Coverage for python/lsst/ip/diffim/dipoleMeasurement.py: 20%
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1# This file is part of ip_diffim.
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
24import lsst.afw.image as afwImage
25import lsst.geom as geom
26import lsst.pex.config as pexConfig
27import lsst.meas.deblender.baseline as deblendBaseline
28from lsst.meas.base.pluginRegistry import register
29from lsst.meas.base import SingleFrameMeasurementTask, SingleFrameMeasurementConfig, \
30 SingleFramePluginConfig, SingleFramePlugin
31import lsst.afw.display as afwDisplay
32from lsst.utils.logging import getLogger
34__all__ = ("DipoleMeasurementConfig", "DipoleMeasurementTask", "DipoleAnalysis", "DipoleDeblender",
35 "SourceFlagChecker", "ClassificationDipoleConfig", "ClassificationDipolePlugin")
38class ClassificationDipoleConfig(SingleFramePluginConfig):
39 """Configuration for classification of detected diaSources as dipole or not"""
40 minSn = pexConfig.Field(
41 doc="Minimum quadrature sum of positive+negative lobe S/N to be considered a dipole",
42 dtype=float, default=np.sqrt(2) * 5.0,
43 )
44 maxFluxRatio = pexConfig.Field(
45 doc="Maximum flux ratio in either lobe to be considered a dipole",
46 dtype=float, default=0.65
47 )
50@register("ip_diffim_ClassificationDipole")
51class ClassificationDipolePlugin(SingleFramePlugin):
52 """A plugin to classify whether a diaSource is a dipole.
53 """
55 ConfigClass = ClassificationDipoleConfig
57 @classmethod
58 def getExecutionOrder(cls):
59 """
60 Returns
61 -------
62 result : `callable`
63 """
64 return cls.APCORR_ORDER
66 def __init__(self, config, name, schema, metadata):
67 SingleFramePlugin.__init__(self, config, name, schema, metadata)
68 self.dipoleAnalysis = DipoleAnalysis()
69 self.keyProbability = schema.addField(name + "_value", type="D",
70 doc="Set to 1 for dipoles, else 0.")
71 self.keyFlag = schema.addField(name + "_flag", type="Flag", doc="Set to 1 for any fatal failure.")
73 def measure(self, measRecord, exposure):
74 passesSn = self.dipoleAnalysis.getSn(measRecord) > self.config.minSn
75 negFlux = np.abs(measRecord.get("ip_diffim_PsfDipoleFlux_neg_instFlux"))
76 negFluxFlag = measRecord.get("ip_diffim_PsfDipoleFlux_neg_flag")
77 posFlux = np.abs(measRecord.get("ip_diffim_PsfDipoleFlux_pos_instFlux"))
78 posFluxFlag = measRecord.get("ip_diffim_PsfDipoleFlux_pos_flag")
80 if negFluxFlag or posFluxFlag:
81 self.fail(measRecord)
82 # continue on to classify
84 totalFlux = negFlux + posFlux
86 # If negFlux or posFlux are NaN, these evaluate to False
87 passesFluxNeg = (negFlux / totalFlux) < self.config.maxFluxRatio
88 passesFluxPos = (posFlux / totalFlux) < self.config.maxFluxRatio
89 if (passesSn and passesFluxPos and passesFluxNeg):
90 val = 1.0
91 else:
92 val = 0.0
94 measRecord.set(self.keyProbability, val)
96 def fail(self, measRecord, error=None):
97 measRecord.set(self.keyFlag, True)
100class DipoleMeasurementConfig(SingleFrameMeasurementConfig):
101 """Measurement of detected diaSources as dipoles"""
103 def setDefaults(self):
104 SingleFrameMeasurementConfig.setDefaults(self)
105 self.plugins = ["base_CircularApertureFlux",
106 "base_PixelFlags",
107 "base_SkyCoord",
108 "base_PsfFlux",
109 "ip_diffim_NaiveDipoleCentroid",
110 "ip_diffim_NaiveDipoleFlux",
111 "ip_diffim_PsfDipoleFlux",
112 "ip_diffim_ClassificationDipole",
113 ]
115 self.slots.calibFlux = None
116 self.slots.modelFlux = None
117 self.slots.gaussianFlux = None
118 self.slots.shape = None
119 self.slots.centroid = "ip_diffim_NaiveDipoleCentroid"
120 self.doReplaceWithNoise = False
123class DipoleMeasurementTask(SingleFrameMeasurementTask):
124 """Measurement of Sources, specifically ones from difference images, for characterization as dipoles
126 Parameters
127 ----------
128 sources : 'lsst.afw.table.SourceCatalog'
129 Sources that will be measured
130 badFlags : `list` of `dict`
131 A list of flags that will be used to determine if there was a measurement problem
133 Notes
134 -----
135 The list of badFlags will be used to make a list of keys to check for measurement flags on. By
136 default the centroid keys are added to this list
138 Description
140 This class provides a default configuration for running Source measurement on image differences.
142 .. code-block:: py
144 class DipoleMeasurementConfig(SingleFrameMeasurementConfig):
145 "Measurement of detected diaSources as dipoles"
146 def setDefaults(self):
147 SingleFrameMeasurementConfig.setDefaults(self)
148 self.plugins = ["base_CircularApertureFlux",
149 "base_PixelFlags",
150 "base_SkyCoord",
151 "base_PsfFlux",
152 "ip_diffim_NaiveDipoleCentroid",
153 "ip_diffim_NaiveDipoleFlux",
154 "ip_diffim_PsfDipoleFlux",
155 "ip_diffim_ClassificationDipole",
156 ]
157 self.slots.calibFlux = None
158 self.slots.modelFlux = None
159 self.slots.instFlux = None
160 self.slots.shape = None
161 self.slots.centroid = "ip_diffim_NaiveDipoleCentroid"
162 self.doReplaceWithNoise = False
164 These plugins enabled by default allow the user to test the hypothesis that the Source is a dipole.
165 This includes a set of measurements derived from intermediate base classes
166 DipoleCentroidAlgorithm and DipoleFluxAlgorithm.
167 Their respective algorithm control classes are defined in
168 DipoleCentroidControl and DipoleFluxControl.
169 Each centroid and flux measurement will have _neg (negative)
170 and _pos (positive lobe) fields.
172 The first set of measurements uses a "naive" alrogithm
173 for centroid and flux measurements, implemented in
174 NaiveDipoleCentroidControl and NaiveDipoleFluxControl.
175 The algorithm uses a naive 3x3 weighted moment around
176 the nominal centroids of each peak in the Source Footprint. These algorithms fill the table fields
177 ip_diffim_NaiveDipoleCentroid* and ip_diffim_NaiveDipoleFlux*
179 The second set of measurements undertakes a joint-Psf model on the negative
180 and positive lobe simultaneously. This fit simultaneously solves for the negative and positive
181 lobe centroids and fluxes using non-linear least squares minimization.
182 The fields are stored in table elements ip_diffim_PsfDipoleFlux*.
184 Because this Task is just a config for SingleFrameMeasurementTask, the same result may be acheived by
185 manually editing the config and running SingleFrameMeasurementTask. For example:
187 .. code-block:: py
189 config = SingleFrameMeasurementConfig()
190 config.plugins.names = ["base_PsfFlux",
191 "ip_diffim_PsfDipoleFlux",
192 "ip_diffim_NaiveDipoleFlux",
193 "ip_diffim_NaiveDipoleCentroid",
194 "ip_diffim_ClassificationDipole",
195 "base_CircularApertureFlux",
196 "base_SkyCoord"]
198 config.slots.calibFlux = None
199 config.slots.modelFlux = None
200 config.slots.instFlux = None
201 config.slots.shape = None
202 config.slots.centroid = "ip_diffim_NaiveDipoleCentroid"
203 config.doReplaceWithNoise = False
205 schema = afwTable.SourceTable.makeMinimalSchema()
206 task = SingleFrameMeasurementTask(schema, config=config)-
208 Debug variables
210 The ``pipetask`` command line interface supports a
211 flag --debug to import @b debug.py from your PYTHONPATH. The relevant contents of debug.py
212 for this Task include:
214 .. code-block:: py
216 import sys
217 import lsstDebug
218 def DebugInfo(name):
219 di = lsstDebug.getInfo(name)
220 if name == "lsst.ip.diffim.dipoleMeasurement":
221 di.display = True # enable debug output
222 di.maskTransparency = 90 # display mask transparency
223 di.displayDiaSources = True # show exposure with dipole results
224 return di
225 lsstDebug.Info = DebugInfo
226 lsstDebug.frame = 1
228 config.slots.calibFlux = None
229 config.slots.modelFlux = None
230 config.slots.gaussianFlux = None
231 config.slots.shape = None
232 config.slots.centroid = "ip_diffim_NaiveDipoleCentroid"
233 config.doReplaceWithNoise = False
235 Start the processing by parsing the command line, where the user has the option of
236 enabling debugging output and/or sending their own image for demonstration
237 (in case they have not downloaded the afwdata package).
239 .. code-block:: py
241 if __name__ == "__main__":
242 import argparse
243 parser = argparse.ArgumentParser(
244 description="Demonstrate the use of SourceDetectionTask and DipoleMeasurementTask")
245 parser.add_argument('--debug', '-d', action="store_true", help="Load debug.py?", default=False)
246 parser.add_argument("--image", "-i", help="User defined image", default=None)
247 args = parser.parse_args()
248 if args.debug:
249 try:
250 import debug
251 debug.lsstDebug.frame = 2
252 except ImportError as e:
253 print(e, file=sys.stderr)
254 run(args)
256 The processing occurs in the run function. We first extract an exposure from disk or afwdata, displaying
257 it if requested:
259 .. code-block:: py
261 def run(args):
262 exposure = loadData(args.image)
263 if args.debug:
264 afwDisplay.Display(frame=1).mtv(exposure)
266 Create a default source schema that we will append fields to as we add more algorithms:
268 .. code-block:: py
270 schema = afwTable.SourceTable.makeMinimalSchema()
272 Create the detection and measurement Tasks, with some minor tweaking of their configs:
274 .. code-block:: py
276 # Create the detection task
277 config = SourceDetectionTask.ConfigClass()
278 config.thresholdPolarity = "both"
279 config.background.isNanSafe = True
280 config.thresholdValue = 3
281 detectionTask = SourceDetectionTask(config=config, schema=schema)
282 # And the measurement Task
283 config = DipoleMeasurementTask.ConfigClass()
284 config.plugins.names.remove('base_SkyCoord')
285 algMetadata = dafBase.PropertyList()
286 measureTask = DipoleMeasurementTask(schema, algMetadata, config=config)
288 Having fully initialied the schema, we create a Source table from it:
290 .. code-block:: py
292 # Create the output table
293 tab = afwTable.SourceTable.make(schema)
295 Run detection:
297 .. code-block:: py
299 # Process the data
300 results = detectionTask.run(tab, exposure)
302 Because we are looking for dipoles, we need to merge the positive and negative detections:
304 .. code-block:: py
306 # Merge the positve and negative sources
307 fpSet = results.fpSets.positive
308 growFootprint = 2
309 fpSet.merge(results.fpSets.negative, growFootprint, growFootprint, False)
310 diaSources = afwTable.SourceCatalog(tab)
311 fpSet.makeSources(diaSources)
312 print("Merged %s Sources into %d diaSources (from %d +ve, %d -ve)" % (len(results.sources),
313 len(diaSources),
314 results.fpSets.numPos,
315 results.fpSets.numNeg))
317 Finally, perform measurement (both standard and dipole-specialized) on the merged sources:
319 .. code-block:: py
321 measureTask.run(diaSources, exposure)
323 Optionally display debugging information:
325 .. code-block:: py
327 # Display dipoles if debug enabled
328 if args.debug:
329 dpa = DipoleAnalysis()
330 dpa.displayDipoles(exposure, diaSources)
332 """
333 ConfigClass = DipoleMeasurementConfig
334 _DefaultName = "dipoleMeasurement"
337#########
338# Other Support classs
339#########
341class SourceFlagChecker(object):
342 """Functor class to check whether a diaSource has flags set that should cause it to be labeled bad."""
344 def __init__(self, sources, badFlags=None):
345 self.badFlags = ['base_PixelFlags_flag_edge', 'base_PixelFlags_flag_interpolatedCenter',
346 'base_PixelFlags_flag_saturatedCenter']
347 if badFlags is not None:
348 for flag in badFlags:
349 self.badFlags.append(flag)
350 self.keys = [sources.getSchema().find(name).key for name in self.badFlags]
351 self.keys.append(sources.table.getCentroidFlagKey())
353 def __call__(self, source):
354 """Call the source flag checker on a single Source
356 Parameters
357 ----------
358 source :
359 Source that will be examined
360 """
361 for k in self.keys:
362 if source.get(k):
363 return False
364 return True
367class DipoleAnalysis(object):
368 """Functor class that provides (S/N, position, orientation) of measured dipoles"""
370 def __init__(self):
371 pass
373 def __call__(self, source):
374 """Parse information returned from dipole measurement
376 Parameters
377 ----------
378 source : `lsst.afw.table.SourceRecord`
379 The source that will be examined"""
380 return self.getSn(source), self.getCentroid(source), self.getOrientation(source)
382 def getSn(self, source):
383 """Get the total signal-to-noise of the dipole; total S/N is from positive and negative lobe
385 Parameters
386 ----------
387 source : `lsst.afw.table.SourceRecord`
388 The source that will be examined"""
390 posflux = source.get("ip_diffim_PsfDipoleFlux_pos_instFlux")
391 posfluxErr = source.get("ip_diffim_PsfDipoleFlux_pos_instFluxErr")
392 negflux = source.get("ip_diffim_PsfDipoleFlux_neg_instFlux")
393 negfluxErr = source.get("ip_diffim_PsfDipoleFlux_neg_instFluxErr")
395 # Not a dipole!
396 if (posflux < 0) is (negflux < 0):
397 return 0
399 return np.sqrt((posflux/posfluxErr)**2 + (negflux/negfluxErr)**2)
401 def getCentroid(self, source):
402 """Get the centroid of the dipole; average of positive and negative lobe
404 Parameters
405 ----------
406 source : `lsst.afw.table.SourceRecord`
407 The source that will be examined"""
409 negCenX = source.get("ip_diffim_PsfDipoleFlux_neg_centroid_x")
410 negCenY = source.get("ip_diffim_PsfDipoleFlux_neg_centroid_y")
411 posCenX = source.get("ip_diffim_PsfDipoleFlux_pos_centroid_x")
412 posCenY = source.get("ip_diffim_PsfDipoleFlux_pos_centroid_y")
413 if (np.isinf(negCenX) or np.isinf(negCenY) or np.isinf(posCenX) or np.isinf(posCenY)):
414 return None
416 center = geom.Point2D(0.5*(negCenX+posCenX),
417 0.5*(negCenY+posCenY))
418 return center
420 def getOrientation(self, source):
421 """Calculate the orientation of dipole; vector from negative to positive lobe
423 Parameters
424 ----------
425 source : `lsst.afw.table.SourceRecord`
426 The source that will be examined"""
428 negCenX = source.get("ip_diffim_PsfDipoleFlux_neg_centroid_x")
429 negCenY = source.get("ip_diffim_PsfDipoleFlux_neg_centroid_y")
430 posCenX = source.get("ip_diffim_PsfDipoleFlux_pos_centroid_x")
431 posCenY = source.get("ip_diffim_PsfDipoleFlux_pos_centroid_y")
432 if (np.isinf(negCenX) or np.isinf(negCenY) or np.isinf(posCenX) or np.isinf(posCenY)):
433 return None
435 dx, dy = posCenX-negCenX, posCenY-negCenY
436 angle = geom.Angle(np.arctan2(dx, dy), geom.radians)
437 return angle
439 def displayDipoles(self, exposure, sources):
440 """Display debugging information on the detected dipoles
442 Parameters
443 ----------
444 exposure : `lsst.afw.image.Exposure`
445 Image the dipoles were measured on
446 sources : `lsst.afw.table.SourceCatalog`
447 The set of diaSources that were measured"""
449 import lsstDebug
450 display = lsstDebug.Info(__name__).display
451 displayDiaSources = lsstDebug.Info(__name__).displayDiaSources
452 maskTransparency = lsstDebug.Info(__name__).maskTransparency
453 if not maskTransparency:
454 maskTransparency = 90
455 disp = afwDisplay.Display(frame=lsstDebug.frame)
456 disp.setMaskTransparency(maskTransparency)
457 disp.mtv(exposure)
459 if display and displayDiaSources:
460 with disp.Buffering():
461 for source in sources:
462 cenX, cenY = source.get("ipdiffim_DipolePsfFlux_centroid")
463 if np.isinf(cenX) or np.isinf(cenY):
464 cenX, cenY = source.getCentroid()
466 isdipole = source.get("ip_diffim_ClassificationDipole_value")
467 if isdipole and np.isfinite(isdipole):
468 # Dipole
469 ctype = afwDisplay.GREEN
470 else:
471 # Not dipole
472 ctype = afwDisplay.RED
474 disp.dot("o", cenX, cenY, size=2, ctype=ctype)
476 negCenX = source.get("ip_diffim_PsfDipoleFlux_neg_centroid_x")
477 negCenY = source.get("ip_diffim_PsfDipoleFlux_neg_centroid_y")
478 posCenX = source.get("ip_diffim_PsfDipoleFlux_pos_centroid_x")
479 posCenY = source.get("ip_diffim_PsfDipoleFlux_pos_centroid_y")
480 if (np.isinf(negCenX) or np.isinf(negCenY) or np.isinf(posCenX) or np.isinf(posCenY)):
481 continue
483 disp.line([(negCenX, negCenY), (posCenX, posCenY)], ctype=afwDisplay.YELLOW)
485 lsstDebug.frame += 1
488class DipoleDeblender(object):
489 """Functor to deblend a source as a dipole, and return a new source with deblended footprints.
491 This necessarily overrides some of the functionality from
492 meas_algorithms/python/lsst/meas/algorithms/deblend.py since we
493 need a single source that contains the blended peaks, not
494 multiple children sources. This directly calls the core
495 deblending code deblendBaseline.deblend (optionally _fitPsf for
496 debugging).
498 Not actively being used, but there is a unit test for it in
499 dipoleAlgorithm.py.
500 """
502 def __init__(self):
503 # Set up defaults to send to deblender
505 # Always deblend as Psf
506 self.psfChisqCut1 = self.psfChisqCut2 = self.psfChisqCut2b = np.inf
507 self.log = getLogger('lsst.ip.diffim.DipoleDeblender')
508 self.sigma2fwhm = 2. * np.sqrt(2. * np.log(2.))
510 def __call__(self, source, exposure):
511 fp = source.getFootprint()
512 peaks = fp.getPeaks()
513 peaksF = [pk.getF() for pk in peaks]
514 fbb = fp.getBBox()
515 fmask = afwImage.Mask(fbb)
516 fmask.setXY0(fbb.getMinX(), fbb.getMinY())
517 fp.spans.setMask(fmask, 1)
519 psf = exposure.getPsf()
520 psfSigPix = psf.computeShape(psf.getAveragePosition()).getDeterminantRadius()
521 psfFwhmPix = psfSigPix * self.sigma2fwhm
522 subimage = afwImage.ExposureF(exposure, bbox=fbb, deep=True)
523 cpsf = deblendBaseline.CachingPsf(psf)
525 # if fewer than 2 peaks, just return a copy of the source
526 if len(peaks) < 2:
527 return source.getTable().copyRecord(source)
529 # make sure you only deblend 2 peaks; take the brighest and faintest
530 speaks = [(p.getPeakValue(), p) for p in peaks]
531 speaks.sort()
532 dpeaks = [speaks[0][1], speaks[-1][1]]
534 # and only set these peaks in the footprint (peaks is mutable)
535 peaks.clear()
536 for peak in dpeaks:
537 peaks.append(peak)
539 if True:
540 # Call top-level deblend task
541 fpres = deblendBaseline.deblend(fp, exposure.getMaskedImage(), psf, psfFwhmPix,
542 log=self.log,
543 psfChisqCut1=self.psfChisqCut1,
544 psfChisqCut2=self.psfChisqCut2,
545 psfChisqCut2b=self.psfChisqCut2b)
546 else:
547 # Call lower-level _fit_psf task
549 # Prepare results structure
550 fpres = deblendBaseline.DeblenderResult(fp, exposure.getMaskedImage(), psf, psfFwhmPix, self.log)
552 for pki, (pk, pkres, pkF) in enumerate(zip(dpeaks, fpres.deblendedParents[0].peaks, peaksF)):
553 self.log.debug('Peak %i', pki)
554 deblendBaseline._fitPsf(fp, fmask, pk, pkF, pkres, fbb, dpeaks, peaksF, self.log,
555 cpsf, psfFwhmPix,
556 subimage.getMaskedImage().getImage(),
557 subimage.getMaskedImage().getVariance(),
558 self.psfChisqCut1, self.psfChisqCut2, self.psfChisqCut2b)
560 deblendedSource = source.getTable().copyRecord(source)
561 deblendedSource.setParent(source.getId())
562 peakList = deblendedSource.getFootprint().getPeaks()
563 peakList.clear()
565 for i, peak in enumerate(fpres.deblendedParents[0].peaks):
566 if peak.psfFitFlux > 0:
567 suffix = "pos"
568 else:
569 suffix = "neg"
570 c = peak.psfFitCenter
571 self.log.info("deblended.centroid.dipole.psf.%s %f %f",
572 suffix, c[0], c[1])
573 self.log.info("deblended.chi2dof.dipole.%s %f",
574 suffix, peak.psfFitChisq / peak.psfFitDof)
575 self.log.info("deblended.flux.dipole.psf.%s %f",
576 suffix, peak.psfFitFlux * np.sum(peak.templateImage.getArray()))
577 peakList.append(peak.peak)
578 return deblendedSource