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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.daf.base as dafBase
25import lsst.pex.config as pexConfig
26import lsst.afw.detection as afwDetect
27import lsst.afw.image as afwImage
28import lsst.afw.math as afwMath
29import lsst.afw.geom as afwGeom
30import lsst.afw.table as afwTable
31import lsst.geom as geom
32import lsst.pipe.base as pipeBase
33from lsst.meas.algorithms import SourceDetectionTask, SubtractBackgroundTask, WarpedPsf
34from lsst.meas.base import SingleFrameMeasurementTask
35from .makeKernelBasisList import makeKernelBasisList
36from .psfMatch import PsfMatchTask, PsfMatchConfigDF, PsfMatchConfigAL
37from . import utils as diffimUtils
38from . import diffimLib
39from . import diffimTools
40import lsst.afw.display as afwDisplay
42__all__ = ["ImagePsfMatchConfig", "ImagePsfMatchTask", "subtractAlgorithmRegistry"]
44sigma2fwhm = 2.*np.sqrt(2.*np.log(2.))
47class ImagePsfMatchConfig(pexConfig.Config):
48 """Configuration for image-to-image Psf matching.
49 """
50 kernel = pexConfig.ConfigChoiceField(
51 doc="kernel type",
52 typemap=dict(
53 AL=PsfMatchConfigAL,
54 DF=PsfMatchConfigDF
55 ),
56 default="AL",
57 )
58 selectDetection = pexConfig.ConfigurableField(
59 target=SourceDetectionTask,
60 doc="Initial detections used to feed stars to kernel fitting",
61 )
62 selectMeasurement = pexConfig.ConfigurableField(
63 target=SingleFrameMeasurementTask,
64 doc="Initial measurements used to feed stars to kernel fitting",
65 )
67 def setDefaults(self):
68 # High sigma detections only
69 self.selectDetection.reEstimateBackground = False
70 self.selectDetection.thresholdValue = 10.0
72 # Minimal set of measurments for star selection
73 self.selectMeasurement.algorithms.names.clear()
74 self.selectMeasurement.algorithms.names = ('base_SdssCentroid', 'base_PsfFlux', 'base_PixelFlags',
75 'base_SdssShape', 'base_GaussianFlux', 'base_SkyCoord')
76 self.selectMeasurement.slots.modelFlux = None
77 self.selectMeasurement.slots.apFlux = None
78 self.selectMeasurement.slots.calibFlux = None
81class ImagePsfMatchTask(PsfMatchTask):
82 """Psf-match two MaskedImages or Exposures using the sources in the images.
84 Parameters
85 ----------
86 args :
87 Arguments to be passed to lsst.ip.diffim.PsfMatchTask.__init__
88 kwargs :
89 Keyword arguments to be passed to lsst.ip.diffim.PsfMatchTask.__init__
91 Notes
92 -----
93 Upon initialization, the kernel configuration is defined by self.config.kernel.active.
94 The task creates an lsst.afw.math.Warper from the subConfig self.config.kernel.active.warpingConfig.
95 A schema for the selection and measurement of candidate lsst.ip.diffim.KernelCandidates is
96 defined, and used to initize subTasks selectDetection (for candidate detection) and selectMeasurement
97 (for candidate measurement).
99 Description
101 Build a Psf-matching kernel using two input images, either as MaskedImages (in which case they need
102 to be astrometrically aligned) or Exposures (in which case astrometric alignment will happen by
103 default but may be turned off). This requires a list of input Sources which may be provided
104 by the calling Task; if not, the Task will perform a coarse source detection
105 and selection for this purpose. Sources are vetted for signal-to-noise and masked pixels
106 (in both the template and science image), and substamps around each acceptable
107 source are extracted and used to create an instance of KernelCandidate.
108 Each KernelCandidate is then placed within a lsst.afw.math.SpatialCellSet, which is used by an ensemble of
109 lsst.afw.math.CandidateVisitor instances to build the Psf-matching kernel. These visitors include, in
110 the order that they are called: BuildSingleKernelVisitor, KernelSumVisitor, BuildSpatialKernelVisitor,
111 and AssessSpatialKernelVisitor.
113 Sigma clipping of KernelCandidates is performed as follows:
115 - BuildSingleKernelVisitor, using the substamp diffim residuals from the per-source kernel fit,
116 if PsfMatchConfig.singleKernelClipping is True
117 - KernelSumVisitor, using the mean and standard deviation of the kernel sum from all candidates,
118 if PsfMatchConfig.kernelSumClipping is True
119 - AssessSpatialKernelVisitor, using the substamp diffim ressiduals from the spatial kernel fit,
120 if PsfMatchConfig.spatialKernelClipping is True
122 The actual solving for the kernel (and differential background model) happens in
123 lsst.ip.diffim.PsfMatchTask._solve. This involves a loop over the SpatialCellSet that first builds the
124 per-candidate matching kernel for the requested number of KernelCandidates per cell
125 (PsfMatchConfig.nStarPerCell). The quality of this initial per-candidate difference image is examined,
126 using moments of the pixel residuals in the difference image normalized by the square root of the variance
127 (i.e. sigma); ideally this should follow a normal (0, 1) distribution,
128 but the rejection thresholds are set
129 by the config (PsfMatchConfig.candidateResidualMeanMax and PsfMatchConfig.candidateResidualStdMax).
130 All candidates that pass this initial build are then examined en masse to find the
131 mean/stdev of the kernel sums across all candidates.
132 Objects that are significantly above or below the mean,
133 typically due to variability or sources that are saturated in one image but not the other,
134 are also rejected.This threshold is defined by PsfMatchConfig.maxKsumSigma.
135 Finally, a spatial model is built using all currently-acceptable candidates,
136 and the spatial model used to derive a second set of (spatial) residuals
137 which are again used to reject bad candidates, using the same thresholds as above.
139 Invoking the Task
141 There is no run() method for this Task. Instead there are 4 methods that
142 may be used to invoke the Psf-matching. These are
143 `~lsst.ip.diffim.imagePsfMatch.ImagePsfMatchTask.matchMaskedImages`,
144 `~lsst.ip.diffim.imagePsfMatch.ImagePsfMatchTask.subtractMaskedImages`,
145 `~lsst.ip.diffim.imagePsfMatch.ImagePsfMatchTask.matchExposures`, and
146 `~lsst.ip.diffim.imagePsfMatch.ImagePsfMatchTask.subtractExposures`.
148 The methods that operate on lsst.afw.image.MaskedImage require that the images already be astrometrically
149 aligned, and are the same shape. The methods that operate on lsst.afw.image.Exposure allow for the
150 input images to be misregistered and potentially be different sizes; by default a
151 lsst.afw.math.LanczosWarpingKernel is used to perform the astrometric alignment. The methods
152 that "match" images return a Psf-matched image, while the methods that "subtract" images
153 return a Psf-matched and template subtracted image.
155 See each method's returned lsst.pipe.base.Struct for more details.
157 Debug variables
159 The lsst.pipe.base.cmdLineTask.CmdLineTask command line task interface supports a
160 flag -d/--debug to import debug.py from your PYTHONPATH. The relevant contents of debug.py
161 for this Task include:
163 .. code-block:: py
165 import sys
166 import lsstDebug
167 def DebugInfo(name):
168 di = lsstDebug.getInfo(name)
169 if name == "lsst.ip.diffim.psfMatch":
170 di.display = True # enable debug output
171 di.maskTransparency = 80 # display mask transparency
172 di.displayCandidates = True # show all the candidates and residuals
173 di.displayKernelBasis = False # show kernel basis functions
174 di.displayKernelMosaic = True # show kernel realized across the image
175 di.plotKernelSpatialModel = False # show coefficients of spatial model
176 di.showBadCandidates = True # show the bad candidates (red) along with good (green)
177 elif name == "lsst.ip.diffim.imagePsfMatch":
178 di.display = True # enable debug output
179 di.maskTransparency = 30 # display mask transparency
180 di.displayTemplate = True # show full (remapped) template
181 di.displaySciIm = True # show science image to match to
182 di.displaySpatialCells = True # show spatial cells
183 di.displayDiffIm = True # show difference image
184 di.showBadCandidates = True # show the bad candidates (red) along with good (green)
185 elif name == "lsst.ip.diffim.diaCatalogSourceSelector":
186 di.display = False # enable debug output
187 di.maskTransparency = 30 # display mask transparency
188 di.displayExposure = True # show exposure with candidates indicated
189 di.pauseAtEnd = False # pause when done
190 return di
191 lsstDebug.Info = DebugInfo
192 lsstDebug.frame = 1
194 Note that if you want addional logging info, you may add to your scripts:
196 .. code-block:: py
198 import lsst.log.utils as logUtils
199 logUtils.traceSetAt("ip.diffim", 4)
201 Examples
202 --------
203 A complete example of using ImagePsfMatchTask
205 This code is imagePsfMatchTask.py in the examples directory, and can be run as e.g.
207 .. code-block:: none
209 examples/imagePsfMatchTask.py --debug
210 examples/imagePsfMatchTask.py --debug --mode="matchExposures"
211 examples/imagePsfMatchTask.py --debug --template /path/to/templateExp.fits
212 --science /path/to/scienceExp.fits
214 Create a subclass of ImagePsfMatchTask that allows us to either match exposures, or subtract exposures:
216 .. code-block:: none
218 class MyImagePsfMatchTask(ImagePsfMatchTask):
220 def __init__(self, args, kwargs):
221 ImagePsfMatchTask.__init__(self, args, kwargs)
223 def run(self, templateExp, scienceExp, mode):
224 if mode == "matchExposures":
225 return self.matchExposures(templateExp, scienceExp)
226 elif mode == "subtractExposures":
227 return self.subtractExposures(templateExp, scienceExp)
229 And allow the user the freedom to either run the script in default mode,
230 or point to their own images on disk.
231 Note that these images must be readable as an lsst.afw.image.Exposure.
233 We have enabled some minor display debugging in this script via the --debug option. However, if you
234 have an lsstDebug debug.py in your PYTHONPATH you will get additional debugging displays. The following
235 block checks for this script:
237 .. code-block:: py
239 if args.debug:
240 try:
241 import debug
242 # Since I am displaying 2 images here, set the starting frame number for the LSST debug LSST
243 debug.lsstDebug.frame = 3
244 except ImportError as e:
245 print(e, file=sys.stderr)
247 Finally, we call a run method that we define below.
248 First set up a Config and modify some of the parameters.
249 E.g. use an "Alard-Lupton" sum-of-Gaussian basis,
250 fit for a differential background, and use low order spatial
251 variation in the kernel and background:
253 .. code-block:: py
255 def run(args):
256 #
257 # Create the Config and use sum of gaussian basis
258 #
259 config = ImagePsfMatchTask.ConfigClass()
260 config.kernel.name = "AL"
261 config.kernel.active.fitForBackground = True
262 config.kernel.active.spatialKernelOrder = 1
263 config.kernel.active.spatialBgOrder = 0
265 Make sure the images (if any) that were sent to the script exist on disk and are readable. If no images
266 are sent, make some fake data up for the sake of this example script (have a look at the code if you want
267 more details on generateFakeImages):
269 .. code-block:: py
271 # Run the requested method of the Task
272 if args.template is not None and args.science is not None:
273 if not os.path.isfile(args.template):
274 raise FileNotFoundError("Template image %s does not exist" % (args.template))
275 if not os.path.isfile(args.science):
276 raise FileNotFoundError("Science image %s does not exist" % (args.science))
277 try:
278 templateExp = afwImage.ExposureF(args.template)
279 except Exception as e:
280 raise RuntimeError("Cannot read template image %s" % (args.template))
281 try:
282 scienceExp = afwImage.ExposureF(args.science)
283 except Exception as e:
284 raise RuntimeError("Cannot read science image %s" % (args.science))
285 else:
286 templateExp, scienceExp = generateFakeImages()
287 config.kernel.active.sizeCellX = 128
288 config.kernel.active.sizeCellY = 128
290 Create and run the Task:
292 .. code-block:: py
294 # Create the Task
295 psfMatchTask = MyImagePsfMatchTask(config=config)
296 # Run the Task
297 result = psfMatchTask.run(templateExp, scienceExp, args.mode)
299 And finally provide some optional debugging displays:
301 .. code-block:: py
303 if args.debug:
304 # See if the LSST debug has incremented the frame number; if not start with frame 3
305 try:
306 frame = debug.lsstDebug.frame + 1
307 except Exception:
308 frame = 3
309 afwDisplay.Display(frame=frame).mtv(result.matchedExposure,
310 title="Example script: Matched Template Image")
311 if "subtractedExposure" in result.getDict():
312 afwDisplay.Display(frame=frame + 1).mtv(result.subtractedExposure,
313 title="Example script: Subtracted Image")
314 """
316 ConfigClass = ImagePsfMatchConfig
318 def __init__(self, *args, **kwargs):
319 """Create the ImagePsfMatchTask.
320 """
321 PsfMatchTask.__init__(self, *args, **kwargs)
322 self.kConfig = self.config.kernel.active
323 self._warper = afwMath.Warper.fromConfig(self.kConfig.warpingConfig)
324 # the background subtraction task uses a config from an unusual location,
325 # so cannot easily be constructed with makeSubtask
326 self.background = SubtractBackgroundTask(config=self.kConfig.afwBackgroundConfig, name="background",
327 parentTask=self)
328 self.selectSchema = afwTable.SourceTable.makeMinimalSchema()
329 self.selectAlgMetadata = dafBase.PropertyList()
330 self.makeSubtask("selectDetection", schema=self.selectSchema)
331 self.makeSubtask("selectMeasurement", schema=self.selectSchema, algMetadata=self.selectAlgMetadata)
333 def getFwhmPix(self, psf):
334 """Return the FWHM in pixels of a Psf.
335 """
336 sigPix = psf.computeShape().getDeterminantRadius()
337 return sigPix*sigma2fwhm
339 @pipeBase.timeMethod
340 def matchExposures(self, templateExposure, scienceExposure,
341 templateFwhmPix=None, scienceFwhmPix=None,
342 candidateList=None, doWarping=True, convolveTemplate=True):
343 """Warp and PSF-match an exposure to the reference.
345 Do the following, in order:
347 - Warp templateExposure to match scienceExposure,
348 if doWarping True and their WCSs do not already match
349 - Determine a PSF matching kernel and differential background model
350 that matches templateExposure to scienceExposure
351 - Convolve templateExposure by PSF matching kernel
353 Parameters
354 ----------
355 templateExposure : `lsst.afw.image.Exposure`
356 Exposure to warp and PSF-match to the reference masked image
357 scienceExposure : `lsst.afw.image.Exposure`
358 Exposure whose WCS and PSF are to be matched to
359 templateFwhmPix :`float`
360 FWHM (in pixels) of the Psf in the template image (image to convolve)
361 scienceFwhmPix : `float`
362 FWHM (in pixels) of the Psf in the science image
363 candidateList : `list`, optional
364 a list of footprints/maskedImages for kernel candidates;
365 if `None` then source detection is run.
367 - Currently supported: list of Footprints or measAlg.PsfCandidateF
369 doWarping : `bool`
370 what to do if ``templateExposure`` and ``scienceExposure`` WCSs do not match:
372 - if `True` then warp ``templateExposure`` to match ``scienceExposure``
373 - if `False` then raise an Exception
375 convolveTemplate : `bool`
376 Whether to convolve the template image or the science image:
378 - if `True`, ``templateExposure`` is warped if doWarping,
379 ``templateExposure`` is convolved
380 - if `False`, ``templateExposure`` is warped if doWarping,
381 ``scienceExposure`` is convolved
383 Returns
384 -------
385 results : `lsst.pipe.base.Struct`
386 An `lsst.pipe.base.Struct` containing these fields:
388 - ``matchedImage`` : the PSF-matched exposure =
389 Warped ``templateExposure`` convolved by psfMatchingKernel. This has:
391 - the same parent bbox, Wcs and PhotoCalib as scienceExposure
392 - the same filter as templateExposure
393 - no Psf (because the PSF-matching process does not compute one)
395 - ``psfMatchingKernel`` : the PSF matching kernel
396 - ``backgroundModel`` : differential background model
397 - ``kernelCellSet`` : SpatialCellSet used to solve for the PSF matching kernel
399 Raises
400 ------
401 RuntimeError
402 Raised if doWarping is False and ``templateExposure`` and
403 ``scienceExposure`` WCSs do not match
404 """
405 if not self._validateWcs(templateExposure, scienceExposure):
406 if doWarping:
407 self.log.info("Astrometrically registering template to science image")
408 templatePsf = templateExposure.getPsf()
409 # Warp PSF before overwriting exposure
410 xyTransform = afwGeom.makeWcsPairTransform(templateExposure.getWcs(),
411 scienceExposure.getWcs())
412 psfWarped = WarpedPsf(templatePsf, xyTransform)
413 templateExposure = self._warper.warpExposure(scienceExposure.getWcs(),
414 templateExposure,
415 destBBox=scienceExposure.getBBox())
416 templateExposure.setPsf(psfWarped)
417 else:
418 self.log.error("ERROR: Input images not registered")
419 raise RuntimeError("Input images not registered")
421 if templateFwhmPix is None:
422 if not templateExposure.hasPsf():
423 self.log.warn("No estimate of Psf FWHM for template image")
424 else:
425 templateFwhmPix = self.getFwhmPix(templateExposure.getPsf())
426 self.log.info("templateFwhmPix: {}".format(templateFwhmPix))
428 if scienceFwhmPix is None:
429 if not scienceExposure.hasPsf():
430 self.log.warn("No estimate of Psf FWHM for science image")
431 else:
432 scienceFwhmPix = self.getFwhmPix(scienceExposure.getPsf())
433 self.log.info("scienceFwhmPix: {}".format(scienceFwhmPix))
435 if convolveTemplate:
436 kernelSize = makeKernelBasisList(self.kConfig, templateFwhmPix, scienceFwhmPix)[0].getWidth()
437 candidateList = self.makeCandidateList(
438 templateExposure, scienceExposure, kernelSize, candidateList)
439 results = self.matchMaskedImages(
440 templateExposure.getMaskedImage(), scienceExposure.getMaskedImage(), candidateList,
441 templateFwhmPix=templateFwhmPix, scienceFwhmPix=scienceFwhmPix)
442 else:
443 kernelSize = makeKernelBasisList(self.kConfig, scienceFwhmPix, templateFwhmPix)[0].getWidth()
444 candidateList = self.makeCandidateList(
445 templateExposure, scienceExposure, kernelSize, candidateList)
446 results = self.matchMaskedImages(
447 scienceExposure.getMaskedImage(), templateExposure.getMaskedImage(), candidateList,
448 templateFwhmPix=scienceFwhmPix, scienceFwhmPix=templateFwhmPix)
450 psfMatchedExposure = afwImage.makeExposure(results.matchedImage, scienceExposure.getWcs())
451 psfMatchedExposure.setFilter(templateExposure.getFilter())
452 psfMatchedExposure.setPhotoCalib(scienceExposure.getPhotoCalib())
453 results.warpedExposure = templateExposure
454 results.matchedExposure = psfMatchedExposure
455 return results
457 @pipeBase.timeMethod
458 def matchMaskedImages(self, templateMaskedImage, scienceMaskedImage, candidateList,
459 templateFwhmPix=None, scienceFwhmPix=None):
460 """PSF-match a MaskedImage (templateMaskedImage) to a reference MaskedImage (scienceMaskedImage).
462 Do the following, in order:
464 - Determine a PSF matching kernel and differential background model
465 that matches templateMaskedImage to scienceMaskedImage
466 - Convolve templateMaskedImage by the PSF matching kernel
468 Parameters
469 ----------
470 templateMaskedImage : `lsst.afw.image.MaskedImage`
471 masked image to PSF-match to the reference masked image;
472 must be warped to match the reference masked image
473 scienceMaskedImage : `lsst.afw.image.MaskedImage`
474 maskedImage whose PSF is to be matched to
475 templateFwhmPix : `float`
476 FWHM (in pixels) of the Psf in the template image (image to convolve)
477 scienceFwhmPix : `float`
478 FWHM (in pixels) of the Psf in the science image
479 candidateList : `list`, optional
480 A list of footprints/maskedImages for kernel candidates;
481 if `None` then source detection is run.
483 - Currently supported: list of Footprints or measAlg.PsfCandidateF
485 Returns
486 -------
487 result : `callable`
488 An `lsst.pipe.base.Struct` containing these fields:
490 - psfMatchedMaskedImage: the PSF-matched masked image =
491 ``templateMaskedImage`` convolved with psfMatchingKernel.
492 This has the same xy0, dimensions and wcs as ``scienceMaskedImage``.
493 - psfMatchingKernel: the PSF matching kernel
494 - backgroundModel: differential background model
495 - kernelCellSet: SpatialCellSet used to solve for the PSF matching kernel
497 Raises
498 ------
499 RuntimeError
500 Raised if input images have different dimensions
501 """
502 import lsstDebug
503 display = lsstDebug.Info(__name__).display
504 displayTemplate = lsstDebug.Info(__name__).displayTemplate
505 displaySciIm = lsstDebug.Info(__name__).displaySciIm
506 displaySpatialCells = lsstDebug.Info(__name__).displaySpatialCells
507 maskTransparency = lsstDebug.Info(__name__).maskTransparency
508 if not maskTransparency:
509 maskTransparency = 0
510 if display:
511 afwDisplay.setDefaultMaskTransparency(maskTransparency)
513 if not candidateList:
514 raise RuntimeError("Candidate list must be populated by makeCandidateList")
516 if not self._validateSize(templateMaskedImage, scienceMaskedImage):
517 self.log.error("ERROR: Input images different size")
518 raise RuntimeError("Input images different size")
520 if display and displayTemplate:
521 disp = afwDisplay.Display(frame=lsstDebug.frame)
522 disp.mtv(templateMaskedImage, title="Image to convolve")
523 lsstDebug.frame += 1
525 if display and displaySciIm:
526 disp = afwDisplay.Display(frame=lsstDebug.frame)
527 disp.mtv(scienceMaskedImage, title="Image to not convolve")
528 lsstDebug.frame += 1
530 kernelCellSet = self._buildCellSet(templateMaskedImage,
531 scienceMaskedImage,
532 candidateList)
534 if display and displaySpatialCells:
535 diffimUtils.showKernelSpatialCells(scienceMaskedImage, kernelCellSet,
536 symb="o", ctype=afwDisplay.CYAN, ctypeUnused=afwDisplay.YELLOW,
537 ctypeBad=afwDisplay.RED, size=4, frame=lsstDebug.frame,
538 title="Image to not convolve")
539 lsstDebug.frame += 1
541 if templateFwhmPix and scienceFwhmPix:
542 self.log.info("Matching Psf FWHM %.2f -> %.2f pix", templateFwhmPix, scienceFwhmPix)
544 if self.kConfig.useBicForKernelBasis:
545 tmpKernelCellSet = self._buildCellSet(templateMaskedImage,
546 scienceMaskedImage,
547 candidateList)
548 nbe = diffimTools.NbasisEvaluator(self.kConfig, templateFwhmPix, scienceFwhmPix)
549 bicDegrees = nbe(tmpKernelCellSet, self.log)
550 basisList = makeKernelBasisList(self.kConfig, templateFwhmPix, scienceFwhmPix,
551 alardDegGauss=bicDegrees[0], metadata=self.metadata)
552 del tmpKernelCellSet
553 else:
554 basisList = makeKernelBasisList(self.kConfig, templateFwhmPix, scienceFwhmPix,
555 metadata=self.metadata)
557 spatialSolution, psfMatchingKernel, backgroundModel = self._solve(kernelCellSet, basisList)
559 psfMatchedMaskedImage = afwImage.MaskedImageF(templateMaskedImage.getBBox())
560 convolutionControl = afwMath.ConvolutionControl()
561 convolutionControl.setDoNormalize(False)
562 afwMath.convolve(psfMatchedMaskedImage, templateMaskedImage, psfMatchingKernel, convolutionControl)
563 return pipeBase.Struct(
564 matchedImage=psfMatchedMaskedImage,
565 psfMatchingKernel=psfMatchingKernel,
566 backgroundModel=backgroundModel,
567 kernelCellSet=kernelCellSet,
568 )
570 @pipeBase.timeMethod
571 def subtractExposures(self, templateExposure, scienceExposure,
572 templateFwhmPix=None, scienceFwhmPix=None,
573 candidateList=None, doWarping=True, convolveTemplate=True):
574 """Register, Psf-match and subtract two Exposures.
576 Do the following, in order:
578 - Warp templateExposure to match scienceExposure, if their WCSs do not already match
579 - Determine a PSF matching kernel and differential background model
580 that matches templateExposure to scienceExposure
581 - PSF-match templateExposure to scienceExposure
582 - Compute subtracted exposure (see return values for equation).
584 Parameters
585 ----------
586 templateExposure : `lsst.afw.image.Exposure`
587 Exposure to PSF-match to scienceExposure
588 scienceExposure : `lsst.afw.image.Exposure`
589 Reference Exposure
590 templateFwhmPix : `float`
591 FWHM (in pixels) of the Psf in the template image (image to convolve)
592 scienceFwhmPix : `float`
593 FWHM (in pixels) of the Psf in the science image
594 candidateList : `list`, optional
595 A list of footprints/maskedImages for kernel candidates;
596 if `None` then source detection is run.
598 - Currently supported: list of Footprints or measAlg.PsfCandidateF
600 doWarping : `bool`
601 What to do if ``templateExposure``` and ``scienceExposure`` WCSs do
602 not match:
604 - if `True` then warp ``templateExposure`` to match ``scienceExposure``
605 - if `False` then raise an Exception
607 convolveTemplate : `bool`
608 Convolve the template image or the science image
610 - if `True`, ``templateExposure`` is warped if doWarping,
611 ``templateExposure`` is convolved
612 - if `False`, ``templateExposure`` is warped if doWarping,
613 ``scienceExposure is`` convolved
615 Returns
616 -------
617 result : `lsst.pipe.base.Struct`
618 An `lsst.pipe.base.Struct` containing these fields:
620 - ``subtractedExposure`` : subtracted Exposure
621 scienceExposure - (matchedImage + backgroundModel)
622 - ``matchedImage`` : ``templateExposure`` after warping to match
623 ``templateExposure`` (if doWarping true),
624 and convolving with psfMatchingKernel
625 - ``psfMatchingKernel`` : PSF matching kernel
626 - ``backgroundModel`` : differential background model
627 - ``kernelCellSet`` : SpatialCellSet used to determine PSF matching kernel
628 """
629 results = self.matchExposures(
630 templateExposure=templateExposure,
631 scienceExposure=scienceExposure,
632 templateFwhmPix=templateFwhmPix,
633 scienceFwhmPix=scienceFwhmPix,
634 candidateList=candidateList,
635 doWarping=doWarping,
636 convolveTemplate=convolveTemplate
637 )
639 subtractedExposure = afwImage.ExposureF(scienceExposure, True)
640 if convolveTemplate:
641 subtractedMaskedImage = subtractedExposure.getMaskedImage()
642 subtractedMaskedImage -= results.matchedExposure.getMaskedImage()
643 subtractedMaskedImage -= results.backgroundModel
644 else:
645 subtractedExposure.setMaskedImage(results.warpedExposure.getMaskedImage())
646 subtractedMaskedImage = subtractedExposure.getMaskedImage()
647 subtractedMaskedImage -= results.matchedExposure.getMaskedImage()
648 subtractedMaskedImage -= results.backgroundModel
650 # Preserve polarity of differences
651 subtractedMaskedImage *= -1
653 # Place back on native photometric scale
654 subtractedMaskedImage /= results.psfMatchingKernel.computeImage(
655 afwImage.ImageD(results.psfMatchingKernel.getDimensions()), False)
657 import lsstDebug
658 display = lsstDebug.Info(__name__).display
659 displayDiffIm = lsstDebug.Info(__name__).displayDiffIm
660 maskTransparency = lsstDebug.Info(__name__).maskTransparency
661 if not maskTransparency:
662 maskTransparency = 0
663 if display:
664 afwDisplay.setDefaultMaskTransparency(maskTransparency)
665 if display and displayDiffIm:
666 disp = afwDisplay.Display(frame=lsstDebug.frame)
667 disp.mtv(templateExposure, title="Template")
668 lsstDebug.frame += 1
669 disp = afwDisplay.Display(frame=lsstDebug.frame)
670 disp.mtv(results.matchedExposure, title="Matched template")
671 lsstDebug.frame += 1
672 disp = afwDisplay.Display(frame=lsstDebug.frame)
673 disp.mtv(scienceExposure, title="Science Image")
674 lsstDebug.frame += 1
675 disp = afwDisplay.Display(frame=lsstDebug.frame)
676 disp.mtv(subtractedExposure, title="Difference Image")
677 lsstDebug.frame += 1
679 results.subtractedExposure = subtractedExposure
680 return results
682 @pipeBase.timeMethod
683 def subtractMaskedImages(self, templateMaskedImage, scienceMaskedImage, candidateList,
684 templateFwhmPix=None, scienceFwhmPix=None):
685 """Psf-match and subtract two MaskedImages.
687 Do the following, in order:
689 - PSF-match templateMaskedImage to scienceMaskedImage
690 - Determine the differential background
691 - Return the difference: scienceMaskedImage
692 ((warped templateMaskedImage convolved with psfMatchingKernel) + backgroundModel)
694 Parameters
695 ----------
696 templateMaskedImage : `lsst.afw.image.MaskedImage`
697 MaskedImage to PSF-match to ``scienceMaskedImage``
698 scienceMaskedImage : `lsst.afw.image.MaskedImage`
699 Reference MaskedImage
700 templateFwhmPix : `float`
701 FWHM (in pixels) of the Psf in the template image (image to convolve)
702 scienceFwhmPix : `float`
703 FWHM (in pixels) of the Psf in the science image
704 candidateList : `list`, optional
705 A list of footprints/maskedImages for kernel candidates;
706 if `None` then source detection is run.
708 - Currently supported: list of Footprints or measAlg.PsfCandidateF
710 Returns
711 -------
712 results : `lsst.pipe.base.Struct`
713 An `lsst.pipe.base.Struct` containing these fields:
715 - ``subtractedMaskedImage`` : ``scienceMaskedImage`` - (matchedImage + backgroundModel)
716 - ``matchedImage`` : templateMaskedImage convolved with psfMatchingKernel
717 - `psfMatchingKernel`` : PSF matching kernel
718 - ``backgroundModel`` : differential background model
719 - ``kernelCellSet`` : SpatialCellSet used to determine PSF matching kernel
721 """
722 if not candidateList:
723 raise RuntimeError("Candidate list must be populated by makeCandidateList")
725 results = self.matchMaskedImages(
726 templateMaskedImage=templateMaskedImage,
727 scienceMaskedImage=scienceMaskedImage,
728 candidateList=candidateList,
729 templateFwhmPix=templateFwhmPix,
730 scienceFwhmPix=scienceFwhmPix,
731 )
733 subtractedMaskedImage = afwImage.MaskedImageF(scienceMaskedImage, True)
734 subtractedMaskedImage -= results.matchedImage
735 subtractedMaskedImage -= results.backgroundModel
736 results.subtractedMaskedImage = subtractedMaskedImage
738 import lsstDebug
739 display = lsstDebug.Info(__name__).display
740 displayDiffIm = lsstDebug.Info(__name__).displayDiffIm
741 maskTransparency = lsstDebug.Info(__name__).maskTransparency
742 if not maskTransparency:
743 maskTransparency = 0
744 if display:
745 afwDisplay.setDefaultMaskTransparency(maskTransparency)
746 if display and displayDiffIm:
747 disp = afwDisplay.Display(frame=lsstDebug.frame)
748 disp.mtv(subtractedMaskedImage, title="Subtracted masked image")
749 lsstDebug.frame += 1
751 return results
753 def getSelectSources(self, exposure, sigma=None, doSmooth=True, idFactory=None):
754 """Get sources to use for Psf-matching.
756 This method runs detection and measurement on an exposure.
757 The returned set of sources will be used as candidates for
758 Psf-matching.
760 Parameters
761 ----------
762 exposure : `lsst.afw.image.Exposure`
763 Exposure on which to run detection/measurement
764 sigma : `float`
765 Detection threshold
766 doSmooth : `bool`
767 Whether or not to smooth the Exposure with Psf before detection
768 idFactory :
769 Factory for the generation of Source ids
771 Returns
772 -------
773 selectSources :
774 source catalog containing candidates for the Psf-matching
775 """
776 if idFactory:
777 table = afwTable.SourceTable.make(self.selectSchema, idFactory)
778 else:
779 table = afwTable.SourceTable.make(self.selectSchema)
780 mi = exposure.getMaskedImage()
782 imArr = mi.getImage().getArray()
783 maskArr = mi.getMask().getArray()
784 miArr = np.ma.masked_array(imArr, mask=maskArr)
785 try:
786 fitBg = self.background.fitBackground(mi)
787 bkgd = fitBg.getImageF(self.background.config.algorithm,
788 self.background.config.undersampleStyle)
789 except Exception:
790 self.log.warn("Failed to get background model. Falling back to median background estimation")
791 bkgd = np.ma.extras.median(miArr)
793 # Take off background for detection
794 mi -= bkgd
795 try:
796 table.setMetadata(self.selectAlgMetadata)
797 detRet = self.selectDetection.run(
798 table=table,
799 exposure=exposure,
800 sigma=sigma,
801 doSmooth=doSmooth
802 )
803 selectSources = detRet.sources
804 self.selectMeasurement.run(measCat=selectSources, exposure=exposure)
805 finally:
806 # Put back on the background in case it is needed down stream
807 mi += bkgd
808 del bkgd
809 return selectSources
811 def makeCandidateList(self, templateExposure, scienceExposure, kernelSize, candidateList=None):
812 """Make a list of acceptable KernelCandidates.
814 Accept or generate a list of candidate sources for
815 Psf-matching, and examine the Mask planes in both of the
816 images for indications of bad pixels
818 Parameters
819 ----------
820 templateExposure : `lsst.afw.image.Exposure`
821 Exposure that will be convolved
822 scienceExposure : `lsst.afw.image.Exposure`
823 Exposure that will be matched-to
824 kernelSize : `float`
825 Dimensions of the Psf-matching Kernel, used to grow detection footprints
826 candidateList : `list`, optional
827 List of Sources to examine. Elements must be of type afw.table.Source
828 or a type that wraps a Source and has a getSource() method, such as
829 meas.algorithms.PsfCandidateF.
831 Returns
832 -------
833 candidateList : `list` of `dict`
834 A list of dicts having a "source" and "footprint"
835 field for the Sources deemed to be appropriate for Psf
836 matching
837 """
838 if candidateList is None:
839 candidateList = self.getSelectSources(scienceExposure)
841 if len(candidateList) < 1:
842 raise RuntimeError("No candidates in candidateList")
844 listTypes = set(type(x) for x in candidateList)
845 if len(listTypes) > 1:
846 raise RuntimeError("Candidate list contains mixed types: %s" % [l for l in listTypes])
848 if not isinstance(candidateList[0], afwTable.SourceRecord):
849 try:
850 candidateList[0].getSource()
851 except Exception as e:
852 raise RuntimeError(f"Candidate List is of type: {type(candidateList[0])} "
853 "Can only make candidate list from list of afwTable.SourceRecords, "
854 f"measAlg.PsfCandidateF or other type with a getSource() method: {e}")
855 candidateList = [c.getSource() for c in candidateList]
857 candidateList = diffimTools.sourceToFootprintList(candidateList,
858 templateExposure, scienceExposure,
859 kernelSize,
860 self.kConfig.detectionConfig,
861 self.log)
862 if len(candidateList) == 0:
863 raise RuntimeError("Cannot find any objects suitable for KernelCandidacy")
865 return candidateList
867 def _adaptCellSize(self, candidateList):
868 """NOT IMPLEMENTED YET.
869 """
870 return self.kConfig.sizeCellX, self.kConfig.sizeCellY
872 def _buildCellSet(self, templateMaskedImage, scienceMaskedImage, candidateList):
873 """Build a SpatialCellSet for use with the solve method.
875 Parameters
876 ----------
877 templateMaskedImage : `lsst.afw.image.MaskedImage`
878 MaskedImage to PSF-matched to scienceMaskedImage
879 scienceMaskedImage : `lsst.afw.image.MaskedImage`
880 Reference MaskedImage
881 candidateList : `list`
882 A list of footprints/maskedImages for kernel candidates;
884 - Currently supported: list of Footprints or measAlg.PsfCandidateF
886 Returns
887 -------
888 kernelCellSet : `lsst.afw.math.SpatialCellSet`
889 a SpatialCellSet for use with self._solve
890 """
891 if not candidateList:
892 raise RuntimeError("Candidate list must be populated by makeCandidateList")
894 sizeCellX, sizeCellY = self._adaptCellSize(candidateList)
896 # Object to store the KernelCandidates for spatial modeling
897 kernelCellSet = afwMath.SpatialCellSet(templateMaskedImage.getBBox(),
898 sizeCellX, sizeCellY)
900 ps = pexConfig.makePropertySet(self.kConfig)
901 # Place candidates within the spatial grid
902 for cand in candidateList:
903 if isinstance(cand, afwDetect.Footprint):
904 bbox = cand.getBBox()
905 else:
906 bbox = cand['footprint'].getBBox()
907 tmi = afwImage.MaskedImageF(templateMaskedImage, bbox)
908 smi = afwImage.MaskedImageF(scienceMaskedImage, bbox)
910 if not isinstance(cand, afwDetect.Footprint):
911 if 'source' in cand:
912 cand = cand['source']
913 xPos = cand.getCentroid()[0]
914 yPos = cand.getCentroid()[1]
915 cand = diffimLib.makeKernelCandidate(xPos, yPos, tmi, smi, ps)
917 self.log.debug("Candidate %d at %f, %f", cand.getId(), cand.getXCenter(), cand.getYCenter())
918 kernelCellSet.insertCandidate(cand)
920 return kernelCellSet
922 def _validateSize(self, templateMaskedImage, scienceMaskedImage):
923 """Return True if two image-like objects are the same size.
924 """
925 return templateMaskedImage.getDimensions() == scienceMaskedImage.getDimensions()
927 def _validateWcs(self, templateExposure, scienceExposure):
928 """Return True if the WCS of the two Exposures have the same origin and extent.
929 """
930 templateWcs = templateExposure.getWcs()
931 scienceWcs = scienceExposure.getWcs()
932 templateBBox = templateExposure.getBBox()
933 scienceBBox = scienceExposure.getBBox()
935 # LLC
936 templateOrigin = templateWcs.pixelToSky(geom.Point2D(templateBBox.getBegin()))
937 scienceOrigin = scienceWcs.pixelToSky(geom.Point2D(scienceBBox.getBegin()))
939 # URC
940 templateLimit = templateWcs.pixelToSky(geom.Point2D(templateBBox.getEnd()))
941 scienceLimit = scienceWcs.pixelToSky(geom.Point2D(scienceBBox.getEnd()))
943 self.log.info("Template Wcs : %f,%f -> %f,%f",
944 templateOrigin[0], templateOrigin[1],
945 templateLimit[0], templateLimit[1])
946 self.log.info("Science Wcs : %f,%f -> %f,%f",
947 scienceOrigin[0], scienceOrigin[1],
948 scienceLimit[0], scienceLimit[1])
950 templateBBox = geom.Box2D(templateOrigin.getPosition(geom.degrees),
951 templateLimit.getPosition(geom.degrees))
952 scienceBBox = geom.Box2D(scienceOrigin.getPosition(geom.degrees),
953 scienceLimit.getPosition(geom.degrees))
954 if not (templateBBox.overlaps(scienceBBox)):
955 raise RuntimeError("Input images do not overlap at all")
957 if ((templateOrigin != scienceOrigin)
958 or (templateLimit != scienceLimit)
959 or (templateExposure.getDimensions() != scienceExposure.getDimensions())):
960 return False
961 return True
964subtractAlgorithmRegistry = pexConfig.makeRegistry(
965 doc="A registry of subtraction algorithms for use as a subtask in imageDifference",
966)
968subtractAlgorithmRegistry.register('al', ImagePsfMatchTask)