lsst.ip.isr g69ac63f7d9+b9cb02afdd
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isrTask.py
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1# This file is part of ip_isr.
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
22__all__ = ["IsrTask", "IsrTaskConfig"]
23
24import math
25import numpy
26
27import lsst.geom
28import lsst.afw.image as afwImage
29import lsst.afw.math as afwMath
30import lsst.pex.config as pexConfig
31import lsst.pipe.base as pipeBase
32import lsst.pipe.base.connectionTypes as cT
33
34from contextlib import contextmanager
35from lsstDebug import getDebugFrame
36
37from lsst.afw.cameraGeom import NullLinearityType
38from lsst.afw.display import getDisplay
39from lsst.meas.algorithms.detection import SourceDetectionTask
40from lsst.utils.timer import timeMethod
41
42from . import isrFunctions
43from . import isrQa
44from . import linearize
45from .defects import Defects
46
47from .assembleCcdTask import AssembleCcdTask
48from .crosstalk import CrosstalkTask, CrosstalkCalib
49from .fringe import FringeTask
50from .isr import maskNans
51from .masking import MaskingTask
52from .overscan import OverscanCorrectionTask
53from .straylight import StrayLightTask
54from .vignette import VignetteTask
55from .ampOffset import AmpOffsetTask
56from .deferredCharge import DeferredChargeTask
57from .isrStatistics import IsrStatisticsTask
58from lsst.daf.butler import DimensionGraph
59
60
61def crosstalkSourceLookup(datasetType, registry, quantumDataId, collections):
62 """Lookup function to identify crosstalkSource entries.
63
64 This should return an empty list under most circumstances. Only
65 when inter-chip crosstalk has been identified should this be
66 populated.
67
68 Parameters
69 ----------
70 datasetType : `str`
71 Dataset to lookup.
72 registry : `lsst.daf.butler.Registry`
73 Butler registry to query.
74 quantumDataId : `lsst.daf.butler.ExpandedDataCoordinate`
75 Data id to transform to identify crosstalkSources. The
76 ``detector`` entry will be stripped.
77 collections : `lsst.daf.butler.CollectionSearch`
78 Collections to search through.
79
80 Returns
81 -------
82 results : `list` [`lsst.daf.butler.DatasetRef`]
83 List of datasets that match the query that will be used as
84 crosstalkSources.
85 """
86 newDataId = quantumDataId.subset(DimensionGraph(registry.dimensions, names=["instrument", "exposure"]))
87 results = set(registry.queryDatasets(datasetType, collections=collections, dataId=newDataId,
88 findFirst=True))
89 # In some contexts, calling `.expanded()` to expand all data IDs in the
90 # query results can be a lot faster because it vectorizes lookups. But in
91 # this case, expandDataId shouldn't need to hit the database at all in the
92 # steady state, because only the detector record is unknown and those are
93 # cached in the registry.
94 return [ref.expanded(registry.expandDataId(ref.dataId, records=newDataId.records)) for ref in results]
95
96
97class IsrTaskConnections(pipeBase.PipelineTaskConnections,
98 dimensions={"instrument", "exposure", "detector"},
99 defaultTemplates={}):
100 ccdExposure = cT.Input(
101 name="raw",
102 doc="Input exposure to process.",
103 storageClass="Exposure",
104 dimensions=["instrument", "exposure", "detector"],
105 )
106 camera = cT.PrerequisiteInput(
107 name="camera",
108 storageClass="Camera",
109 doc="Input camera to construct complete exposures.",
110 dimensions=["instrument"],
111 isCalibration=True,
112 )
113
114 crosstalk = cT.PrerequisiteInput(
115 name="crosstalk",
116 doc="Input crosstalk object",
117 storageClass="CrosstalkCalib",
118 dimensions=["instrument", "detector"],
119 isCalibration=True,
120 minimum=0, # can fall back to cameraGeom
121 )
122 crosstalkSources = cT.PrerequisiteInput(
123 name="isrOverscanCorrected",
124 doc="Overscan corrected input images.",
125 storageClass="Exposure",
126 dimensions=["instrument", "exposure", "detector"],
127 deferLoad=True,
128 multiple=True,
129 lookupFunction=crosstalkSourceLookup,
130 minimum=0, # not needed for all instruments, no config to control this
131 )
132 bias = cT.PrerequisiteInput(
133 name="bias",
134 doc="Input bias calibration.",
135 storageClass="ExposureF",
136 dimensions=["instrument", "detector"],
137 isCalibration=True,
138 )
139 dark = cT.PrerequisiteInput(
140 name='dark',
141 doc="Input dark calibration.",
142 storageClass="ExposureF",
143 dimensions=["instrument", "detector"],
144 isCalibration=True,
145 )
146 flat = cT.PrerequisiteInput(
147 name="flat",
148 doc="Input flat calibration.",
149 storageClass="ExposureF",
150 dimensions=["instrument", "physical_filter", "detector"],
151 isCalibration=True,
152 )
153 ptc = cT.PrerequisiteInput(
154 name="ptc",
155 doc="Input Photon Transfer Curve dataset",
156 storageClass="PhotonTransferCurveDataset",
157 dimensions=["instrument", "detector"],
158 isCalibration=True,
159 )
160 fringes = cT.PrerequisiteInput(
161 name="fringe",
162 doc="Input fringe calibration.",
163 storageClass="ExposureF",
164 dimensions=["instrument", "physical_filter", "detector"],
165 isCalibration=True,
166 minimum=0, # only needed for some bands, even when enabled
167 )
168 strayLightData = cT.PrerequisiteInput(
169 name='yBackground',
170 doc="Input stray light calibration.",
171 storageClass="StrayLightData",
172 dimensions=["instrument", "physical_filter", "detector"],
173 deferLoad=True,
174 isCalibration=True,
175 minimum=0, # only needed for some bands, even when enabled
176 )
177 bfKernel = cT.PrerequisiteInput(
178 name='bfKernel',
179 doc="Input brighter-fatter kernel.",
180 storageClass="NumpyArray",
181 dimensions=["instrument"],
182 isCalibration=True,
183 minimum=0, # can use either bfKernel or newBFKernel
184 )
185 newBFKernel = cT.PrerequisiteInput(
186 name='brighterFatterKernel',
187 doc="Newer complete kernel + gain solutions.",
188 storageClass="BrighterFatterKernel",
189 dimensions=["instrument", "detector"],
190 isCalibration=True,
191 minimum=0, # can use either bfKernel or newBFKernel
192 )
193 defects = cT.PrerequisiteInput(
194 name='defects',
195 doc="Input defect tables.",
196 storageClass="Defects",
197 dimensions=["instrument", "detector"],
198 isCalibration=True,
199 )
200 linearizer = cT.PrerequisiteInput(
201 name='linearizer',
202 storageClass="Linearizer",
203 doc="Linearity correction calibration.",
204 dimensions=["instrument", "detector"],
205 isCalibration=True,
206 minimum=0, # can fall back to cameraGeom
207 )
208 opticsTransmission = cT.PrerequisiteInput(
209 name="transmission_optics",
210 storageClass="TransmissionCurve",
211 doc="Transmission curve due to the optics.",
212 dimensions=["instrument"],
213 isCalibration=True,
214 )
215 filterTransmission = cT.PrerequisiteInput(
216 name="transmission_filter",
217 storageClass="TransmissionCurve",
218 doc="Transmission curve due to the filter.",
219 dimensions=["instrument", "physical_filter"],
220 isCalibration=True,
221 )
222 sensorTransmission = cT.PrerequisiteInput(
223 name="transmission_sensor",
224 storageClass="TransmissionCurve",
225 doc="Transmission curve due to the sensor.",
226 dimensions=["instrument", "detector"],
227 isCalibration=True,
228 )
229 atmosphereTransmission = cT.PrerequisiteInput(
230 name="transmission_atmosphere",
231 storageClass="TransmissionCurve",
232 doc="Transmission curve due to the atmosphere.",
233 dimensions=["instrument"],
234 isCalibration=True,
235 )
236 illumMaskedImage = cT.PrerequisiteInput(
237 name="illum",
238 doc="Input illumination correction.",
239 storageClass="MaskedImageF",
240 dimensions=["instrument", "physical_filter", "detector"],
241 isCalibration=True,
242 )
243 deferredChargeCalib = cT.PrerequisiteInput(
244 name="deferredCharge",
245 doc="Deferred charge/CTI correction dataset.",
246 storageClass="IsrCalib",
247 dimensions=["instrument", "detector"],
248 isCalibration=True,
249 )
250
251 outputExposure = cT.Output(
252 name='postISRCCD',
253 doc="Output ISR processed exposure.",
254 storageClass="Exposure",
255 dimensions=["instrument", "exposure", "detector"],
256 )
257 preInterpExposure = cT.Output(
258 name='preInterpISRCCD',
259 doc="Output ISR processed exposure, with pixels left uninterpolated.",
260 storageClass="ExposureF",
261 dimensions=["instrument", "exposure", "detector"],
262 )
263 outputOssThumbnail = cT.Output(
264 name="OssThumb",
265 doc="Output Overscan-subtracted thumbnail image.",
266 storageClass="Thumbnail",
267 dimensions=["instrument", "exposure", "detector"],
268 )
269 outputFlattenedThumbnail = cT.Output(
270 name="FlattenedThumb",
271 doc="Output flat-corrected thumbnail image.",
272 storageClass="Thumbnail",
273 dimensions=["instrument", "exposure", "detector"],
274 )
275 outputStatistics = cT.Output(
276 name="isrStatistics",
277 doc="Output of additional statistics table.",
278 storageClass="StructuredDataDict",
279 dimensions=["instrument", "exposure", "detector"],
280 )
281
282 def __init__(self, *, config=None):
283 super().__init__(config=config)
284
285 if config.doBias is not True:
286 self.prerequisiteInputs.remove("bias")
287 if config.doLinearize is not True:
288 self.prerequisiteInputs.remove("linearizer")
289 if config.doCrosstalk is not True:
290 self.prerequisiteInputs.remove("crosstalkSources")
291 self.prerequisiteInputs.remove("crosstalk")
292 if config.doBrighterFatter is not True:
293 self.prerequisiteInputs.remove("bfKernel")
294 self.prerequisiteInputs.remove("newBFKernel")
295 if config.doDefect is not True:
296 self.prerequisiteInputs.remove("defects")
297 if config.doDark is not True:
298 self.prerequisiteInputs.remove("dark")
299 if config.doFlat is not True:
300 self.prerequisiteInputs.remove("flat")
301 if config.doFringe is not True:
302 self.prerequisiteInputs.remove("fringes")
303 if config.doStrayLight is not True:
304 self.prerequisiteInputs.remove("strayLightData")
305 if config.usePtcGains is not True and config.usePtcReadNoise is not True:
306 self.prerequisiteInputs.remove("ptc")
307 if config.doAttachTransmissionCurve is not True:
308 self.prerequisiteInputs.remove("opticsTransmission")
309 self.prerequisiteInputs.remove("filterTransmission")
310 self.prerequisiteInputs.remove("sensorTransmission")
311 self.prerequisiteInputs.remove("atmosphereTransmission")
312 else:
313 if config.doUseOpticsTransmission is not True:
314 self.prerequisiteInputs.remove("opticsTransmission")
315 if config.doUseFilterTransmission is not True:
316 self.prerequisiteInputs.remove("filterTransmission")
317 if config.doUseSensorTransmission is not True:
318 self.prerequisiteInputs.remove("sensorTransmission")
319 if config.doUseAtmosphereTransmission is not True:
320 self.prerequisiteInputs.remove("atmosphereTransmission")
321 if config.doIlluminationCorrection is not True:
322 self.prerequisiteInputs.remove("illumMaskedImage")
323 if config.doDeferredCharge is not True:
324 self.prerequisiteInputs.remove("deferredChargeCalib")
325
326 if config.doWrite is not True:
327 self.outputs.remove("outputExposure")
328 self.outputs.remove("preInterpExposure")
329 self.outputs.remove("outputFlattenedThumbnail")
330 self.outputs.remove("outputOssThumbnail")
331 self.outputs.remove("outputStatistics")
332
333 if config.doSaveInterpPixels is not True:
334 self.outputs.remove("preInterpExposure")
335 if config.qa.doThumbnailOss is not True:
336 self.outputs.remove("outputOssThumbnail")
337 if config.qa.doThumbnailFlattened is not True:
338 self.outputs.remove("outputFlattenedThumbnail")
339 if config.doCalculateStatistics is not True:
340 self.outputs.remove("outputStatistics")
341
342
343class IsrTaskConfig(pipeBase.PipelineTaskConfig,
344 pipelineConnections=IsrTaskConnections):
345 """Configuration parameters for IsrTask.
346
347 Items are grouped in the order in which they are executed by the task.
348 """
349 datasetType = pexConfig.Field(
350 dtype=str,
351 doc="Dataset type for input data; users will typically leave this alone, "
352 "but camera-specific ISR tasks will override it",
353 default="raw",
354 )
355
356 fallbackFilterName = pexConfig.Field(
357 dtype=str,
358 doc="Fallback default filter name for calibrations.",
359 optional=True
360 )
361 useFallbackDate = pexConfig.Field(
362 dtype=bool,
363 doc="Pass observation date when using fallback filter.",
364 default=False,
365 )
366 expectWcs = pexConfig.Field(
367 dtype=bool,
368 default=True,
369 doc="Expect input science images to have a WCS (set False for e.g. spectrographs)."
370 )
371 fwhm = pexConfig.Field(
372 dtype=float,
373 doc="FWHM of PSF in arcseconds.",
374 default=1.0,
375 )
376 qa = pexConfig.ConfigField(
377 dtype=isrQa.IsrQaConfig,
378 doc="QA related configuration options.",
379 )
380
381 # Image conversion configuration
382 doConvertIntToFloat = pexConfig.Field(
383 dtype=bool,
384 doc="Convert integer raw images to floating point values?",
385 default=True,
386 )
387
388 # Saturated pixel handling.
389 doSaturation = pexConfig.Field(
390 dtype=bool,
391 doc="Mask saturated pixels? NB: this is totally independent of the"
392 " interpolation option - this is ONLY setting the bits in the mask."
393 " To have them interpolated make sure doSaturationInterpolation=True",
394 default=True,
395 )
396 saturatedMaskName = pexConfig.Field(
397 dtype=str,
398 doc="Name of mask plane to use in saturation detection and interpolation",
399 default="SAT",
400 )
401 saturation = pexConfig.Field(
402 dtype=float,
403 doc="The saturation level to use if no Detector is present in the Exposure (ignored if NaN)",
404 default=float("NaN"),
405 )
406 growSaturationFootprintSize = pexConfig.Field(
407 dtype=int,
408 doc="Number of pixels by which to grow the saturation footprints",
409 default=1,
410 )
411
412 # Suspect pixel handling.
413 doSuspect = pexConfig.Field(
414 dtype=bool,
415 doc="Mask suspect pixels?",
416 default=False,
417 )
418 suspectMaskName = pexConfig.Field(
419 dtype=str,
420 doc="Name of mask plane to use for suspect pixels",
421 default="SUSPECT",
422 )
423 numEdgeSuspect = pexConfig.Field(
424 dtype=int,
425 doc="Number of edge pixels to be flagged as untrustworthy.",
426 default=0,
427 )
428 edgeMaskLevel = pexConfig.ChoiceField(
429 dtype=str,
430 doc="Mask edge pixels in which coordinate frame: DETECTOR or AMP?",
431 default="DETECTOR",
432 allowed={
433 'DETECTOR': 'Mask only the edges of the full detector.',
434 'AMP': 'Mask edges of each amplifier.',
435 },
436 )
437
438 # Initial masking options.
439 doSetBadRegions = pexConfig.Field(
440 dtype=bool,
441 doc="Should we set the level of all BAD patches of the chip to the chip's average value?",
442 default=True,
443 )
444 badStatistic = pexConfig.ChoiceField(
445 dtype=str,
446 doc="How to estimate the average value for BAD regions.",
447 default='MEANCLIP',
448 allowed={
449 "MEANCLIP": "Correct using the (clipped) mean of good data",
450 "MEDIAN": "Correct using the median of the good data",
451 },
452 )
453
454 # Overscan subtraction configuration.
455 doOverscan = pexConfig.Field(
456 dtype=bool,
457 doc="Do overscan subtraction?",
458 default=True,
459 )
460 overscan = pexConfig.ConfigurableField(
461 target=OverscanCorrectionTask,
462 doc="Overscan subtraction task for image segments.",
463 )
464
465 # Amplifier to CCD assembly configuration
466 doAssembleCcd = pexConfig.Field(
467 dtype=bool,
468 default=True,
469 doc="Assemble amp-level exposures into a ccd-level exposure?"
470 )
471 assembleCcd = pexConfig.ConfigurableField(
472 target=AssembleCcdTask,
473 doc="CCD assembly task",
474 )
475
476 # General calibration configuration.
477 doAssembleIsrExposures = pexConfig.Field(
478 dtype=bool,
479 default=False,
480 doc="Assemble amp-level calibration exposures into ccd-level exposure?"
481 )
482 doTrimToMatchCalib = pexConfig.Field(
483 dtype=bool,
484 default=False,
485 doc="Trim raw data to match calibration bounding boxes?"
486 )
487
488 # Bias subtraction.
489 doBias = pexConfig.Field(
490 dtype=bool,
491 doc="Apply bias frame correction?",
492 default=True,
493 )
494 biasDataProductName = pexConfig.Field(
495 dtype=str,
496 doc="Name of the bias data product",
497 default="bias",
498 )
499 doBiasBeforeOverscan = pexConfig.Field(
500 dtype=bool,
501 doc="Reverse order of overscan and bias correction.",
502 default=False
503 )
504
505 # Deferred charge correction.
506 doDeferredCharge = pexConfig.Field(
507 dtype=bool,
508 doc="Apply deferred charge correction?",
509 default=False,
510 )
511 deferredChargeCorrection = pexConfig.ConfigurableField(
512 target=DeferredChargeTask,
513 doc="Deferred charge correction task.",
514 )
515
516 # Variance construction
517 doVariance = pexConfig.Field(
518 dtype=bool,
519 doc="Calculate variance?",
520 default=True
521 )
522 gain = pexConfig.Field(
523 dtype=float,
524 doc="The gain to use if no Detector is present in the Exposure (ignored if NaN)",
525 default=float("NaN"),
526 )
527 readNoise = pexConfig.Field(
528 dtype=float,
529 doc="The read noise to use if no Detector is present in the Exposure",
530 default=0.0,
531 )
532 doEmpiricalReadNoise = pexConfig.Field(
533 dtype=bool,
534 default=False,
535 doc="Calculate empirical read noise instead of value from AmpInfo data?"
536 )
537 usePtcReadNoise = pexConfig.Field(
538 dtype=bool,
539 default=False,
540 doc="Use readnoise values from the Photon Transfer Curve?"
541 )
542 maskNegativeVariance = pexConfig.Field(
543 dtype=bool,
544 default=True,
545 doc="Mask pixels that claim a negative variance? This likely indicates a failure "
546 "in the measurement of the overscan at an edge due to the data falling off faster "
547 "than the overscan model can account for it."
548 )
549 negativeVarianceMaskName = pexConfig.Field(
550 dtype=str,
551 default="BAD",
552 doc="Mask plane to use to mark pixels with negative variance, if `maskNegativeVariance` is True.",
553 )
554 # Linearization.
555 doLinearize = pexConfig.Field(
556 dtype=bool,
557 doc="Correct for nonlinearity of the detector's response?",
558 default=True,
559 )
560
561 # Crosstalk.
562 doCrosstalk = pexConfig.Field(
563 dtype=bool,
564 doc="Apply intra-CCD crosstalk correction?",
565 default=False,
566 )
567 doCrosstalkBeforeAssemble = pexConfig.Field(
568 dtype=bool,
569 doc="Apply crosstalk correction before CCD assembly, and before trimming?",
570 default=False,
571 )
572 crosstalk = pexConfig.ConfigurableField(
573 target=CrosstalkTask,
574 doc="Intra-CCD crosstalk correction",
575 )
576
577 # Masking options.
578 doDefect = pexConfig.Field(
579 dtype=bool,
580 doc="Apply correction for CCD defects, e.g. hot pixels?",
581 default=True,
582 )
583 doNanMasking = pexConfig.Field(
584 dtype=bool,
585 doc="Mask non-finite (NAN, inf) pixels?",
586 default=True,
587 )
588 doWidenSaturationTrails = pexConfig.Field(
589 dtype=bool,
590 doc="Widen bleed trails based on their width?",
591 default=True
592 )
593
594 # Brighter-Fatter correction.
595 doBrighterFatter = pexConfig.Field(
596 dtype=bool,
597 default=False,
598 doc="Apply the brighter-fatter correction?"
599 )
600 brighterFatterLevel = pexConfig.ChoiceField(
601 dtype=str,
602 default="DETECTOR",
603 doc="The level at which to correct for brighter-fatter.",
604 allowed={
605 "AMP": "Every amplifier treated separately.",
606 "DETECTOR": "One kernel per detector",
607 }
608 )
609 brighterFatterMaxIter = pexConfig.Field(
610 dtype=int,
611 default=10,
612 doc="Maximum number of iterations for the brighter-fatter correction"
613 )
614 brighterFatterThreshold = pexConfig.Field(
615 dtype=float,
616 default=1000,
617 doc="Threshold used to stop iterating the brighter-fatter correction. It is the "
618 "absolute value of the difference between the current corrected image and the one "
619 "from the previous iteration summed over all the pixels."
620 )
621 brighterFatterApplyGain = pexConfig.Field(
622 dtype=bool,
623 default=True,
624 doc="Should the gain be applied when applying the brighter-fatter correction?"
625 )
626 brighterFatterMaskListToInterpolate = pexConfig.ListField(
627 dtype=str,
628 doc="List of mask planes that should be interpolated over when applying the brighter-fatter "
629 "correction.",
630 default=["SAT", "BAD", "NO_DATA", "UNMASKEDNAN"],
631 )
632 brighterFatterMaskGrowSize = pexConfig.Field(
633 dtype=int,
634 default=0,
635 doc="Number of pixels to grow the masks listed in config.brighterFatterMaskListToInterpolate "
636 "when brighter-fatter correction is applied."
637 )
638
639 # Dark subtraction.
640 doDark = pexConfig.Field(
641 dtype=bool,
642 doc="Apply dark frame correction?",
643 default=True,
644 )
645 darkDataProductName = pexConfig.Field(
646 dtype=str,
647 doc="Name of the dark data product",
648 default="dark",
649 )
650
651 # Camera-specific stray light removal.
652 doStrayLight = pexConfig.Field(
653 dtype=bool,
654 doc="Subtract stray light in the y-band (due to encoder LEDs)?",
655 default=False,
656 )
657 strayLight = pexConfig.ConfigurableField(
658 target=StrayLightTask,
659 doc="y-band stray light correction"
660 )
661
662 # Flat correction.
663 doFlat = pexConfig.Field(
664 dtype=bool,
665 doc="Apply flat field correction?",
666 default=True,
667 )
668 flatDataProductName = pexConfig.Field(
669 dtype=str,
670 doc="Name of the flat data product",
671 default="flat",
672 )
673 flatScalingType = pexConfig.ChoiceField(
674 dtype=str,
675 doc="The method for scaling the flat on the fly.",
676 default='USER',
677 allowed={
678 "USER": "Scale by flatUserScale",
679 "MEAN": "Scale by the inverse of the mean",
680 "MEDIAN": "Scale by the inverse of the median",
681 },
682 )
683 flatUserScale = pexConfig.Field(
684 dtype=float,
685 doc="If flatScalingType is 'USER' then scale flat by this amount; ignored otherwise",
686 default=1.0,
687 )
688 doTweakFlat = pexConfig.Field(
689 dtype=bool,
690 doc="Tweak flats to match observed amplifier ratios?",
691 default=False
692 )
693
694 # Amplifier normalization based on gains instead of using flats
695 # configuration.
696 doApplyGains = pexConfig.Field(
697 dtype=bool,
698 doc="Correct the amplifiers for their gains instead of applying flat correction",
699 default=False,
700 )
701 usePtcGains = pexConfig.Field(
702 dtype=bool,
703 doc="Use the gain values from the Photon Transfer Curve?",
704 default=False,
705 )
706 normalizeGains = pexConfig.Field(
707 dtype=bool,
708 doc="Normalize all the amplifiers in each CCD to have the same median value.",
709 default=False,
710 )
711
712 # Fringe correction.
713 doFringe = pexConfig.Field(
714 dtype=bool,
715 doc="Apply fringe correction?",
716 default=True,
717 )
718 fringe = pexConfig.ConfigurableField(
719 target=FringeTask,
720 doc="Fringe subtraction task",
721 )
722 fringeAfterFlat = pexConfig.Field(
723 dtype=bool,
724 doc="Do fringe subtraction after flat-fielding?",
725 default=True,
726 )
727
728 # Amp offset correction.
729 doAmpOffset = pexConfig.Field(
730 doc="Calculate and apply amp offset corrections?",
731 dtype=bool,
732 default=False,
733 )
734 ampOffset = pexConfig.ConfigurableField(
735 doc="Amp offset correction task.",
736 target=AmpOffsetTask,
737 )
738
739 # Initial CCD-level background statistics options.
740 doMeasureBackground = pexConfig.Field(
741 dtype=bool,
742 doc="Measure the background level on the reduced image?",
743 default=False,
744 )
745
746 # Camera-specific masking configuration.
747 doCameraSpecificMasking = pexConfig.Field(
748 dtype=bool,
749 doc="Mask camera-specific bad regions?",
750 default=False,
751 )
752 masking = pexConfig.ConfigurableField(
753 target=MaskingTask,
754 doc="Masking task."
755 )
756
757 # Interpolation options.
758 doInterpolate = pexConfig.Field(
759 dtype=bool,
760 doc="Interpolate masked pixels?",
761 default=True,
762 )
763 doSaturationInterpolation = pexConfig.Field(
764 dtype=bool,
765 doc="Perform interpolation over pixels masked as saturated?"
766 " NB: This is independent of doSaturation; if that is False this plane"
767 " will likely be blank, resulting in a no-op here.",
768 default=True,
769 )
770 doNanInterpolation = pexConfig.Field(
771 dtype=bool,
772 doc="Perform interpolation over pixels masked as NaN?"
773 " NB: This is independent of doNanMasking; if that is False this plane"
774 " will likely be blank, resulting in a no-op here.",
775 default=True,
776 )
777 doNanInterpAfterFlat = pexConfig.Field(
778 dtype=bool,
779 doc=("If True, ensure we interpolate NaNs after flat-fielding, even if we "
780 "also have to interpolate them before flat-fielding."),
781 default=False,
782 )
783 maskListToInterpolate = pexConfig.ListField(
784 dtype=str,
785 doc="List of mask planes that should be interpolated.",
786 default=['SAT', 'BAD'],
787 )
788 doSaveInterpPixels = pexConfig.Field(
789 dtype=bool,
790 doc="Save a copy of the pre-interpolated pixel values?",
791 default=False,
792 )
793
794 # Default photometric calibration options.
795 fluxMag0T1 = pexConfig.DictField(
796 keytype=str,
797 itemtype=float,
798 doc="The approximate flux of a zero-magnitude object in a one-second exposure, per filter.",
799 default=dict((f, pow(10.0, 0.4*m)) for f, m in (("Unknown", 28.0),
800 ))
801 )
802 defaultFluxMag0T1 = pexConfig.Field(
803 dtype=float,
804 doc="Default value for fluxMag0T1 (for an unrecognized filter).",
805 default=pow(10.0, 0.4*28.0)
806 )
807
808 # Vignette correction configuration.
809 doVignette = pexConfig.Field(
810 dtype=bool,
811 doc=("Compute and attach the validPolygon defining the unvignetted region to the exposure "
812 "according to vignetting parameters?"),
813 default=False,
814 )
815 doMaskVignettePolygon = pexConfig.Field(
816 dtype=bool,
817 doc=("Add a mask bit for pixels within the vignetted region. Ignored if doVignette "
818 "is False"),
819 default=True,
820 )
821 vignetteValue = pexConfig.Field(
822 dtype=float,
823 doc="Value to replace image array pixels with in the vignetted region? Ignored if None.",
824 optional=True,
825 default=None,
826 )
827 vignette = pexConfig.ConfigurableField(
828 target=VignetteTask,
829 doc="Vignetting task.",
830 )
831
832 # Transmission curve configuration.
833 doAttachTransmissionCurve = pexConfig.Field(
834 dtype=bool,
835 default=False,
836 doc="Construct and attach a wavelength-dependent throughput curve for this CCD image?"
837 )
838 doUseOpticsTransmission = pexConfig.Field(
839 dtype=bool,
840 default=True,
841 doc="Load and use transmission_optics (if doAttachTransmissionCurve is True)?"
842 )
843 doUseFilterTransmission = pexConfig.Field(
844 dtype=bool,
845 default=True,
846 doc="Load and use transmission_filter (if doAttachTransmissionCurve is True)?"
847 )
848 doUseSensorTransmission = pexConfig.Field(
849 dtype=bool,
850 default=True,
851 doc="Load and use transmission_sensor (if doAttachTransmissionCurve is True)?"
852 )
853 doUseAtmosphereTransmission = pexConfig.Field(
854 dtype=bool,
855 default=True,
856 doc="Load and use transmission_atmosphere (if doAttachTransmissionCurve is True)?"
857 )
858
859 # Illumination correction.
860 doIlluminationCorrection = pexConfig.Field(
861 dtype=bool,
862 default=False,
863 doc="Perform illumination correction?"
864 )
865 illuminationCorrectionDataProductName = pexConfig.Field(
866 dtype=str,
867 doc="Name of the illumination correction data product.",
868 default="illumcor",
869 )
870 illumScale = pexConfig.Field(
871 dtype=float,
872 doc="Scale factor for the illumination correction.",
873 default=1.0,
874 )
875 illumFilters = pexConfig.ListField(
876 dtype=str,
877 default=[],
878 doc="Only perform illumination correction for these filters."
879 )
880
881 # Calculate additional statistics?
882 doCalculateStatistics = pexConfig.Field(
883 dtype=bool,
884 doc="Should additional ISR statistics be calculated?",
885 default=False,
886 )
887 isrStats = pexConfig.ConfigurableField(
888 target=IsrStatisticsTask,
889 doc="Task to calculate additional statistics.",
890 )
891
892 # Write the outputs to disk. If ISR is run as a subtask, this may not
893 # be needed.
894 doWrite = pexConfig.Field(
895 dtype=bool,
896 doc="Persist postISRCCD?",
897 default=True,
898 )
899
900 def validate(self):
901 super().validate()
902 if self.doFlat and self.doApplyGains:
903 raise ValueError("You may not specify both doFlat and doApplyGains")
905 raise ValueError("You may not specify both doBiasBeforeOverscan and doTrimToMatchCalib")
910 if self.doNanInterpolation and "UNMASKEDNAN" not in self.maskListToInterpolate:
911 self.maskListToInterpolate.append("UNMASKEDNAN")
912
913
914class IsrTask(pipeBase.PipelineTask):
915 """Apply common instrument signature correction algorithms to a raw frame.
916
917 The process for correcting imaging data is very similar from
918 camera to camera. This task provides a vanilla implementation of
919 doing these corrections, including the ability to turn certain
920 corrections off if they are not needed. The inputs to the primary
921 method, `run()`, are a raw exposure to be corrected and the
922 calibration data products. The raw input is a single chip sized
923 mosaic of all amps including overscans and other non-science
924 pixels.
925
926 The __init__ method sets up the subtasks for ISR processing, using
927 the defaults from `lsst.ip.isr`.
928
929 Parameters
930 ----------
931 args : `list`
932 Positional arguments passed to the Task constructor.
933 None used at this time.
934 kwargs : `dict`, optional
935 Keyword arguments passed on to the Task constructor.
936 None used at this time.
937 """
938 ConfigClass = IsrTaskConfig
939 _DefaultName = "isr"
940
941 def __init__(self, **kwargs):
942 super().__init__(**kwargs)
943 self.makeSubtask("assembleCcd")
944 self.makeSubtask("crosstalk")
945 self.makeSubtask("strayLight")
946 self.makeSubtask("fringe")
947 self.makeSubtask("masking")
948 self.makeSubtask("overscan")
949 self.makeSubtask("vignette")
950 self.makeSubtask("ampOffset")
951 self.makeSubtask("deferredChargeCorrection")
952 self.makeSubtask("isrStats")
953
954 def runQuantum(self, butlerQC, inputRefs, outputRefs):
955 inputs = butlerQC.get(inputRefs)
956
957 try:
958 inputs['detectorNum'] = inputRefs.ccdExposure.dataId['detector']
959 except Exception as e:
960 raise ValueError("Failure to find valid detectorNum value for Dataset %s: %s." %
961 (inputRefs, e))
962
963 detector = inputs['ccdExposure'].getDetector()
964
965 if self.config.doCrosstalk is True:
966 # Crosstalk sources need to be defined by the pipeline
967 # yaml if they exist.
968 if 'crosstalk' in inputs and inputs['crosstalk'] is not None:
969 if not isinstance(inputs['crosstalk'], CrosstalkCalib):
970 inputs['crosstalk'] = CrosstalkCalib.fromTable(inputs['crosstalk'])
971 else:
972 coeffVector = (self.config.crosstalk.crosstalkValues
973 if self.config.crosstalk.useConfigCoefficients else None)
974 crosstalkCalib = CrosstalkCalib().fromDetector(detector, coeffVector=coeffVector)
975 inputs['crosstalk'] = crosstalkCalib
976 if inputs['crosstalk'].interChip and len(inputs['crosstalk'].interChip) > 0:
977 if 'crosstalkSources' not in inputs:
978 self.log.warning("No crosstalkSources found for chip with interChip terms!")
979
980 if self.doLinearize(detector) is True:
981 if 'linearizer' in inputs:
982 if isinstance(inputs['linearizer'], dict):
983 linearizer = linearize.Linearizer(detector=detector, log=self.log)
984 linearizer.fromYaml(inputs['linearizer'])
985 self.log.warning("Dictionary linearizers will be deprecated in DM-28741.")
986 elif isinstance(inputs['linearizer'], numpy.ndarray):
987 linearizer = linearize.Linearizer(table=inputs.get('linearizer', None),
988 detector=detector,
989 log=self.log)
990 self.log.warning("Bare lookup table linearizers will be deprecated in DM-28741.")
991 else:
992 linearizer = inputs['linearizer']
993 linearizer.log = self.log
994 inputs['linearizer'] = linearizer
995 else:
996 inputs['linearizer'] = linearize.Linearizer(detector=detector, log=self.log)
997 self.log.warning("Constructing linearizer from cameraGeom information.")
998
999 if self.config.doDefect is True:
1000 if "defects" in inputs and inputs['defects'] is not None:
1001 # defects is loaded as a BaseCatalog with columns
1002 # x0, y0, width, height. Masking expects a list of defects
1003 # defined by their bounding box
1004 if not isinstance(inputs["defects"], Defects):
1005 inputs["defects"] = Defects.fromTable(inputs["defects"])
1006
1007 # Load the correct style of brighter-fatter kernel, and repack
1008 # the information as a numpy array.
1009 if self.config.doBrighterFatter:
1010 brighterFatterKernel = inputs.pop('newBFKernel', None)
1011 if brighterFatterKernel is None:
1012 brighterFatterKernel = inputs.get('bfKernel', None)
1013
1014 if brighterFatterKernel is not None and not isinstance(brighterFatterKernel, numpy.ndarray):
1015 # This is a ISR calib kernel
1016 detName = detector.getName()
1017 level = brighterFatterKernel.level
1018
1019 # This is expected to be a dictionary of amp-wise gains.
1020 inputs['bfGains'] = brighterFatterKernel.gain
1021 if self.config.brighterFatterLevel == 'DETECTOR':
1022 if level == 'DETECTOR':
1023 if detName in brighterFatterKernel.detKernels:
1024 inputs['bfKernel'] = brighterFatterKernel.detKernels[detName]
1025 else:
1026 raise RuntimeError("Failed to extract kernel from new-style BF kernel.")
1027 elif level == 'AMP':
1028 self.log.warning("Making DETECTOR level kernel from AMP based brighter "
1029 "fatter kernels.")
1030 brighterFatterKernel.makeDetectorKernelFromAmpwiseKernels(detName)
1031 inputs['bfKernel'] = brighterFatterKernel.detKernels[detName]
1032 elif self.config.brighterFatterLevel == 'AMP':
1033 raise NotImplementedError("Per-amplifier brighter-fatter correction not implemented")
1034
1035 if self.config.doFringe is True and self.fringe.checkFilter(inputs['ccdExposure']):
1036 expId = inputs['ccdExposure'].info.id
1037 inputs['fringes'] = self.fringe.loadFringes(inputs['fringes'],
1038 expId=expId,
1039 assembler=self.assembleCcd
1040 if self.config.doAssembleIsrExposures else None)
1041 else:
1042 inputs['fringes'] = pipeBase.Struct(fringes=None)
1043
1044 if self.config.doStrayLight is True and self.strayLight.checkFilter(inputs['ccdExposure']):
1045 if 'strayLightData' not in inputs:
1046 inputs['strayLightData'] = None
1047
1048 outputs = self.run(**inputs)
1049 butlerQC.put(outputs, outputRefs)
1050
1051 @timeMethod
1052 def run(self, ccdExposure, *, camera=None, bias=None, linearizer=None,
1053 crosstalk=None, crosstalkSources=None,
1054 dark=None, flat=None, ptc=None, bfKernel=None, bfGains=None, defects=None,
1055 fringes=pipeBase.Struct(fringes=None), opticsTransmission=None, filterTransmission=None,
1056 sensorTransmission=None, atmosphereTransmission=None,
1057 detectorNum=None, strayLightData=None, illumMaskedImage=None,
1058 deferredCharge=None,
1059 ):
1060 """Perform instrument signature removal on an exposure.
1061
1062 Steps included in the ISR processing, in order performed, are:
1063
1064 - saturation and suspect pixel masking
1065 - overscan subtraction
1066 - CCD assembly of individual amplifiers
1067 - bias subtraction
1068 - variance image construction
1069 - linearization of non-linear response
1070 - crosstalk masking
1071 - brighter-fatter correction
1072 - dark subtraction
1073 - fringe correction
1074 - stray light subtraction
1075 - flat correction
1076 - masking of known defects and camera specific features
1077 - vignette calculation
1078 - appending transmission curve and distortion model
1079
1080 Parameters
1081 ----------
1082 ccdExposure : `lsst.afw.image.Exposure`
1083 The raw exposure that is to be run through ISR. The
1084 exposure is modified by this method.
1085 camera : `lsst.afw.cameraGeom.Camera`, optional
1086 The camera geometry for this exposure. Required if
1087 one or more of ``ccdExposure``, ``bias``, ``dark``, or
1088 ``flat`` does not have an associated detector.
1089 bias : `lsst.afw.image.Exposure`, optional
1090 Bias calibration frame.
1091 linearizer : `lsst.ip.isr.linearize.LinearizeBase`, optional
1092 Functor for linearization.
1093 crosstalk : `lsst.ip.isr.crosstalk.CrosstalkCalib`, optional
1094 Calibration for crosstalk.
1095 crosstalkSources : `list`, optional
1096 List of possible crosstalk sources.
1097 dark : `lsst.afw.image.Exposure`, optional
1098 Dark calibration frame.
1099 flat : `lsst.afw.image.Exposure`, optional
1100 Flat calibration frame.
1102 Photon transfer curve dataset, with, e.g., gains
1103 and read noise.
1104 bfKernel : `numpy.ndarray`, optional
1105 Brighter-fatter kernel.
1106 bfGains : `dict` of `float`, optional
1107 Gains used to override the detector's nominal gains for the
1108 brighter-fatter correction. A dict keyed by amplifier name for
1109 the detector in question.
1110 defects : `lsst.ip.isr.Defects`, optional
1111 List of defects.
1112 fringes : `lsst.pipe.base.Struct`, optional
1113 Struct containing the fringe correction data, with
1114 elements:
1115
1116 ``fringes``
1117 fringe calibration frame (`lsst.afw.image.Exposure`)
1118 ``seed``
1119 random seed derived from the ``ccdExposureId`` for random
1120 number generator (`numpy.uint32`)
1121 opticsTransmission: `lsst.afw.image.TransmissionCurve`, optional
1122 A ``TransmissionCurve`` that represents the throughput of the,
1123 optics, to be evaluated in focal-plane coordinates.
1124 filterTransmission : `lsst.afw.image.TransmissionCurve`
1125 A ``TransmissionCurve`` that represents the throughput of the
1126 filter itself, to be evaluated in focal-plane coordinates.
1127 sensorTransmission : `lsst.afw.image.TransmissionCurve`
1128 A ``TransmissionCurve`` that represents the throughput of the
1129 sensor itself, to be evaluated in post-assembly trimmed detector
1130 coordinates.
1131 atmosphereTransmission : `lsst.afw.image.TransmissionCurve`
1132 A ``TransmissionCurve`` that represents the throughput of the
1133 atmosphere, assumed to be spatially constant.
1134 detectorNum : `int`, optional
1135 The integer number for the detector to process.
1136 strayLightData : `object`, optional
1137 Opaque object containing calibration information for stray-light
1138 correction. If `None`, no correction will be performed.
1139 illumMaskedImage : `lsst.afw.image.MaskedImage`, optional
1140 Illumination correction image.
1141
1142 Returns
1143 -------
1144 result : `lsst.pipe.base.Struct`
1145 Result struct with component:
1146
1147 ``exposure``
1148 The fully ISR corrected exposure.
1150 ``outputExposure``
1151 An alias for ``exposure``. (`lsst.afw.image.Exposure`)
1152 ``ossThumb``
1153 Thumbnail image of the exposure after overscan subtraction.
1154 (`numpy.ndarray`)
1155 ``flattenedThumb``
1156 Thumbnail image of the exposure after flat-field correction.
1157 (`numpy.ndarray`)
1158 ``outputStatistics``
1159 Values of the additional statistics calculated.
1160
1161 Raises
1162 ------
1163 RuntimeError
1164 Raised if a configuration option is set to `True`, but the
1165 required calibration data has not been specified.
1166
1167 Notes
1168 -----
1169 The current processed exposure can be viewed by setting the
1170 appropriate `lsstDebug` entries in the ``debug.display``
1171 dictionary. The names of these entries correspond to some of
1172 the `IsrTaskConfig` Boolean options, with the value denoting the
1173 frame to use. The exposure is shown inside the matching
1174 option check and after the processing of that step has
1175 finished. The steps with debug points are:
1176
1177 * doAssembleCcd
1178 * doBias
1179 * doCrosstalk
1180 * doBrighterFatter
1181 * doDark
1182 * doFringe
1183 * doStrayLight
1184 * doFlat
1185
1186 In addition, setting the ``postISRCCD`` entry displays the
1187 exposure after all ISR processing has finished.
1188 """
1189
1190 ccdExposure = self.ensureExposure(ccdExposure, camera, detectorNum)
1191 bias = self.ensureExposure(bias, camera, detectorNum)
1192 dark = self.ensureExposure(dark, camera, detectorNum)
1193 flat = self.ensureExposure(flat, camera, detectorNum)
1194
1195 ccd = ccdExposure.getDetector()
1196 filterLabel = ccdExposure.getFilter()
1197 physicalFilter = isrFunctions.getPhysicalFilter(filterLabel, self.log)
1198
1199 if not ccd:
1200 assert not self.config.doAssembleCcd, "You need a Detector to run assembleCcd."
1201 ccd = [FakeAmp(ccdExposure, self.config)]
1202
1203 # Validate Input
1204 if self.config.doBias and bias is None:
1205 raise RuntimeError("Must supply a bias exposure if config.doBias=True.")
1206 if self.doLinearize(ccd) and linearizer is None:
1207 raise RuntimeError("Must supply a linearizer if config.doLinearize=True for this detector.")
1208 if self.config.doBrighterFatter and bfKernel is None:
1209 raise RuntimeError("Must supply a kernel if config.doBrighterFatter=True.")
1210 if self.config.doDark and dark is None:
1211 raise RuntimeError("Must supply a dark exposure if config.doDark=True.")
1212 if self.config.doFlat and flat is None:
1213 raise RuntimeError("Must supply a flat exposure if config.doFlat=True.")
1214 if self.config.doDefect and defects is None:
1215 raise RuntimeError("Must supply defects if config.doDefect=True.")
1216 if (self.config.doFringe and physicalFilter in self.fringe.config.filters
1217 and fringes.fringes is None):
1218 # The `fringes` object needs to be a pipeBase.Struct, as
1219 # we use it as a `dict` for the parameters of
1220 # `FringeTask.run()`. The `fringes.fringes` `list` may
1221 # not be `None` if `doFringe=True`. Otherwise, raise.
1222 raise RuntimeError("Must supply fringe exposure as a pipeBase.Struct.")
1223 if (self.config.doIlluminationCorrection and physicalFilter in self.config.illumFilters
1224 and illumMaskedImage is None):
1225 raise RuntimeError("Must supply an illumcor if config.doIlluminationCorrection=True.")
1226 if (self.config.doDeferredCharge and deferredCharge is None):
1227 raise RuntimeError("Must supply a deferred charge calibration if config.doDeferredCharge=True.")
1228
1229 # Begin ISR processing.
1230 if self.config.doConvertIntToFloat:
1231 self.log.info("Converting exposure to floating point values.")
1232 ccdExposure = self.convertIntToFloat(ccdExposure)
1233
1234 if self.config.doBias and self.config.doBiasBeforeOverscan:
1235 self.log.info("Applying bias correction.")
1236 isrFunctions.biasCorrection(ccdExposure.getMaskedImage(), bias.getMaskedImage(),
1237 trimToFit=self.config.doTrimToMatchCalib)
1238 self.debugView(ccdExposure, "doBias")
1239
1240 # Amplifier level processing.
1241 overscans = []
1242 for amp in ccd:
1243 # if ccdExposure is one amp,
1244 # check for coverage to prevent performing ops multiple times
1245 if ccdExposure.getBBox().contains(amp.getBBox()):
1246 # Check for fully masked bad amplifiers,
1247 # and generate masks for SUSPECT and SATURATED values.
1248 badAmp = self.maskAmplifier(ccdExposure, amp, defects)
1249
1250 if self.config.doOverscan and not badAmp:
1251 # Overscan correction on amp-by-amp basis.
1252 overscanResults = self.overscanCorrection(ccdExposure, amp)
1253 self.log.debug("Corrected overscan for amplifier %s.", amp.getName())
1254 if overscanResults is not None and \
1255 self.config.qa is not None and self.config.qa.saveStats is True:
1256
1257 self.metadata[f"FIT MEDIAN {amp.getName()}"] = overscanResults.overscanMean
1258 self.metadata[f"FIT STDEV {amp.getName()}"] = overscanResults.overscanSigma
1259 self.log.debug(" Overscan stats for amplifer %s: %f +/- %f",
1260 amp.getName(), overscanResults.overscanMean,
1261 overscanResults.overscanSigma)
1262
1263 self.metadata[f"RESIDUAL MEDIAN {amp.getName()}"] = overscanResults.residualMean
1264 self.metadata[f"RESIDUAL STDEV {amp.getName()}"] = overscanResults.residualSigma
1265 self.log.debug(" Overscan stats for amplifer %s after correction: %f +/- %f",
1266 amp.getName(), overscanResults.residualMean,
1267 overscanResults.residualSigma)
1268
1269 ccdExposure.getMetadata().set('OVERSCAN', "Overscan corrected")
1270 else:
1271 if badAmp:
1272 self.log.warning("Amplifier %s is bad.", amp.getName())
1273 overscanResults = None
1274
1275 overscans.append(overscanResults if overscanResults is not None else None)
1276 else:
1277 self.log.info("Skipped OSCAN for %s.", amp.getName())
1278
1279 if self.config.doDeferredCharge:
1280 self.log.info("Applying deferred charge/CTI correction.")
1281 self.deferredChargeCorrection.run(ccdExposure, deferredCharge)
1282 self.debugView(ccdExposure, "doDeferredCharge")
1283
1284 if self.config.doCrosstalk and self.config.doCrosstalkBeforeAssemble:
1285 self.log.info("Applying crosstalk correction.")
1286 self.crosstalk.run(ccdExposure, crosstalk=crosstalk,
1287 crosstalkSources=crosstalkSources, camera=camera)
1288 self.debugView(ccdExposure, "doCrosstalk")
1289
1290 if self.config.doAssembleCcd:
1291 self.log.info("Assembling CCD from amplifiers.")
1292 ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
1293
1294 if self.config.expectWcs and not ccdExposure.getWcs():
1295 self.log.warning("No WCS found in input exposure.")
1296 self.debugView(ccdExposure, "doAssembleCcd")
1297
1298 ossThumb = None
1299 if self.config.qa.doThumbnailOss:
1300 ossThumb = isrQa.makeThumbnail(ccdExposure, isrQaConfig=self.config.qa)
1301
1302 if self.config.doBias and not self.config.doBiasBeforeOverscan:
1303 self.log.info("Applying bias correction.")
1304 isrFunctions.biasCorrection(ccdExposure.getMaskedImage(), bias.getMaskedImage(),
1305 trimToFit=self.config.doTrimToMatchCalib)
1306 self.debugView(ccdExposure, "doBias")
1307
1308 if self.config.doVariance:
1309 for amp, overscanResults in zip(ccd, overscans):
1310 if ccdExposure.getBBox().contains(amp.getBBox()):
1311 self.log.debug("Constructing variance map for amplifer %s.", amp.getName())
1312 ampExposure = ccdExposure.Factory(ccdExposure, amp.getBBox())
1313 if overscanResults is not None:
1314 self.updateVariance(ampExposure, amp,
1315 overscanImage=overscanResults.overscanImage,
1316 ptcDataset=ptc)
1317 else:
1318 self.updateVariance(ampExposure, amp,
1319 overscanImage=None,
1320 ptcDataset=ptc)
1321 if self.config.qa is not None and self.config.qa.saveStats is True:
1322 qaStats = afwMath.makeStatistics(ampExposure.getVariance(),
1323 afwMath.MEDIAN | afwMath.STDEVCLIP)
1324 self.metadata[f"ISR VARIANCE {amp.getName()} MEDIAN"] = \
1325 qaStats.getValue(afwMath.MEDIAN)
1326 self.metadata[f"ISR VARIANCE {amp.getName()} STDEV"] = \
1327 qaStats.getValue(afwMath.STDEVCLIP)
1328 self.log.debug(" Variance stats for amplifer %s: %f +/- %f.",
1329 amp.getName(), qaStats.getValue(afwMath.MEDIAN),
1330 qaStats.getValue(afwMath.STDEVCLIP))
1331 if self.config.maskNegativeVariance:
1332 self.maskNegativeVariance(ccdExposure)
1333
1334 if self.doLinearize(ccd):
1335 self.log.info("Applying linearizer.")
1336 linearizer.applyLinearity(image=ccdExposure.getMaskedImage().getImage(),
1337 detector=ccd, log=self.log)
1338
1339 if self.config.doCrosstalk and not self.config.doCrosstalkBeforeAssemble:
1340 self.log.info("Applying crosstalk correction.")
1341 self.crosstalk.run(ccdExposure, crosstalk=crosstalk,
1342 crosstalkSources=crosstalkSources, isTrimmed=True)
1343 self.debugView(ccdExposure, "doCrosstalk")
1344
1345 # Masking block. Optionally mask known defects, NAN/inf pixels,
1346 # widen trails, and do anything else the camera needs. Saturated and
1347 # suspect pixels have already been masked.
1348 if self.config.doDefect:
1349 self.log.info("Masking defects.")
1350 self.maskDefect(ccdExposure, defects)
1351
1352 if self.config.numEdgeSuspect > 0:
1353 self.log.info("Masking edges as SUSPECT.")
1354 self.maskEdges(ccdExposure, numEdgePixels=self.config.numEdgeSuspect,
1355 maskPlane="SUSPECT", level=self.config.edgeMaskLevel)
1356
1357 if self.config.doNanMasking:
1358 self.log.info("Masking non-finite (NAN, inf) value pixels.")
1359 self.maskNan(ccdExposure)
1360
1361 if self.config.doWidenSaturationTrails:
1362 self.log.info("Widening saturation trails.")
1363 isrFunctions.widenSaturationTrails(ccdExposure.getMaskedImage().getMask())
1364
1365 if self.config.doCameraSpecificMasking:
1366 self.log.info("Masking regions for camera specific reasons.")
1367 self.masking.run(ccdExposure)
1368
1369 if self.config.doBrighterFatter:
1370 # We need to apply flats and darks before we can interpolate, and
1371 # we need to interpolate before we do B-F, but we do B-F without
1372 # the flats and darks applied so we can work in units of electrons
1373 # or holes. This context manager applies and then removes the darks
1374 # and flats.
1375 #
1376 # We also do not want to interpolate values here, so operate on
1377 # temporary images so we can apply only the BF-correction and roll
1378 # back the interpolation.
1379 interpExp = ccdExposure.clone()
1380 with self.flatContext(interpExp, flat, dark):
1381 isrFunctions.interpolateFromMask(
1382 maskedImage=interpExp.getMaskedImage(),
1383 fwhm=self.config.fwhm,
1384 growSaturatedFootprints=self.config.growSaturationFootprintSize,
1385 maskNameList=list(self.config.brighterFatterMaskListToInterpolate)
1386 )
1387 bfExp = interpExp.clone()
1388
1389 self.log.info("Applying brighter-fatter correction using kernel type %s / gains %s.",
1390 type(bfKernel), type(bfGains))
1391 bfResults = isrFunctions.brighterFatterCorrection(bfExp, bfKernel,
1392 self.config.brighterFatterMaxIter,
1393 self.config.brighterFatterThreshold,
1394 self.config.brighterFatterApplyGain,
1395 bfGains)
1396 if bfResults[1] == self.config.brighterFatterMaxIter:
1397 self.log.warning("Brighter-fatter correction did not converge, final difference %f.",
1398 bfResults[0])
1399 else:
1400 self.log.info("Finished brighter-fatter correction in %d iterations.",
1401 bfResults[1])
1402 image = ccdExposure.getMaskedImage().getImage()
1403 bfCorr = bfExp.getMaskedImage().getImage()
1404 bfCorr -= interpExp.getMaskedImage().getImage()
1405 image += bfCorr
1406
1407 # Applying the brighter-fatter correction applies a
1408 # convolution to the science image. At the edges this
1409 # convolution may not have sufficient valid pixels to
1410 # produce a valid correction. Mark pixels within the size
1411 # of the brighter-fatter kernel as EDGE to warn of this
1412 # fact.
1413 self.log.info("Ensuring image edges are masked as EDGE to the brighter-fatter kernel size.")
1414 self.maskEdges(ccdExposure, numEdgePixels=numpy.max(bfKernel.shape) // 2,
1415 maskPlane="EDGE")
1416
1417 if self.config.brighterFatterMaskGrowSize > 0:
1418 self.log.info("Growing masks to account for brighter-fatter kernel convolution.")
1419 for maskPlane in self.config.brighterFatterMaskListToInterpolate:
1420 isrFunctions.growMasks(ccdExposure.getMask(),
1421 radius=self.config.brighterFatterMaskGrowSize,
1422 maskNameList=maskPlane,
1423 maskValue=maskPlane)
1424
1425 self.debugView(ccdExposure, "doBrighterFatter")
1426
1427 if self.config.doDark:
1428 self.log.info("Applying dark correction.")
1429 self.darkCorrection(ccdExposure, dark)
1430 self.debugView(ccdExposure, "doDark")
1431
1432 if self.config.doFringe and not self.config.fringeAfterFlat:
1433 self.log.info("Applying fringe correction before flat.")
1434 self.fringe.run(ccdExposure, **fringes.getDict())
1435 self.debugView(ccdExposure, "doFringe")
1436
1437 if self.config.doStrayLight and self.strayLight.check(ccdExposure):
1438 self.log.info("Checking strayLight correction.")
1439 self.strayLight.run(ccdExposure, strayLightData)
1440 self.debugView(ccdExposure, "doStrayLight")
1441
1442 if self.config.doFlat:
1443 self.log.info("Applying flat correction.")
1444 self.flatCorrection(ccdExposure, flat)
1445 self.debugView(ccdExposure, "doFlat")
1446
1447 if self.config.doApplyGains:
1448 self.log.info("Applying gain correction instead of flat.")
1449 if self.config.usePtcGains:
1450 self.log.info("Using gains from the Photon Transfer Curve.")
1451 isrFunctions.applyGains(ccdExposure, self.config.normalizeGains,
1452 ptcGains=ptc.gain)
1453 else:
1454 isrFunctions.applyGains(ccdExposure, self.config.normalizeGains)
1455
1456 if self.config.doFringe and self.config.fringeAfterFlat:
1457 self.log.info("Applying fringe correction after flat.")
1458 self.fringe.run(ccdExposure, **fringes.getDict())
1459
1460 if self.config.doVignette:
1461 if self.config.doMaskVignettePolygon:
1462 self.log.info("Constructing, attaching, and masking vignette polygon.")
1463 else:
1464 self.log.info("Constructing and attaching vignette polygon.")
1465 self.vignettePolygon = self.vignette.run(
1466 exposure=ccdExposure, doUpdateMask=self.config.doMaskVignettePolygon,
1467 vignetteValue=self.config.vignetteValue, log=self.log)
1468
1469 if self.config.doAttachTransmissionCurve:
1470 self.log.info("Adding transmission curves.")
1471 isrFunctions.attachTransmissionCurve(ccdExposure, opticsTransmission=opticsTransmission,
1472 filterTransmission=filterTransmission,
1473 sensorTransmission=sensorTransmission,
1474 atmosphereTransmission=atmosphereTransmission)
1475
1476 flattenedThumb = None
1477 if self.config.qa.doThumbnailFlattened:
1478 flattenedThumb = isrQa.makeThumbnail(ccdExposure, isrQaConfig=self.config.qa)
1479
1480 if self.config.doIlluminationCorrection and physicalFilter in self.config.illumFilters:
1481 self.log.info("Performing illumination correction.")
1482 isrFunctions.illuminationCorrection(ccdExposure.getMaskedImage(),
1483 illumMaskedImage, illumScale=self.config.illumScale,
1484 trimToFit=self.config.doTrimToMatchCalib)
1485
1486 preInterpExp = None
1487 if self.config.doSaveInterpPixels:
1488 preInterpExp = ccdExposure.clone()
1489
1490 # Reset and interpolate bad pixels.
1491 #
1492 # Large contiguous bad regions (which should have the BAD mask
1493 # bit set) should have their values set to the image median.
1494 # This group should include defects and bad amplifiers. As the
1495 # area covered by these defects are large, there's little
1496 # reason to expect that interpolation would provide a more
1497 # useful value.
1498 #
1499 # Smaller defects can be safely interpolated after the larger
1500 # regions have had their pixel values reset. This ensures
1501 # that the remaining defects adjacent to bad amplifiers (as an
1502 # example) do not attempt to interpolate extreme values.
1503 if self.config.doSetBadRegions:
1504 badPixelCount, badPixelValue = isrFunctions.setBadRegions(ccdExposure)
1505 if badPixelCount > 0:
1506 self.log.info("Set %d BAD pixels to %f.", badPixelCount, badPixelValue)
1507
1508 if self.config.doInterpolate:
1509 self.log.info("Interpolating masked pixels.")
1510 isrFunctions.interpolateFromMask(
1511 maskedImage=ccdExposure.getMaskedImage(),
1512 fwhm=self.config.fwhm,
1513 growSaturatedFootprints=self.config.growSaturationFootprintSize,
1514 maskNameList=list(self.config.maskListToInterpolate)
1515 )
1516
1517 self.roughZeroPoint(ccdExposure)
1518
1519 # correct for amp offsets within the CCD
1520 if self.config.doAmpOffset:
1521 self.log.info("Correcting amp offsets.")
1522 self.ampOffset.run(ccdExposure)
1523
1524 if self.config.doMeasureBackground:
1525 self.log.info("Measuring background level.")
1526 self.measureBackground(ccdExposure, self.config.qa)
1527
1528 if self.config.qa is not None and self.config.qa.saveStats is True:
1529 for amp in ccd:
1530 ampExposure = ccdExposure.Factory(ccdExposure, amp.getBBox())
1531 qaStats = afwMath.makeStatistics(ampExposure.getImage(),
1532 afwMath.MEDIAN | afwMath.STDEVCLIP)
1533 self.metadata[f"ISR BACKGROUND {amp.getName()} MEDIAN"] = qaStats.getValue(afwMath.MEDIAN)
1534 self.metadata[f"ISR BACKGROUND {amp.getName()} STDEV"] = \
1535 qaStats.getValue(afwMath.STDEVCLIP)
1536 self.log.debug(" Background stats for amplifer %s: %f +/- %f",
1537 amp.getName(), qaStats.getValue(afwMath.MEDIAN),
1538 qaStats.getValue(afwMath.STDEVCLIP))
1539
1540 # calculate additional statistics.
1541 outputStatistics = None
1542 if self.config.doCalculateStatistics:
1543 outputStatistics = self.isrStats.run(ccdExposure, overscanResults=overscans,
1544 ptc=ptc).results
1545
1546 self.debugView(ccdExposure, "postISRCCD")
1547
1548 return pipeBase.Struct(
1549 exposure=ccdExposure,
1550 ossThumb=ossThumb,
1551 flattenedThumb=flattenedThumb,
1552
1553 preInterpExposure=preInterpExp,
1554 outputExposure=ccdExposure,
1555 outputOssThumbnail=ossThumb,
1556 outputFlattenedThumbnail=flattenedThumb,
1557 outputStatistics=outputStatistics,
1558 )
1559
1560 def ensureExposure(self, inputExp, camera=None, detectorNum=None):
1561 """Ensure that the data returned by Butler is a fully constructed exp.
1562
1563 ISR requires exposure-level image data for historical reasons, so if we
1564 did not recieve that from Butler, construct it from what we have,
1565 modifying the input in place.
1566
1567 Parameters
1568 ----------
1569 inputExp : `lsst.afw.image` image-type.
1570 The input data structure obtained from Butler.
1571 Can be `lsst.afw.image.Exposure`,
1572 `lsst.afw.image.DecoratedImageU`,
1573 or `lsst.afw.image.ImageF`
1574 camera : `lsst.afw.cameraGeom.camera`, optional
1575 The camera associated with the image. Used to find the appropriate
1576 detector if detector is not already set.
1577 detectorNum : `int`, optional
1578 The detector in the camera to attach, if the detector is not
1579 already set.
1580
1581 Returns
1582 -------
1583 inputExp : `lsst.afw.image.Exposure`
1584 The re-constructed exposure, with appropriate detector parameters.
1585
1586 Raises
1587 ------
1588 TypeError
1589 Raised if the input data cannot be used to construct an exposure.
1590 """
1591 if isinstance(inputExp, afwImage.DecoratedImageU):
1592 inputExp = afwImage.makeExposure(afwImage.makeMaskedImage(inputExp))
1593 elif isinstance(inputExp, afwImage.ImageF):
1594 inputExp = afwImage.makeExposure(afwImage.makeMaskedImage(inputExp))
1595 elif isinstance(inputExp, afwImage.MaskedImageF):
1596 inputExp = afwImage.makeExposure(inputExp)
1597 elif isinstance(inputExp, afwImage.Exposure):
1598 pass
1599 elif inputExp is None:
1600 # Assume this will be caught by the setup if it is a problem.
1601 return inputExp
1602 else:
1603 raise TypeError("Input Exposure is not known type in isrTask.ensureExposure: %s." %
1604 (type(inputExp), ))
1605
1606 if inputExp.getDetector() is None:
1607 if camera is None or detectorNum is None:
1608 raise RuntimeError('Must supply both a camera and detector number when using exposures '
1609 'without a detector set.')
1610 inputExp.setDetector(camera[detectorNum])
1611
1612 return inputExp
1613
1614 def convertIntToFloat(self, exposure):
1615 """Convert exposure image from uint16 to float.
1616
1617 If the exposure does not need to be converted, the input is
1618 immediately returned. For exposures that are converted to use
1619 floating point pixels, the variance is set to unity and the
1620 mask to zero.
1621
1622 Parameters
1623 ----------
1624 exposure : `lsst.afw.image.Exposure`
1625 The raw exposure to be converted.
1626
1627 Returns
1628 -------
1629 newexposure : `lsst.afw.image.Exposure`
1630 The input ``exposure``, converted to floating point pixels.
1631
1632 Raises
1633 ------
1634 RuntimeError
1635 Raised if the exposure type cannot be converted to float.
1636
1637 """
1638 if isinstance(exposure, afwImage.ExposureF):
1639 # Nothing to be done
1640 self.log.debug("Exposure already of type float.")
1641 return exposure
1642 if not hasattr(exposure, "convertF"):
1643 raise RuntimeError("Unable to convert exposure (%s) to float." % type(exposure))
1644
1645 newexposure = exposure.convertF()
1646 newexposure.variance[:] = 1
1647 newexposure.mask[:] = 0x0
1648
1649 return newexposure
1650
1651 def maskAmplifier(self, ccdExposure, amp, defects):
1652 """Identify bad amplifiers, saturated and suspect pixels.
1653
1654 Parameters
1655 ----------
1656 ccdExposure : `lsst.afw.image.Exposure`
1657 Input exposure to be masked.
1659 Catalog of parameters defining the amplifier on this
1660 exposure to mask.
1661 defects : `lsst.ip.isr.Defects`
1662 List of defects. Used to determine if the entire
1663 amplifier is bad.
1664
1665 Returns
1666 -------
1667 badAmp : `Bool`
1668 If this is true, the entire amplifier area is covered by
1669 defects and unusable.
1670
1671 """
1672 maskedImage = ccdExposure.getMaskedImage()
1673
1674 badAmp = False
1675
1676 # Check if entire amp region is defined as a defect
1677 # NB: need to use amp.getBBox() for correct comparison with current
1678 # defects definition.
1679 if defects is not None:
1680 badAmp = bool(sum([v.getBBox().contains(amp.getBBox()) for v in defects]))
1681
1682 # In the case of a bad amp, we will set mask to "BAD"
1683 # (here use amp.getRawBBox() for correct association with pixels in
1684 # current ccdExposure).
1685 if badAmp:
1686 dataView = afwImage.MaskedImageF(maskedImage, amp.getRawBBox(),
1687 afwImage.PARENT)
1688 maskView = dataView.getMask()
1689 maskView |= maskView.getPlaneBitMask("BAD")
1690 del maskView
1691 return badAmp
1692
1693 # Mask remaining defects after assembleCcd() to allow for defects that
1694 # cross amplifier boundaries. Saturation and suspect pixels can be
1695 # masked now, though.
1696 limits = dict()
1697 if self.config.doSaturation and not badAmp:
1698 limits.update({self.config.saturatedMaskName: amp.getSaturation()})
1699 if self.config.doSuspect and not badAmp:
1700 limits.update({self.config.suspectMaskName: amp.getSuspectLevel()})
1701 if math.isfinite(self.config.saturation):
1702 limits.update({self.config.saturatedMaskName: self.config.saturation})
1703
1704 for maskName, maskThreshold in limits.items():
1705 if not math.isnan(maskThreshold):
1706 dataView = maskedImage.Factory(maskedImage, amp.getRawBBox())
1707 isrFunctions.makeThresholdMask(
1708 maskedImage=dataView,
1709 threshold=maskThreshold,
1710 growFootprints=0,
1711 maskName=maskName
1712 )
1713
1714 # Determine if we've fully masked this amplifier with SUSPECT and
1715 # SAT pixels.
1716 maskView = afwImage.Mask(maskedImage.getMask(), amp.getRawDataBBox(),
1717 afwImage.PARENT)
1718 maskVal = maskView.getPlaneBitMask([self.config.saturatedMaskName,
1719 self.config.suspectMaskName])
1720 if numpy.all(maskView.getArray() & maskVal > 0):
1721 badAmp = True
1722 maskView |= maskView.getPlaneBitMask("BAD")
1723
1724 return badAmp
1725
1726 def overscanCorrection(self, ccdExposure, amp):
1727 """Apply overscan correction in place.
1728
1729 This method does initial pixel rejection of the overscan
1730 region. The overscan can also be optionally segmented to
1731 allow for discontinuous overscan responses to be fit
1732 separately. The actual overscan subtraction is performed by
1733 the `lsst.ip.isr.overscan.OverscanTask`, which is called here
1734 after the amplifier is preprocessed.
1735
1736 Parameters
1737 ----------
1738 ccdExposure : `lsst.afw.image.Exposure`
1739 Exposure to have overscan correction performed.
1740 amp : `lsst.afw.cameraGeom.Amplifer`
1741 The amplifier to consider while correcting the overscan.
1742
1743 Returns
1744 -------
1745 overscanResults : `lsst.pipe.base.Struct`
1746 Result struct with components:
1747
1748 ``imageFit``
1749 Value or fit subtracted from the amplifier image data.
1750 (scalar or `lsst.afw.image.Image`)
1751 ``overscanFit``
1752 Value or fit subtracted from the overscan image data.
1753 (scalar or `lsst.afw.image.Image`)
1754 ``overscanImage``
1755 Image of the overscan region with the overscan
1756 correction applied. This quantity is used to estimate
1757 the amplifier read noise empirically.
1759 ``edgeMask``
1760 Mask of the suspect pixels. (`lsst.afw.image.Mask`)
1761 ``overscanMean``
1762 Median overscan fit value. (`float`)
1763 ``overscanSigma``
1764 Clipped standard deviation of the overscan after
1765 correction. (`float`)
1766
1767 Raises
1768 ------
1769 RuntimeError
1770 Raised if the ``amp`` does not contain raw pixel information.
1771
1772 See Also
1773 --------
1774 lsst.ip.isr.overscan.OverscanTask
1775
1776 """
1777 if amp.getRawHorizontalOverscanBBox().isEmpty():
1778 self.log.info("ISR_OSCAN: No overscan region. Not performing overscan correction.")
1779 return None
1780
1781 # Perform overscan correction on subregions.
1782 overscanResults = self.overscan.run(ccdExposure, amp)
1783
1784 metadata = ccdExposure.getMetadata()
1785 ampNum = amp.getName()
1786 metadata[f"ISR_OSCAN_LEVEL{ampNum}"] = overscanResults.overscanMean
1787 metadata[f"ISR_OSCAN_SIGMA{ampNum}"] = overscanResults.overscanSigma
1788
1789 return overscanResults
1790
1791 def updateVariance(self, ampExposure, amp, overscanImage=None, ptcDataset=None):
1792 """Set the variance plane using the gain and read noise
1793
1794 The read noise is calculated from the ``overscanImage`` if the
1795 ``doEmpiricalReadNoise`` option is set in the configuration; otherwise
1796 the value from the amplifier data is used.
1797
1798 Parameters
1799 ----------
1800 ampExposure : `lsst.afw.image.Exposure`
1801 Exposure to process.
1802 amp : `lsst.afw.cameraGeom.Amplifier` or `FakeAmp`
1803 Amplifier detector data.
1804 overscanImage : `lsst.afw.image.MaskedImage`, optional.
1805 Image of overscan, required only for empirical read noise.
1806 ptcDataset : `lsst.ip.isr.PhotonTransferCurveDataset`, optional
1807 PTC dataset containing the gains and read noise.
1808
1809 Raises
1810 ------
1811 RuntimeError
1812 Raised if either ``usePtcGains`` of ``usePtcReadNoise``
1813 are ``True``, but ptcDataset is not provided.
1814
1815 Raised if ```doEmpiricalReadNoise`` is ``True`` but
1816 ``overscanImage`` is ``None``.
1817
1818 See also
1819 --------
1820 lsst.ip.isr.isrFunctions.updateVariance
1821 """
1822 maskPlanes = [self.config.saturatedMaskName, self.config.suspectMaskName]
1823 if self.config.usePtcGains:
1824 if ptcDataset is None:
1825 raise RuntimeError("No ptcDataset provided to use PTC gains.")
1826 else:
1827 gain = ptcDataset.gain[amp.getName()]
1828 self.log.info("Using gain from Photon Transfer Curve.")
1829 else:
1830 gain = amp.getGain()
1831
1832 if math.isnan(gain):
1833 gain = 1.0
1834 self.log.warning("Gain set to NAN! Updating to 1.0 to generate Poisson variance.")
1835 elif gain <= 0:
1836 patchedGain = 1.0
1837 self.log.warning("Gain for amp %s == %g <= 0; setting to %f.",
1838 amp.getName(), gain, patchedGain)
1839 gain = patchedGain
1840
1841 if self.config.doEmpiricalReadNoise and overscanImage is None:
1842 raise RuntimeError("Overscan is none for EmpiricalReadNoise.")
1843
1844 if self.config.doEmpiricalReadNoise and overscanImage is not None:
1845 stats = afwMath.StatisticsControl()
1846 stats.setAndMask(overscanImage.mask.getPlaneBitMask(maskPlanes))
1847 readNoise = afwMath.makeStatistics(overscanImage.getImage(),
1848 afwMath.STDEVCLIP, stats).getValue()
1849 self.log.info("Calculated empirical read noise for amp %s: %f.",
1850 amp.getName(), readNoise)
1851 elif self.config.usePtcReadNoise:
1852 if ptcDataset is None:
1853 raise RuntimeError("No ptcDataset provided to use PTC readnoise.")
1854 else:
1855 readNoise = ptcDataset.noise[amp.getName()]
1856 self.log.info("Using read noise from Photon Transfer Curve.")
1857 else:
1858 readNoise = amp.getReadNoise()
1859
1860 isrFunctions.updateVariance(
1861 maskedImage=ampExposure.getMaskedImage(),
1862 gain=gain,
1863 readNoise=readNoise,
1864 )
1865
1866 def maskNegativeVariance(self, exposure):
1867 """Identify and mask pixels with negative variance values.
1868
1869 Parameters
1870 ----------
1871 exposure : `lsst.afw.image.Exposure`
1872 Exposure to process.
1873
1874 See Also
1875 --------
1876 lsst.ip.isr.isrFunctions.updateVariance
1877 """
1878 maskPlane = exposure.getMask().getPlaneBitMask(self.config.negativeVarianceMaskName)
1879 bad = numpy.where(exposure.getVariance().getArray() <= 0.0)
1880 exposure.mask.array[bad] |= maskPlane
1881
1882 def darkCorrection(self, exposure, darkExposure, invert=False):
1883 """Apply dark correction in place.
1884
1885 Parameters
1886 ----------
1887 exposure : `lsst.afw.image.Exposure`
1888 Exposure to process.
1889 darkExposure : `lsst.afw.image.Exposure`
1890 Dark exposure of the same size as ``exposure``.
1891 invert : `Bool`, optional
1892 If True, re-add the dark to an already corrected image.
1893
1894 Raises
1895 ------
1896 RuntimeError
1897 Raised if either ``exposure`` or ``darkExposure`` do not
1898 have their dark time defined.
1899
1900 See Also
1901 --------
1902 lsst.ip.isr.isrFunctions.darkCorrection
1903 """
1904 expScale = exposure.getInfo().getVisitInfo().getDarkTime()
1905 if math.isnan(expScale):
1906 raise RuntimeError("Exposure darktime is NAN.")
1907 if darkExposure.getInfo().getVisitInfo() is not None \
1908 and not math.isnan(darkExposure.getInfo().getVisitInfo().getDarkTime()):
1909 darkScale = darkExposure.getInfo().getVisitInfo().getDarkTime()
1910 else:
1911 # DM-17444: darkExposure.getInfo.getVisitInfo() is None
1912 # so getDarkTime() does not exist.
1913 self.log.warning("darkExposure.getInfo().getVisitInfo() does not exist. Using darkScale = 1.0.")
1914 darkScale = 1.0
1915
1916 isrFunctions.darkCorrection(
1917 maskedImage=exposure.getMaskedImage(),
1918 darkMaskedImage=darkExposure.getMaskedImage(),
1919 expScale=expScale,
1920 darkScale=darkScale,
1921 invert=invert,
1922 trimToFit=self.config.doTrimToMatchCalib
1923 )
1924
1925 def doLinearize(self, detector):
1926 """Check if linearization is needed for the detector cameraGeom.
1927
1928 Checks config.doLinearize and the linearity type of the first
1929 amplifier.
1930
1931 Parameters
1932 ----------
1933 detector : `lsst.afw.cameraGeom.Detector`
1934 Detector to get linearity type from.
1935
1936 Returns
1937 -------
1938 doLinearize : `Bool`
1939 If True, linearization should be performed.
1940 """
1941 return self.config.doLinearize and \
1942 detector.getAmplifiers()[0].getLinearityType() != NullLinearityType
1943
1944 def flatCorrection(self, exposure, flatExposure, invert=False):
1945 """Apply flat correction in place.
1946
1947 Parameters
1948 ----------
1949 exposure : `lsst.afw.image.Exposure`
1950 Exposure to process.
1951 flatExposure : `lsst.afw.image.Exposure`
1952 Flat exposure of the same size as ``exposure``.
1953 invert : `Bool`, optional
1954 If True, unflatten an already flattened image.
1955
1956 See Also
1957 --------
1958 lsst.ip.isr.isrFunctions.flatCorrection
1959 """
1960 isrFunctions.flatCorrection(
1961 maskedImage=exposure.getMaskedImage(),
1962 flatMaskedImage=flatExposure.getMaskedImage(),
1963 scalingType=self.config.flatScalingType,
1964 userScale=self.config.flatUserScale,
1965 invert=invert,
1966 trimToFit=self.config.doTrimToMatchCalib
1967 )
1968
1969 def saturationDetection(self, exposure, amp):
1970 """Detect and mask saturated pixels in config.saturatedMaskName.
1971
1972 Parameters
1973 ----------
1974 exposure : `lsst.afw.image.Exposure`
1975 Exposure to process. Only the amplifier DataSec is processed.
1977 Amplifier detector data.
1978
1979 See Also
1980 --------
1981 lsst.ip.isr.isrFunctions.makeThresholdMask
1982 """
1983 if not math.isnan(amp.getSaturation()):
1984 maskedImage = exposure.getMaskedImage()
1985 dataView = maskedImage.Factory(maskedImage, amp.getRawBBox())
1986 isrFunctions.makeThresholdMask(
1987 maskedImage=dataView,
1988 threshold=amp.getSaturation(),
1989 growFootprints=0,
1990 maskName=self.config.saturatedMaskName,
1991 )
1992
1993 def saturationInterpolation(self, exposure):
1994 """Interpolate over saturated pixels, in place.
1995
1996 This method should be called after `saturationDetection`, to
1997 ensure that the saturated pixels have been identified in the
1998 SAT mask. It should also be called after `assembleCcd`, since
1999 saturated regions may cross amplifier boundaries.
2000
2001 Parameters
2002 ----------
2003 exposure : `lsst.afw.image.Exposure`
2004 Exposure to process.
2005
2006 See Also
2007 --------
2008 lsst.ip.isr.isrTask.saturationDetection
2009 lsst.ip.isr.isrFunctions.interpolateFromMask
2010 """
2011 isrFunctions.interpolateFromMask(
2012 maskedImage=exposure.getMaskedImage(),
2013 fwhm=self.config.fwhm,
2014 growSaturatedFootprints=self.config.growSaturationFootprintSize,
2015 maskNameList=list(self.config.saturatedMaskName),
2016 )
2017
2018 def suspectDetection(self, exposure, amp):
2019 """Detect and mask suspect pixels in config.suspectMaskName.
2020
2021 Parameters
2022 ----------
2023 exposure : `lsst.afw.image.Exposure`
2024 Exposure to process. Only the amplifier DataSec is processed.
2026 Amplifier detector data.
2027
2028 See Also
2029 --------
2030 lsst.ip.isr.isrFunctions.makeThresholdMask
2031
2032 Notes
2033 -----
2034 Suspect pixels are pixels whose value is greater than
2035 amp.getSuspectLevel(). This is intended to indicate pixels that may be
2036 affected by unknown systematics; for example if non-linearity
2037 corrections above a certain level are unstable then that would be a
2038 useful value for suspectLevel. A value of `nan` indicates that no such
2039 level exists and no pixels are to be masked as suspicious.
2040 """
2041 suspectLevel = amp.getSuspectLevel()
2042 if math.isnan(suspectLevel):
2043 return
2044
2045 maskedImage = exposure.getMaskedImage()
2046 dataView = maskedImage.Factory(maskedImage, amp.getRawBBox())
2047 isrFunctions.makeThresholdMask(
2048 maskedImage=dataView,
2049 threshold=suspectLevel,
2050 growFootprints=0,
2051 maskName=self.config.suspectMaskName,
2052 )
2053
2054 def maskDefect(self, exposure, defectBaseList):
2055 """Mask defects using mask plane "BAD", in place.
2056
2057 Parameters
2058 ----------
2059 exposure : `lsst.afw.image.Exposure`
2060 Exposure to process.
2061 defectBaseList : defect-type
2062 List of defects to mask. Can be of type `lsst.ip.isr.Defects`
2063 or `list` of `lsst.afw.image.DefectBase`.
2064
2065 Notes
2066 -----
2067 Call this after CCD assembly, since defects may cross amplifier
2068 boundaries.
2069 """
2070 maskedImage = exposure.getMaskedImage()
2071 if not isinstance(defectBaseList, Defects):
2072 # Promotes DefectBase to Defect
2073 defectList = Defects(defectBaseList)
2074 else:
2075 defectList = defectBaseList
2076 defectList.maskPixels(maskedImage, maskName="BAD")
2077
2078 def maskEdges(self, exposure, numEdgePixels=0, maskPlane="SUSPECT", level='DETECTOR'):
2079 """Mask edge pixels with applicable mask plane.
2080
2081 Parameters
2082 ----------
2083 exposure : `lsst.afw.image.Exposure`
2084 Exposure to process.
2085 numEdgePixels : `int`, optional
2086 Number of edge pixels to mask.
2087 maskPlane : `str`, optional
2088 Mask plane name to use.
2089 level : `str`, optional
2090 Level at which to mask edges.
2091 """
2092 maskedImage = exposure.getMaskedImage()
2093 maskBitMask = maskedImage.getMask().getPlaneBitMask(maskPlane)
2094
2095 if numEdgePixels > 0:
2096 if level == 'DETECTOR':
2097 boxes = [maskedImage.getBBox()]
2098 elif level == 'AMP':
2099 boxes = [amp.getBBox() for amp in exposure.getDetector()]
2100
2101 for box in boxes:
2102 # This makes a bbox numEdgeSuspect pixels smaller than the
2103 # image on each side
2104 subImage = maskedImage[box]
2105 box.grow(-numEdgePixels)
2106 # Mask pixels outside box
2107 SourceDetectionTask.setEdgeBits(
2108 subImage,
2109 box,
2110 maskBitMask)
2111
2112 def maskAndInterpolateDefects(self, exposure, defectBaseList):
2113 """Mask and interpolate defects using mask plane "BAD", in place.
2114
2115 Parameters
2116 ----------
2117 exposure : `lsst.afw.image.Exposure`
2118 Exposure to process.
2119 defectBaseList : defects-like
2120 List of defects to mask and interpolate. Can be
2122
2123 See Also
2124 --------
2125 lsst.ip.isr.isrTask.maskDefect
2126 """
2127 self.maskDefect(exposure, defectBaseList)
2128 self.maskEdges(exposure, numEdgePixels=self.config.numEdgeSuspect,
2129 maskPlane="SUSPECT", level=self.config.edgeMaskLevel)
2130 isrFunctions.interpolateFromMask(
2131 maskedImage=exposure.getMaskedImage(),
2132 fwhm=self.config.fwhm,
2133 growSaturatedFootprints=0,
2134 maskNameList=["BAD"],
2135 )
2136
2137 def maskNan(self, exposure):
2138 """Mask NaNs using mask plane "UNMASKEDNAN", in place.
2139
2140 Parameters
2141 ----------
2142 exposure : `lsst.afw.image.Exposure`
2143 Exposure to process.
2144
2145 Notes
2146 -----
2147 We mask over all non-finite values (NaN, inf), including those
2148 that are masked with other bits (because those may or may not be
2149 interpolated over later, and we want to remove all NaN/infs).
2150 Despite this behaviour, the "UNMASKEDNAN" mask plane is used to
2151 preserve the historical name.
2152 """
2153 maskedImage = exposure.getMaskedImage()
2154
2155 # Find and mask NaNs
2156 maskedImage.getMask().addMaskPlane("UNMASKEDNAN")
2157 maskVal = maskedImage.getMask().getPlaneBitMask("UNMASKEDNAN")
2158 numNans = maskNans(maskedImage, maskVal)
2159 self.metadata["NUMNANS"] = numNans
2160 if numNans > 0:
2161 self.log.warning("There were %d unmasked NaNs.", numNans)
2162
2163 def maskAndInterpolateNan(self, exposure):
2164 """"Mask and interpolate NaN/infs using mask plane "UNMASKEDNAN",
2165 in place.
2166
2167 Parameters
2168 ----------
2169 exposure : `lsst.afw.image.Exposure`
2170 Exposure to process.
2171
2172 See Also
2173 --------
2174 lsst.ip.isr.isrTask.maskNan
2175 """
2176 self.maskNan(exposure)
2177 isrFunctions.interpolateFromMask(
2178 maskedImage=exposure.getMaskedImage(),
2179 fwhm=self.config.fwhm,
2180 growSaturatedFootprints=0,
2181 maskNameList=["UNMASKEDNAN"],
2182 )
2183
2184 def measureBackground(self, exposure, IsrQaConfig=None):
2185 """Measure the image background in subgrids, for quality control.
2186
2187 Parameters
2188 ----------
2189 exposure : `lsst.afw.image.Exposure`
2190 Exposure to process.
2191 IsrQaConfig : `lsst.ip.isr.isrQa.IsrQaConfig`
2192 Configuration object containing parameters on which background
2193 statistics and subgrids to use.
2194 """
2195 if IsrQaConfig is not None:
2196 statsControl = afwMath.StatisticsControl(IsrQaConfig.flatness.clipSigma,
2197 IsrQaConfig.flatness.nIter)
2198 maskVal = exposure.getMaskedImage().getMask().getPlaneBitMask(["BAD", "SAT", "DETECTED"])
2199 statsControl.setAndMask(maskVal)
2200 maskedImage = exposure.getMaskedImage()
2201 stats = afwMath.makeStatistics(maskedImage, afwMath.MEDIAN | afwMath.STDEVCLIP, statsControl)
2202 skyLevel = stats.getValue(afwMath.MEDIAN)
2203 skySigma = stats.getValue(afwMath.STDEVCLIP)
2204 self.log.info("Flattened sky level: %f +/- %f.", skyLevel, skySigma)
2205 metadata = exposure.getMetadata()
2206 metadata["SKYLEVEL"] = skyLevel
2207 metadata["SKYSIGMA"] = skySigma
2208
2209 # calcluating flatlevel over the subgrids
2210 stat = afwMath.MEANCLIP if IsrQaConfig.flatness.doClip else afwMath.MEAN
2211 meshXHalf = int(IsrQaConfig.flatness.meshX/2.)
2212 meshYHalf = int(IsrQaConfig.flatness.meshY/2.)
2213 nX = int((exposure.getWidth() + meshXHalf) / IsrQaConfig.flatness.meshX)
2214 nY = int((exposure.getHeight() + meshYHalf) / IsrQaConfig.flatness.meshY)
2215 skyLevels = numpy.zeros((nX, nY))
2216
2217 for j in range(nY):
2218 yc = meshYHalf + j * IsrQaConfig.flatness.meshY
2219 for i in range(nX):
2220 xc = meshXHalf + i * IsrQaConfig.flatness.meshX
2221
2222 xLLC = xc - meshXHalf
2223 yLLC = yc - meshYHalf
2224 xURC = xc + meshXHalf - 1
2225 yURC = yc + meshYHalf - 1
2226
2227 bbox = lsst.geom.Box2I(lsst.geom.Point2I(xLLC, yLLC), lsst.geom.Point2I(xURC, yURC))
2228 miMesh = maskedImage.Factory(exposure.getMaskedImage(), bbox, afwImage.LOCAL)
2229
2230 skyLevels[i, j] = afwMath.makeStatistics(miMesh, stat, statsControl).getValue()
2231
2232 good = numpy.where(numpy.isfinite(skyLevels))
2233 skyMedian = numpy.median(skyLevels[good])
2234 flatness = (skyLevels[good] - skyMedian) / skyMedian
2235 flatness_rms = numpy.std(flatness)
2236 flatness_pp = flatness.max() - flatness.min() if len(flatness) > 0 else numpy.nan
2237
2238 self.log.info("Measuring sky levels in %dx%d grids: %f.", nX, nY, skyMedian)
2239 self.log.info("Sky flatness in %dx%d grids - pp: %f rms: %f.",
2240 nX, nY, flatness_pp, flatness_rms)
2241
2242 metadata["FLATNESS_PP"] = float(flatness_pp)
2243 metadata["FLATNESS_RMS"] = float(flatness_rms)
2244 metadata["FLATNESS_NGRIDS"] = '%dx%d' % (nX, nY)
2245 metadata["FLATNESS_MESHX"] = IsrQaConfig.flatness.meshX
2246 metadata["FLATNESS_MESHY"] = IsrQaConfig.flatness.meshY
2247
2248 def roughZeroPoint(self, exposure):
2249 """Set an approximate magnitude zero point for the exposure.
2250
2251 Parameters
2252 ----------
2253 exposure : `lsst.afw.image.Exposure`
2254 Exposure to process.
2255 """
2256 filterLabel = exposure.getFilter()
2257 physicalFilter = isrFunctions.getPhysicalFilter(filterLabel, self.log)
2258
2259 if physicalFilter in self.config.fluxMag0T1:
2260 fluxMag0 = self.config.fluxMag0T1[physicalFilter]
2261 else:
2262 self.log.warning("No rough magnitude zero point defined for filter %s.", physicalFilter)
2263 fluxMag0 = self.config.defaultFluxMag0T1
2264
2265 expTime = exposure.getInfo().getVisitInfo().getExposureTime()
2266 if not expTime > 0: # handle NaN as well as <= 0
2267 self.log.warning("Non-positive exposure time; skipping rough zero point.")
2268 return
2269
2270 self.log.info("Setting rough magnitude zero point for filter %s: %f",
2271 physicalFilter, 2.5*math.log10(fluxMag0*expTime))
2272 exposure.setPhotoCalib(afwImage.makePhotoCalibFromCalibZeroPoint(fluxMag0*expTime, 0.0))
2273
2274 @contextmanager
2275 def flatContext(self, exp, flat, dark=None):
2276 """Context manager that applies and removes flats and darks,
2277 if the task is configured to apply them.
2278
2279 Parameters
2280 ----------
2282 Exposure to process.
2284 Flat exposure the same size as ``exp``.
2285 dark : `lsst.afw.image.Exposure`, optional
2286 Dark exposure the same size as ``exp``.
2287
2288 Yields
2289 ------
2291 The flat and dark corrected exposure.
2292 """
2293 if self.config.doDark and dark is not None:
2294 self.darkCorrection(exp, dark)
2295 if self.config.doFlat:
2296 self.flatCorrection(exp, flat)
2297 try:
2298 yield exp
2299 finally:
2300 if self.config.doFlat:
2301 self.flatCorrection(exp, flat, invert=True)
2302 if self.config.doDark and dark is not None:
2303 self.darkCorrection(exp, dark, invert=True)
2304
2305 def debugView(self, exposure, stepname):
2306 """Utility function to examine ISR exposure at different stages.
2307
2308 Parameters
2309 ----------
2310 exposure : `lsst.afw.image.Exposure`
2311 Exposure to view.
2312 stepname : `str`
2313 State of processing to view.
2314 """
2315 frame = getDebugFrame(self._display, stepname)
2316 if frame:
2317 display = getDisplay(frame)
2318 display.scale('asinh', 'zscale')
2319 display.mtv(exposure)
2320 prompt = "Press Enter to continue [c]... "
2321 while True:
2322 ans = input(prompt).lower()
2323 if ans in ("", "c",):
2324 break
2325
2326
2327class FakeAmp(object):
2328 """A Detector-like object that supports returning gain and saturation level
2329
2330 This is used when the input exposure does not have a detector.
2331
2332 Parameters
2333 ----------
2334 exposure : `lsst.afw.image.Exposure`
2335 Exposure to generate a fake amplifier for.
2336 config : `lsst.ip.isr.isrTaskConfig`
2337 Configuration to apply to the fake amplifier.
2338 """
2339
2340 def __init__(self, exposure, config):
2341 self._bbox = exposure.getBBox(afwImage.LOCAL)
2343 self._gain = config.gain
2344 self._readNoise = config.readNoise
2345 self._saturation = config.saturation
2346
2347 def getBBox(self):
2348 return self._bbox
2349
2350 def getRawBBox(self):
2351 return self._bbox
2352
2354 return self._RawHorizontalOverscanBBox
2355
2356 def getGain(self):
2357 return self._gain
2358
2359 def getReadNoise(self):
2360 return self._readNoise
2361
2362 def getSaturation(self):
2363 return self._saturation
2364
2366 return float("NaN")
def getRawHorizontalOverscanBBox(self)
Definition: isrTask.py:2353
def __init__(self, exposure, config)
Definition: isrTask.py:2340
def __init__(self, *config=None)
Definition: isrTask.py:282
def flatCorrection(self, exposure, flatExposure, invert=False)
Definition: isrTask.py:1944
def maskAndInterpolateNan(self, exposure)
Definition: isrTask.py:2163
def saturationInterpolation(self, exposure)
Definition: isrTask.py:1993
def maskNan(self, exposure)
Definition: isrTask.py:2137
def maskAmplifier(self, ccdExposure, amp, defects)
Definition: isrTask.py:1651
def debugView(self, exposure, stepname)
Definition: isrTask.py:2305
def ensureExposure(self, inputExp, camera=None, detectorNum=None)
Definition: isrTask.py:1560
def maskNegativeVariance(self, exposure)
Definition: isrTask.py:1866
def saturationDetection(self, exposure, amp)
Definition: isrTask.py:1969
def maskDefect(self, exposure, defectBaseList)
Definition: isrTask.py:2054
def __init__(self, **kwargs)
Definition: isrTask.py:941
def runQuantum(self, butlerQC, inputRefs, outputRefs)
Definition: isrTask.py:954
def maskEdges(self, exposure, numEdgePixels=0, maskPlane="SUSPECT", level='DETECTOR')
Definition: isrTask.py:2078
def overscanCorrection(self, ccdExposure, amp)
Definition: isrTask.py:1726
def run(self, ccdExposure, *camera=None, bias=None, linearizer=None, crosstalk=None, crosstalkSources=None, dark=None, flat=None, ptc=None, bfKernel=None, bfGains=None, defects=None, fringes=pipeBase.Struct(fringes=None), opticsTransmission=None, filterTransmission=None, sensorTransmission=None, atmosphereTransmission=None, detectorNum=None, strayLightData=None, illumMaskedImage=None, deferredCharge=None)
Definition: isrTask.py:1059
def measureBackground(self, exposure, IsrQaConfig=None)
Definition: isrTask.py:2184
def roughZeroPoint(self, exposure)
Definition: isrTask.py:2248
def maskAndInterpolateDefects(self, exposure, defectBaseList)
Definition: isrTask.py:2112
def doLinearize(self, detector)
Definition: isrTask.py:1925
def flatContext(self, exp, flat, dark=None)
Definition: isrTask.py:2275
def convertIntToFloat(self, exposure)
Definition: isrTask.py:1614
def suspectDetection(self, exposure, amp)
Definition: isrTask.py:2018
def updateVariance(self, ampExposure, amp, overscanImage=None, ptcDataset=None)
Definition: isrTask.py:1791
def darkCorrection(self, exposure, darkExposure, invert=False)
Definition: isrTask.py:1882
def crosstalkSourceLookup(datasetType, registry, quantumDataId, collections)
Definition: isrTask.py:61