTable minimal schema will be transferred
393 to the main source Schema. If None, no fields will be transferred
394 from the Peaks.
395 filters : list of str
396 Names of the filters used for the eposures. This is needed to store
397 the SED as a field
398 **kwargs
399 Passed to Task.__init__.
400 """
401 pipeBase.Task.__init__(self, **kwargs)
403 peakMinimalSchema = afwDet.PeakTable.makeMinimalSchema()
404 if peakSchema is None:
405 # In this case, the peakSchemaMapper will transfer nothing, but
406 # we'll still have one
407 # to simplify downstream code
408 self.peakSchemaMapper = afwTable.SchemaMapper(peakMinimalSchema, schema)
409 else:
410 self.peakSchemaMapper = afwTable.SchemaMapper(peakSchema, schema)
411 for item in peakSchema:
412 if item.key not in peakMinimalSchema:
413 self.peakSchemaMapper.addMapping(item.key, item.field)
414 # Because SchemaMapper makes a copy of the output schema
415 # you give its ctor, it isn't updating this Schema in
416 # place. That's probably a design flaw, but in the
417 # meantime, we'll keep that schema in sync with the
418 # peakSchemaMapper.getOutputSchema() manually, by adding
419 # the same fields to both.
420 schema.addField(item.field)
421 assert schema == self.peakSchemaMapper.getOutputSchema(), "Logic bug mapping schemas"
422 self._addSchemaKeys(schema)
423 self.schema = schema
425 def _addSchemaKeys(self, schema):
426 """Add deblender specific keys to the schema
427 """
428 self.runtimeKey = schema.addField('deblend_runtime', type=np.float32, doc='runtime in ms')
430 self.iterKey = schema.addField('deblend_iterations', type=np.int32, doc='iterations to converge')
432 self.nChildKey = schema.addField('deblend_nChild', type=np.int32,
433 doc='Number of children this object has (defaults to 0)')
434 self.psfKey = schema.addField('deblend_deblendedAsPsf', type='Flag',
435 doc='Deblender thought this source looked like a PSF')
436 self.tooManyPeaksKey = schema.addField('deblend_tooManyPeaks', type='Flag',
437 doc='Source had too many peaks; '
438 'only the brightest were included')
439 self.tooBigKey = schema.addField('deblend_parentTooBig', type='Flag',
440 doc='Parent footprint covered too many pixels')
441 self.maskedKey = schema.addField('deblend_masked', type='Flag',
442 doc='Parent footprint was predominantly masked')
443 self.sedNotConvergedKey = schema.addField('deblend_sedConvergenceFailed', type='Flag',
444 doc='scarlet sed optimization did not converge before'
445 'config.maxIter')
446 self.morphNotConvergedKey = schema.addField('deblend_morphConvergenceFailed', type='Flag',
447 doc='scarlet morph optimization did not converge before'
448 'config.maxIter')
449 self.blendConvergenceFailedFlagKey = schema.addField('deblend_blendConvergenceFailedFlag',
450 type='Flag',
451 doc='at least one source in the blend'
452 'failed to converge')
453 self.edgePixelsKey = schema.addField('deblend_edgePixels', type='Flag',
454 doc='Source had flux on the edge of the parent footprint')
455 self.deblendFailedKey = schema.addField('deblend_failed', type='Flag',
456 doc="Deblending failed on source")
457 self.deblendErrorKey = schema.addField('deblend_error', type="String", size=25,
458 doc='Name of error if the blend failed')
459 self.deblendSkippedKey = schema.addField('deblend_skipped', type='Flag',
460 doc="Deblender skipped this source")
461 self.peakCenter = afwTable.Point2IKey.addFields(schema, name="deblend_peak_center",
462 doc="Center used to apply constraints in scarlet",
463 unit="pixel")
464 self.peakIdKey = schema.addField("deblend_peakId", type=np.int32,
465 doc="ID of the peak in the parent footprint. "
466 "This is not unique, but the combination of 'parent'"
467 "and 'peakId' should be for all child sources. "
468 "Top level blends with no parents have 'peakId=0'")
469 self.modelCenterFlux = schema.addField('deblend_peak_instFlux', type=float, units='count',
470 doc="The instFlux at the peak position of deblended mode")
471 self.modelTypeKey = schema.addField("deblend_modelType", type="String", size=20,
472 doc="The type of model used, for example "
473 "MultiExtendedSource, SingleExtendedSource, PointSource")
474 self.edgeFluxFlagKey = schema.addField("deblend_edgeFluxFlag", type="Flag",
475 doc="Source has flux on the edge of the image")
476 self.nPeaksKey = schema.addField("deblend_nPeaks", type=np.int32,
477 doc="Number of initial peaks in the blend. "
478 "This includes peaks that may have been culled "
479 "during deblending or failed to deblend")
480 self.parentNPeaksKey = schema.addField("deblend_parentNPeaks", type=np.int32,
481 doc="Same as deblend_n_peaks, but the number of peaks "
482 "in the parent footprint")
483 self.scarletFluxKey = schema.addField("deblend_scarletFlux", type=np.float32,
484 doc="Flux measurement from scarlet")
485 self.scarletLogLKey = schema.addField("deblend_logL", type=np.float32,
486 doc="Final logL, used to identify regressions in scarlet.")
488 # self.log.trace('Added keys to schema: %s', ", ".join(str(x) for x in
489 # (self.nChildKey, self.tooManyPeaksKey, self.tooBigKey))
490 # )
492 @pipeBase.timeMethod
493 def run(self, mExposure, mergedSources):
494 """Get the psf from each exposure and then run deblend().
496 Parameters
497 ----------
498 mExposure : `MultibandExposure`
499 The exposures should be co-added images of the same
500 shape and region of the sky.
501 mergedSources : `SourceCatalog`
502 The merged `SourceCatalog` that contains parent footprints
503 to (potentially) deblend.
505 Returns
506 -------
507 fluxCatalogs: dict or None
508 Keys are the names of the filters and the values are
509 `lsst.afw.table.source.source.SourceCatalog`'s.
510 These are the flux-conserved catalogs with heavy footprints with
511 the image data weighted by the multiband templates.
512 If `self.config.conserveFlux` is `False`, then this item will be
513 None
514 templateCatalogs: dict or None
515 Keys are the names of the filters and the values are
516 `lsst.afw.table.source.source.SourceCatalog`'s.
517 These are catalogs with heavy footprints that are the templates
518 created by the multiband templates.
519 If `self.config.saveTemplates` is `False`, then this item will be
520 None
521 """
522 return self.deblend(mExposure, mergedSources)
524 @pipeBase.timeMethod
525 def deblend(self, mExposure, sources):
526 """Deblend a data cube of multiband images
528 Parameters
529 ----------
530 mExposure : `MultibandExposure`
531 The exposures should be co-added images of the same
532 shape and region of the sky.
533 sources : `SourceCatalog`
534 The merged `SourceCatalog` that contains parent footprints
535 to (potentially) deblend.
537 Returns
538 -------
539 fluxCatalogs : dict or None
540 Keys are the names of the filters and the values are
541 `lsst.afw.table.source.source.SourceCatalog`'s.
542 These are the flux-conserved catalogs with heavy footprints with
543 the image data weighted by the multiband templates.
544 If `self.config.conserveFlux` is `False`, then this item will be
545 None
546 templateCatalogs : dict or None
547 Keys are the names of the filters and the values are
548 `lsst.afw.table.source.source.SourceCatalog`'s.
549 These are catalogs with heavy footprints that are the templates
550 created by the multiband templates.
551 If `self.config.saveTemplates` is `False`, then this item will be
552 None
553 """
554 import time
556 filters = mExposure.filters
557 self.log.info("Deblending {0} sources in {1} exposure bands".format(len(sources), len(mExposure)))
559 # Create the output catalogs
560 templateCatalogs = {}
561 # This must be returned but is not calculated right now, setting it to
562 # None to be consistent with doc string
563 fluxCatalogs = None
564 for f in filters:
565 _catalog = afwTable.SourceCatalog(sources.table.clone())
566 _catalog.extend(sources)
567 templateCatalogs[f] = _catalog
569 n0 = len(sources)
570 nparents = 0
571 for pk, src in enumerate(sources):
572 foot = src.getFootprint()
573 bbox = foot.getBBox()
574 peaks = foot.getPeaks()
576 # Since we use the first peak for the parent object, we should
577 # propagate its flags to the parent source.
578 src.assign(peaks[0], self.peakSchemaMapper)
580 # Block of Skipping conditions
581 if len(peaks) < 2 and not self.config.processSingles:
582 for f in filters:
583 templateCatalogs[f][pk].set(self.runtimeKey, 0)
584 continue
585 if self._isLargeFootprint(foot):
586 src.set(self.tooBigKey, True)
587 self._skipParent(src, mExposure.mask)
588 self.log.trace('Parent %i: skipping large footprint', int(src.getId()))
589 continue
590 if self._isMasked(foot, mExposure):
591 src.set(self.maskedKey, True)
592 mask = np.bitwise_or.reduce(mExposure.mask[:, bbox].array, axis=0)
593 mask = afwImage.MaskX(mask, xy0=bbox.getMin())
594 self._skipParent(src, mask)
595 self.log.trace('Parent %i: skipping masked footprint', int(src.getId()))
596 continue
597 if self.config.maxNumberOfPeaks > 0 and len(peaks) > self.config.maxNumberOfPeaks:
598 src.set(self.tooManyPeaksKey, True)
599 self._skipParent(src, mExposure.mask)
600 msg = 'Parent {0}: Too many peaks, skipping blend'
601 self.log.trace(msg.format(int(src.getId())))
602 # Unlike meas_deblender, in scarlet we skip the entire blend
603 # if the number of peaks exceeds max peaks, since neglecting
604 # to model any peaks often results in catastrophic failure
605 # of scarlet to generate models for the brighter sources.
606 continue
608 nparents += 1
609 self.log.trace('Parent %i: deblending %i peaks', int(src.getId()), len(peaks))
610 # Run the deblender
611 blendError = None
612 try:
613 t0 = time.time()
614 # Build the parameter lists with the same ordering
615 blend, skipped = deblend(mExposure, foot, self.config)
616 tf = time.time()
617 runtime = (tf-t0)*1000
618 src.set(self.deblendFailedKey, False)
619 src.set(self.runtimeKey, runtime)
620 converged = _checkBlendConvergence(blend, self.config.relativeError)
621 src.set(self.blendConvergenceFailedFlagKey, converged)
622 sources = [src for src in blend.sources]
623 # Re-insert place holders for skipped sources
624 # to propagate them in the catalog so
625 # that the peaks stay consistent
626 for k in skipped:
627 sources.insert(k, None)
628 # Catch all errors and filter out the ones that we know about
629 except Exception as e:
630 blendError = type(e).__name__
631 if isinstance(e, ScarletGradientError):
632 src.set(self.iterKey, e.iterations)
633 elif not isinstance(e, IncompleteDataError):
634 blendError = "UnknownError"
635 self._skipParent(src, mExposure.mask)
636 if self.config.catchFailures:
637 # Make it easy to find UnknownErrors in the log file
638 self.log.warn("UnknownError")
639 import traceback
640 traceback.print_exc()
641 else:
642 raise
644 self.log.warn("Unable to deblend source %d: %s" % (src.getId(), blendError))
645 src.set(self.deblendFailedKey, True)
646 src.set(self.deblendErrorKey, blendError)
647 self._skipParent(src, mExposure.mask)
648 continue
650 # Add the merged source as a parent in the catalog for each band
651 templateParents = {}
652 parentId = src.getId()
653 for f in filters:
654 templateParents[f] = templateCatalogs[f][pk]
655 templateParents[f].set(self.nPeaksKey, len(foot.peaks))
656 templateParents[f].set(self.runtimeKey, runtime)
657 templateParents[f].set(self.iterKey, len(blend.loss))
658 logL = blend.loss[-1]-blend.observations[0].log_norm
659 templateParents[f].set(self.scarletLogLKey, logL)
661 # Add each source to the catalogs in each band
662 nchild = 0
663 for k, source in enumerate(sources):
664 # Skip any sources with no flux or that scarlet skipped because
665 # it could not initialize
666 if k in skipped:
667 # No need to propagate anything
668 continue
669 else:
670 src.set(self.deblendSkippedKey, False)
671 models = modelToHeavy(source, filters, xy0=bbox.getMin(),
672 observation=blend.observations[0])
674 flux = scarlet.measure.flux(source)
675 for fidx, f in enumerate(filters):
676 if len(models[f].getPeaks()) != 1:
677 err = "Heavy footprint should have a single peak, got {0}"
678 raise ValueError(err.format(len(models[f].peaks)))
679 cat = templateCatalogs[f]
680 child = self._addChild(parentId, cat, models[f], source, converged,
681 xy0=bbox.getMin(), flux=flux[fidx])
682 if parentId == 0:
683 child.setId(src.getId())
684 child.set(self.runtimeKey, runtime)
685 nchild += 1
687 # Set the number of children for each parent
688 for f in filters:
689 templateParents[f].set(self.nChildKey, nchild)
691 K = len(list(templateCatalogs.values())[0])
692 self.log.info('Deblended: of %i sources, %i were deblended, creating %i children, total %i sources'
693 % (n0, nparents, K-n0, K))
694 return fluxCatalogs, templateCatalogs
696 def _isLargeFootprint(self, footprint):
697 """Returns whether a Footprint is large
699 'Large' is defined by thresholds on the area, size and axis ratio.
700 These may be disabled independently by configuring them to be
701 non-positive.
703 This is principally intended to get rid of satellite streaks, which the
704 deblender or other downstream processing can have trouble dealing with
705 (e.g., multiple large HeavyFootprints can chew up memory).
706 """
707 if self.config.maxFootprintArea > 0 and footprint.getArea() > self.config.maxFootprintArea:
708 return True
709 if self.config.maxFootprintSize > 0:
710 bbox = footprint.getBBox()
711 if max(bbox.getWidth(), bbox.getHeight()) > self.config.maxFootprintSize:
712 return True
713 if self.config.minFootprintAxisRatio > 0:
714 axes = afwEll.Axes(footprint.getShape())
715 if axes.getB() < self.config.minFootprintAxisRatio*axes.getA():
716 return True
717 return False
719 def _isMasked(self, footprint, mExposure):
720 """Returns whether the footprint violates the mask limits"""
721 bbox = footprint.getBBox()
722 mask = np.bitwise_or.reduce(mExposure.mask[:, bbox].array, axis=0)
723 size = float(footprint.getArea())
724 for maskName, limit in self.config.maskLimits.items():
725 maskVal = mExposure.mask.getPlaneBitMask(maskName)
726 _mask = afwImage.MaskX(mask & maskVal, xy0=bbox.getMin())
727 unmaskedSpan = footprint.spans.intersectNot(_mask) # spanset of unmasked pixels
728 if (size - unmaskedSpan.getArea())/size > limit:
729 return True
730 return False
732 def _skipParent(self, source, masks):
733 """Indicate that the parent source is not being deblended
735 We set the appropriate flags and masks for each exposure.
737 Parameters
738 ----------
739 source : `lsst.afw.table.source.source.SourceRecord`
740 The source to flag as skipped
741 masks : list of `lsst.afw.image.MaskX`
742 The mask in each band to update with the non-detection
743 """
744 fp = source.getFootprint()
745 source.set(self.deblendSkippedKey, True)
746 if self.config.notDeblendedMask:
747 for mask in masks:
748 mask.addMaskPlane(self.config.notDeblendedMask)
749 fp.spans.setMask(mask, mask.getPlaneBitMask(self.config.notDeblendedMask))
750 # The deblender didn't run on this source, so it has zero runtime
751 source.set(self.runtimeKey, 0)
752 # Set the center of the parent
753 bbox = fp.getBBox()
754 centerX = int(bbox.getMinX()+bbox.getWidth()/2)
755 centerY = int(bbox.getMinY()+bbox.getHeight()/2)
756 source.set(self.peakCenter, Point2I(centerX, centerY))
757 # There are no deblended children, so nChild = 0
758 source.set(self.nChildKey, 0)
759 # But we also want to know how many peaks that we would have
760 # deblended if the parent wasn't skipped.
761 source.set(self.nPeaksKey, len(fp.peaks))
762 # The blend was skipped, so it didn't take any iterations
763 source.set(self.iterKey, 0)
764 # Top level parents are not a detected peak, so they have no peakId
765 source.set(self.peakIdKey, 0)
766 # Top level parents also have no parentNPeaks
767 source.set(self.parentNPeaksKey, 0)
769 def _addChild(self, parentId, sources, heavy, scarletSource, blend_converged, xy0, flux):
770 """Add a child to a catalog
772 This creates a new child in the source catalog,
773 assigning it a parent id, adding a footprint,
774 and setting all appropriate flags based on the
775 deblender result.
776 """
777 assert len(heavy.getPeaks()) == 1
778 src = sources.addNew()
779 src.assign(heavy.getPeaks()[0], self.peakSchemaMapper)
780 src.setParent(parentId)
781 src.setFootprint(heavy)
782 # Set the psf key based on whether or not the source was
783 # deblended using the PointSource model.
784 # This key is not that useful anymore since we now keep track of
785 # `modelType`, but we continue to propagate it in case code downstream
786 # is expecting it.
787 src.set(self.psfKey, scarletSource.__class__.__name__ == "PointSource")
788 src.set(self.runtimeKey, 0)
789 src.set(self.blendConvergenceFailedFlagKey, not blend_converged)
791 # Set the position of the peak from the parent footprint
792 # This will make it easier to match the same source across
793 # deblenders and across observations, where the peak
794 # position is unlikely to change unless enough time passes
795 # for a source to move on the sky.
796 peak = scarletSource.detectedPeak
797 src.set(self.peakCenter, Point2I(peak["i_x"], peak["i_y"]))
798 src.set(self.peakIdKey, peak["id"])
800 # The children have a single peak
801 src.set(self.nPeaksKey, 1)
803 # Store the flux at the center of the model and the total
804 # scarlet flux measurement.
805 morph = afwDet.multiband.heavyFootprintToImage(heavy).image.array
807 # Set the flux at the center of the model (for SNR)
808 try:
809 cy, cx = scarletSource.center
810 cy = np.max([np.min([int(np.round(cy)), morph.shape[0]-1]), 0])
811 cx = np.max([np.min([int(np.round(cx)), morph.shape[1]-1]), 0])
812 src.set(self.modelCenterFlux, morph[cy, cx])
813 except AttributeError:
814 msg = "Did not recognize coordinates for source type of `{0}`, "
815 msg += "could not write coordinates or center flux. "
816 msg += "Add `{0}` to meas_extensions_scarlet to properly persist this information."
817 logger.warning(msg.format(type(scarletSource)))
819 src.set(self.modelTypeKey, scarletSource.__class__.__name__)
820 src.set(self.edgeFluxFlagKey, scarletSource.isEdge)
821 # Include the source flux in the model space in the catalog.
822 # This uses the narrower model PSF, which ensures that all sources
823 # not located on an edge have all of their flux included in the
824 # measurement.
825 src.set(self.scarletFluxKey, flux)
826 return src