Coverage for python/lsst/ip/diffim/psfMatch.py: 31%
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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/>.
22__all__ = ["DetectionConfig", "PsfMatchConfig", "PsfMatchConfigAL", "PsfMatchConfigDF", "PsfMatchTask"]
24import time
26import numpy as np
28import lsst.afw.image as afwImage
29import lsst.pex.config as pexConfig
30import lsst.afw.math as afwMath
31import lsst.afw.display as afwDisplay
32import lsst.pipe.base as pipeBase
33from lsst.meas.algorithms import SubtractBackgroundConfig
34from lsst.utils.logging import getTraceLogger
35from lsst.utils.timer import timeMethod
36from . import utils as diutils
37from . import diffimLib
40class DetectionConfig(pexConfig.Config):
41 """Configuration for detecting sources on images for building a
42 PSF-matching kernel
44 Configuration for turning detected lsst.afw.detection.FootPrints into an
45 acceptable (unmasked, high signal-to-noise, not too large or not too small)
46 list of `lsst.ip.diffim.KernelSources` that are used to build the
47 Psf-matching kernel"""
49 detThreshold = pexConfig.Field( 49 ↛ exitline 49 didn't jump to the function exit
50 dtype=float,
51 doc="Value of footprint detection threshold",
52 default=10.0,
53 check=lambda x: x >= 3.0
54 )
55 detThresholdType = pexConfig.ChoiceField(
56 dtype=str,
57 doc="Type of detection threshold",
58 default="pixel_stdev",
59 allowed={
60 "value": "Use counts as the detection threshold type",
61 "stdev": "Use standard deviation of image plane",
62 "variance": "Use variance of image plane",
63 "pixel_stdev": "Use stdev derived from variance plane"
64 }
65 )
66 detOnTemplate = pexConfig.Field(
67 dtype=bool,
68 doc="""If true run detection on the template (image to convolve);
69 if false run detection on the science image""",
70 default=True
71 )
72 badMaskPlanes = pexConfig.ListField(
73 dtype=str,
74 doc="""Mask planes that lead to an invalid detection.
75 Options: NO_DATA EDGE SAT BAD CR INTRP""",
76 default=("NO_DATA", "EDGE", "SAT")
77 )
78 fpNpixMin = pexConfig.Field( 78 ↛ exitline 78 didn't jump to the function exit
79 dtype=int,
80 doc="Minimum number of pixels in an acceptable Footprint",
81 default=5,
82 check=lambda x: x >= 5
83 )
84 fpNpixMax = pexConfig.Field( 84 ↛ exitline 84 didn't jump to the function exit
85 dtype=int,
86 doc="""Maximum number of pixels in an acceptable Footprint;
87 too big and the subsequent convolutions become unwieldy""",
88 default=500,
89 check=lambda x: x <= 500
90 )
91 fpGrowKernelScaling = pexConfig.Field( 91 ↛ exitline 91 didn't jump to the function exit
92 dtype=float,
93 doc="""If config.scaleByFwhm, grow the footprint based on
94 the final kernelSize. Each footprint will be
95 2*fpGrowKernelScaling*kernelSize x
96 2*fpGrowKernelScaling*kernelSize. With the value
97 of 1.0, the remaining pixels in each KernelCandiate
98 after convolution by the basis functions will be
99 equal to the kernel size itself.""",
100 default=1.0,
101 check=lambda x: x >= 1.0
102 )
103 fpGrowPix = pexConfig.Field( 103 ↛ exitline 103 didn't jump to the function exit
104 dtype=int,
105 doc="""Growing radius (in pixels) for each raw detection
106 footprint. The smaller the faster; however the
107 kernel sum does not converge if the stamp is too
108 small; and the kernel is not constrained at all if
109 the stamp is the size of the kernel. The grown stamp
110 is 2 * fpGrowPix pixels larger in each dimension.
111 This is overridden by fpGrowKernelScaling if scaleByFwhm""",
112 default=30,
113 check=lambda x: x >= 10
114 )
115 scaleByFwhm = pexConfig.Field(
116 dtype=bool,
117 doc="Scale fpGrowPix by input Fwhm?",
118 default=True,
119 )
122class PsfMatchConfig(pexConfig.Config):
123 """Base configuration for Psf-matching
125 The base configuration of the Psf-matching kernel, and of the warping, detection,
126 and background modeling subTasks."""
128 warpingConfig = pexConfig.ConfigField("Config for warping exposures to a common alignment",
129 afwMath.WarperConfig)
130 detectionConfig = pexConfig.ConfigField("Controlling the detection of sources for kernel building",
131 DetectionConfig)
132 afwBackgroundConfig = pexConfig.ConfigField("Controlling the Afw background fitting",
133 SubtractBackgroundConfig)
135 useAfwBackground = pexConfig.Field(
136 dtype=bool,
137 doc="Use afw background subtraction instead of ip_diffim",
138 default=False,
139 )
140 fitForBackground = pexConfig.Field(
141 dtype=bool,
142 doc="Include terms (including kernel cross terms) for background in ip_diffim",
143 default=False,
144 )
145 kernelBasisSet = pexConfig.ChoiceField(
146 dtype=str,
147 doc="Type of basis set for PSF matching kernel.",
148 default="alard-lupton",
149 allowed={
150 "alard-lupton": """Alard-Lupton sum-of-gaussians basis set,
151 * The first term has no spatial variation
152 * The kernel sum is conserved
153 * You may want to turn off 'usePcaForSpatialKernel'""",
154 "delta-function": """Delta-function kernel basis set,
155 * You may enable the option useRegularization
156 * You should seriously consider usePcaForSpatialKernel, which will also
157 enable kernel sum conservation for the delta function kernels"""
158 }
159 )
160 kernelSize = pexConfig.Field(
161 dtype=int,
162 doc="""Number of rows/columns in the convolution kernel; should be odd-valued.
163 Modified by kernelSizeFwhmScaling if scaleByFwhm = true""",
164 default=21,
165 )
166 scaleByFwhm = pexConfig.Field(
167 dtype=bool,
168 doc="Scale kernelSize, alardGaussians by input Fwhm",
169 default=True,
170 )
171 kernelSizeFwhmScaling = pexConfig.Field( 171 ↛ exitline 171 didn't jump to the function exit
172 dtype=float,
173 doc="Multiplier of the largest AL Gaussian basis sigma to get the kernel bbox (pixel) size.",
174 default=6.0,
175 check=lambda x: x >= 1.0
176 )
177 kernelSizeMin = pexConfig.Field(
178 dtype=int,
179 doc="Minimum kernel bbox (pixel) size.",
180 default=21,
181 )
182 kernelSizeMax = pexConfig.Field(
183 dtype=int,
184 doc="Maximum kernel bbox (pixel) size.",
185 default=35,
186 )
187 spatialModelType = pexConfig.ChoiceField(
188 dtype=str,
189 doc="Type of spatial functions for kernel and background",
190 default="chebyshev1",
191 allowed={
192 "chebyshev1": "Chebyshev polynomial of the first kind",
193 "polynomial": "Standard x,y polynomial",
194 }
195 )
196 spatialKernelOrder = pexConfig.Field( 196 ↛ exitline 196 didn't jump to the function exit
197 dtype=int,
198 doc="Spatial order of convolution kernel variation",
199 default=2,
200 check=lambda x: x >= 0
201 )
202 spatialBgOrder = pexConfig.Field( 202 ↛ exitline 202 didn't jump to the function exit
203 dtype=int,
204 doc="Spatial order of differential background variation",
205 default=1,
206 check=lambda x: x >= 0
207 )
208 sizeCellX = pexConfig.Field( 208 ↛ exitline 208 didn't jump to the function exit
209 dtype=int,
210 doc="Size (rows) in pixels of each SpatialCell for spatial modeling",
211 default=128,
212 check=lambda x: x >= 32
213 )
214 sizeCellY = pexConfig.Field( 214 ↛ exitline 214 didn't jump to the function exit
215 dtype=int,
216 doc="Size (columns) in pixels of each SpatialCell for spatial modeling",
217 default=128,
218 check=lambda x: x >= 32
219 )
220 nStarPerCell = pexConfig.Field( 220 ↛ exitline 220 didn't jump to the function exit
221 dtype=int,
222 doc="Number of KernelCandidates in each SpatialCell to use in the spatial fitting",
223 default=3,
224 check=lambda x: x >= 1
225 )
226 maxSpatialIterations = pexConfig.Field( 226 ↛ exitline 226 didn't jump to the function exit
227 dtype=int,
228 doc="Maximum number of iterations for rejecting bad KernelCandidates in spatial fitting",
229 default=3,
230 check=lambda x: x >= 1 and x <= 5
231 )
232 usePcaForSpatialKernel = pexConfig.Field(
233 dtype=bool,
234 doc="""Use Pca to reduce the dimensionality of the kernel basis sets.
235 This is particularly useful for delta-function kernels.
236 Functionally, after all Cells have their raw kernels determined, we run
237 a Pca on these Kernels, re-fit the Cells using the eigenKernels and then
238 fit those for spatial variation using the same technique as for Alard-Lupton kernels.
239 If this option is used, the first term will have no spatial variation and the
240 kernel sum will be conserved.""",
241 default=False,
242 )
243 subtractMeanForPca = pexConfig.Field(
244 dtype=bool,
245 doc="Subtract off the mean feature before doing the Pca",
246 default=True,
247 )
248 numPrincipalComponents = pexConfig.Field( 248 ↛ exitline 248 didn't jump to the function exit
249 dtype=int,
250 doc="""Number of principal components to use for Pca basis, including the
251 mean kernel if requested.""",
252 default=5,
253 check=lambda x: x >= 3
254 )
255 singleKernelClipping = pexConfig.Field(
256 dtype=bool,
257 doc="Do sigma clipping on each raw kernel candidate",
258 default=True,
259 )
260 kernelSumClipping = pexConfig.Field(
261 dtype=bool,
262 doc="Do sigma clipping on the ensemble of kernel sums",
263 default=True,
264 )
265 spatialKernelClipping = pexConfig.Field(
266 dtype=bool,
267 doc="Do sigma clipping after building the spatial model",
268 default=True,
269 )
270 checkConditionNumber = pexConfig.Field(
271 dtype=bool,
272 doc="""Test for maximum condition number when inverting a kernel matrix.
273 Anything above maxConditionNumber is not used and the candidate is set as BAD.
274 Also used to truncate inverse matrix in estimateBiasedRisk. However,
275 if you are doing any deconvolution you will want to turn this off, or use
276 a large maxConditionNumber""",
277 default=False,
278 )
279 badMaskPlanes = pexConfig.ListField(
280 dtype=str,
281 doc="""Mask planes to ignore when calculating diffim statistics
282 Options: NO_DATA EDGE SAT BAD CR INTRP""",
283 default=("NO_DATA", "EDGE", "SAT")
284 )
285 candidateResidualMeanMax = pexConfig.Field( 285 ↛ exitline 285 didn't jump to the function exit
286 dtype=float,
287 doc="""Rejects KernelCandidates yielding bad difference image quality.
288 Used by BuildSingleKernelVisitor, AssessSpatialKernelVisitor.
289 Represents average over pixels of (image/sqrt(variance)).""",
290 default=0.25,
291 check=lambda x: x >= 0.0
292 )
293 candidateResidualStdMax = pexConfig.Field( 293 ↛ exitline 293 didn't jump to the function exit
294 dtype=float,
295 doc="""Rejects KernelCandidates yielding bad difference image quality.
296 Used by BuildSingleKernelVisitor, AssessSpatialKernelVisitor.
297 Represents stddev over pixels of (image/sqrt(variance)).""",
298 default=1.50,
299 check=lambda x: x >= 0.0
300 )
301 useCoreStats = pexConfig.Field(
302 dtype=bool,
303 doc="""Use the core of the footprint for the quality statistics, instead of the entire footprint.
304 WARNING: if there is deconvolution we probably will need to turn this off""",
305 default=False,
306 )
307 candidateCoreRadius = pexConfig.Field( 307 ↛ exitline 307 didn't jump to the function exit
308 dtype=int,
309 doc="""Radius for calculation of stats in 'core' of KernelCandidate diffim.
310 Total number of pixels used will be (2*radius)**2.
311 This is used both for 'core' diffim quality as well as ranking of
312 KernelCandidates by their total flux in this core""",
313 default=3,
314 check=lambda x: x >= 1
315 )
316 maxKsumSigma = pexConfig.Field( 316 ↛ exitline 316 didn't jump to the function exit
317 dtype=float,
318 doc="""Maximum allowed sigma for outliers from kernel sum distribution.
319 Used to reject variable objects from the kernel model""",
320 default=3.0,
321 check=lambda x: x >= 0.0
322 )
323 maxConditionNumber = pexConfig.Field( 323 ↛ exitline 323 didn't jump to the function exit
324 dtype=float,
325 doc="Maximum condition number for a well conditioned matrix",
326 default=5.0e7,
327 check=lambda x: x >= 0.0
328 )
329 conditionNumberType = pexConfig.ChoiceField(
330 dtype=str,
331 doc="Use singular values (SVD) or eigen values (EIGENVALUE) to determine condition number",
332 default="EIGENVALUE",
333 allowed={
334 "SVD": "Use singular values",
335 "EIGENVALUE": "Use eigen values (faster)",
336 }
337 )
338 maxSpatialConditionNumber = pexConfig.Field( 338 ↛ exitline 338 didn't jump to the function exit
339 dtype=float,
340 doc="Maximum condition number for a well conditioned spatial matrix",
341 default=1.0e10,
342 check=lambda x: x >= 0.0
343 )
344 iterateSingleKernel = pexConfig.Field(
345 dtype=bool,
346 doc="""Remake KernelCandidate using better variance estimate after first pass?
347 Primarily useful when convolving a single-depth image, otherwise not necessary.""",
348 default=False,
349 )
350 constantVarianceWeighting = pexConfig.Field(
351 dtype=bool,
352 doc="""Use constant variance weighting in single kernel fitting?
353 In some cases this is better for bright star residuals.""",
354 default=True,
355 )
356 calculateKernelUncertainty = pexConfig.Field(
357 dtype=bool,
358 doc="""Calculate kernel and background uncertainties for each kernel candidate?
359 This comes from the inverse of the covariance matrix.
360 Warning: regularization can cause problems for this step.""",
361 default=False,
362 )
363 useBicForKernelBasis = pexConfig.Field(
364 dtype=bool,
365 doc="""Use Bayesian Information Criterion to select the number of bases going into the kernel""",
366 default=False,
367 )
370class PsfMatchConfigAL(PsfMatchConfig):
371 """The parameters specific to the "Alard-Lupton" (sum-of-Gaussian) Psf-matching basis"""
373 def setDefaults(self):
374 PsfMatchConfig.setDefaults(self)
375 self.kernelBasisSet = "alard-lupton"
376 self.maxConditionNumber = 5.0e7
378 alardNGauss = pexConfig.Field( 378 ↛ exitline 378 didn't jump to the function exit
379 dtype=int,
380 doc="Number of base Gaussians in alard-lupton kernel basis function generation.",
381 default=3,
382 check=lambda x: x >= 1
383 )
384 alardDegGauss = pexConfig.ListField(
385 dtype=int,
386 doc="Polynomial order of spatial modification of base Gaussians. "
387 "List length must be `alardNGauss`.",
388 default=(4, 2, 2),
389 )
390 alardSigGauss = pexConfig.ListField(
391 dtype=float,
392 doc="Default sigma values in pixels of base Gaussians. "
393 "List length must be `alardNGauss`.",
394 default=(0.7, 1.5, 3.0),
395 )
396 alardGaussBeta = pexConfig.Field( 396 ↛ exitline 396 didn't jump to the function exit
397 dtype=float,
398 doc="Used if `scaleByFwhm==True`, scaling multiplier of base "
399 "Gaussian sigmas for automated sigma determination",
400 default=2.0,
401 check=lambda x: x >= 0.0,
402 )
403 alardMinSig = pexConfig.Field( 403 ↛ exitline 403 didn't jump to the function exit
404 dtype=float,
405 doc="Used if `scaleByFwhm==True`, minimum sigma (pixels) for base Gaussians",
406 default=0.7,
407 check=lambda x: x >= 0.25
408 )
409 alardDegGaussDeconv = pexConfig.Field( 409 ↛ exitline 409 didn't jump to the function exit
410 dtype=int,
411 doc="Used if `scaleByFwhm==True`, degree of spatial modification of ALL base Gaussians "
412 "in AL basis during deconvolution",
413 default=3,
414 check=lambda x: x >= 1
415 )
416 alardMinSigDeconv = pexConfig.Field( 416 ↛ exitline 416 didn't jump to the function exit
417 dtype=float,
418 doc="Used if `scaleByFwhm==True`, minimum sigma (pixels) for base Gaussians during deconvolution; "
419 "make smaller than `alardMinSig` as this is only indirectly used",
420 default=0.4,
421 check=lambda x: x >= 0.25
422 )
423 alardNGaussDeconv = pexConfig.Field( 423 ↛ exitline 423 didn't jump to the function exit
424 dtype=int,
425 doc="Used if `scaleByFwhm==True`, number of base Gaussians in AL basis during deconvolution",
426 default=3,
427 check=lambda x: x >= 1
428 )
431class PsfMatchConfigDF(PsfMatchConfig):
432 """The parameters specific to the delta-function (one basis per-pixel) Psf-matching basis"""
434 def setDefaults(self):
435 PsfMatchConfig.setDefaults(self)
436 self.kernelBasisSet = "delta-function"
437 self.maxConditionNumber = 5.0e6
438 self.usePcaForSpatialKernel = True
439 self.subtractMeanForPca = True
440 self.useBicForKernelBasis = False
442 useRegularization = pexConfig.Field(
443 dtype=bool,
444 doc="Use regularization to smooth the delta function kernels",
445 default=True,
446 )
447 regularizationType = pexConfig.ChoiceField(
448 dtype=str,
449 doc="Type of regularization.",
450 default="centralDifference",
451 allowed={
452 "centralDifference": "Penalize second derivative using 2-D stencil of central finite difference",
453 "forwardDifference": "Penalize first, second, third derivatives using forward finite differeces"
454 }
455 )
456 centralRegularizationStencil = pexConfig.ChoiceField(
457 dtype=int,
458 doc="Type of stencil to approximate central derivative (for centralDifference only)",
459 default=9,
460 allowed={
461 5: "5-point stencil including only adjacent-in-x,y elements",
462 9: "9-point stencil including diagonal elements"
463 }
464 )
465 forwardRegularizationOrders = pexConfig.ListField( 465 ↛ exitline 465 didn't jump to the function exit
466 dtype=int,
467 doc="Array showing which order derivatives to penalize (for forwardDifference only)",
468 default=(1, 2),
469 itemCheck=lambda x: (x > 0) and (x < 4)
470 )
471 regularizationBorderPenalty = pexConfig.Field( 471 ↛ exitline 471 didn't jump to the function exit
472 dtype=float,
473 doc="Value of the penalty for kernel border pixels",
474 default=3.0,
475 check=lambda x: x >= 0.0
476 )
477 lambdaType = pexConfig.ChoiceField(
478 dtype=str,
479 doc="How to choose the value of the regularization strength",
480 default="absolute",
481 allowed={
482 "absolute": "Use lambdaValue as the value of regularization strength",
483 "relative": "Use lambdaValue as fraction of the default regularization strength (N.R. 18.5.8)",
484 "minimizeBiasedRisk": "Minimize biased risk estimate",
485 "minimizeUnbiasedRisk": "Minimize unbiased risk estimate",
486 }
487 )
488 lambdaValue = pexConfig.Field(
489 dtype=float,
490 doc="Value used for absolute determinations of regularization strength",
491 default=0.2,
492 )
493 lambdaScaling = pexConfig.Field(
494 dtype=float,
495 doc="Fraction of the default lambda strength (N.R. 18.5.8) to use. 1e-4 or 1e-5",
496 default=1e-4,
497 )
498 lambdaStepType = pexConfig.ChoiceField(
499 dtype=str,
500 doc="""If a scan through lambda is needed (minimizeBiasedRisk, minimizeUnbiasedRisk),
501 use log or linear steps""",
502 default="log",
503 allowed={
504 "log": "Step in log intervals; e.g. lambdaMin, lambdaMax, lambdaStep = -1.0, 2.0, 0.1",
505 "linear": "Step in linear intervals; e.g. lambdaMin, lambdaMax, lambdaStep = 0.1, 100, 0.1",
506 }
507 )
508 lambdaMin = pexConfig.Field(
509 dtype=float,
510 doc="""If scan through lambda needed (minimizeBiasedRisk, minimizeUnbiasedRisk),
511 start at this value. If lambdaStepType = log:linear, suggest -1:0.1""",
512 default=-1.0,
513 )
514 lambdaMax = pexConfig.Field(
515 dtype=float,
516 doc="""If scan through lambda needed (minimizeBiasedRisk, minimizeUnbiasedRisk),
517 stop at this value. If lambdaStepType = log:linear, suggest 2:100""",
518 default=2.0,
519 )
520 lambdaStep = pexConfig.Field(
521 dtype=float,
522 doc="""If scan through lambda needed (minimizeBiasedRisk, minimizeUnbiasedRisk),
523 step in these increments. If lambdaStepType = log:linear, suggest 0.1:0.1""",
524 default=0.1,
525 )
528class PsfMatchTask(pipeBase.Task):
529 """Base class for Psf Matching; should not be called directly
531 Notes
532 -----
533 PsfMatchTask is a base class that implements the core functionality for matching the
534 Psfs of two images using a spatially varying Psf-matching `lsst.afw.math.LinearCombinationKernel`.
535 The Task requires the user to provide an instance of an `lsst.afw.math.SpatialCellSet`,
536 filled with `lsst.ip.diffim.KernelCandidate` instances, and a list of `lsst.afw.math.Kernels`
537 of basis shapes that will be used for the decomposition. If requested, the Task
538 also performs background matching and returns the differential background model as an
539 `lsst.afw.math.Kernel.SpatialFunction`.
541 **Invoking the Task**
543 As a base class, this Task is not directly invoked. However, ``run()`` methods that are
544 implemented on derived classes will make use of the core ``_solve()`` functionality,
545 which defines a sequence of `lsst.afw.math.CandidateVisitor` classes that iterate
546 through the KernelCandidates, first building up a per-candidate solution and then
547 building up a spatial model from the ensemble of candidates. Sigma clipping is
548 performed using the mean and standard deviation of all kernel sums (to reject
549 variable objects), on the per-candidate substamp diffim residuals
550 (to indicate a bad choice of kernel basis shapes for that particular object),
551 and on the substamp diffim residuals using the spatial kernel fit (to indicate a bad
552 choice of spatial kernel order, or poor constraints on the spatial model). The
553 ``_diagnostic()`` method logs information on the quality of the spatial fit, and also
554 modifies the Task metadata.
556 .. list-table:: Quantities set in Metadata
557 :header-rows: 1
559 * - Parameter
560 - Description
561 * - ``spatialConditionNum``
562 - Condition number of the spatial kernel fit
563 * - ``spatialKernelSum``
564 - Kernel sum (10^{-0.4 * ``Delta``; zeropoint}) of the spatial Psf-matching kernel
565 * - ``ALBasisNGauss``
566 - If using sum-of-Gaussian basis, the number of gaussians used
567 * - ``ALBasisDegGauss``
568 - If using sum-of-Gaussian basis, the deg of spatial variation of the Gaussians
569 * - ``ALBasisSigGauss``
570 - If using sum-of-Gaussian basis, the widths (sigma) of the Gaussians
571 * - ``ALKernelSize``
572 - If using sum-of-Gaussian basis, the kernel size
573 * - ``NFalsePositivesTotal``
574 - Total number of diaSources
575 * - ``NFalsePositivesRefAssociated``
576 - Number of diaSources that associate with the reference catalog
577 * - ``NFalsePositivesRefAssociated``
578 - Number of diaSources that associate with the source catalog
579 * - ``NFalsePositivesUnassociated``
580 - Number of diaSources that are orphans
581 * - ``metric_MEAN``
582 - Mean value of substamp diffim quality metrics across all KernelCandidates,
583 for both the per-candidate (LOCAL) and SPATIAL residuals
584 * - ``metric_MEDIAN``
585 - Median value of substamp diffim quality metrics across all KernelCandidates,
586 for both the per-candidate (LOCAL) and SPATIAL residuals
587 * - ``metric_STDEV``
588 - Standard deviation of substamp diffim quality metrics across all KernelCandidates,
589 for both the per-candidate (LOCAL) and SPATIAL residuals
591 **Debug variables**
593 The `lsst.pipe.base.cmdLineTask.CmdLineTask` command line task interface supports a
594 flag -d/--debug to import @b debug.py from your PYTHONPATH. The relevant contents of debug.py
595 for this Task include:
597 .. code-block:: py
599 import sys
600 import lsstDebug
601 def DebugInfo(name):
602 di = lsstDebug.getInfo(name)
603 if name == "lsst.ip.diffim.psfMatch":
604 # enable debug output
605 di.display = True
606 # display mask transparency
607 di.maskTransparency = 80
608 # show all the candidates and residuals
609 di.displayCandidates = True
610 # show kernel basis functions
611 di.displayKernelBasis = False
612 # show kernel realized across the image
613 di.displayKernelMosaic = True
614 # show coefficients of spatial model
615 di.plotKernelSpatialModel = False
616 # show fixed and spatial coefficients and coefficient histograms
617 di.plotKernelCoefficients = True
618 # show the bad candidates (red) along with good (green)
619 di.showBadCandidates = True
620 return di
621 lsstDebug.Info = DebugInfo
622 lsstDebug.frame = 1
624 Note that if you want additional logging info, you may add to your scripts:
626 .. code-block:: py
628 import lsst.utils.logging as logUtils
629 logUtils.trace_set_at("lsst.ip.diffim", 4)
630 """
631 ConfigClass = PsfMatchConfig
632 _DefaultName = "psfMatch"
634 def __init__(self, *args, **kwargs):
635 """Create the psf-matching Task
637 Parameters
638 ----------
639 *args
640 Arguments to be passed to ``lsst.pipe.base.task.Task.__init__``
641 **kwargs
642 Keyword arguments to be passed to ``lsst.pipe.base.task.Task.__init__``
644 Notes
645 -----
646 The initialization sets the Psf-matching kernel configuration using the value of
647 self.config.kernel.active. If the kernel is requested with regularization to moderate
648 the bias/variance tradeoff, currently only used when a delta function kernel basis
649 is provided, it creates a regularization matrix stored as member variable
650 self.hMat.
651 """
652 pipeBase.Task.__init__(self, *args, **kwargs)
653 self.kConfig = self.config.kernel.active
655 if 'useRegularization' in self.kConfig:
656 self.useRegularization = self.kConfig.useRegularization
657 else:
658 self.useRegularization = False
660 if self.useRegularization:
661 self.hMat = diffimLib.makeRegularizationMatrix(pexConfig.makePropertySet(self.kConfig))
663 def _diagnostic(self, kernelCellSet, spatialSolution, spatialKernel, spatialBg):
664 """Provide logging diagnostics on quality of spatial kernel fit
666 Parameters
667 ----------
668 kernelCellSet : `lsst.afw.math.SpatialCellSet`
669 Cellset that contains the KernelCandidates used in the fitting
670 spatialSolution : `lsst.ip.diffim.SpatialKernelSolution`
671 KernelSolution of best-fit
672 spatialKernel : `lsst.afw.math.LinearCombinationKernel`
673 Best-fit spatial Kernel model
674 spatialBg : `lsst.afw.math.Function2D`
675 Best-fit spatial background model
676 """
677 # What is the final kernel sum
678 kImage = afwImage.ImageD(spatialKernel.getDimensions())
679 kSum = spatialKernel.computeImage(kImage, False)
680 self.log.info("Final spatial kernel sum %.3f", kSum)
682 # Look at how well conditioned the matrix is
683 conditionNum = spatialSolution.getConditionNumber(
684 getattr(diffimLib.KernelSolution, self.kConfig.conditionNumberType))
685 self.log.info("Spatial model condition number %.3e", conditionNum)
687 if conditionNum < 0.0:
688 self.log.warning("Condition number is negative (%.3e)", conditionNum)
689 if conditionNum > self.kConfig.maxSpatialConditionNumber:
690 self.log.warning("Spatial solution exceeds max condition number (%.3e > %.3e)",
691 conditionNum, self.kConfig.maxSpatialConditionNumber)
693 self.metadata["spatialConditionNum"] = conditionNum
694 self.metadata["spatialKernelSum"] = kSum
696 # Look at how well the solution is constrained
697 nBasisKernels = spatialKernel.getNBasisKernels()
698 nKernelTerms = spatialKernel.getNSpatialParameters()
699 if nKernelTerms == 0: # order 0
700 nKernelTerms = 1
702 # Not fit for
703 nBgTerms = spatialBg.getNParameters()
704 if nBgTerms == 1:
705 if spatialBg.getParameters()[0] == 0.0:
706 nBgTerms = 0
708 nGood = 0
709 nBad = 0
710 nTot = 0
711 for cell in kernelCellSet.getCellList():
712 for cand in cell.begin(False): # False = include bad candidates
713 nTot += 1
714 if cand.getStatus() == afwMath.SpatialCellCandidate.GOOD:
715 nGood += 1
716 if cand.getStatus() == afwMath.SpatialCellCandidate.BAD:
717 nBad += 1
719 self.log.info("Doing stats of kernel candidates used in the spatial fit.")
721 # Counting statistics
722 if nBad > 2*nGood:
723 self.log.warning("Many more candidates rejected than accepted; %d total, %d rejected, %d used",
724 nTot, nBad, nGood)
725 else:
726 self.log.info("%d candidates total, %d rejected, %d used", nTot, nBad, nGood)
728 # Some judgements on the quality of the spatial models
729 if nGood < nKernelTerms:
730 self.log.warning("Spatial kernel model underconstrained; %d candidates, %d terms, %d bases",
731 nGood, nKernelTerms, nBasisKernels)
732 self.log.warning("Consider lowering the spatial order")
733 elif nGood <= 2*nKernelTerms:
734 self.log.warning("Spatial kernel model poorly constrained; %d candidates, %d terms, %d bases",
735 nGood, nKernelTerms, nBasisKernels)
736 self.log.warning("Consider lowering the spatial order")
737 else:
738 self.log.info("Spatial kernel model well constrained; %d candidates, %d terms, %d bases",
739 nGood, nKernelTerms, nBasisKernels)
741 if nGood < nBgTerms:
742 self.log.warning("Spatial background model underconstrained; %d candidates, %d terms",
743 nGood, nBgTerms)
744 self.log.warning("Consider lowering the spatial order")
745 elif nGood <= 2*nBgTerms:
746 self.log.warning("Spatial background model poorly constrained; %d candidates, %d terms",
747 nGood, nBgTerms)
748 self.log.warning("Consider lowering the spatial order")
749 else:
750 self.log.info("Spatial background model appears well constrained; %d candidates, %d terms",
751 nGood, nBgTerms)
753 def _displayDebug(self, kernelCellSet, spatialKernel, spatialBackground):
754 """Provide visualization of the inputs and ouputs to the Psf-matching code
756 Parameters
757 ----------
758 kernelCellSet : `lsst.afw.math.SpatialCellSet`
759 The SpatialCellSet used in determining the matching kernel and background
760 spatialKernel : `lsst.afw.math.LinearCombinationKernel`
761 Spatially varying Psf-matching kernel
762 spatialBackground : `lsst.afw.math.Function2D`
763 Spatially varying background-matching function
764 """
765 import lsstDebug
766 displayCandidates = lsstDebug.Info(__name__).displayCandidates
767 displayKernelBasis = lsstDebug.Info(__name__).displayKernelBasis
768 displayKernelMosaic = lsstDebug.Info(__name__).displayKernelMosaic
769 plotKernelSpatialModel = lsstDebug.Info(__name__).plotKernelSpatialModel
770 plotKernelCoefficients = lsstDebug.Info(__name__).plotKernelCoefficients
771 showBadCandidates = lsstDebug.Info(__name__).showBadCandidates
772 maskTransparency = lsstDebug.Info(__name__).maskTransparency
773 if not maskTransparency:
774 maskTransparency = 0
775 afwDisplay.setDefaultMaskTransparency(maskTransparency)
777 if displayCandidates:
778 diutils.showKernelCandidates(kernelCellSet, kernel=spatialKernel, background=spatialBackground,
779 frame=lsstDebug.frame,
780 showBadCandidates=showBadCandidates)
781 lsstDebug.frame += 1
782 diutils.showKernelCandidates(kernelCellSet, kernel=spatialKernel, background=spatialBackground,
783 frame=lsstDebug.frame,
784 showBadCandidates=showBadCandidates,
785 kernels=True)
786 lsstDebug.frame += 1
787 diutils.showKernelCandidates(kernelCellSet, kernel=spatialKernel, background=spatialBackground,
788 frame=lsstDebug.frame,
789 showBadCandidates=showBadCandidates,
790 resids=True)
791 lsstDebug.frame += 1
793 if displayKernelBasis:
794 diutils.showKernelBasis(spatialKernel, frame=lsstDebug.frame)
795 lsstDebug.frame += 1
797 if displayKernelMosaic:
798 diutils.showKernelMosaic(kernelCellSet.getBBox(), spatialKernel, frame=lsstDebug.frame)
799 lsstDebug.frame += 1
801 if plotKernelSpatialModel:
802 diutils.plotKernelSpatialModel(spatialKernel, kernelCellSet, showBadCandidates=showBadCandidates)
804 if plotKernelCoefficients:
805 diutils.plotKernelCoefficients(spatialKernel, kernelCellSet)
807 def _createPcaBasis(self, kernelCellSet, nStarPerCell, ps):
808 """Create Principal Component basis
810 If a principal component analysis is requested, typically when using a delta function basis,
811 perform the PCA here and return a new basis list containing the new principal components.
813 Parameters
814 ----------
815 kernelCellSet : `lsst.afw.math.SpatialCellSet`
816 a SpatialCellSet containing KernelCandidates, from which components are derived
817 nStarPerCell : `int`
818 the number of stars per cell to visit when doing the PCA
819 ps : `lsst.daf.base.PropertySet`
820 input property set controlling the single kernel visitor
822 Returns
823 -------
824 nRejectedPca : `int`
825 number of KernelCandidates rejected during PCA loop
826 spatialBasisList : `list` of `lsst.afw.math.kernel.FixedKernel`
827 basis list containing the principal shapes as Kernels
829 Raises
830 ------
831 RuntimeError
832 If the Eigenvalues sum to zero.
833 """
834 nComponents = self.kConfig.numPrincipalComponents
835 imagePca = diffimLib.KernelPcaD()
836 importStarVisitor = diffimLib.KernelPcaVisitorF(imagePca)
837 kernelCellSet.visitCandidates(importStarVisitor, nStarPerCell)
838 if self.kConfig.subtractMeanForPca:
839 importStarVisitor.subtractMean()
840 imagePca.analyze()
842 eigenValues = imagePca.getEigenValues()
843 pcaBasisList = importStarVisitor.getEigenKernels()
845 eSum = np.sum(eigenValues)
846 if eSum == 0.0:
847 raise RuntimeError("Eigenvalues sum to zero")
848 trace_logger = getTraceLogger(self.log.getChild("_solve"), 5)
849 for j in range(len(eigenValues)):
850 trace_logger.debug("Eigenvalue %d : %f (%f)", j, eigenValues[j], eigenValues[j]/eSum)
852 nToUse = min(nComponents, len(eigenValues))
853 trimBasisList = []
854 for j in range(nToUse):
855 # Check for NaNs?
856 kimage = afwImage.ImageD(pcaBasisList[j].getDimensions())
857 pcaBasisList[j].computeImage(kimage, False)
858 if not (True in np.isnan(kimage.getArray())):
859 trimBasisList.append(pcaBasisList[j])
861 # Put all the power in the first kernel, which will not vary spatially
862 spatialBasisList = diffimLib.renormalizeKernelList(trimBasisList)
864 # New Kernel visitor for this new basis list (no regularization explicitly)
865 singlekvPca = diffimLib.BuildSingleKernelVisitorF(spatialBasisList, ps)
866 singlekvPca.setSkipBuilt(False)
867 kernelCellSet.visitCandidates(singlekvPca, nStarPerCell)
868 singlekvPca.setSkipBuilt(True)
869 nRejectedPca = singlekvPca.getNRejected()
871 return nRejectedPca, spatialBasisList
873 def _buildCellSet(self, *args):
874 """Fill a SpatialCellSet with KernelCandidates for the Psf-matching process;
875 override in derived classes"""
876 return
878 @timeMethod
879 def _solve(self, kernelCellSet, basisList, returnOnExcept=False):
880 """Solve for the PSF matching kernel
882 Parameters
883 ----------
884 kernelCellSet : `lsst.afw.math.SpatialCellSet`
885 a SpatialCellSet to use in determining the matching kernel
886 (typically as provided by _buildCellSet)
887 basisList : `list` of `lsst.afw.math.kernel.FixedKernel`
888 list of Kernels to be used in the decomposition of the spatially varying kernel
889 (typically as provided by makeKernelBasisList)
890 returnOnExcept : `bool`, optional
891 if True then return (None, None) if an error occurs, else raise the exception
893 Returns
894 -------
895 psfMatchingKernel : `lsst.afw.math.LinearCombinationKernel`
896 Spatially varying Psf-matching kernel
897 backgroundModel : `lsst.afw.math.Function2D`
898 Spatially varying background-matching function
900 Raises
901 ------
902 RuntimeError :
903 If unable to determine PSF matching kernel and ``returnOnExcept==False``.
904 """
906 import lsstDebug
907 display = lsstDebug.Info(__name__).display
909 maxSpatialIterations = self.kConfig.maxSpatialIterations
910 nStarPerCell = self.kConfig.nStarPerCell
911 usePcaForSpatialKernel = self.kConfig.usePcaForSpatialKernel
913 # Visitor for the single kernel fit
914 ps = pexConfig.makePropertySet(self.kConfig)
915 if self.useRegularization:
916 singlekv = diffimLib.BuildSingleKernelVisitorF(basisList, ps, self.hMat)
917 else:
918 singlekv = diffimLib.BuildSingleKernelVisitorF(basisList, ps)
920 # Visitor for the kernel sum rejection
921 ksv = diffimLib.KernelSumVisitorF(ps)
923 # Main loop
924 trace_loggers = [getTraceLogger(self.log.getChild("_solve"), i) for i in range(5)]
925 t0 = time.time()
926 try:
927 totalIterations = 0
928 thisIteration = 0
929 while (thisIteration < maxSpatialIterations):
931 # Make sure there are no uninitialized candidates as active occupants of Cell
932 nRejectedSkf = -1
933 while (nRejectedSkf != 0):
934 trace_loggers[1].debug("Building single kernels...")
935 kernelCellSet.visitCandidates(singlekv, nStarPerCell)
936 nRejectedSkf = singlekv.getNRejected()
937 trace_loggers[1].debug(
938 "Iteration %d, rejected %d candidates due to initial kernel fit",
939 thisIteration, nRejectedSkf
940 )
942 # Reject outliers in kernel sum
943 ksv.resetKernelSum()
944 ksv.setMode(diffimLib.KernelSumVisitorF.AGGREGATE)
945 kernelCellSet.visitCandidates(ksv, nStarPerCell)
946 ksv.processKsumDistribution()
947 ksv.setMode(diffimLib.KernelSumVisitorF.REJECT)
948 kernelCellSet.visitCandidates(ksv, nStarPerCell)
950 nRejectedKsum = ksv.getNRejected()
951 trace_loggers[1].debug(
952 "Iteration %d, rejected %d candidates due to kernel sum",
953 thisIteration, nRejectedKsum
954 )
956 # Do we jump back to the top without incrementing thisIteration?
957 if nRejectedKsum > 0:
958 totalIterations += 1
959 continue
961 # At this stage we can either apply the spatial fit to
962 # the kernels, or we run a PCA, use these as a *new*
963 # basis set with lower dimensionality, and then apply
964 # the spatial fit to these kernels
966 if (usePcaForSpatialKernel):
967 trace_loggers[0].debug("Building Pca basis")
969 nRejectedPca, spatialBasisList = self._createPcaBasis(kernelCellSet, nStarPerCell, ps)
970 trace_loggers[1].debug(
971 "Iteration %d, rejected %d candidates due to Pca kernel fit",
972 thisIteration, nRejectedPca
973 )
975 # We don't want to continue on (yet) with the
976 # spatial modeling, because we have bad objects
977 # contributing to the Pca basis. We basically
978 # need to restart from the beginning of this loop,
979 # since the cell-mates of those objects that were
980 # rejected need their original Kernels built by
981 # singleKernelFitter.
983 # Don't count against thisIteration
984 if (nRejectedPca > 0):
985 totalIterations += 1
986 continue
987 else:
988 spatialBasisList = basisList
990 # We have gotten on to the spatial modeling part
991 regionBBox = kernelCellSet.getBBox()
992 spatialkv = diffimLib.BuildSpatialKernelVisitorF(spatialBasisList, regionBBox, ps)
993 kernelCellSet.visitCandidates(spatialkv, nStarPerCell)
994 spatialkv.solveLinearEquation()
995 trace_loggers[2].debug("Spatial kernel built with %d candidates", spatialkv.getNCandidates())
996 spatialKernel, spatialBackground = spatialkv.getSolutionPair()
998 # Check the quality of the spatial fit (look at residuals)
999 assesskv = diffimLib.AssessSpatialKernelVisitorF(spatialKernel, spatialBackground, ps)
1000 kernelCellSet.visitCandidates(assesskv, nStarPerCell)
1001 nRejectedSpatial = assesskv.getNRejected()
1002 nGoodSpatial = assesskv.getNGood()
1003 trace_loggers[1].debug(
1004 "Iteration %d, rejected %d candidates due to spatial kernel fit",
1005 thisIteration, nRejectedSpatial
1006 )
1007 trace_loggers[1].debug("%d candidates used in fit", nGoodSpatial)
1009 # If only nGoodSpatial == 0, might be other candidates in the cells
1010 if nGoodSpatial == 0 and nRejectedSpatial == 0:
1011 raise RuntimeError("No kernel candidates for spatial fit")
1013 if nRejectedSpatial == 0:
1014 # Nothing rejected, finished with spatial fit
1015 break
1017 # Otherwise, iterate on...
1018 thisIteration += 1
1020 # Final fit if above did not converge
1021 if (nRejectedSpatial > 0) and (thisIteration == maxSpatialIterations):
1022 trace_loggers[1].debug("Final spatial fit")
1023 if (usePcaForSpatialKernel):
1024 nRejectedPca, spatialBasisList = self._createPcaBasis(kernelCellSet, nStarPerCell, ps)
1025 regionBBox = kernelCellSet.getBBox()
1026 spatialkv = diffimLib.BuildSpatialKernelVisitorF(spatialBasisList, regionBBox, ps)
1027 kernelCellSet.visitCandidates(spatialkv, nStarPerCell)
1028 spatialkv.solveLinearEquation()
1029 trace_loggers[2].debug("Spatial kernel built with %d candidates", spatialkv.getNCandidates())
1030 spatialKernel, spatialBackground = spatialkv.getSolutionPair()
1032 spatialSolution = spatialkv.getKernelSolution()
1034 except Exception as e:
1035 self.log.error("ERROR: Unable to calculate psf matching kernel")
1037 trace_loggers[1].debug("%s", e)
1038 raise e
1040 t1 = time.time()
1041 trace_loggers[0].debug("Total time to compute the spatial kernel : %.2f s", (t1 - t0))
1043 if display:
1044 self._displayDebug(kernelCellSet, spatialKernel, spatialBackground)
1046 self._diagnostic(kernelCellSet, spatialSolution, spatialKernel, spatialBackground)
1048 return spatialSolution, spatialKernel, spatialBackground
1051PsfMatch = PsfMatchTask