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1# This file is part of cp_pipe.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
21#
22import numpy as np
23import matplotlib.pyplot as plt
24from collections import Counter
26import lsst.afw.math as afwMath
27import lsst.pex.config as pexConfig
28import lsst.pipe.base as pipeBase
29from .utils import (fitLeastSq, fitBootstrap, funcPolynomial, funcAstier)
30from scipy.optimize import least_squares
32import datetime
34from .astierCovPtcUtils import (fftSize, CovFft, computeCovDirect, fitData)
35from .linearity import LinearitySolveTask
36from .photodiode import getBOTphotodiodeData
38from lsst.pipe.tasks.getRepositoryData import DataRefListRunner
39from lsst.ip.isr import PhotonTransferCurveDataset
41__all__ = ['MeasurePhotonTransferCurveTask',
42 'MeasurePhotonTransferCurveTaskConfig']
45class MeasurePhotonTransferCurveTaskConfig(pexConfig.Config):
46 """Config class for photon transfer curve measurement task"""
47 ccdKey = pexConfig.Field(
48 dtype=str,
49 doc="The key by which to pull a detector from a dataId, e.g. 'ccd' or 'detector'.",
50 default='ccd',
51 )
52 ptcFitType = pexConfig.ChoiceField(
53 dtype=str,
54 doc="Fit PTC to Eq. 16, Eq. 20 in Astier+19, or to a polynomial.",
55 default="POLYNOMIAL",
56 allowed={
57 "POLYNOMIAL": "n-degree polynomial (use 'polynomialFitDegree' to set 'n').",
58 "EXPAPPROXIMATION": "Approximation in Astier+19 (Eq. 16).",
59 "FULLCOVARIANCE": "Full covariances model in Astier+19 (Eq. 20)"
60 }
61 )
62 sigmaClipFullFitCovariancesAstier = pexConfig.Field(
63 dtype=float,
64 doc="sigma clip for full model fit for FULLCOVARIANCE ptcFitType ",
65 default=5.0,
66 )
67 maxIterFullFitCovariancesAstier = pexConfig.Field(
68 dtype=int,
69 doc="Maximum number of iterations in full model fit for FULLCOVARIANCE ptcFitType",
70 default=3,
71 )
72 maximumRangeCovariancesAstier = pexConfig.Field(
73 dtype=int,
74 doc="Maximum range of covariances as in Astier+19",
75 default=8,
76 )
77 covAstierRealSpace = pexConfig.Field(
78 dtype=bool,
79 doc="Calculate covariances in real space or via FFT? (see appendix A of Astier+19).",
80 default=False,
81 )
82 polynomialFitDegree = pexConfig.Field(
83 dtype=int,
84 doc="Degree of polynomial to fit the PTC, when 'ptcFitType'=POLYNOMIAL.",
85 default=3,
86 )
87 linearity = pexConfig.ConfigurableField(
88 target=LinearitySolveTask,
89 doc="Task to solve the linearity."
90 )
92 doCreateLinearizer = pexConfig.Field(
93 dtype=bool,
94 doc="Calculate non-linearity and persist linearizer?",
95 default=False,
96 )
98 binSize = pexConfig.Field(
99 dtype=int,
100 doc="Bin the image by this factor in both dimensions.",
101 default=1,
102 )
103 minMeanSignal = pexConfig.Field(
104 dtype=float,
105 doc="Minimum value (inclusive) of mean signal (in DN) above which to consider.",
106 default=0,
107 )
108 maxMeanSignal = pexConfig.Field(
109 dtype=float,
110 doc="Maximum value (inclusive) of mean signal (in DN) below which to consider.",
111 default=9e6,
112 )
113 initialNonLinearityExclusionThresholdPositive = pexConfig.RangeField(
114 dtype=float,
115 doc="Initially exclude data points with a variance that are more than a factor of this from being"
116 " linear in the positive direction, from the PTC fit. Note that these points will also be"
117 " excluded from the non-linearity fit. This is done before the iterative outlier rejection,"
118 " to allow an accurate determination of the sigmas for said iterative fit.",
119 default=0.12,
120 min=0.0,
121 max=1.0,
122 )
123 initialNonLinearityExclusionThresholdNegative = pexConfig.RangeField(
124 dtype=float,
125 doc="Initially exclude data points with a variance that are more than a factor of this from being"
126 " linear in the negative direction, from the PTC fit. Note that these points will also be"
127 " excluded from the non-linearity fit. This is done before the iterative outlier rejection,"
128 " to allow an accurate determination of the sigmas for said iterative fit.",
129 default=0.25,
130 min=0.0,
131 max=1.0,
132 )
133 sigmaCutPtcOutliers = pexConfig.Field(
134 dtype=float,
135 doc="Sigma cut for outlier rejection in PTC.",
136 default=5.0,
137 )
138 maskNameList = pexConfig.ListField(
139 dtype=str,
140 doc="Mask list to exclude from statistics calculations.",
141 default=['SUSPECT', 'BAD', 'NO_DATA'],
142 )
143 nSigmaClipPtc = pexConfig.Field(
144 dtype=float,
145 doc="Sigma cut for afwMath.StatisticsControl()",
146 default=5.5,
147 )
148 nIterSigmaClipPtc = pexConfig.Field(
149 dtype=int,
150 doc="Number of sigma-clipping iterations for afwMath.StatisticsControl()",
151 default=1,
152 )
153 maxIterationsPtcOutliers = pexConfig.Field(
154 dtype=int,
155 doc="Maximum number of iterations for outlier rejection in PTC.",
156 default=2,
157 )
158 doFitBootstrap = pexConfig.Field(
159 dtype=bool,
160 doc="Use bootstrap for the PTC fit parameters and errors?.",
161 default=False,
162 )
163 doPhotodiode = pexConfig.Field(
164 dtype=bool,
165 doc="Apply a correction based on the photodiode readings if available?",
166 default=True,
167 )
168 photodiodeDataPath = pexConfig.Field(
169 dtype=str,
170 doc="Gen2 only: path to locate the data photodiode data files.",
171 default=""
172 )
173 instrumentName = pexConfig.Field(
174 dtype=str,
175 doc="Instrument name.",
176 default='',
177 )
180class MeasurePhotonTransferCurveTask(pipeBase.CmdLineTask):
181 """A class to calculate, fit, and plot a PTC from a set of flat pairs.
183 The Photon Transfer Curve (var(signal) vs mean(signal)) is a standard tool
184 used in astronomical detectors characterization (e.g., Janesick 2001,
185 Janesick 2007). If ptcFitType is "EXPAPPROXIMATION" or "POLYNOMIAL", this task calculates the
186 PTC from a series of pairs of flat-field images; each pair taken at identical exposure
187 times. The difference image of each pair is formed to eliminate fixed pattern noise,
188 and then the variance of the difference image and the mean of the average image
189 are used to produce the PTC. An n-degree polynomial or the approximation in Equation
190 16 of Astier+19 ("The Shape of the Photon Transfer Curve of CCD sensors",
191 arXiv:1905.08677) can be fitted to the PTC curve. These models include
192 parameters such as the gain (e/DN) and readout noise.
194 Linearizers to correct for signal-chain non-linearity are also calculated.
195 The `Linearizer` class, in general, can support per-amp linearizers, but in this
196 task this is not supported.
198 If ptcFitType is "FULLCOVARIANCE", the covariances of the difference images are calculated via the
199 DFT methods described in Astier+19 and the variances for the PTC are given by the cov[0,0] elements
200 at each signal level. The full model in Equation 20 of Astier+19 is fit to the PTC to get the gain
201 and the noise.
203 Parameters
204 ----------
206 *args: `list`
207 Positional arguments passed to the Task constructor. None used at this
208 time.
209 **kwargs: `dict`
210 Keyword arguments passed on to the Task constructor. None used at this
211 time.
213 """
215 RunnerClass = DataRefListRunner
216 ConfigClass = MeasurePhotonTransferCurveTaskConfig
217 _DefaultName = "measurePhotonTransferCurve"
219 def __init__(self, *args, **kwargs):
220 pipeBase.CmdLineTask.__init__(self, *args, **kwargs)
221 self.makeSubtask("linearity")
222 plt.interactive(False) # stop windows popping up when plotting. When headless, use 'agg' backend too
223 self.config.validate()
224 self.config.freeze()
226 @pipeBase.timeMethod
227 def runDataRef(self, dataRefList):
228 """Run the Photon Transfer Curve (PTC) measurement task.
230 For a dataRef (which is each detector here),
231 and given a list of exposure pairs (postISR) at different exposure times,
232 measure the PTC.
234 Parameters
235 ----------
236 dataRefList : `list` [`lsst.daf.peristence.ButlerDataRef`]
237 Data references for exposures for detectors to process.
238 """
239 if len(dataRefList) < 2:
240 raise RuntimeError("Insufficient inputs to combine.")
242 # setup necessary objects
243 dataRef = dataRefList[0]
245 detNum = dataRef.dataId[self.config.ccdKey]
246 camera = dataRef.get('camera')
247 detector = camera[dataRef.dataId[self.config.ccdKey]]
249 amps = detector.getAmplifiers()
250 ampNames = [amp.getName() for amp in amps]
251 datasetPtc = PhotonTransferCurveDataset(ampNames, self.config.ptcFitType)
253 # Get the pairs of flat indexed by expTime
254 expPairs = self.makePairs(dataRefList)
255 expIds = []
256 for (exp1, exp2) in expPairs.values():
257 id1 = exp1.getInfo().getVisitInfo().getExposureId()
258 id2 = exp2.getInfo().getVisitInfo().getExposureId()
259 expIds.append((id1, id2))
260 self.log.info(f"Measuring PTC using {expIds} exposures for detector {detector.getId()}")
262 # get photodiode data early so that logic can be put in to only use the
263 # data if all files are found, as partial corrections are not possible
264 # or at least require significant logic to deal with
265 if self.config.doPhotodiode:
266 for (expId1, expId2) in expIds:
267 charges = [-1, -1] # necessary to have a not-found value to keep lists in step
268 for i, expId in enumerate([expId1, expId2]):
269 # //1000 is a Gen2 only hack, working around the fact an
270 # exposure's ID is not the same as the expId in the
271 # registry. Currently expId is concatenated with the
272 # zero-padded detector ID. This will all go away in Gen3.
273 dataRef.dataId['expId'] = expId//1000
274 if self.config.photodiodeDataPath:
275 photodiodeData = getBOTphotodiodeData(dataRef, self.config.photodiodeDataPath)
276 else:
277 photodiodeData = getBOTphotodiodeData(dataRef)
278 if photodiodeData: # default path stored in function def to keep task clean
279 charges[i] = photodiodeData.getCharge()
280 else:
281 # full expId (not //1000) here, as that encodes the
282 # the detector number as so is fully qualifying
283 self.log.warn(f"No photodiode data found for {expId}")
285 for ampName in ampNames:
286 datasetPtc.photoCharge[ampName].append((charges[0], charges[1]))
287 else:
288 # Can't be an empty list, as initialized, because astropy.Table won't allow it
289 # when saving as fits
290 for ampName in ampNames:
291 datasetPtc.photoCharge[ampName] = np.repeat(np.nan, len(expIds))
293 for ampName in ampNames:
294 datasetPtc.inputExpIdPairs[ampName] = expIds
296 tupleRecords = []
297 allTags = []
298 for expTime, (exp1, exp2) in expPairs.items():
299 expId1 = exp1.getInfo().getVisitInfo().getExposureId()
300 expId2 = exp2.getInfo().getVisitInfo().getExposureId()
301 tupleRows = []
302 nAmpsNan = 0
303 for ampNumber, amp in enumerate(detector):
304 ampName = amp.getName()
305 # covAstier: (i, j, var (cov[0,0]), cov, npix)
306 doRealSpace = self.config.covAstierRealSpace
307 muDiff, varDiff, covAstier = self.measureMeanVarCov(exp1, exp2, region=amp.getBBox(),
308 covAstierRealSpace=doRealSpace)
309 datasetPtc.rawExpTimes[ampName].append(expTime)
310 datasetPtc.rawMeans[ampName].append(muDiff)
311 datasetPtc.rawVars[ampName].append(varDiff)
313 if np.isnan(muDiff) or np.isnan(varDiff) or (covAstier is None):
314 msg = (f"NaN mean or var, or None cov in amp {ampName} in exposure pair {expId1},"
315 f" {expId2} of detector {detNum}.")
316 self.log.warn(msg)
317 nAmpsNan += 1
318 continue
319 tags = ['mu', 'i', 'j', 'var', 'cov', 'npix', 'ext', 'expTime', 'ampName']
320 if (muDiff <= self.config.minMeanSignal) or (muDiff >= self.config.maxMeanSignal):
321 continue
323 tupleRows += [(muDiff, ) + covRow + (ampNumber, expTime, ampName) for covRow in covAstier]
324 if nAmpsNan == len(ampNames):
325 msg = f"NaN mean in all amps of exposure pair {expId1}, {expId2} of detector {detNum}."
326 self.log.warn(msg)
327 continue
328 allTags += tags
329 tupleRecords += tupleRows
330 covariancesWithTags = np.core.records.fromrecords(tupleRecords, names=allTags)
332 if self.config.ptcFitType in ["FULLCOVARIANCE", ]:
333 # Calculate covariances and fit them, including the PTC, to Astier+19 full model (Eq. 20)
334 datasetPtc = self.fitCovariancesAstier(datasetPtc, covariancesWithTags)
335 elif self.config.ptcFitType in ["EXPAPPROXIMATION", "POLYNOMIAL"]:
336 # Fit the PTC to a polynomial or to Astier+19 exponential approximation (Eq. 16)
337 # Fill up PhotonTransferCurveDataset object.
338 datasetPtc = self.fitPtc(datasetPtc, self.config.ptcFitType)
340 detName = detector.getName()
341 now = datetime.datetime.utcnow()
342 calibDate = now.strftime("%Y-%m-%d")
343 butler = dataRef.getButler()
345 datasetPtc.updateMetadata(setDate=True, camera=camera, detector=detector)
347 # Fit a poynomial to calculate non-linearity and persist linearizer.
348 if self.config.doCreateLinearizer:
349 # Fit (non)linearity of signal vs time curve.
350 # Fill up PhotonTransferCurveDataset object.
351 # Fill up array for LUT linearizer (tableArray).
352 # Produce coefficients for Polynomial and Squared linearizers.
353 # Build linearizer objects.
354 dimensions = {'camera': camera.getName(), 'detector': detector.getId()}
355 linearityResults = self.linearity.run(datasetPtc, camera, dimensions)
356 linearizer = linearityResults.outputLinearizer
358 self.log.info("Writing linearizer:")
359 butler.put(linearizer, datasetType='Linearizer', dataId={'detector': detNum,
360 'detectorName': detName, 'calibDate': calibDate})
362 self.log.info(f"Writing PTC data.")
363 butler.put(datasetPtc, datasetType='photonTransferCurveDataset', dataId={'detector': detNum,
364 'detectorName': detName, 'calibDate': calibDate})
366 return pipeBase.Struct(exitStatus=0)
368 def makePairs(self, dataRefList):
369 """Produce a list of flat pairs indexed by exposure time.
371 Parameters
372 ----------
373 dataRefList : `list` [`lsst.daf.peristence.ButlerDataRef`]
374 Data references for exposures for detectors to process.
376 Return
377 ------
378 flatPairs : `dict` [`float`, `lsst.afw.image.exposure.exposure.ExposureF`]
379 Dictionary that groups flat-field exposures that have the same exposure time (seconds).
381 Notes
382 -----
383 We use the difference of one pair of flat-field images taken at the same exposure time when
384 calculating the PTC to reduce Fixed Pattern Noise. If there are > 2 flat-field images with the
385 same exposure time, the first two are kept and the rest discarded.
386 """
388 # Organize exposures by observation date.
389 expDict = {}
390 for dataRef in dataRefList:
391 try:
392 tempFlat = dataRef.get("postISRCCD")
393 except RuntimeError:
394 self.log.warn("postISR exposure could not be retrieved. Ignoring flat.")
395 continue
396 expDate = tempFlat.getInfo().getVisitInfo().getDate().get()
397 expDict.setdefault(expDate, tempFlat)
398 sortedExps = {k: expDict[k] for k in sorted(expDict)}
400 flatPairs = {}
401 for exp in sortedExps:
402 tempFlat = sortedExps[exp]
403 expTime = tempFlat.getInfo().getVisitInfo().getExposureTime()
404 listAtExpTime = flatPairs.setdefault(expTime, [])
405 if len(listAtExpTime) >= 2:
406 self.log.warn(f"Already found 2 exposures at expTime {expTime}. "
407 f"Ignoring exposure {tempFlat.getInfo().getVisitInfo().getExposureId()}")
408 else:
409 listAtExpTime.append(tempFlat)
411 keysToDrop = []
412 for (key, value) in flatPairs.items():
413 if len(value) < 2:
414 keysToDrop.append(key)
416 if len(keysToDrop):
417 for key in keysToDrop:
418 self.log.warn(f"Only one exposure found at expTime {key}. Dropping exposure "
419 f"{flatPairs[key][0].getInfo().getVisitInfo().getExposureId()}.")
420 flatPairs.pop(key)
421 return flatPairs
423 def fitCovariancesAstier(self, dataset, covariancesWithTagsArray):
424 """Fit measured flat covariances to full model in Astier+19.
426 Parameters
427 ----------
428 dataset : `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
429 The dataset containing information such as the means, variances and exposure times.
431 covariancesWithTagsArray : `numpy.recarray`
432 Tuple with at least (mu, cov, var, i, j, npix), where:
433 mu : 0.5*(m1 + m2), where:
434 mu1: mean value of flat1
435 mu2: mean value of flat2
436 cov: covariance value at lag(i, j)
437 var: variance(covariance value at lag(0, 0))
438 i: lag dimension
439 j: lag dimension
440 npix: number of pixels used for covariance calculation.
442 Returns
443 -------
444 dataset: `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
445 This is the same dataset as the input paramter, however, it has been modified
446 to include information such as the fit vectors and the fit parameters. See
447 the class `PhotonTransferCurveDatase`.
448 """
450 covFits, covFitsNoB = fitData(covariancesWithTagsArray, maxMu=self.config.maxMeanSignal,
451 r=self.config.maximumRangeCovariancesAstier,
452 nSigmaFullFit=self.config.sigmaClipFullFitCovariancesAstier,
453 maxIterFullFit=self.config.maxIterFullFitCovariancesAstier)
455 dataset = self.getOutputPtcDataCovAstier(dataset, covFits, covFitsNoB)
457 return dataset
459 def getOutputPtcDataCovAstier(self, dataset, covFits, covFitsNoB):
460 """Get output data for PhotonTransferCurveCovAstierDataset from CovFit objects.
462 Parameters
463 ----------
464 dataset : `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
465 The dataset containing information such as the means, variances and exposure times.
467 covFits: `dict`
468 Dictionary of CovFit objects, with amp names as keys.
470 covFitsNoB : `dict`
471 Dictionary of CovFit objects, with amp names as keys, and 'b=0' in Eq. 20 of Astier+19.
473 Returns
474 -------
475 dataset : `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
476 This is the same dataset as the input paramter, however, it has been modified
477 to include extra information such as the mask 1D array, gains, reoudout noise, measured signal,
478 measured variance, modeled variance, a, and b coefficient matrices (see Astier+19) per amplifier.
479 See the class `PhotonTransferCurveDatase`.
480 """
481 assert(len(covFits) == len(covFitsNoB))
483 for i, amp in enumerate(dataset.ampNames):
484 lenInputTimes = len(dataset.rawExpTimes[amp])
485 # Not used when ptcFitType is 'FULLCOVARIANCE'
486 dataset.ptcFitPars[amp] = np.nan
487 dataset.ptcFitParsError[amp] = np.nan
488 dataset.ptcFitChiSq[amp] = np.nan
489 if amp in covFits:
490 fit = covFits[amp]
491 fitNoB = covFitsNoB[amp]
492 # Save full covariances, covariances models, and their weights
493 dataset.covariances[amp] = fit.cov
494 dataset.covariancesModel[amp] = fit.evalCovModel()
495 dataset.covariancesSqrtWeights[amp] = fit.sqrtW
496 dataset.aMatrix[amp] = fit.getA()
497 dataset.bMatrix[amp] = fit.getB()
498 dataset.covariancesNoB[amp] = fitNoB.cov
499 dataset.covariancesModelNoB[amp] = fitNoB.evalCovModel()
500 dataset.covariancesSqrtWeightsNoB[amp] = fitNoB.sqrtW
501 dataset.aMatrixNoB[amp] = fitNoB.getA()
503 (meanVecFinal, varVecFinal, varVecModel,
504 wc, varMask) = fit.getFitData(0, 0, divideByMu=False, returnMasked=True)
505 gain = fit.getGain()
506 dataset.expIdMask[amp] = varMask
507 dataset.gain[amp] = gain
508 dataset.gainErr[amp] = fit.getGainErr()
509 dataset.noise[amp] = np.sqrt(fit.getRon())
510 dataset.noiseErr[amp] = fit.getRonErr()
512 padLength = lenInputTimes - len(varVecFinal)
513 dataset.finalVars[amp] = np.pad(varVecFinal/(gain**2), (0, padLength), 'constant',
514 constant_values=np.nan)
515 dataset.finalModelVars[amp] = np.pad(varVecModel/(gain**2), (0, padLength), 'constant',
516 constant_values=np.nan)
517 dataset.finalMeans[amp] = np.pad(meanVecFinal/gain, (0, padLength), 'constant',
518 constant_values=np.nan)
519 else:
520 # Bad amp
521 # Entries need to have proper dimensions so read/write with astropy.Table works.
522 matrixSide = self.config.maximumRangeCovariancesAstier
523 nanMatrix = np.full((matrixSide, matrixSide), np.nan)
524 listNanMatrix = np.full((lenInputTimes, matrixSide, matrixSide), np.nan)
526 dataset.covariances[amp] = listNanMatrix
527 dataset.covariancesModel[amp] = listNanMatrix
528 dataset.covariancesSqrtWeights[amp] = listNanMatrix
529 dataset.aMatrix[amp] = nanMatrix
530 dataset.bMatrix[amp] = nanMatrix
531 dataset.covariancesNoB[amp] = listNanMatrix
532 dataset.covariancesModelNoB[amp] = listNanMatrix
533 dataset.covariancesSqrtWeightsNoB[amp] = listNanMatrix
534 dataset.aMatrixNoB[amp] = nanMatrix
536 dataset.expIdMask[amp] = np.repeat(np.nan, lenInputTimes)
537 dataset.gain[amp] = np.nan
538 dataset.gainErr[amp] = np.nan
539 dataset.noise[amp] = np.nan
540 dataset.noiseErr[amp] = np.nan
541 dataset.finalVars[amp] = np.repeat(np.nan, lenInputTimes)
542 dataset.finalModelVars[amp] = np.repeat(np.nan, lenInputTimes)
543 dataset.finalMeans[amp] = np.repeat(np.nan, lenInputTimes)
545 return dataset
547 def measureMeanVarCov(self, exposure1, exposure2, region=None, covAstierRealSpace=False):
548 """Calculate the mean of each of two exposures and the variance and covariance of their difference.
550 The variance is calculated via afwMath, and the covariance via the methods in Astier+19 (appendix A).
551 In theory, var = covariance[0,0]. This should be validated, and in the future, we may decide to just
552 keep one (covariance).
554 Parameters
555 ----------
556 exposure1 : `lsst.afw.image.exposure.exposure.ExposureF`
557 First exposure of flat field pair.
559 exposure2 : `lsst.afw.image.exposure.exposure.ExposureF`
560 Second exposure of flat field pair.
562 region : `lsst.geom.Box2I`, optional
563 Region of each exposure where to perform the calculations (e.g, an amplifier).
565 covAstierRealSpace : `bool`, optional
566 Should the covariannces in Astier+19 be calculated in real space or via FFT?
567 See Appendix A of Astier+19.
569 Returns
570 -------
571 mu : `float` or `NaN`
572 0.5*(mu1 + mu2), where mu1, and mu2 are the clipped means of the regions in
573 both exposures. If either mu1 or m2 are NaN's, the returned value is NaN.
575 varDiff : `float` or `NaN`
576 Half of the clipped variance of the difference of the regions inthe two input
577 exposures. If either mu1 or m2 are NaN's, the returned value is NaN.
579 covDiffAstier : `list` or `NaN`
580 List with tuples of the form (dx, dy, var, cov, npix), where:
581 dx : `int`
582 Lag in x
583 dy : `int`
584 Lag in y
585 var : `float`
586 Variance at (dx, dy).
587 cov : `float`
588 Covariance at (dx, dy).
589 nPix : `int`
590 Number of pixel pairs used to evaluate var and cov.
591 If either mu1 or m2 are NaN's, the returned value is NaN.
592 """
594 if region is not None:
595 im1Area = exposure1.maskedImage[region]
596 im2Area = exposure2.maskedImage[region]
597 else:
598 im1Area = exposure1.maskedImage
599 im2Area = exposure2.maskedImage
601 if self.config.binSize > 1:
602 im1Area = afwMath.binImage(im1Area, self.config.binSize)
603 im2Area = afwMath.binImage(im2Area, self.config.binSize)
605 im1MaskVal = exposure1.getMask().getPlaneBitMask(self.config.maskNameList)
606 im1StatsCtrl = afwMath.StatisticsControl(self.config.nSigmaClipPtc,
607 self.config.nIterSigmaClipPtc,
608 im1MaskVal)
609 im1StatsCtrl.setNanSafe(True)
610 im1StatsCtrl.setAndMask(im1MaskVal)
612 im2MaskVal = exposure2.getMask().getPlaneBitMask(self.config.maskNameList)
613 im2StatsCtrl = afwMath.StatisticsControl(self.config.nSigmaClipPtc,
614 self.config.nIterSigmaClipPtc,
615 im2MaskVal)
616 im2StatsCtrl.setNanSafe(True)
617 im2StatsCtrl.setAndMask(im2MaskVal)
619 # Clipped mean of images; then average of mean.
620 mu1 = afwMath.makeStatistics(im1Area, afwMath.MEANCLIP, im1StatsCtrl).getValue()
621 mu2 = afwMath.makeStatistics(im2Area, afwMath.MEANCLIP, im2StatsCtrl).getValue()
622 if np.isnan(mu1) or np.isnan(mu2):
623 return np.nan, np.nan, None
624 mu = 0.5*(mu1 + mu2)
626 # Take difference of pairs
627 # symmetric formula: diff = (mu2*im1-mu1*im2)/(0.5*(mu1+mu2))
628 temp = im2Area.clone()
629 temp *= mu1
630 diffIm = im1Area.clone()
631 diffIm *= mu2
632 diffIm -= temp
633 diffIm /= mu
635 diffImMaskVal = diffIm.getMask().getPlaneBitMask(self.config.maskNameList)
636 diffImStatsCtrl = afwMath.StatisticsControl(self.config.nSigmaClipPtc,
637 self.config.nIterSigmaClipPtc,
638 diffImMaskVal)
639 diffImStatsCtrl.setNanSafe(True)
640 diffImStatsCtrl.setAndMask(diffImMaskVal)
642 varDiff = 0.5*(afwMath.makeStatistics(diffIm, afwMath.VARIANCECLIP, diffImStatsCtrl).getValue())
644 # Get the mask and identify good pixels as '1', and the rest as '0'.
645 w1 = np.where(im1Area.getMask().getArray() == 0, 1, 0)
646 w2 = np.where(im2Area.getMask().getArray() == 0, 1, 0)
648 w12 = w1*w2
649 wDiff = np.where(diffIm.getMask().getArray() == 0, 1, 0)
650 w = w12*wDiff
652 maxRangeCov = self.config.maximumRangeCovariancesAstier
653 if covAstierRealSpace:
654 covDiffAstier = computeCovDirect(diffIm.getImage().getArray(), w, maxRangeCov)
655 else:
656 shapeDiff = diffIm.getImage().getArray().shape
657 fftShape = (fftSize(shapeDiff[0] + maxRangeCov), fftSize(shapeDiff[1]+maxRangeCov))
658 c = CovFft(diffIm.getImage().getArray(), w, fftShape, maxRangeCov)
659 covDiffAstier = c.reportCovFft(maxRangeCov)
661 return mu, varDiff, covDiffAstier
663 def computeCovDirect(self, diffImage, weightImage, maxRange):
664 """Compute covariances of diffImage in real space.
666 For lags larger than ~25, it is slower than the FFT way.
667 Taken from https://github.com/PierreAstier/bfptc/
669 Parameters
670 ----------
671 diffImage : `numpy.array`
672 Image to compute the covariance of.
674 weightImage : `numpy.array`
675 Weight image of diffImage (1's and 0's for good and bad pixels, respectively).
677 maxRange : `int`
678 Last index of the covariance to be computed.
680 Returns
681 -------
682 outList : `list`
683 List with tuples of the form (dx, dy, var, cov, npix), where:
684 dx : `int`
685 Lag in x
686 dy : `int`
687 Lag in y
688 var : `float`
689 Variance at (dx, dy).
690 cov : `float`
691 Covariance at (dx, dy).
692 nPix : `int`
693 Number of pixel pairs used to evaluate var and cov.
694 """
695 outList = []
696 var = 0
697 # (dy,dx) = (0,0) has to be first
698 for dy in range(maxRange + 1):
699 for dx in range(0, maxRange + 1):
700 if (dx*dy > 0):
701 cov1, nPix1 = self.covDirectValue(diffImage, weightImage, dx, dy)
702 cov2, nPix2 = self.covDirectValue(diffImage, weightImage, dx, -dy)
703 cov = 0.5*(cov1 + cov2)
704 nPix = nPix1 + nPix2
705 else:
706 cov, nPix = self.covDirectValue(diffImage, weightImage, dx, dy)
707 if (dx == 0 and dy == 0):
708 var = cov
709 outList.append((dx, dy, var, cov, nPix))
711 return outList
713 def covDirectValue(self, diffImage, weightImage, dx, dy):
714 """Compute covariances of diffImage in real space at lag (dx, dy).
716 Taken from https://github.com/PierreAstier/bfptc/ (c.f., appendix of Astier+19).
718 Parameters
719 ----------
720 diffImage : `numpy.array`
721 Image to compute the covariance of.
723 weightImage : `numpy.array`
724 Weight image of diffImage (1's and 0's for good and bad pixels, respectively).
726 dx : `int`
727 Lag in x.
729 dy : `int`
730 Lag in y.
732 Returns
733 -------
734 cov : `float`
735 Covariance at (dx, dy)
737 nPix : `int`
738 Number of pixel pairs used to evaluate var and cov.
739 """
740 (nCols, nRows) = diffImage.shape
741 # switching both signs does not change anything:
742 # it just swaps im1 and im2 below
743 if (dx < 0):
744 (dx, dy) = (-dx, -dy)
745 # now, we have dx >0. We have to distinguish two cases
746 # depending on the sign of dy
747 if dy >= 0:
748 im1 = diffImage[dy:, dx:]
749 w1 = weightImage[dy:, dx:]
750 im2 = diffImage[:nCols - dy, :nRows - dx]
751 w2 = weightImage[:nCols - dy, :nRows - dx]
752 else:
753 im1 = diffImage[:nCols + dy, dx:]
754 w1 = weightImage[:nCols + dy, dx:]
755 im2 = diffImage[-dy:, :nRows - dx]
756 w2 = weightImage[-dy:, :nRows - dx]
757 # use the same mask for all 3 calculations
758 wAll = w1*w2
759 # do not use mean() because weightImage=0 pixels would then count
760 nPix = wAll.sum()
761 im1TimesW = im1*wAll
762 s1 = im1TimesW.sum()/nPix
763 s2 = (im2*wAll).sum()/nPix
764 p = (im1TimesW*im2).sum()/nPix
765 cov = p - s1*s2
767 return cov, nPix
769 @staticmethod
770 def _initialParsForPolynomial(order):
771 assert(order >= 2)
772 pars = np.zeros(order, dtype=np.float)
773 pars[0] = 10
774 pars[1] = 1
775 pars[2:] = 0.0001
776 return pars
778 @staticmethod
779 def _boundsForPolynomial(initialPars):
780 lowers = [np.NINF for p in initialPars]
781 uppers = [np.inf for p in initialPars]
782 lowers[1] = 0 # no negative gains
783 return (lowers, uppers)
785 @staticmethod
786 def _boundsForAstier(initialPars):
787 lowers = [np.NINF for p in initialPars]
788 uppers = [np.inf for p in initialPars]
789 return (lowers, uppers)
791 @staticmethod
792 def _getInitialGoodPoints(means, variances, maxDeviationPositive, maxDeviationNegative):
793 """Return a boolean array to mask bad points.
795 Parameters
796 ----------
797 means : `numpy.array`
798 Input array with mean signal values.
800 variances : `numpy.array`
801 Input array with variances at each mean value.
803 maxDeviationPositive : `float`
804 Maximum deviation from being constant for the variance/mean
805 ratio, in the positive direction.
807 maxDeviationNegative : `float`
808 Maximum deviation from being constant for the variance/mean
809 ratio, in the negative direction.
811 Return
812 ------
813 goodPoints : `numpy.array` [`bool`]
814 Boolean array to select good (`True`) and bad (`False`)
815 points.
817 Notes
818 -----
819 A linear function has a constant ratio, so find the median
820 value of the ratios, and exclude the points that deviate
821 from that by more than a factor of maxDeviationPositive/negative.
822 Asymmetric deviations are supported as we expect the PTC to turn
823 down as the flux increases, but sometimes it anomalously turns
824 upwards just before turning over, which ruins the fits, so it
825 is wise to be stricter about restricting positive outliers than
826 negative ones.
828 Too high and points that are so bad that fit will fail will be included
829 Too low and the non-linear points will be excluded, biasing the NL fit."""
831 assert(len(means) == len(variances))
832 ratios = [b/a for (a, b) in zip(means, variances)]
833 medianRatio = np.nanmedian(ratios)
834 ratioDeviations = [(r/medianRatio)-1 for r in ratios]
836 # so that it doesn't matter if the deviation is expressed as positive or negative
837 maxDeviationPositive = abs(maxDeviationPositive)
838 maxDeviationNegative = -1. * abs(maxDeviationNegative)
840 goodPoints = np.array([True if (r < maxDeviationPositive and r > maxDeviationNegative)
841 else False for r in ratioDeviations])
842 return goodPoints
844 def _makeZeroSafe(self, array, warn=True, substituteValue=1e-9):
845 """"""
846 nBad = Counter(array)[0]
847 if nBad == 0:
848 return array
850 if warn:
851 msg = f"Found {nBad} zeros in array at elements {[x for x in np.where(array==0)[0]]}"
852 self.log.warn(msg)
854 array[array == 0] = substituteValue
855 return array
857 def fitPtc(self, dataset, ptcFitType):
858 """Fit the photon transfer curve to a polynimial or to Astier+19 approximation.
860 Fit the photon transfer curve with either a polynomial of the order
861 specified in the task config, or using the Astier approximation.
863 Sigma clipping is performed iteratively for the fit, as well as an
864 initial clipping of data points that are more than
865 config.initialNonLinearityExclusionThreshold away from lying on a
866 straight line. This other step is necessary because the photon transfer
867 curve turns over catastrophically at very high flux (because saturation
868 drops the variance to ~0) and these far outliers cause the initial fit
869 to fail, meaning the sigma cannot be calculated to perform the
870 sigma-clipping.
872 Parameters
873 ----------
874 dataset : `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
875 The dataset containing the means, variances and exposure times
877 ptcFitType : `str`
878 Fit a 'POLYNOMIAL' (degree: 'polynomialFitDegree') or
879 'EXPAPPROXIMATION' (Eq. 16 of Astier+19) to the PTC
881 Returns
882 -------
883 dataset: `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
884 This is the same dataset as the input paramter, however, it has been modified
885 to include information such as the fit vectors and the fit parameters. See
886 the class `PhotonTransferCurveDatase`.
887 """
889 matrixSide = self.config.maximumRangeCovariancesAstier
890 nanMatrix = np.empty((matrixSide, matrixSide))
891 nanMatrix[:] = np.nan
893 for amp in dataset.ampNames:
894 lenInputTimes = len(dataset.rawExpTimes[amp])
895 listNanMatrix = np.empty((lenInputTimes, matrixSide, matrixSide))
896 listNanMatrix[:] = np.nan
898 dataset.covariances[amp] = listNanMatrix
899 dataset.covariancesModel[amp] = listNanMatrix
900 dataset.covariancesSqrtWeights[amp] = listNanMatrix
901 dataset.aMatrix[amp] = nanMatrix
902 dataset.bMatrix[amp] = nanMatrix
903 dataset.covariancesNoB[amp] = listNanMatrix
904 dataset.covariancesModelNoB[amp] = listNanMatrix
905 dataset.covariancesSqrtWeightsNoB[amp] = listNanMatrix
906 dataset.aMatrixNoB[amp] = nanMatrix
908 def errFunc(p, x, y):
909 return ptcFunc(p, x) - y
911 sigmaCutPtcOutliers = self.config.sigmaCutPtcOutliers
912 maxIterationsPtcOutliers = self.config.maxIterationsPtcOutliers
914 for i, ampName in enumerate(dataset.ampNames):
915 timeVecOriginal = np.array(dataset.rawExpTimes[ampName])
916 meanVecOriginal = np.array(dataset.rawMeans[ampName])
917 varVecOriginal = np.array(dataset.rawVars[ampName])
918 varVecOriginal = self._makeZeroSafe(varVecOriginal)
920 mask = ((meanVecOriginal >= self.config.minMeanSignal) &
921 (meanVecOriginal <= self.config.maxMeanSignal))
923 goodPoints = self._getInitialGoodPoints(meanVecOriginal, varVecOriginal,
924 self.config.initialNonLinearityExclusionThresholdPositive,
925 self.config.initialNonLinearityExclusionThresholdNegative)
926 if not (mask.any() and goodPoints.any()):
927 msg = (f"\nSERIOUS: All points in either mask: {mask} or goodPoints: {goodPoints} are bad."
928 f"Setting {ampName} to BAD.")
929 self.log.warn(msg)
930 # The first and second parameters of initial fit are discarded (bias and gain)
931 # for the final NL coefficients
932 dataset.badAmps.append(ampName)
933 dataset.expIdMask[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
934 dataset.gain[ampName] = np.nan
935 dataset.gainErr[ampName] = np.nan
936 dataset.noise[ampName] = np.nan
937 dataset.noiseErr[ampName] = np.nan
938 dataset.ptcFitPars[ampName] = (np.repeat(np.nan, self.config.polynomialFitDegree + 1) if
939 ptcFitType in ["POLYNOMIAL", ] else np.repeat(np.nan, 3))
940 dataset.ptcFitParsError[ampName] = (np.repeat(np.nan, self.config.polynomialFitDegree + 1) if
941 ptcFitType in ["POLYNOMIAL", ] else np.repeat(np.nan, 3))
942 dataset.ptcFitChiSq[ampName] = np.nan
943 dataset.finalVars[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
944 dataset.finalModelVars[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
945 dataset.finalMeans[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
946 continue
948 mask = mask & goodPoints
950 if ptcFitType == 'EXPAPPROXIMATION':
951 ptcFunc = funcAstier
952 parsIniPtc = [-1e-9, 1.0, 10.] # a00, gain, noise
953 bounds = self._boundsForAstier(parsIniPtc)
954 if ptcFitType == 'POLYNOMIAL':
955 ptcFunc = funcPolynomial
956 parsIniPtc = self._initialParsForPolynomial(self.config.polynomialFitDegree + 1)
957 bounds = self._boundsForPolynomial(parsIniPtc)
959 # Before bootstrap fit, do an iterative fit to get rid of outliers
960 count = 1
961 while count <= maxIterationsPtcOutliers:
962 # Note that application of the mask actually shrinks the array
963 # to size rather than setting elements to zero (as we want) so
964 # always update mask itself and re-apply to the original data
965 meanTempVec = meanVecOriginal[mask]
966 varTempVec = varVecOriginal[mask]
967 res = least_squares(errFunc, parsIniPtc, bounds=bounds, args=(meanTempVec, varTempVec))
968 pars = res.x
970 # change this to the original from the temp because the masks are ANDed
971 # meaning once a point is masked it's always masked, and the masks must
972 # always be the same length for broadcasting
973 sigResids = (varVecOriginal - ptcFunc(pars, meanVecOriginal))/np.sqrt(varVecOriginal)
974 newMask = np.array([True if np.abs(r) < sigmaCutPtcOutliers else False for r in sigResids])
975 mask = mask & newMask
976 if not (mask.any() and newMask.any()):
977 msg = (f"\nSERIOUS: All points in either mask: {mask} or newMask: {newMask} are bad. "
978 f"Setting {ampName} to BAD.")
979 self.log.warn(msg)
980 # The first and second parameters of initial fit are discarded (bias and gain)
981 # for the final NL coefficients
982 dataset.badAmps.append(ampName)
983 dataset.expIdMask[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
984 dataset.gain[ampName] = np.nan
985 dataset.gainErr[ampName] = np.nan
986 dataset.noise[ampName] = np.nan
987 dataset.noiseErr[ampName] = np.nan
988 dataset.ptcFitPars[ampName] = (np.repeat(np.nan, self.config.polynomialFitDegree + 1)
989 if ptcFitType in ["POLYNOMIAL", ] else
990 np.repeat(np.nan, 3))
991 dataset.ptcFitParsError[ampName] = (np.repeat(np.nan, self.config.polynomialFitDegree + 1)
992 if ptcFitType in ["POLYNOMIAL", ] else
993 np.repeat(np.nan, 3))
994 dataset.ptcFitChiSq[ampName] = np.nan
995 dataset.finalVars[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
996 dataset.finalModelVars[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
997 dataset.finalMeans[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
998 break
999 nDroppedTotal = Counter(mask)[False]
1000 self.log.debug(f"Iteration {count}: discarded {nDroppedTotal} points in total for {ampName}")
1001 count += 1
1002 # objects should never shrink
1003 assert (len(mask) == len(timeVecOriginal) == len(meanVecOriginal) == len(varVecOriginal))
1005 if not (mask.any() and newMask.any()):
1006 continue
1007 dataset.expIdMask[ampName] = mask # store the final mask
1008 parsIniPtc = pars
1009 meanVecFinal = meanVecOriginal[mask]
1010 varVecFinal = varVecOriginal[mask]
1012 if Counter(mask)[False] > 0:
1013 self.log.info((f"Number of points discarded in PTC of amplifier {ampName}:" +
1014 f" {Counter(mask)[False]} out of {len(meanVecOriginal)}"))
1016 if (len(meanVecFinal) < len(parsIniPtc)):
1017 msg = (f"\nSERIOUS: Not enough data points ({len(meanVecFinal)}) compared to the number of"
1018 f"parameters of the PTC model({len(parsIniPtc)}). Setting {ampName} to BAD.")
1019 self.log.warn(msg)
1020 # The first and second parameters of initial fit are discarded (bias and gain)
1021 # for the final NL coefficients
1022 dataset.badAmps.append(ampName)
1023 dataset.expIdMask[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
1024 dataset.gain[ampName] = np.nan
1025 dataset.gainErr[ampName] = np.nan
1026 dataset.noise[ampName] = np.nan
1027 dataset.noiseErr[ampName] = np.nan
1028 dataset.ptcFitPars[ampName] = (np.repeat(np.nan, self.config.polynomialFitDegree + 1) if
1029 ptcFitType in ["POLYNOMIAL", ] else np.repeat(np.nan, 3))
1030 dataset.ptcFitParsError[ampName] = (np.repeat(np.nan, self.config.polynomialFitDegree + 1) if
1031 ptcFitType in ["POLYNOMIAL", ] else np.repeat(np.nan, 3))
1032 dataset.ptcFitChiSq[ampName] = np.nan
1033 dataset.finalVars[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
1034 dataset.finalModelVars[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
1035 dataset.finalMeans[ampName] = np.repeat(np.nan, len(dataset.rawExpTimes[ampName]))
1036 continue
1038 # Fit the PTC
1039 if self.config.doFitBootstrap:
1040 parsFit, parsFitErr, reducedChiSqPtc = fitBootstrap(parsIniPtc, meanVecFinal,
1041 varVecFinal, ptcFunc,
1042 weightsY=1./np.sqrt(varVecFinal))
1043 else:
1044 parsFit, parsFitErr, reducedChiSqPtc = fitLeastSq(parsIniPtc, meanVecFinal,
1045 varVecFinal, ptcFunc,
1046 weightsY=1./np.sqrt(varVecFinal))
1047 dataset.ptcFitPars[ampName] = parsFit
1048 dataset.ptcFitParsError[ampName] = parsFitErr
1049 dataset.ptcFitChiSq[ampName] = reducedChiSqPtc
1050 # Masked variances (measured and modeled) and means. Need to pad the array so astropy.Table does
1051 # not crash (the mask may vary per amp).
1052 padLength = len(dataset.rawExpTimes[ampName]) - len(varVecFinal)
1053 dataset.finalVars[ampName] = np.pad(varVecFinal, (0, padLength), 'constant',
1054 constant_values=np.nan)
1055 dataset.finalModelVars[ampName] = np.pad(ptcFunc(parsFit, meanVecFinal), (0, padLength),
1056 'constant', constant_values=np.nan)
1057 dataset.finalMeans[ampName] = np.pad(meanVecFinal, (0, padLength), 'constant',
1058 constant_values=np.nan)
1060 if ptcFitType == 'EXPAPPROXIMATION':
1061 ptcGain = parsFit[1]
1062 ptcGainErr = parsFitErr[1]
1063 ptcNoise = np.sqrt(np.fabs(parsFit[2]))
1064 ptcNoiseErr = 0.5*(parsFitErr[2]/np.fabs(parsFit[2]))*np.sqrt(np.fabs(parsFit[2]))
1065 if ptcFitType == 'POLYNOMIAL':
1066 ptcGain = 1./parsFit[1]
1067 ptcGainErr = np.fabs(1./parsFit[1])*(parsFitErr[1]/parsFit[1])
1068 ptcNoise = np.sqrt(np.fabs(parsFit[0]))*ptcGain
1069 ptcNoiseErr = (0.5*(parsFitErr[0]/np.fabs(parsFit[0]))*(np.sqrt(np.fabs(parsFit[0]))))*ptcGain
1070 dataset.gain[ampName] = ptcGain
1071 dataset.gainErr[ampName] = ptcGainErr
1072 dataset.noise[ampName] = ptcNoise
1073 dataset.noiseErr[ampName] = ptcNoiseErr
1074 if not len(dataset.ptcFitType) == 0:
1075 dataset.ptcFitType = ptcFitType
1076 if len(dataset.badAmps) == 0:
1077 dataset.badAmps = np.repeat(np.nan, len(list(dataset.rawExpTimes.values())[0]))
1079 return dataset