Coverage for python/lsst/ip/isr/isrTask.py: 18%
765 statements
« prev ^ index » next coverage.py v6.4.4, created at 2022-09-20 02:39 -0700
« prev ^ index » next coverage.py v6.4.4, created at 2022-09-20 02:39 -0700
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/>.
22__all__ = ["IsrTask", "IsrTaskConfig"]
24import math
25import numpy
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
34from contextlib import contextmanager
35from lsstDebug import getDebugFrame
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
42from . import isrFunctions
43from . import isrQa
44from . import linearize
45from .defects import Defects
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
61def crosstalkSourceLookup(datasetType, registry, quantumDataId, collections):
62 """Lookup function to identify crosstalkSource entries.
64 This should return an empty list under most circumstances. Only
65 when inter-chip crosstalk has been identified should this be
66 populated.
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.
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]
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 )
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 )
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 )
282 def __init__(self, *, config=None):
283 super().__init__(config=config)
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")
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")
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")
343class IsrTaskConfig(pipeBase.PipelineTaskConfig,
344 pipelineConnections=IsrTaskConnections):
345 """Configuration parameters for IsrTask.
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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")
904 if self.doBiasBeforeOverscan and self.doTrimToMatchCalib:
905 raise ValueError("You may not specify both doBiasBeforeOverscan and doTrimToMatchCalib")
906 if self.doSaturationInterpolation and self.saturatedMaskName not in self.maskListToInterpolate:
907 self.maskListToInterpolate.append(self.saturatedMaskName)
908 if not self.doSaturationInterpolation and self.saturatedMaskName in self.maskListToInterpolate:
909 self.maskListToInterpolate.remove(self.saturatedMaskName)
910 if self.doNanInterpolation and "UNMASKEDNAN" not in self.maskListToInterpolate:
911 self.maskListToInterpolate.append("UNMASKEDNAN")
914class IsrTask(pipeBase.PipelineTask):
915 """Apply common instrument signature correction algorithms to a raw frame.
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.
926 The __init__ method sets up the subtasks for ISR processing, using
927 the defaults from `lsst.ip.isr`.
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"
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")
954 def runQuantum(self, butlerQC, inputRefs, outputRefs):
955 inputs = butlerQC.get(inputRefs)
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))
963 detector = inputs['ccdExposure'].getDetector()
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!")
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.")
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"])
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)
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
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")
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)
1044 if self.config.doStrayLight is True and self.strayLight.checkFilter(inputs['ccdExposure']):
1045 if 'strayLightData' not in inputs:
1046 inputs['strayLightData'] = None
1048 outputs = self.run(**inputs)
1049 butlerQC.put(outputs, outputRefs)
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.
1062 Steps included in the ISR processing, in order performed, are:
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
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.
1101 ptc : `lsst.ip.isr.PhotonTransferCurveDataset`, optional
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:
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.
1142 Returns
1143 -------
1144 result : `lsst.pipe.base.Struct`
1145 Result struct with component:
1147 ``exposure``
1148 The fully ISR corrected exposure.
1149 (`lsst.afw.image.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.
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.
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:
1177 * doAssembleCcd
1178 * doBias
1179 * doCrosstalk
1180 * doBrighterFatter
1181 * doDark
1182 * doFringe
1183 * doStrayLight
1184 * doFlat
1186 In addition, setting the ``postISRCCD`` entry displays the
1187 exposure after all ISR processing has finished.
1188 """
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)
1195 ccd = ccdExposure.getDetector()
1196 filterLabel = ccdExposure.getFilter()
1197 physicalFilter = isrFunctions.getPhysicalFilter(filterLabel, self.log)
1199 if not ccd:
1200 assert not self.config.doAssembleCcd, "You need a Detector to run assembleCcd."
1201 ccd = [FakeAmp(ccdExposure, self.config)]
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.")
1229 # Begin ISR processing.
1230 if self.config.doConvertIntToFloat:
1231 self.log.info("Converting exposure to floating point values.")
1232 ccdExposure = self.convertIntToFloat(ccdExposure)
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")
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)
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:
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)
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)
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
1275 overscans.append(overscanResults if overscanResults is not None else None)
1276 else:
1277 self.log.info("Skipped OSCAN for %s.", amp.getName())
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")
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")
1290 if self.config.doAssembleCcd:
1291 self.log.info("Assembling CCD from amplifiers.")
1292 ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
1294 if self.config.expectWcs and not ccdExposure.getWcs():
1295 self.log.warning("No WCS found in input exposure.")
1296 self.debugView(ccdExposure, "doAssembleCcd")
1298 ossThumb = None
1299 if self.config.qa.doThumbnailOss:
1300 ossThumb = isrQa.makeThumbnail(ccdExposure, isrQaConfig=self.config.qa)
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")
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)
1334 if self.doLinearize(ccd):
1335 self.log.info("Applying linearizer.")
1336 linearizer.applyLinearity(image=ccdExposure.getMaskedImage().getImage(),
1337 detector=ccd, log=self.log)
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")
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)
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)
1357 if self.config.doNanMasking:
1358 self.log.info("Masking non-finite (NAN, inf) value pixels.")
1359 self.maskNan(ccdExposure)
1361 if self.config.doWidenSaturationTrails:
1362 self.log.info("Widening saturation trails.")
1363 isrFunctions.widenSaturationTrails(ccdExposure.getMaskedImage().getMask())
1365 if self.config.doCameraSpecificMasking:
1366 self.log.info("Masking regions for camera specific reasons.")
1367 self.masking.run(ccdExposure)
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()
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
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")
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)
1425 self.debugView(ccdExposure, "doBrighterFatter")
1427 if self.config.doDark:
1428 self.log.info("Applying dark correction.")
1429 self.darkCorrection(ccdExposure, dark)
1430 self.debugView(ccdExposure, "doDark")
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")
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")
1442 if self.config.doFlat:
1443 self.log.info("Applying flat correction.")
1444 self.flatCorrection(ccdExposure, flat)
1445 self.debugView(ccdExposure, "doFlat")
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)
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())
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)
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)
1476 flattenedThumb = None
1477 if self.config.qa.doThumbnailFlattened:
1478 flattenedThumb = isrQa.makeThumbnail(ccdExposure, isrQaConfig=self.config.qa)
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)
1486 preInterpExp = None
1487 if self.config.doSaveInterpPixels:
1488 preInterpExp = ccdExposure.clone()
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)
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 )
1517 self.roughZeroPoint(ccdExposure)
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)
1524 if self.config.doMeasureBackground:
1525 self.log.info("Measuring background level.")
1526 self.measureBackground(ccdExposure, self.config.qa)
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))
1540 # calculate additional statistics.
1541 outputStatistics = None
1542 if self.config.doCalculateStatistics:
1543 outputStatistics = self.isrStats.run(ccdExposure, overscanResults=overscans,
1544 ptc=ptc).results
1546 self.debugView(ccdExposure, "postISRCCD")
1548 return pipeBase.Struct(
1549 exposure=ccdExposure,
1550 ossThumb=ossThumb,
1551 flattenedThumb=flattenedThumb,
1553 preInterpExposure=preInterpExp,
1554 outputExposure=ccdExposure,
1555 outputOssThumbnail=ossThumb,
1556 outputFlattenedThumbnail=flattenedThumb,
1557 outputStatistics=outputStatistics,
1558 )
1560 def ensureExposure(self, inputExp, camera=None, detectorNum=None):
1561 """Ensure that the data returned by Butler is a fully constructed exp.
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.
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.
1581 Returns
1582 -------
1583 inputExp : `lsst.afw.image.Exposure`
1584 The re-constructed exposure, with appropriate detector parameters.
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), ))
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])
1612 return inputExp
1614 def convertIntToFloat(self, exposure):
1615 """Convert exposure image from uint16 to float.
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.
1622 Parameters
1623 ----------
1624 exposure : `lsst.afw.image.Exposure`
1625 The raw exposure to be converted.
1627 Returns
1628 -------
1629 newexposure : `lsst.afw.image.Exposure`
1630 The input ``exposure``, converted to floating point pixels.
1632 Raises
1633 ------
1634 RuntimeError
1635 Raised if the exposure type cannot be converted to float.
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))
1645 newexposure = exposure.convertF()
1646 newexposure.variance[:] = 1
1647 newexposure.mask[:] = 0x0
1649 return newexposure
1651 def maskAmplifier(self, ccdExposure, amp, defects):
1652 """Identify bad amplifiers, saturated and suspect pixels.
1654 Parameters
1655 ----------
1656 ccdExposure : `lsst.afw.image.Exposure`
1657 Input exposure to be masked.
1658 amp : `lsst.afw.cameraGeom.Amplifier`
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.
1665 Returns
1666 -------
1667 badAmp : `Bool`
1668 If this is true, the entire amplifier area is covered by
1669 defects and unusable.
1671 """
1672 maskedImage = ccdExposure.getMaskedImage()
1674 badAmp = False
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]))
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
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})
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 )
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")
1724 return badAmp
1726 def overscanCorrection(self, ccdExposure, amp):
1727 """Apply overscan correction in place.
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.
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.
1743 Returns
1744 -------
1745 overscanResults : `lsst.pipe.base.Struct`
1746 Result struct with components:
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.
1758 (`lsst.afw.image.Image`)
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`)
1767 Raises
1768 ------
1769 RuntimeError
1770 Raised if the ``amp`` does not contain raw pixel information.
1772 See Also
1773 --------
1774 lsst.ip.isr.overscan.OverscanTask
1776 """
1777 if amp.getRawHorizontalOverscanBBox().isEmpty():
1778 self.log.info("ISR_OSCAN: No overscan region. Not performing overscan correction.")
1779 return None
1781 # Perform overscan correction on subregions.
1782 overscanResults = self.overscan.run(ccdExposure, amp)
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
1789 return overscanResults
1791 def updateVariance(self, ampExposure, amp, overscanImage=None, ptcDataset=None):
1792 """Set the variance plane using the gain and read noise
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.
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.
1809 Raises
1810 ------
1811 RuntimeError
1812 Raised if either ``usePtcGains`` of ``usePtcReadNoise``
1813 are ``True``, but ptcDataset is not provided.
1815 Raised if ```doEmpiricalReadNoise`` is ``True`` but
1816 ``overscanImage`` is ``None``.
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()
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
1841 if self.config.doEmpiricalReadNoise and overscanImage is None:
1842 badPixels = isrFunctions.countMaskedPixels(ampExposure.getMaskedImage(),
1843 [self.config.saturatedMaskName,
1844 self.config.suspectMaskName,
1845 "BAD", "NO_DATA"])
1846 allPixels = ampExposure.getWidth() * ampExposure.getHeight()
1847 if allPixels == badPixels:
1848 # If the image is bad, do not raise.
1849 self.log.info("Skipping empirical read noise for amp %s. No good pixels.",
1850 amp.getName())
1851 else:
1852 raise RuntimeError("Overscan is none for EmpiricalReadNoise.")
1854 if self.config.doEmpiricalReadNoise and overscanImage is not None:
1855 stats = afwMath.StatisticsControl()
1856 stats.setAndMask(overscanImage.mask.getPlaneBitMask(maskPlanes))
1857 readNoise = afwMath.makeStatistics(overscanImage.getImage(),
1858 afwMath.STDEVCLIP, stats).getValue()
1859 self.log.info("Calculated empirical read noise for amp %s: %f.",
1860 amp.getName(), readNoise)
1861 elif self.config.usePtcReadNoise:
1862 if ptcDataset is None:
1863 raise RuntimeError("No ptcDataset provided to use PTC readnoise.")
1864 else:
1865 readNoise = ptcDataset.noise[amp.getName()]
1866 self.log.info("Using read noise from Photon Transfer Curve.")
1867 else:
1868 readNoise = amp.getReadNoise()
1870 isrFunctions.updateVariance(
1871 maskedImage=ampExposure.getMaskedImage(),
1872 gain=gain,
1873 readNoise=readNoise,
1874 )
1876 def maskNegativeVariance(self, exposure):
1877 """Identify and mask pixels with negative variance values.
1879 Parameters
1880 ----------
1881 exposure : `lsst.afw.image.Exposure`
1882 Exposure to process.
1884 See Also
1885 --------
1886 lsst.ip.isr.isrFunctions.updateVariance
1887 """
1888 maskPlane = exposure.getMask().getPlaneBitMask(self.config.negativeVarianceMaskName)
1889 bad = numpy.where(exposure.getVariance().getArray() <= 0.0)
1890 exposure.mask.array[bad] |= maskPlane
1892 def darkCorrection(self, exposure, darkExposure, invert=False):
1893 """Apply dark correction in place.
1895 Parameters
1896 ----------
1897 exposure : `lsst.afw.image.Exposure`
1898 Exposure to process.
1899 darkExposure : `lsst.afw.image.Exposure`
1900 Dark exposure of the same size as ``exposure``.
1901 invert : `Bool`, optional
1902 If True, re-add the dark to an already corrected image.
1904 Raises
1905 ------
1906 RuntimeError
1907 Raised if either ``exposure`` or ``darkExposure`` do not
1908 have their dark time defined.
1910 See Also
1911 --------
1912 lsst.ip.isr.isrFunctions.darkCorrection
1913 """
1914 expScale = exposure.getInfo().getVisitInfo().getDarkTime()
1915 if math.isnan(expScale):
1916 raise RuntimeError("Exposure darktime is NAN.")
1917 if darkExposure.getInfo().getVisitInfo() is not None \
1918 and not math.isnan(darkExposure.getInfo().getVisitInfo().getDarkTime()):
1919 darkScale = darkExposure.getInfo().getVisitInfo().getDarkTime()
1920 else:
1921 # DM-17444: darkExposure.getInfo.getVisitInfo() is None
1922 # so getDarkTime() does not exist.
1923 self.log.warning("darkExposure.getInfo().getVisitInfo() does not exist. Using darkScale = 1.0.")
1924 darkScale = 1.0
1926 isrFunctions.darkCorrection(
1927 maskedImage=exposure.getMaskedImage(),
1928 darkMaskedImage=darkExposure.getMaskedImage(),
1929 expScale=expScale,
1930 darkScale=darkScale,
1931 invert=invert,
1932 trimToFit=self.config.doTrimToMatchCalib
1933 )
1935 def doLinearize(self, detector):
1936 """Check if linearization is needed for the detector cameraGeom.
1938 Checks config.doLinearize and the linearity type of the first
1939 amplifier.
1941 Parameters
1942 ----------
1943 detector : `lsst.afw.cameraGeom.Detector`
1944 Detector to get linearity type from.
1946 Returns
1947 -------
1948 doLinearize : `Bool`
1949 If True, linearization should be performed.
1950 """
1951 return self.config.doLinearize and \
1952 detector.getAmplifiers()[0].getLinearityType() != NullLinearityType
1954 def flatCorrection(self, exposure, flatExposure, invert=False):
1955 """Apply flat correction in place.
1957 Parameters
1958 ----------
1959 exposure : `lsst.afw.image.Exposure`
1960 Exposure to process.
1961 flatExposure : `lsst.afw.image.Exposure`
1962 Flat exposure of the same size as ``exposure``.
1963 invert : `Bool`, optional
1964 If True, unflatten an already flattened image.
1966 See Also
1967 --------
1968 lsst.ip.isr.isrFunctions.flatCorrection
1969 """
1970 isrFunctions.flatCorrection(
1971 maskedImage=exposure.getMaskedImage(),
1972 flatMaskedImage=flatExposure.getMaskedImage(),
1973 scalingType=self.config.flatScalingType,
1974 userScale=self.config.flatUserScale,
1975 invert=invert,
1976 trimToFit=self.config.doTrimToMatchCalib
1977 )
1979 def saturationDetection(self, exposure, amp):
1980 """Detect and mask saturated pixels in config.saturatedMaskName.
1982 Parameters
1983 ----------
1984 exposure : `lsst.afw.image.Exposure`
1985 Exposure to process. Only the amplifier DataSec is processed.
1986 amp : `lsst.afw.cameraGeom.Amplifier`
1987 Amplifier detector data.
1989 See Also
1990 --------
1991 lsst.ip.isr.isrFunctions.makeThresholdMask
1992 """
1993 if not math.isnan(amp.getSaturation()):
1994 maskedImage = exposure.getMaskedImage()
1995 dataView = maskedImage.Factory(maskedImage, amp.getRawBBox())
1996 isrFunctions.makeThresholdMask(
1997 maskedImage=dataView,
1998 threshold=amp.getSaturation(),
1999 growFootprints=0,
2000 maskName=self.config.saturatedMaskName,
2001 )
2003 def saturationInterpolation(self, exposure):
2004 """Interpolate over saturated pixels, in place.
2006 This method should be called after `saturationDetection`, to
2007 ensure that the saturated pixels have been identified in the
2008 SAT mask. It should also be called after `assembleCcd`, since
2009 saturated regions may cross amplifier boundaries.
2011 Parameters
2012 ----------
2013 exposure : `lsst.afw.image.Exposure`
2014 Exposure to process.
2016 See Also
2017 --------
2018 lsst.ip.isr.isrTask.saturationDetection
2019 lsst.ip.isr.isrFunctions.interpolateFromMask
2020 """
2021 isrFunctions.interpolateFromMask(
2022 maskedImage=exposure.getMaskedImage(),
2023 fwhm=self.config.fwhm,
2024 growSaturatedFootprints=self.config.growSaturationFootprintSize,
2025 maskNameList=list(self.config.saturatedMaskName),
2026 )
2028 def suspectDetection(self, exposure, amp):
2029 """Detect and mask suspect pixels in config.suspectMaskName.
2031 Parameters
2032 ----------
2033 exposure : `lsst.afw.image.Exposure`
2034 Exposure to process. Only the amplifier DataSec is processed.
2035 amp : `lsst.afw.cameraGeom.Amplifier`
2036 Amplifier detector data.
2038 See Also
2039 --------
2040 lsst.ip.isr.isrFunctions.makeThresholdMask
2042 Notes
2043 -----
2044 Suspect pixels are pixels whose value is greater than
2045 amp.getSuspectLevel(). This is intended to indicate pixels that may be
2046 affected by unknown systematics; for example if non-linearity
2047 corrections above a certain level are unstable then that would be a
2048 useful value for suspectLevel. A value of `nan` indicates that no such
2049 level exists and no pixels are to be masked as suspicious.
2050 """
2051 suspectLevel = amp.getSuspectLevel()
2052 if math.isnan(suspectLevel):
2053 return
2055 maskedImage = exposure.getMaskedImage()
2056 dataView = maskedImage.Factory(maskedImage, amp.getRawBBox())
2057 isrFunctions.makeThresholdMask(
2058 maskedImage=dataView,
2059 threshold=suspectLevel,
2060 growFootprints=0,
2061 maskName=self.config.suspectMaskName,
2062 )
2064 def maskDefect(self, exposure, defectBaseList):
2065 """Mask defects using mask plane "BAD", in place.
2067 Parameters
2068 ----------
2069 exposure : `lsst.afw.image.Exposure`
2070 Exposure to process.
2071 defectBaseList : defect-type
2072 List of defects to mask. Can be of type `lsst.ip.isr.Defects`
2073 or `list` of `lsst.afw.image.DefectBase`.
2075 Notes
2076 -----
2077 Call this after CCD assembly, since defects may cross amplifier
2078 boundaries.
2079 """
2080 maskedImage = exposure.getMaskedImage()
2081 if not isinstance(defectBaseList, Defects):
2082 # Promotes DefectBase to Defect
2083 defectList = Defects(defectBaseList)
2084 else:
2085 defectList = defectBaseList
2086 defectList.maskPixels(maskedImage, maskName="BAD")
2088 def maskEdges(self, exposure, numEdgePixels=0, maskPlane="SUSPECT", level='DETECTOR'):
2089 """Mask edge pixels with applicable mask plane.
2091 Parameters
2092 ----------
2093 exposure : `lsst.afw.image.Exposure`
2094 Exposure to process.
2095 numEdgePixels : `int`, optional
2096 Number of edge pixels to mask.
2097 maskPlane : `str`, optional
2098 Mask plane name to use.
2099 level : `str`, optional
2100 Level at which to mask edges.
2101 """
2102 maskedImage = exposure.getMaskedImage()
2103 maskBitMask = maskedImage.getMask().getPlaneBitMask(maskPlane)
2105 if numEdgePixels > 0:
2106 if level == 'DETECTOR':
2107 boxes = [maskedImage.getBBox()]
2108 elif level == 'AMP':
2109 boxes = [amp.getBBox() for amp in exposure.getDetector()]
2111 for box in boxes:
2112 # This makes a bbox numEdgeSuspect pixels smaller than the
2113 # image on each side
2114 subImage = maskedImage[box]
2115 box.grow(-numEdgePixels)
2116 # Mask pixels outside box
2117 SourceDetectionTask.setEdgeBits(
2118 subImage,
2119 box,
2120 maskBitMask)
2122 def maskAndInterpolateDefects(self, exposure, defectBaseList):
2123 """Mask and interpolate defects using mask plane "BAD", in place.
2125 Parameters
2126 ----------
2127 exposure : `lsst.afw.image.Exposure`
2128 Exposure to process.
2129 defectBaseList : defects-like
2130 List of defects to mask and interpolate. Can be
2131 `lsst.ip.isr.Defects` or `list` of `lsst.afw.image.DefectBase`.
2133 See Also
2134 --------
2135 lsst.ip.isr.isrTask.maskDefect
2136 """
2137 self.maskDefect(exposure, defectBaseList)
2138 self.maskEdges(exposure, numEdgePixels=self.config.numEdgeSuspect,
2139 maskPlane="SUSPECT", level=self.config.edgeMaskLevel)
2140 isrFunctions.interpolateFromMask(
2141 maskedImage=exposure.getMaskedImage(),
2142 fwhm=self.config.fwhm,
2143 growSaturatedFootprints=0,
2144 maskNameList=["BAD"],
2145 )
2147 def maskNan(self, exposure):
2148 """Mask NaNs using mask plane "UNMASKEDNAN", in place.
2150 Parameters
2151 ----------
2152 exposure : `lsst.afw.image.Exposure`
2153 Exposure to process.
2155 Notes
2156 -----
2157 We mask over all non-finite values (NaN, inf), including those
2158 that are masked with other bits (because those may or may not be
2159 interpolated over later, and we want to remove all NaN/infs).
2160 Despite this behaviour, the "UNMASKEDNAN" mask plane is used to
2161 preserve the historical name.
2162 """
2163 maskedImage = exposure.getMaskedImage()
2165 # Find and mask NaNs
2166 maskedImage.getMask().addMaskPlane("UNMASKEDNAN")
2167 maskVal = maskedImage.getMask().getPlaneBitMask("UNMASKEDNAN")
2168 numNans = maskNans(maskedImage, maskVal)
2169 self.metadata["NUMNANS"] = numNans
2170 if numNans > 0:
2171 self.log.warning("There were %d unmasked NaNs.", numNans)
2173 def maskAndInterpolateNan(self, exposure):
2174 """"Mask and interpolate NaN/infs using mask plane "UNMASKEDNAN",
2175 in place.
2177 Parameters
2178 ----------
2179 exposure : `lsst.afw.image.Exposure`
2180 Exposure to process.
2182 See Also
2183 --------
2184 lsst.ip.isr.isrTask.maskNan
2185 """
2186 self.maskNan(exposure)
2187 isrFunctions.interpolateFromMask(
2188 maskedImage=exposure.getMaskedImage(),
2189 fwhm=self.config.fwhm,
2190 growSaturatedFootprints=0,
2191 maskNameList=["UNMASKEDNAN"],
2192 )
2194 def measureBackground(self, exposure, IsrQaConfig=None):
2195 """Measure the image background in subgrids, for quality control.
2197 Parameters
2198 ----------
2199 exposure : `lsst.afw.image.Exposure`
2200 Exposure to process.
2201 IsrQaConfig : `lsst.ip.isr.isrQa.IsrQaConfig`
2202 Configuration object containing parameters on which background
2203 statistics and subgrids to use.
2204 """
2205 if IsrQaConfig is not None:
2206 statsControl = afwMath.StatisticsControl(IsrQaConfig.flatness.clipSigma,
2207 IsrQaConfig.flatness.nIter)
2208 maskVal = exposure.getMaskedImage().getMask().getPlaneBitMask(["BAD", "SAT", "DETECTED"])
2209 statsControl.setAndMask(maskVal)
2210 maskedImage = exposure.getMaskedImage()
2211 stats = afwMath.makeStatistics(maskedImage, afwMath.MEDIAN | afwMath.STDEVCLIP, statsControl)
2212 skyLevel = stats.getValue(afwMath.MEDIAN)
2213 skySigma = stats.getValue(afwMath.STDEVCLIP)
2214 self.log.info("Flattened sky level: %f +/- %f.", skyLevel, skySigma)
2215 metadata = exposure.getMetadata()
2216 metadata["SKYLEVEL"] = skyLevel
2217 metadata["SKYSIGMA"] = skySigma
2219 # calcluating flatlevel over the subgrids
2220 stat = afwMath.MEANCLIP if IsrQaConfig.flatness.doClip else afwMath.MEAN
2221 meshXHalf = int(IsrQaConfig.flatness.meshX/2.)
2222 meshYHalf = int(IsrQaConfig.flatness.meshY/2.)
2223 nX = int((exposure.getWidth() + meshXHalf) / IsrQaConfig.flatness.meshX)
2224 nY = int((exposure.getHeight() + meshYHalf) / IsrQaConfig.flatness.meshY)
2225 skyLevels = numpy.zeros((nX, nY))
2227 for j in range(nY):
2228 yc = meshYHalf + j * IsrQaConfig.flatness.meshY
2229 for i in range(nX):
2230 xc = meshXHalf + i * IsrQaConfig.flatness.meshX
2232 xLLC = xc - meshXHalf
2233 yLLC = yc - meshYHalf
2234 xURC = xc + meshXHalf - 1
2235 yURC = yc + meshYHalf - 1
2237 bbox = lsst.geom.Box2I(lsst.geom.Point2I(xLLC, yLLC), lsst.geom.Point2I(xURC, yURC))
2238 miMesh = maskedImage.Factory(exposure.getMaskedImage(), bbox, afwImage.LOCAL)
2240 skyLevels[i, j] = afwMath.makeStatistics(miMesh, stat, statsControl).getValue()
2242 good = numpy.where(numpy.isfinite(skyLevels))
2243 skyMedian = numpy.median(skyLevels[good])
2244 flatness = (skyLevels[good] - skyMedian) / skyMedian
2245 flatness_rms = numpy.std(flatness)
2246 flatness_pp = flatness.max() - flatness.min() if len(flatness) > 0 else numpy.nan
2248 self.log.info("Measuring sky levels in %dx%d grids: %f.", nX, nY, skyMedian)
2249 self.log.info("Sky flatness in %dx%d grids - pp: %f rms: %f.",
2250 nX, nY, flatness_pp, flatness_rms)
2252 metadata["FLATNESS_PP"] = float(flatness_pp)
2253 metadata["FLATNESS_RMS"] = float(flatness_rms)
2254 metadata["FLATNESS_NGRIDS"] = '%dx%d' % (nX, nY)
2255 metadata["FLATNESS_MESHX"] = IsrQaConfig.flatness.meshX
2256 metadata["FLATNESS_MESHY"] = IsrQaConfig.flatness.meshY
2258 def roughZeroPoint(self, exposure):
2259 """Set an approximate magnitude zero point for the exposure.
2261 Parameters
2262 ----------
2263 exposure : `lsst.afw.image.Exposure`
2264 Exposure to process.
2265 """
2266 filterLabel = exposure.getFilter()
2267 physicalFilter = isrFunctions.getPhysicalFilter(filterLabel, self.log)
2269 if physicalFilter in self.config.fluxMag0T1:
2270 fluxMag0 = self.config.fluxMag0T1[physicalFilter]
2271 else:
2272 self.log.warning("No rough magnitude zero point defined for filter %s.", physicalFilter)
2273 fluxMag0 = self.config.defaultFluxMag0T1
2275 expTime = exposure.getInfo().getVisitInfo().getExposureTime()
2276 if not expTime > 0: # handle NaN as well as <= 0
2277 self.log.warning("Non-positive exposure time; skipping rough zero point.")
2278 return
2280 self.log.info("Setting rough magnitude zero point for filter %s: %f",
2281 physicalFilter, 2.5*math.log10(fluxMag0*expTime))
2282 exposure.setPhotoCalib(afwImage.makePhotoCalibFromCalibZeroPoint(fluxMag0*expTime, 0.0))
2284 @contextmanager
2285 def flatContext(self, exp, flat, dark=None):
2286 """Context manager that applies and removes flats and darks,
2287 if the task is configured to apply them.
2289 Parameters
2290 ----------
2291 exp : `lsst.afw.image.Exposure`
2292 Exposure to process.
2293 flat : `lsst.afw.image.Exposure`
2294 Flat exposure the same size as ``exp``.
2295 dark : `lsst.afw.image.Exposure`, optional
2296 Dark exposure the same size as ``exp``.
2298 Yields
2299 ------
2300 exp : `lsst.afw.image.Exposure`
2301 The flat and dark corrected exposure.
2302 """
2303 if self.config.doDark and dark is not None:
2304 self.darkCorrection(exp, dark)
2305 if self.config.doFlat:
2306 self.flatCorrection(exp, flat)
2307 try:
2308 yield exp
2309 finally:
2310 if self.config.doFlat:
2311 self.flatCorrection(exp, flat, invert=True)
2312 if self.config.doDark and dark is not None:
2313 self.darkCorrection(exp, dark, invert=True)
2315 def debugView(self, exposure, stepname):
2316 """Utility function to examine ISR exposure at different stages.
2318 Parameters
2319 ----------
2320 exposure : `lsst.afw.image.Exposure`
2321 Exposure to view.
2322 stepname : `str`
2323 State of processing to view.
2324 """
2325 frame = getDebugFrame(self._display, stepname)
2326 if frame:
2327 display = getDisplay(frame)
2328 display.scale('asinh', 'zscale')
2329 display.mtv(exposure)
2330 prompt = "Press Enter to continue [c]... "
2331 while True:
2332 ans = input(prompt).lower()
2333 if ans in ("", "c",):
2334 break
2337class FakeAmp(object):
2338 """A Detector-like object that supports returning gain and saturation level
2340 This is used when the input exposure does not have a detector.
2342 Parameters
2343 ----------
2344 exposure : `lsst.afw.image.Exposure`
2345 Exposure to generate a fake amplifier for.
2346 config : `lsst.ip.isr.isrTaskConfig`
2347 Configuration to apply to the fake amplifier.
2348 """
2350 def __init__(self, exposure, config):
2351 self._bbox = exposure.getBBox(afwImage.LOCAL)
2352 self._RawHorizontalOverscanBBox = lsst.geom.Box2I()
2353 self._gain = config.gain
2354 self._readNoise = config.readNoise
2355 self._saturation = config.saturation
2357 def getBBox(self):
2358 return self._bbox
2360 def getRawBBox(self):
2361 return self._bbox
2363 def getRawHorizontalOverscanBBox(self):
2364 return self._RawHorizontalOverscanBBox
2366 def getGain(self):
2367 return self._gain
2369 def getReadNoise(self):
2370 return self._readNoise
2372 def getSaturation(self):
2373 return self._saturation
2375 def getSuspectLevel(self):
2376 return float("NaN")