lsst.ip.isr 22.0.1-29-g4a3d635+366db6d849
isrMock.py
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21
22import copy
23import numpy as np
24import tempfile
25
26import lsst.geom
27import lsst.afw.geom as afwGeom
28import lsst.afw.image as afwImage
29
30import lsst.afw.cameraGeom.utils as afwUtils
31import lsst.afw.cameraGeom.testUtils as afwTestUtils
32import lsst.pex.config as pexConfig
33import lsst.pipe.base as pipeBase
34from .crosstalk import CrosstalkCalib
35from .defects import Defects
36
37__all__ = ["IsrMockConfig", "IsrMock", "RawMock", "TrimmedRawMock", "RawDictMock",
38 "CalibratedRawMock", "MasterMock",
39 "BiasMock", "DarkMock", "FlatMock", "FringeMock", "UntrimmedFringeMock",
40 "BfKernelMock", "DefectMock", "CrosstalkCoeffMock", "TransmissionMock",
41 "DataRefMock"]
42
43
44class IsrMockConfig(pexConfig.Config):
45 """Configuration parameters for isrMock.
46
47 These parameters produce generic fixed position signals from
48 various sources, and combine them in a way that matches how those
49 signals are combined to create real data. The camera used is the
50 test camera defined by the afwUtils code.
51 """
52 # Detector parameters. "Exposure" parameters.
53 isLsstLike = pexConfig.Field(
54 dtype=bool,
55 default=False,
56 doc="If True, products have one raw image per amplifier, otherwise, one raw image per detector.",
57 )
58 plateScale = pexConfig.Field(
59 dtype=float,
60 default=20.0,
61 doc="Plate scale used in constructing mock camera.",
62 )
63 radialDistortion = pexConfig.Field(
64 dtype=float,
65 default=0.925,
66 doc="Radial distortion term used in constructing mock camera.",
67 )
68 isTrimmed = pexConfig.Field(
69 dtype=bool,
70 default=True,
71 doc="If True, amplifiers have been trimmed and mosaicked to remove regions outside the data BBox.",
72 )
73 detectorIndex = pexConfig.Field(
74 dtype=int,
75 default=20,
76 doc="Index for the detector to use. The default value uses a standard 2x4 array of amps.",
77 )
78 rngSeed = pexConfig.Field(
79 dtype=int,
80 default=20000913,
81 doc="Seed for random number generator used to add noise.",
82 )
83 # TODO: DM-18345 Check that mocks scale correctly when gain != 1.0
84 gain = pexConfig.Field(
85 dtype=float,
86 default=1.0,
87 doc="Gain for simulated data in e^-/DN.",
88 )
89 readNoise = pexConfig.Field(
90 dtype=float,
91 default=5.0,
92 doc="Read noise of the detector in e-.",
93 )
94 expTime = pexConfig.Field(
95 dtype=float,
96 default=5.0,
97 doc="Exposure time for simulated data.",
98 )
99
100 # Signal parameters
101 skyLevel = pexConfig.Field(
102 dtype=float,
103 default=1000.0,
104 doc="Background contribution to be generated from 'the sky' in DN.",
105 )
106 sourceFlux = pexConfig.ListField(
107 dtype=float,
108 default=[45000.0],
109 doc="Peak flux level (in DN) of simulated 'astronomical sources'.",
110 )
111 sourceAmp = pexConfig.ListField(
112 dtype=int,
113 default=[0],
114 doc="Amplifier to place simulated 'astronomical sources'.",
115 )
116 sourceX = pexConfig.ListField(
117 dtype=float,
118 default=[50.0],
119 doc="Peak position (in amplifier coordinates) of simulated 'astronomical sources'.",
120 )
121 sourceY = pexConfig.ListField(
122 dtype=float,
123 default=[25.0],
124 doc="Peak position (in amplifier coordinates) of simulated 'astronomical sources'.",
125 )
126 overscanScale = pexConfig.Field(
127 dtype=float,
128 default=100.0,
129 doc="Amplitude (in DN) of the ramp function to add to overscan data.",
130 )
131 biasLevel = pexConfig.Field(
132 dtype=float,
133 default=8000.0,
134 doc="Background contribution to be generated from the bias offset in DN.",
135 )
136 darkRate = pexConfig.Field(
137 dtype=float,
138 default=5.0,
139 doc="Background level contribution (in e-/s) to be generated from dark current.",
140 )
141 darkTime = pexConfig.Field(
142 dtype=float,
143 default=5.0,
144 doc="Exposure time for the dark current contribution.",
145 )
146 flatDrop = pexConfig.Field(
147 dtype=float,
148 default=0.1,
149 doc="Fractional flux drop due to flat from center to edge of detector along x-axis.",
150 )
151 fringeScale = pexConfig.ListField(
152 dtype=float,
153 default=[200.0],
154 doc="Peak fluxes for the components of the fringe ripple in DN.",
155 )
156 fringeX0 = pexConfig.ListField(
157 dtype=float,
158 default=[-100],
159 doc="Center position for the fringe ripples.",
160 )
161 fringeY0 = pexConfig.ListField(
162 dtype=float,
163 default=[-0],
164 doc="Center position for the fringe ripples.",
165 )
166
167 # Inclusion parameters
168 doAddSky = pexConfig.Field(
169 dtype=bool,
170 default=True,
171 doc="Apply 'sky' signal to output image.",
172 )
173 doAddSource = pexConfig.Field(
174 dtype=bool,
175 default=True,
176 doc="Add simulated source to output image.",
177 )
178 doAddCrosstalk = pexConfig.Field(
179 dtype=bool,
180 default=False,
181 doc="Apply simulated crosstalk to output image. This cannot be corrected by ISR, "
182 "as detector.hasCrosstalk()==False.",
183 )
184 doAddOverscan = pexConfig.Field(
185 dtype=bool,
186 default=True,
187 doc="If untrimmed, add overscan ramp to overscan and data regions.",
188 )
189 doAddBias = pexConfig.Field(
190 dtype=bool,
191 default=True,
192 doc="Add bias signal to data.",
193 )
194 doAddDark = pexConfig.Field(
195 dtype=bool,
196 default=True,
197 doc="Add dark signal to data.",
198 )
199 doAddFlat = pexConfig.Field(
200 dtype=bool,
201 default=True,
202 doc="Add flat signal to data.",
203 )
204 doAddFringe = pexConfig.Field(
205 dtype=bool,
206 default=True,
207 doc="Add fringe signal to data.",
208 )
209
210 # Datasets to create and return instead of generating an image.
211 doTransmissionCurve = pexConfig.Field(
212 dtype=bool,
213 default=False,
214 doc="Return a simulated transmission curve.",
215 )
216 doDefects = pexConfig.Field(
217 dtype=bool,
218 default=False,
219 doc="Return a simulated defect list.",
220 )
221 doBrighterFatter = pexConfig.Field(
222 dtype=bool,
223 default=False,
224 doc="Return a simulated brighter-fatter kernel.",
225 )
226 doCrosstalkCoeffs = pexConfig.Field(
227 dtype=bool,
228 default=False,
229 doc="Return the matrix of crosstalk coefficients.",
230 )
231 doDataRef = pexConfig.Field(
232 dtype=bool,
233 default=False,
234 doc="Return a simulated gen2 butler dataRef.",
235 )
236 doGenerateImage = pexConfig.Field(
237 dtype=bool,
238 default=False,
239 doc="Return the generated output image if True.",
240 )
241 doGenerateData = pexConfig.Field(
242 dtype=bool,
243 default=False,
244 doc="Return a non-image data structure if True.",
245 )
246 doGenerateAmpDict = pexConfig.Field(
247 dtype=bool,
248 default=False,
249 doc="Return a dict of exposure amplifiers instead of an afwImage.Exposure.",
250 )
251
252
253class IsrMock(pipeBase.Task):
254 """Class to generate consistent mock images for ISR testing.
255
256 ISR testing currently relies on one-off fake images that do not
257 accurately mimic the full set of detector effects. This class
258 uses the test camera/detector/amplifier structure defined in
259 `lsst.afw.cameraGeom.testUtils` to avoid making the test data
260 dependent on any of the actual obs package formats.
261 """
262 ConfigClass = IsrMockConfig
263 _DefaultName = "isrMock"
264
265 def __init__(self, **kwargs):
266 super().__init__(**kwargs)
267 self.rngrng = np.random.RandomState(self.config.rngSeed)
268 self.crosstalkCoeffscrosstalkCoeffs = np.array([[0.0, 0.0, 0.0, 0.0, 0.0, -1e-3, 0.0, 0.0],
269 [1e-2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
270 [1e-2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
271 [1e-2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
272 [1e-2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
273 [1e-2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
274 [1e-2, 0.0, 0.0, 2.2e-2, 0.0, 0.0, 0.0, 0.0],
275 [1e-2, 5e-3, 5e-4, 3e-3, 4e-2, 5e-3, 5e-3, 0.0]])
276
277 self.bfKernelbfKernel = np.array([[1., 4., 7., 4., 1.],
278 [4., 16., 26., 16., 4.],
279 [7., 26., 41., 26., 7.],
280 [4., 16., 26., 16., 4.],
281 [1., 4., 7., 4., 1.]]) / 273.0
282
283 def run(self):
284 """Generate a mock ISR product, and return it.
285
286 Returns
287 -------
289 Simulated ISR image with signals added.
290 dataProduct :
291 Simulated ISR data products.
292 None :
293 Returned if no valid configuration was found.
294
295 Raises
296 ------
297 RuntimeError
298 Raised if both doGenerateImage and doGenerateData are specified.
299 """
300 if self.config.doGenerateImage and self.config.doGenerateData:
301 raise RuntimeError("Only one of doGenerateImage and doGenerateData may be specified.")
302 elif self.config.doGenerateImage:
303 return self.makeImagemakeImage()
304 elif self.config.doGenerateData:
305 return self.makeDatamakeData()
306 else:
307 return None
308
309 def makeData(self):
310 """Generate simulated ISR data.
311
312 Currently, only the class defined crosstalk coefficient
313 matrix, brighter-fatter kernel, a constant unity transmission
314 curve, or a simple single-entry defect list can be generated.
315
316 Returns
317 -------
318 dataProduct :
319 Simulated ISR data product.
320 """
321 if sum(map(bool, [self.config.doBrighterFatter,
322 self.config.doDefects,
323 self.config.doTransmissionCurve,
324 self.config.doCrosstalkCoeffs])) != 1:
325 raise RuntimeError("Only one data product can be generated at a time.")
326 elif self.config.doBrighterFatter is True:
327 return self.makeBfKernelmakeBfKernel()
328 elif self.config.doDefects is True:
329 return self.makeDefectListmakeDefectList()
330 elif self.config.doTransmissionCurve is True:
331 return self.makeTransmissionCurvemakeTransmissionCurve()
332 elif self.config.doCrosstalkCoeffs is True:
333 return self.crosstalkCoeffscrosstalkCoeffs
334 else:
335 return None
336
337 def makeBfKernel(self):
338 """Generate a simple Gaussian brighter-fatter kernel.
339
340 Returns
341 -------
342 kernel : `numpy.ndarray`
343 Simulated brighter-fatter kernel.
344 """
345 return self.bfKernelbfKernel
346
347 def makeDefectList(self):
348 """Generate a simple single-entry defect list.
349
350 Returns
351 -------
352 defectList : `lsst.meas.algorithms.Defects`
353 Simulated defect list
354 """
356 lsst.geom.Extent2I(40, 50))])
357
359 """Generate the simulated crosstalk coefficients.
360
361 Returns
362 -------
363 coeffs : `numpy.ndarray`
364 Simulated crosstalk coefficients.
365 """
366
367 return self.crosstalkCoeffscrosstalkCoeffs
368
370 """Generate a simulated flat transmission curve.
371
372 Returns
373 -------
374 transmission : `lsst.afw.image.TransmissionCurve`
375 Simulated transmission curve.
376 """
377
378 return afwImage.TransmissionCurve.makeIdentity()
379
380 def makeImage(self):
381 """Generate a simulated ISR image.
382
383 Returns
384 -------
385 exposure : `lsst.afw.image.Exposure` or `dict`
386 Simulated ISR image data.
387
388 Notes
389 -----
390 This method currently constructs a "raw" data image by:
391 * Generating a simulated sky with noise
392 * Adding a single Gaussian "star"
393 * Adding the fringe signal
394 * Multiplying the frame by the simulated flat
395 * Adding dark current (and noise)
396 * Adding a bias offset (and noise)
397 * Adding an overscan gradient parallel to the pixel y-axis
398 * Simulating crosstalk by adding a scaled version of each
399 amplifier to each other amplifier.
400
401 The exposure with image data constructed this way is in one of
402 three formats.
403 * A single image, with overscan and prescan regions retained
404 * A single image, with overscan and prescan regions trimmed
405 * A `dict`, containing the amplifer data indexed by the
406 amplifier name.
407
408 The nonlinearity, CTE, and brighter fatter are currently not
409 implemented.
410
411 Note that this method generates an image in the reverse
412 direction as the ISR processing, as the output image here has
413 had a series of instrument effects added to an idealized
414 exposure.
415 """
416 exposure = self.getExposuregetExposure()
417
418 for idx, amp in enumerate(exposure.getDetector()):
419 bbox = None
420 if self.config.isTrimmed is True:
421 bbox = amp.getBBox()
422 else:
423 bbox = amp.getRawDataBBox()
424
425 ampData = exposure.image[bbox]
426
427 if self.config.doAddSky is True:
428 self.amplifierAddNoiseamplifierAddNoise(ampData, self.config.skyLevel, np.sqrt(self.config.skyLevel))
429
430 if self.config.doAddSource is True:
431 for sourceAmp, sourceFlux, sourceX, sourceY in zip(self.config.sourceAmp,
432 self.config.sourceFlux,
433 self.config.sourceX,
434 self.config.sourceY):
435 if idx == sourceAmp:
436 self.amplifierAddSourceamplifierAddSource(ampData, sourceFlux, sourceX, sourceY)
437
438 if self.config.doAddFringe is True:
439 self.amplifierAddFringeamplifierAddFringe(amp, ampData, np.array(self.config.fringeScale),
440 x0=np.array(self.config.fringeX0),
441 y0=np.array(self.config.fringeY0))
442
443 if self.config.doAddFlat is True:
444 if ampData.getArray().sum() == 0.0:
445 self.amplifierAddNoiseamplifierAddNoise(ampData, 1.0, 0.0)
446 u0 = exposure.getDimensions().getX()
447 v0 = exposure.getDimensions().getY()
448 self.amplifierMultiplyFlatamplifierMultiplyFlat(amp, ampData, self.config.flatDrop, u0=u0, v0=v0)
449
450 if self.config.doAddDark is True:
451 self.amplifierAddNoiseamplifierAddNoise(ampData,
452 self.config.darkRate * self.config.darkTime / self.config.gain,
453 np.sqrt(self.config.darkRate
454 * self.config.darkTime / self.config.gain))
455
456 if self.config.doAddCrosstalk is True:
457 ctCalib = CrosstalkCalib()
458 for idxS, ampS in enumerate(exposure.getDetector()):
459 for idxT, ampT in enumerate(exposure.getDetector()):
460 ampDataT = exposure.image[ampT.getBBox()
461 if self.config.isTrimmed else ampT.getRawDataBBox()]
462 outAmp = ctCalib.extractAmp(exposure.getImage(), ampS, ampT,
463 isTrimmed=self.config.isTrimmed)
464 self.amplifierAddCTamplifierAddCT(outAmp, ampDataT, self.crosstalkCoeffscrosstalkCoeffs[idxT][idxS])
465
466 for amp in exposure.getDetector():
467 bbox = None
468 if self.config.isTrimmed is True:
469 bbox = amp.getBBox()
470 else:
471 bbox = amp.getRawDataBBox()
472
473 ampData = exposure.image[bbox]
474
475 if self.config.doAddBias is True:
476 self.amplifierAddNoiseamplifierAddNoise(ampData, self.config.biasLevel,
477 self.config.readNoise / self.config.gain)
478
479 if self.config.doAddOverscan is True:
480 oscanBBox = amp.getRawHorizontalOverscanBBox()
481 oscanData = exposure.image[oscanBBox]
482 self.amplifierAddNoiseamplifierAddNoise(oscanData, self.config.biasLevel,
483 self.config.readNoise / self.config.gain)
484
485 self.amplifierAddYGradientamplifierAddYGradient(ampData, -1.0 * self.config.overscanScale,
486 1.0 * self.config.overscanScale)
487 self.amplifierAddYGradientamplifierAddYGradient(oscanData, -1.0 * self.config.overscanScale,
488 1.0 * self.config.overscanScale)
489
490 if self.config.doGenerateAmpDict is True:
491 expDict = dict()
492 for amp in exposure.getDetector():
493 expDict[amp.getName()] = exposure
494 return expDict
495 else:
496 return exposure
497
498 # afw primatives to construct the image structure
499 def getCamera(self):
500 """Construct a test camera object.
501
502 Returns
503 -------
504 camera : `lsst.afw.cameraGeom.camera`
505 Test camera.
506 """
507 cameraWrapper = afwTestUtils.CameraWrapper(
508 plateScale=self.config.plateScale,
509 radialDistortion=self.config.radialDistortion,
510 isLsstLike=self.config.isLsstLike,
511 )
512 camera = cameraWrapper.camera
513 return camera
514
515 def getExposure(self):
516 """Construct a test exposure.
517
518 The test exposure has a simple WCS set, as well as a list of
519 unlikely header keywords that can be removed during ISR
520 processing to exercise that code.
521
522 Returns
523 -------
524 exposure : `lsst.afw.exposure.Exposure`
525 Construct exposure containing masked image of the
526 appropriate size.
527 """
528 camera = self.getCameragetCamera()
529 detector = camera[self.config.detectorIndex]
530 image = afwUtils.makeImageFromCcd(detector,
531 isTrimmed=self.config.isTrimmed,
532 showAmpGain=False,
533 rcMarkSize=0,
534 binSize=1,
535 imageFactory=afwImage.ImageF)
536
537 var = afwImage.ImageF(image.getDimensions())
538 mask = afwImage.Mask(image.getDimensions())
539 image.assign(0.0)
540
541 maskedImage = afwImage.makeMaskedImage(image, mask, var)
542 exposure = afwImage.makeExposure(maskedImage)
543 exposure.setDetector(detector)
544 exposure.setWcs(self.getWcsgetWcs())
545
546 visitInfo = afwImage.VisitInfo(exposureTime=self.config.expTime, darkTime=self.config.darkTime)
547 exposure.getInfo().setVisitInfo(visitInfo)
548
549 metadata = exposure.getMetadata()
550 metadata.add("SHEEP", 7.3, "number of sheep on farm")
551 metadata.add("MONKEYS", 155, "monkeys per tree")
552 metadata.add("VAMPIRES", 4, "How scary are vampires.")
553
554 ccd = exposure.getDetector()
555 newCcd = ccd.rebuild()
556 newCcd.clear()
557 for amp in ccd:
558 newAmp = amp.rebuild()
559 newAmp.setLinearityCoeffs((0., 1., 0., 0.))
560 newAmp.setLinearityType("Polynomial")
561 newAmp.setGain(self.config.gain)
562 newAmp.setSuspectLevel(25000.0)
563 newAmp.setSaturation(32000.0)
564 newCcd.append(newAmp)
565 exposure.setDetector(newCcd.finish())
566
567 exposure.image.array[:] = np.zeros(exposure.getImage().getDimensions()).transpose()
568 exposure.mask.array[:] = np.zeros(exposure.getMask().getDimensions()).transpose()
569 exposure.variance.array[:] = np.zeros(exposure.getVariance().getDimensions()).transpose()
570
571 return exposure
572
573 def getWcs(self):
574 """Construct a dummy WCS object.
575
576 Taken from the deprecated ip_isr/examples/exampleUtils.py.
577
578 This is not guaranteed, given the distortion and pixel scale
579 listed in the afwTestUtils camera definition.
580
581 Returns
582 -------
584 Test WCS transform.
585 """
586 return afwGeom.makeSkyWcs(crpix=lsst.geom.Point2D(0.0, 100.0),
587 crval=lsst.geom.SpherePoint(45.0, 25.0, lsst.geom.degrees),
588 cdMatrix=afwGeom.makeCdMatrix(scale=1.0*lsst.geom.degrees))
589
590 def localCoordToExpCoord(self, ampData, x, y):
591 """Convert between a local amplifier coordinate and the full
592 exposure coordinate.
593
594 Parameters
595 ----------
596 ampData : `lsst.afw.image.ImageF`
597 Amplifier image to use for conversions.
598 x : `int`
599 X-coordinate of the point to transform.
600 y : `int`
601 Y-coordinate of the point to transform.
602
603 Returns
604 -------
605 u : `int`
606 Transformed x-coordinate.
607 v : `int`
608 Transformed y-coordinate.
609
610 Notes
611 -----
612 The output is transposed intentionally here, to match the
613 internal transpose between numpy and afw.image coordinates.
614 """
615 u = x + ampData.getBBox().getBeginX()
616 v = y + ampData.getBBox().getBeginY()
617
618 return (v, u)
619
620 # Simple data values.
621 def amplifierAddNoise(self, ampData, mean, sigma):
622 """Add Gaussian noise to an amplifier's image data.
623
624 This method operates in the amplifier coordinate frame.
625
626 Parameters
627 ----------
628 ampData : `lsst.afw.image.ImageF`
629 Amplifier image to operate on.
630 mean : `float`
631 Mean value of the Gaussian noise.
632 sigma : `float`
633 Sigma of the Gaussian noise.
634 """
635 ampArr = ampData.array
636 ampArr[:] = ampArr[:] + self.rngrng.normal(mean, sigma,
637 size=ampData.getDimensions()).transpose()
638
639 def amplifierAddYGradient(self, ampData, start, end):
640 """Add a y-axis linear gradient to an amplifier's image data.
641
642 This method operates in the amplifier coordinate frame.
643
644 Parameters
645 ----------
646 ampData : `lsst.afw.image.ImageF`
647 Amplifier image to operate on.
648 start : `float`
649 Start value of the gradient (at y=0).
650 end : `float`
651 End value of the gradient (at y=ymax).
652 """
653 nPixY = ampData.getDimensions().getY()
654 ampArr = ampData.array
655 ampArr[:] = ampArr[:] + (np.interp(range(nPixY), (0, nPixY - 1), (start, end)).reshape(nPixY, 1)
656 + np.zeros(ampData.getDimensions()).transpose())
657
658 def amplifierAddSource(self, ampData, scale, x0, y0):
659 """Add a single Gaussian source to an amplifier.
660
661 This method operates in the amplifier coordinate frame.
662
663 Parameters
664 ----------
665 ampData : `lsst.afw.image.ImageF`
666 Amplifier image to operate on.
667 scale : `float`
668 Peak flux of the source to add.
669 x0 : `float`
670 X-coordinate of the source peak.
671 y0 : `float`
672 Y-coordinate of the source peak.
673 """
674 for x in range(0, ampData.getDimensions().getX()):
675 for y in range(0, ampData.getDimensions().getY()):
676 ampData.array[y][x] = (ampData.array[y][x]
677 + scale * np.exp(-0.5 * ((x - x0)**2 + (y - y0)**2) / 3.0**2))
678
679 def amplifierAddCT(self, ampDataSource, ampDataTarget, scale):
680 """Add a scaled copy of an amplifier to another, simulating crosstalk.
681
682 This method operates in the amplifier coordinate frame.
683
684 Parameters
685 ----------
686 ampDataSource : `lsst.afw.image.ImageF`
687 Amplifier image to add scaled copy from.
688 ampDataTarget : `lsst.afw.image.ImageF`
689 Amplifier image to add scaled copy to.
690 scale : `float`
691 Flux scale of the copy to add to the target.
692
693 Notes
694 -----
695 This simulates simple crosstalk between amplifiers.
696 """
697 ampDataTarget.array[:] = (ampDataTarget.array[:]
698 + scale * ampDataSource.array[:])
699
700 # Functional form data values.
701 def amplifierAddFringe(self, amp, ampData, scale, x0=100, y0=0):
702 """Add a fringe-like ripple pattern to an amplifier's image data.
703
704 Parameters
705 ----------
706 amp : `~lsst.afw.ampInfo.AmpInfoRecord`
707 Amplifier to operate on. Needed for amp<->exp coordinate transforms.
708 ampData : `lsst.afw.image.ImageF`
709 Amplifier image to operate on.
710 scale : `numpy.array` or `float`
711 Peak intensity scaling for the ripple.
712 x0 : `numpy.array` or `float`, optional
713 Fringe center
714 y0 : `numpy.array` or `float`, optional
715 Fringe center
716
717 Notes
718 -----
719 This uses an offset sinc function to generate a ripple
720 pattern. True fringes have much finer structure, but this
721 pattern should be visually identifiable. The (x, y)
722 coordinates are in the frame of the amplifier, and (u, v) in
723 the frame of the full trimmed image.
724 """
725 for x in range(0, ampData.getDimensions().getX()):
726 for y in range(0, ampData.getDimensions().getY()):
727 (u, v) = self.localCoordToExpCoordlocalCoordToExpCoord(amp, x, y)
728 ampData.getArray()[y][x] = np.sum((ampData.getArray()[y][x]
729 + scale * np.sinc(((u - x0) / 50)**2
730 + ((v - y0) / 50)**2)))
731
732 def amplifierMultiplyFlat(self, amp, ampData, fracDrop, u0=100.0, v0=100.0):
733 """Multiply an amplifier's image data by a flat-like pattern.
734
735 Parameters
736 ----------
737 amp : `lsst.afw.ampInfo.AmpInfoRecord`
738 Amplifier to operate on. Needed for amp<->exp coordinate transforms.
739 ampData : `lsst.afw.image.ImageF`
740 Amplifier image to operate on.
741 fracDrop : `float`
742 Fractional drop from center to edge of detector along x-axis.
743 u0 : `float`
744 Peak location in detector coordinates.
745 v0 : `float`
746 Peak location in detector coordinates.
747
748 Notes
749 -----
750 This uses a 2-d Gaussian to simulate an illumination pattern
751 that falls off towards the edge of the detector. The (x, y)
752 coordinates are in the frame of the amplifier, and (u, v) in
753 the frame of the full trimmed image.
754 """
755 if fracDrop >= 1.0:
756 raise RuntimeError("Flat fractional drop cannot be greater than 1.0")
757
758 sigma = u0 / np.sqrt(-2.0 * np.log(fracDrop))
759
760 for x in range(0, ampData.getDimensions().getX()):
761 for y in range(0, ampData.getDimensions().getY()):
762 (u, v) = self.localCoordToExpCoordlocalCoordToExpCoord(amp, x, y)
763 f = np.exp(-0.5 * ((u - u0)**2 + (v - v0)**2) / sigma**2)
764 ampData.array[y][x] = (ampData.array[y][x] * f)
765
766
768 """Generate a raw exposure suitable for ISR.
769 """
770 def __init__(self, **kwargs):
771 super().__init__(**kwargs)
772 self.config.isTrimmed = False
773 self.config.doGenerateImage = True
774 self.config.doGenerateAmpDict = False
775 self.config.doAddOverscan = True
776 self.config.doAddSky = True
777 self.config.doAddSource = True
778 self.config.doAddCrosstalk = False
779 self.config.doAddBias = True
780 self.config.doAddDark = True
781
782
784 """Generate a trimmed raw exposure.
785 """
786 def __init__(self, **kwargs):
787 super().__init__(**kwargs)
788 self.config.isTrimmed = True
789 self.config.doAddOverscan = False
790
791
793 """Generate a trimmed raw exposure.
794 """
795 def __init__(self, **kwargs):
796 super().__init__(**kwargs)
797 self.config.isTrimmed = True
798 self.config.doGenerateImage = True
799 self.config.doAddOverscan = False
800 self.config.doAddSky = True
801 self.config.doAddSource = True
802 self.config.doAddCrosstalk = False
803
804 self.config.doAddBias = False
805 self.config.doAddDark = False
806 self.config.doAddFlat = False
807 self.config.doAddFringe = True
808
809 self.config.biasLevel = 0.0
810 self.config.readNoise = 10.0
811
812
814 """Generate a raw exposure dict suitable for ISR.
815 """
816 def __init__(self, **kwargs):
817 super().__init__(**kwargs)
818 self.config.doGenerateAmpDict = True
819
820
822 """Parent class for those that make master calibrations.
823 """
824 def __init__(self, **kwargs):
825 super().__init__(**kwargs)
826 self.config.isTrimmed = True
827 self.config.doGenerateImage = True
828 self.config.doAddOverscan = False
829 self.config.doAddSky = False
830 self.config.doAddSource = False
831 self.config.doAddCrosstalk = False
832
833 self.config.doAddBias = False
834 self.config.doAddDark = False
835 self.config.doAddFlat = False
836 self.config.doAddFringe = False
837
838
840 """Simulated master bias calibration.
841 """
842 def __init__(self, **kwargs):
843 super().__init__(**kwargs)
844 self.config.doAddBias = True
845 self.config.readNoise = 10.0
846
847
849 """Simulated master dark calibration.
850 """
851 def __init__(self, **kwargs):
852 super().__init__(**kwargs)
853 self.config.doAddDark = True
854 self.config.darkTime = 1.0
855
856
858 """Simulated master flat calibration.
859 """
860 def __init__(self, **kwargs):
861 super().__init__(**kwargs)
862 self.config.doAddFlat = True
863
864
866 """Simulated master fringe calibration.
867 """
868 def __init__(self, **kwargs):
869 super().__init__(**kwargs)
870 self.config.doAddFringe = True
871
872
874 """Simulated untrimmed master fringe calibration.
875 """
876 def __init__(self, **kwargs):
877 super().__init__(**kwargs)
878 self.config.isTrimmed = False
879
880
882 """Simulated brighter-fatter kernel.
883 """
884 def __init__(self, **kwargs):
885 super().__init__(**kwargs)
886 self.config.doGenerateImage = False
887 self.config.doGenerateData = True
888 self.config.doBrighterFatter = True
889 self.config.doDefects = False
890 self.config.doCrosstalkCoeffs = False
891 self.config.doTransmissionCurve = False
892
893
895 """Simulated defect list.
896 """
897 def __init__(self, **kwargs):
898 super().__init__(**kwargs)
899 self.config.doGenerateImage = False
900 self.config.doGenerateData = True
901 self.config.doBrighterFatter = False
902 self.config.doDefects = True
903 self.config.doCrosstalkCoeffs = False
904 self.config.doTransmissionCurve = False
905
906
908 """Simulated crosstalk coefficient matrix.
909 """
910 def __init__(self, **kwargs):
911 super().__init__(**kwargs)
912 self.config.doGenerateImage = False
913 self.config.doGenerateData = True
914 self.config.doBrighterFatter = False
915 self.config.doDefects = False
916 self.config.doCrosstalkCoeffs = True
917 self.config.doTransmissionCurve = False
918
919
921 """Simulated transmission curve.
922 """
923 def __init__(self, **kwargs):
924 super().__init__(**kwargs)
925 self.config.doGenerateImage = False
926 self.config.doGenerateData = True
927 self.config.doBrighterFatter = False
928 self.config.doDefects = False
929 self.config.doCrosstalkCoeffs = False
930 self.config.doTransmissionCurve = True
931
932
933class DataRefMock(object):
934 """Simulated gen2 butler data ref.
935
936 Currently only supports get and put operations, which are most
937 likely to be called for data in ISR processing.
938
939 """
940 dataId = "isrMock Fake Data"
941 darkval = 2. # e-/sec
942 oscan = 250. # DN
943 gradient = .10
944 exptime = 15.0 # seconds
945 darkexptime = 15.0 # seconds
946
947 def __init__(self, **kwargs):
948 if 'config' in kwargs.keys():
949 self.configconfig = kwargs['config']
950 else:
951 self.configconfig = None
952
953 def expectImage(self):
954 if self.configconfig is None:
955 self.configconfig = IsrMockConfig()
956 self.configconfig.doGenerateImage = True
957 self.configconfig.doGenerateData = False
958
959 def expectData(self):
960 if self.configconfig is None:
961 self.configconfig = IsrMockConfig()
962 self.configconfig.doGenerateImage = False
963 self.configconfig.doGenerateData = True
964
965 def get(self, dataType, **kwargs):
966 """Return an appropriate data product.
967
968 Parameters
969 ----------
970 dataType : `str`
971 Type of data product to return.
972
973 Returns
974 -------
975 mock : IsrMock.run() result
976 The output product.
977 """
978 if "_filename" in dataType:
979 self.expectDataexpectData()
980 return tempfile.mktemp(), "mock"
981 elif 'transmission_' in dataType:
982 self.expectDataexpectData()
983 return TransmissionMock(config=self.configconfig).run()
984 elif dataType == 'ccdExposureId':
985 self.expectDataexpectData()
986 return 20090913
987 elif dataType == 'camera':
988 self.expectDataexpectData()
989 return IsrMock(config=self.configconfig).getCamera()
990 elif dataType == 'raw':
991 self.expectImageexpectImage()
992 return RawMock(config=self.configconfig).run()
993 elif dataType == 'bias':
994 self.expectImageexpectImage()
995 return BiasMock(config=self.configconfig).run()
996 elif dataType == 'dark':
997 self.expectImageexpectImage()
998 return DarkMock(config=self.configconfig).run()
999 elif dataType == 'flat':
1000 self.expectImageexpectImage()
1001 return FlatMock(config=self.configconfig).run()
1002 elif dataType == 'fringe':
1003 self.expectImageexpectImage()
1004 return FringeMock(config=self.configconfig).run()
1005 elif dataType == 'defects':
1006 self.expectDataexpectData()
1007 return DefectMock(config=self.configconfig).run()
1008 elif dataType == 'bfKernel':
1009 self.expectDataexpectData()
1010 return BfKernelMock(config=self.configconfig).run()
1011 elif dataType == 'linearizer':
1012 return None
1013 elif dataType == 'crosstalkSources':
1014 return None
1015 else:
1016 raise RuntimeError("ISR DataRefMock cannot return %s.", dataType)
1017
1018 def put(self, exposure, filename):
1019 """Write an exposure to a FITS file.
1020
1021 Parameters
1022 ----------
1023 exposure : `lsst.afw.image.Exposure`
1024 Image data to write out.
1025 filename : `str`
1026 Base name of the output file.
1027 """
1028 exposure.writeFits(filename+".fits")
1029
1030
1031class FringeDataRefMock(object):
1032 """Simulated gen2 butler data ref.
1033
1034 Currently only supports get and put operations, which are most
1035 likely to be called for data in ISR processing.
1036
1037 """
1038 dataId = "isrMock Fake Data"
1039 darkval = 2. # e-/sec
1040 oscan = 250. # DN
1041 gradient = .10
1042 exptime = 15 # seconds
1043 darkexptime = 40. # seconds
1044
1045 def __init__(self, **kwargs):
1046 if 'config' in kwargs.keys():
1047 self.configconfig = kwargs['config']
1048 else:
1049 self.configconfig = IsrMockConfig()
1050 self.configconfig.isTrimmed = True
1051 self.configconfig.doAddFringe = True
1052 self.configconfig.readNoise = 10.0
1053
1054 def get(self, dataType, **kwargs):
1055 """Return an appropriate data product.
1056
1057 Parameters
1058 ----------
1059 dataType : `str`
1060 Type of data product to return.
1061
1062 Returns
1063 -------
1064 mock : IsrMock.run() result
1065 The output product.
1066 """
1067 if "_filename" in dataType:
1068 return tempfile.mktemp(), "mock"
1069 elif 'transmission_' in dataType:
1070 return TransmissionMock(config=self.configconfig).run()
1071 elif dataType == 'ccdExposureId':
1072 return 20090913
1073 elif dataType == 'camera':
1074 return IsrMock(config=self.configconfig).getCamera()
1075 elif dataType == 'raw':
1076 return CalibratedRawMock(config=self.configconfig).run()
1077 elif dataType == 'bias':
1078 return BiasMock(config=self.configconfig).run()
1079 elif dataType == 'dark':
1080 return DarkMock(config=self.configconfig).run()
1081 elif dataType == 'flat':
1082 return FlatMock(config=self.configconfig).run()
1083 elif dataType == 'fringe':
1084 fringes = []
1085 configCopy = copy.deepcopy(self.configconfig)
1086 for scale, x, y in zip(self.configconfig.fringeScale, self.configconfig.fringeX0, self.configconfig.fringeY0):
1087 configCopy.fringeScale = [1.0]
1088 configCopy.fringeX0 = [x]
1089 configCopy.fringeY0 = [y]
1090 fringes.append(FringeMock(config=configCopy).run())
1091 return fringes
1092 elif dataType == 'defects':
1093 return DefectMock(config=self.configconfig).run()
1094 elif dataType == 'bfKernel':
1095 return BfKernelMock(config=self.configconfig).run()
1096 elif dataType == 'linearizer':
1097 return None
1098 elif dataType == 'crosstalkSources':
1099 return None
1100 else:
1101 return None
1102
1103 def put(self, exposure, filename):
1104 """Write an exposure to a FITS file.
1105
1106 Parameters
1107 ----------
1108 exposure : `lsst.afw.image.Exposure`
1109 Image data to write out.
1110 filename : `str`
1111 Base name of the output file.
1112 """
1113 exposure.writeFits(filename+".fits")
def __init__(self, **kwargs)
Definition: isrMock.py:884
def __init__(self, **kwargs)
Definition: isrMock.py:842
def __init__(self, **kwargs)
Definition: isrMock.py:851
def put(self, exposure, filename)
Definition: isrMock.py:1018
def get(self, dataType, **kwargs)
Definition: isrMock.py:965
def __init__(self, **kwargs)
Definition: isrMock.py:947
def __init__(self, **kwargs)
Definition: isrMock.py:897
def __init__(self, **kwargs)
Definition: isrMock.py:860
def put(self, exposure, filename)
Definition: isrMock.py:1103
def get(self, dataType, **kwargs)
Definition: isrMock.py:1054
def __init__(self, **kwargs)
Definition: isrMock.py:868
def amplifierAddSource(self, ampData, scale, x0, y0)
Definition: isrMock.py:658
def __init__(self, **kwargs)
Definition: isrMock.py:265
def amplifierAddNoise(self, ampData, mean, sigma)
Definition: isrMock.py:621
def amplifierAddYGradient(self, ampData, start, end)
Definition: isrMock.py:639
def amplifierAddCT(self, ampDataSource, ampDataTarget, scale)
Definition: isrMock.py:679
def amplifierMultiplyFlat(self, amp, ampData, fracDrop, u0=100.0, v0=100.0)
Definition: isrMock.py:732
def amplifierAddFringe(self, amp, ampData, scale, x0=100, y0=0)
Definition: isrMock.py:701
def localCoordToExpCoord(self, ampData, x, y)
Definition: isrMock.py:590
def __init__(self, **kwargs)
Definition: isrMock.py:824
def __init__(self, **kwargs)
Definition: isrMock.py:816
def __init__(self, **kwargs)
Definition: isrMock.py:770
def __init__(self, **kwargs)
Definition: isrMock.py:786