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1# This file is part of cp_pipe
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
21import itertools
22import numpy as np
24from collections import defaultdict
26import lsst.pipe.base as pipeBase
27import lsst.pipe.base.connectionTypes as cT
29from lsstDebug import getDebugFrame
30from lsst.afw.detection import FootprintSet, Threshold
31from lsst.afw.display import getDisplay
32from lsst.pex.config import Config, Field, ListField, ConfigurableField
33from lsst.ip.isr import CrosstalkCalib, IsrProvenance
34from lsst.pipe.tasks.getRepositoryData import DataRefListRunner
35from lsst.cp.pipe.utils import (ddict2dict, sigmaClipCorrection)
37from ._lookupStaticCalibration import lookupStaticCalibration
39__all__ = ["CrosstalkExtractConfig", "CrosstalkExtractTask",
40 "CrosstalkSolveTask", "CrosstalkSolveConfig",
41 "MeasureCrosstalkConfig", "MeasureCrosstalkTask"]
44class CrosstalkExtractConnections(pipeBase.PipelineTaskConnections,
45 dimensions=("instrument", "exposure", "detector")):
46 inputExp = cT.Input(
47 name="crosstalkInputs",
48 doc="Input post-ISR processed exposure to measure crosstalk from.",
49 storageClass="Exposure",
50 dimensions=("instrument", "exposure", "detector"),
51 multiple=False,
52 )
53 # TODO: Depends on DM-21904.
54 sourceExp = cT.Input(
55 name="crosstalkSource",
56 doc="Post-ISR exposure to measure for inter-chip crosstalk onto inputExp.",
57 storageClass="Exposure",
58 dimensions=("instrument", "exposure", "detector"),
59 multiple=True,
60 deferLoad=True,
61 # lookupFunction=None,
62 )
64 outputRatios = cT.Output(
65 name="crosstalkRatios",
66 doc="Extracted crosstalk pixel ratios.",
67 storageClass="StructuredDataDict",
68 dimensions=("instrument", "exposure", "detector"),
69 )
70 outputFluxes = cT.Output(
71 name="crosstalkFluxes",
72 doc="Source pixel fluxes used in ratios.",
73 storageClass="StructuredDataDict",
74 dimensions=("instrument", "exposure", "detector"),
75 )
77 def __init__(self, *, config=None):
78 super().__init__(config=config)
79 # Discard sourceExp until DM-21904 allows full interchip
80 # measurements.
81 self.inputs.discard("sourceExp")
84class CrosstalkExtractConfig(pipeBase.PipelineTaskConfig,
85 pipelineConnections=CrosstalkExtractConnections):
86 """Configuration for the measurement of pixel ratios.
87 """
88 doMeasureInterchip = Field(
89 dtype=bool,
90 default=False,
91 doc="Measure inter-chip crosstalk as well?",
92 )
93 threshold = Field(
94 dtype=float,
95 default=30000,
96 doc="Minimum level of source pixels for which to measure crosstalk."
97 )
98 ignoreSaturatedPixels = Field(
99 dtype=bool,
100 default=True,
101 doc="Should saturated pixels be ignored?"
102 )
103 badMask = ListField(
104 dtype=str,
105 default=["BAD", "INTRP"],
106 doc="Mask planes to ignore when identifying source pixels."
107 )
108 isTrimmed = Field(
109 dtype=bool,
110 default=True,
111 doc="Is the input exposure trimmed?"
112 )
114 def validate(self):
115 super().validate()
117 # Ensure the handling of the SAT mask plane is consistent
118 # with the ignoreSaturatedPixels value.
119 if self.ignoreSaturatedPixels:
120 if 'SAT' not in self.badMask:
121 self.badMask.append('SAT')
122 else:
123 if 'SAT' in self.badMask:
124 self.badMask = [mask for mask in self.badMask if mask != 'SAT']
127class CrosstalkExtractTask(pipeBase.PipelineTask,
128 pipeBase.CmdLineTask):
129 """Task to measure pixel ratios to find crosstalk.
130 """
131 ConfigClass = CrosstalkExtractConfig
132 _DefaultName = 'cpCrosstalkExtract'
134 def run(self, inputExp, sourceExps=[]):
135 """Measure pixel ratios between amplifiers in inputExp.
137 Extract crosstalk ratios between different amplifiers.
139 For pixels above ``config.threshold``, we calculate the ratio
140 between each background-subtracted target amp and the source
141 amp. We return a list of ratios for each pixel for each
142 target/source combination, as nested dictionary containing the
143 ratio.
145 Parameters
146 ----------
147 inputExp : `lsst.afw.image.Exposure`
148 Input exposure to measure pixel ratios on.
149 sourceExp : `list` [`lsst.afw.image.Exposure`], optional
150 List of chips to use as sources to measure inter-chip
151 crosstalk.
153 Returns
154 -------
155 results : `lsst.pipe.base.Struct`
156 The results struct containing:
158 ``outputRatios`` : `dict` [`dict` [`dict` [`dict` [`list`]]]]
159 A catalog of ratio lists. The dictionaries are
160 indexed such that:
161 outputRatios[targetChip][sourceChip][targetAmp][sourceAmp]
162 contains the ratio list for that combination.
163 ``outputFluxes`` : `dict` [`dict` [`list`]]
164 A catalog of flux lists. The dictionaries are
165 indexed such that:
166 outputFluxes[sourceChip][sourceAmp]
167 contains the flux list used in the outputRatios.
169 Notes
170 -----
171 The lsstDebug.Info() method can be rewritten for __name__ =
172 `lsst.cp.pipe.measureCrosstalk`, and supports the parameters:
174 debug.display['extract'] : `bool`
175 Display the exposure under consideration, with the pixels used
176 for crosstalk measurement indicated by the DETECTED mask plane.
177 debug.display['pixels'] : `bool`
178 Display a plot of the ratio calculated for each pixel used in this
179 exposure, split by amplifier pairs. The median value is listed
180 for reference.
181 """
182 outputRatios = defaultdict(lambda: defaultdict(dict))
183 outputFluxes = defaultdict(lambda: defaultdict(dict))
185 threshold = self.config.threshold
186 badPixels = list(self.config.badMask)
188 targetDetector = inputExp.getDetector()
189 targetChip = targetDetector.getName()
191 # Always look at the target chip first, then go to any other supplied exposures.
192 sourceExtractExps = [inputExp]
193 sourceExtractExps.extend(sourceExps)
195 self.log.info("Measuring full detector background for target: %s", targetChip)
196 targetIm = inputExp.getMaskedImage()
197 FootprintSet(targetIm, Threshold(threshold), "DETECTED")
198 detected = targetIm.getMask().getPlaneBitMask("DETECTED")
199 bg = CrosstalkCalib.calculateBackground(targetIm, badPixels + ["DETECTED"])
201 self.debugView('extract', inputExp)
203 for sourceExp in sourceExtractExps:
204 sourceDetector = sourceExp.getDetector()
205 sourceChip = sourceDetector.getName()
206 sourceIm = sourceExp.getMaskedImage()
207 bad = sourceIm.getMask().getPlaneBitMask(badPixels)
208 self.log.info("Measuring crosstalk from source: %s", sourceChip)
210 if sourceExp != inputExp:
211 FootprintSet(sourceIm, Threshold(threshold), "DETECTED")
212 detected = sourceIm.getMask().getPlaneBitMask("DETECTED")
214 # The dictionary of amp-to-amp ratios for this pair of source->target detectors.
215 ratioDict = defaultdict(lambda: defaultdict(list))
216 extractedCount = 0
218 for sourceAmp in sourceDetector:
219 sourceAmpName = sourceAmp.getName()
220 sourceAmpBBox = sourceAmp.getBBox() if self.config.isTrimmed else sourceAmp.getRawDataBBox()
221 sourceAmpImage = sourceIm[sourceAmpBBox]
222 sourceMask = sourceAmpImage.mask.array
223 select = ((sourceMask & detected > 0)
224 & (sourceMask & bad == 0)
225 & np.isfinite(sourceAmpImage.image.array))
226 count = np.sum(select)
227 self.log.debug(" Source amplifier: %s", sourceAmpName)
229 outputFluxes[sourceChip][sourceAmpName] = sourceAmpImage.image.array[select].tolist()
231 for targetAmp in targetDetector:
232 # iterate over targetExposure
233 targetAmpName = targetAmp.getName()
234 if sourceAmpName == targetAmpName and sourceChip == targetChip:
235 ratioDict[sourceAmpName][targetAmpName] = []
236 continue
237 self.log.debug(" Target amplifier: %s", targetAmpName)
239 targetAmpImage = CrosstalkCalib.extractAmp(targetIm.image,
240 targetAmp, sourceAmp,
241 isTrimmed=self.config.isTrimmed)
242 ratios = (targetAmpImage.array[select] - bg)/sourceAmpImage.image.array[select]
243 ratioDict[targetAmpName][sourceAmpName] = ratios.tolist()
244 extractedCount += count
246 self.debugPixels('pixels',
247 sourceAmpImage.image.array[select],
248 targetAmpImage.array[select] - bg,
249 sourceAmpName, targetAmpName)
251 self.log.info("Extracted %d pixels from %s -> %s (targetBG: %f)",
252 extractedCount, sourceChip, targetChip, bg)
253 outputRatios[targetChip][sourceChip] = ratioDict
255 return pipeBase.Struct(
256 outputRatios=ddict2dict(outputRatios),
257 outputFluxes=ddict2dict(outputFluxes)
258 )
260 def debugView(self, stepname, exposure):
261 """Utility function to examine the image being processed.
263 Parameters
264 ----------
265 stepname : `str`
266 State of processing to view.
267 exposure : `lsst.afw.image.Exposure`
268 Exposure to view.
269 """
270 frame = getDebugFrame(self._display, stepname)
271 if frame:
272 display = getDisplay(frame)
273 display.scale('asinh', 'zscale')
274 display.mtv(exposure)
276 prompt = "Press Enter to continue: "
277 while True:
278 ans = input(prompt).lower()
279 if ans in ("", "c",):
280 break
282 def debugPixels(self, stepname, pixelsIn, pixelsOut, sourceName, targetName):
283 """Utility function to examine the CT ratio pixel values.
285 Parameters
286 ----------
287 stepname : `str`
288 State of processing to view.
289 pixelsIn : `np.ndarray`
290 Pixel values from the potential crosstalk source.
291 pixelsOut : `np.ndarray`
292 Pixel values from the potential crosstalk target.
293 sourceName : `str`
294 Source amplifier name
295 targetName : `str`
296 Target amplifier name
297 """
298 frame = getDebugFrame(self._display, stepname)
299 if frame:
300 import matplotlib.pyplot as plt
301 figure = plt.figure(1)
302 figure.clear()
304 axes = figure.add_axes((0.1, 0.1, 0.8, 0.8))
305 axes.plot(pixelsIn, pixelsOut / pixelsIn, 'k+')
306 plt.xlabel("Source amplifier pixel value")
307 plt.ylabel("Measured pixel ratio")
308 plt.title(f"(Source {sourceName} -> Target {targetName}) median ratio: "
309 f"{(np.median(pixelsOut / pixelsIn))}")
310 figure.show()
312 prompt = "Press Enter to continue: "
313 while True:
314 ans = input(prompt).lower()
315 if ans in ("", "c",):
316 break
317 plt.close()
320class CrosstalkSolveConnections(pipeBase.PipelineTaskConnections,
321 dimensions=("instrument", "detector")):
322 inputRatios = cT.Input(
323 name="crosstalkRatios",
324 doc="Ratios measured for an input exposure.",
325 storageClass="StructuredDataDict",
326 dimensions=("instrument", "exposure", "detector"),
327 multiple=True,
328 )
329 inputFluxes = cT.Input(
330 name="crosstalkFluxes",
331 doc="Fluxes of CT source pixels, for nonlinear fits.",
332 storageClass="StructuredDataDict",
333 dimensions=("instrument", "exposure", "detector"),
334 multiple=True,
335 )
336 camera = cT.PrerequisiteInput(
337 name="camera",
338 doc="Camera the input data comes from.",
339 storageClass="Camera",
340 dimensions=("instrument",),
341 isCalibration=True,
342 lookupFunction=lookupStaticCalibration,
343 )
345 outputCrosstalk = cT.Output(
346 name="crosstalk",
347 doc="Output proposed crosstalk calibration.",
348 storageClass="CrosstalkCalib",
349 dimensions=("instrument", "detector"),
350 multiple=False,
351 isCalibration=True,
352 )
354 def __init__(self, *, config=None):
355 super().__init__(config=config)
357 if config.fluxOrder == 0:
358 self.inputs.discard("inputFluxes")
361class CrosstalkSolveConfig(pipeBase.PipelineTaskConfig,
362 pipelineConnections=CrosstalkSolveConnections):
363 """Configuration for the solving of crosstalk from pixel ratios.
364 """
365 rejIter = Field(
366 dtype=int,
367 default=3,
368 doc="Number of rejection iterations for final coefficient calculation.",
369 )
370 rejSigma = Field(
371 dtype=float,
372 default=2.0,
373 doc="Rejection threshold (sigma) for final coefficient calculation.",
374 )
375 fluxOrder = Field(
376 dtype=int,
377 default=0,
378 doc="Polynomial order in source flux to fit crosstalk.",
379 )
380 doFiltering = Field(
381 dtype=bool,
382 default=False,
383 doc="Filter generated crosstalk to remove marginal measurements.",
384 )
387class CrosstalkSolveTask(pipeBase.PipelineTask,
388 pipeBase.CmdLineTask):
389 """Task to solve crosstalk from pixel ratios.
390 """
391 ConfigClass = CrosstalkSolveConfig
392 _DefaultName = 'cpCrosstalkSolve'
394 def runQuantum(self, butlerQC, inputRefs, outputRefs):
395 """Ensure that the input and output dimensions are passed along.
397 Parameters
398 ----------
399 butlerQC : `lsst.daf.butler.butlerQuantumContext.ButlerQuantumContext`
400 Butler to operate on.
401 inputRefs : `lsst.pipe.base.connections.InputQuantizedConnection`
402 Input data refs to load.
403 ouptutRefs : `lsst.pipe.base.connections.OutputQuantizedConnection`
404 Output data refs to persist.
405 """
406 inputs = butlerQC.get(inputRefs)
408 # Use the dimensions to set calib/provenance information.
409 inputs['inputDims'] = [exp.dataId.byName() for exp in inputRefs.inputRatios]
410 inputs['outputDims'] = outputRefs.outputCrosstalk.dataId.byName()
412 outputs = self.run(**inputs)
413 butlerQC.put(outputs, outputRefs)
415 def run(self, inputRatios, inputFluxes=None, camera=None, inputDims=None, outputDims=None):
416 """Combine ratios to produce crosstalk coefficients.
418 Parameters
419 ----------
420 inputRatios : `list` [`dict` [`dict` [`dict` [`dict` [`list`]]]]]
421 A list of nested dictionaries of ratios indexed by target
422 and source chip, then by target and source amplifier.
423 inputFluxes : `list` [`dict` [`dict` [`list`]]]
424 A list of nested dictionaries of source pixel fluxes, indexed
425 by source chip and amplifier.
426 camera : `lsst.afw.cameraGeom.Camera`
427 Input camera.
428 inputDims : `list` [`lsst.daf.butler.DataCoordinate`]
429 DataIds to use to construct provenance.
430 outputDims : `list` [`lsst.daf.butler.DataCoordinate`]
431 DataIds to use to populate the output calibration.
433 Returns
434 -------
435 results : `lsst.pipe.base.Struct`
436 The results struct containing:
438 ``outputCrosstalk`` : `lsst.ip.isr.CrosstalkCalib`
439 Final crosstalk calibration.
440 ``outputProvenance`` : `lsst.ip.isr.IsrProvenance`
441 Provenance data for the new calibration.
443 Raises
444 ------
445 RuntimeError
446 Raised if the input data contains multiple target detectors.
448 Notes
449 -----
450 The lsstDebug.Info() method can be rewritten for __name__ =
451 `lsst.ip.isr.measureCrosstalk`, and supports the parameters:
453 debug.display['reduce'] : `bool`
454 Display a histogram of the combined ratio measurements for
455 a pair of source/target amplifiers from all input
456 exposures/detectors.
458 """
459 if outputDims:
460 calibChip = outputDims['detector']
461 instrument = outputDims['instrument']
462 else:
463 # calibChip needs to be set manually in Gen2.
464 calibChip = None
465 instrument = None
467 self.log.info("Combining measurements from %d ratios and %d fluxes",
468 len(inputRatios), len(inputFluxes) if inputFluxes else 0)
470 if inputFluxes is None:
471 inputFluxes = [None for exp in inputRatios]
473 combinedRatios = defaultdict(lambda: defaultdict(list))
474 combinedFluxes = defaultdict(lambda: defaultdict(list))
475 for ratioDict, fluxDict in zip(inputRatios, inputFluxes):
476 for targetChip in ratioDict:
477 if calibChip and targetChip != calibChip:
478 raise RuntimeError("Received multiple target chips!")
480 sourceChip = targetChip
481 if sourceChip in ratioDict[targetChip]:
482 ratios = ratioDict[targetChip][sourceChip]
484 for targetAmp in ratios:
485 for sourceAmp in ratios[targetAmp]:
486 combinedRatios[targetAmp][sourceAmp].extend(ratios[targetAmp][sourceAmp])
487 if fluxDict:
488 combinedFluxes[targetAmp][sourceAmp].extend(fluxDict[sourceChip][sourceAmp])
489 # TODO: DM-21904
490 # Iterating over all other entries in ratioDict[targetChip] will yield
491 # inter-chip terms.
493 for targetAmp in combinedRatios:
494 for sourceAmp in combinedRatios[targetAmp]:
495 self.log.info("Read %d pixels for %s -> %s",
496 len(combinedRatios[targetAmp][sourceAmp]),
497 targetAmp, sourceAmp)
498 if len(combinedRatios[targetAmp][sourceAmp]) > 1:
499 self.debugRatios('reduce', combinedRatios, targetAmp, sourceAmp)
501 if self.config.fluxOrder == 0:
502 self.log.info("Fitting crosstalk coefficients.")
503 calib = self.measureCrosstalkCoefficients(combinedRatios,
504 self.config.rejIter, self.config.rejSigma)
505 else:
506 raise NotImplementedError("Non-linear crosstalk terms are not yet supported.")
508 self.log.info("Number of valid coefficients: %d", np.sum(calib.coeffValid))
510 if self.config.doFiltering:
511 # This step will apply the calculated validity values to
512 # censor poorly measured coefficients.
513 self.log.info("Filtering measured crosstalk to remove invalid solutions.")
514 calib = self.filterCrosstalkCalib(calib)
516 # Populate the remainder of the calibration information.
517 calib.hasCrosstalk = True
518 calib.interChip = {}
520 # calibChip is the detector dimension, which is the detector Id
521 calib._detectorId = calibChip
522 if camera:
523 calib._detectorName = camera[calibChip].getName()
524 calib._detectorSerial = camera[calibChip].getSerial()
526 calib._instrument = instrument
527 calib.updateMetadata(setCalibId=True, setDate=True)
529 # Make an IsrProvenance().
530 provenance = IsrProvenance(calibType="CROSSTALK")
531 provenance._detectorName = calibChip
532 if inputDims:
533 provenance.fromDataIds(inputDims)
534 provenance._instrument = instrument
535 provenance.updateMetadata()
537 return pipeBase.Struct(
538 outputCrosstalk=calib,
539 outputProvenance=provenance,
540 )
542 def measureCrosstalkCoefficients(self, ratios, rejIter, rejSigma):
543 """Measure crosstalk coefficients from the ratios.
545 Given a list of ratios for each target/source amp combination,
546 we measure a sigma clipped mean and error.
548 The coefficient errors returned are the standard deviation of
549 the final set of clipped input ratios.
551 Parameters
552 ----------
553 ratios : `dict` of `dict` of `numpy.ndarray`
554 Catalog of arrays of ratios.
555 rejIter : `int`
556 Number of rejection iterations.
557 rejSigma : `float`
558 Rejection threshold (sigma).
560 Returns
561 -------
562 calib : `lsst.ip.isr.CrosstalkCalib`
563 The output crosstalk calibration.
565 Notes
566 -----
567 The lsstDebug.Info() method can be rewritten for __name__ =
568 `lsst.ip.isr.measureCrosstalk`, and supports the parameters:
570 debug.display['measure'] : `bool`
571 Display the CDF of the combined ratio measurements for
572 a pair of source/target amplifiers from the final set of
573 clipped input ratios.
574 """
575 calib = CrosstalkCalib(nAmp=len(ratios))
577 # Calibration stores coefficients as a numpy ndarray.
578 ordering = list(ratios.keys())
579 for ii, jj in itertools.product(range(calib.nAmp), range(calib.nAmp)):
580 if ii == jj:
581 values = [0.0]
582 else:
583 values = np.array(ratios[ordering[ii]][ordering[jj]])
584 values = values[np.abs(values) < 1.0] # Discard unreasonable values
586 calib.coeffNum[ii][jj] = len(values)
588 if len(values) == 0:
589 self.log.warn("No values for matrix element %d,%d" % (ii, jj))
590 calib.coeffs[ii][jj] = np.nan
591 calib.coeffErr[ii][jj] = np.nan
592 calib.coeffValid[ii][jj] = False
593 else:
594 if ii != jj:
595 for rej in range(rejIter):
596 lo, med, hi = np.percentile(values, [25.0, 50.0, 75.0])
597 sigma = 0.741*(hi - lo)
598 good = np.abs(values - med) < rejSigma*sigma
599 if good.sum() == len(good):
600 break
601 values = values[good]
603 calib.coeffs[ii][jj] = np.mean(values)
604 if calib.coeffNum[ii][jj] == 1:
605 calib.coeffErr[ii][jj] = np.nan
606 else:
607 correctionFactor = sigmaClipCorrection(rejSigma)
608 calib.coeffErr[ii][jj] = np.std(values) * correctionFactor
609 calib.coeffValid[ii][jj] = (np.abs(calib.coeffs[ii][jj])
610 > calib.coeffErr[ii][jj] / np.sqrt(calib.coeffNum[ii][jj]))
612 if calib.coeffNum[ii][jj] > 1:
613 self.debugRatios('measure', ratios, ordering[ii], ordering[jj],
614 calib.coeffs[ii][jj], calib.coeffValid[ii][jj])
616 return calib
618 @staticmethod
619 def filterCrosstalkCalib(inCalib):
620 """Apply valid constraints to the measured values.
622 Any measured coefficient that is determined to be invalid is
623 set to zero, and has the error set to nan. The validation is
624 determined by checking that the measured coefficient is larger
625 than the calculated standard error of the mean.
627 Parameters
628 ----------
629 inCalib : `lsst.ip.isr.CrosstalkCalib`
630 Input calibration to filter.
632 Returns
633 -------
634 outCalib : `lsst.ip.isr.CrosstalkCalib`
635 Filtered calibration.
636 """
637 outCalib = CrosstalkCalib()
638 outCalib.numAmps = inCalib.numAmps
640 outCalib.coeffs = inCalib.coeffs
641 outCalib.coeffs[~inCalib.coeffValid] = 0.0
643 outCalib.coeffErr = inCalib.coeffErr
644 outCalib.coeffErr[~inCalib.coeffValid] = np.nan
646 outCalib.coeffNum = inCalib.coeffNum
647 outCalib.coeffValid = inCalib.coeffValid
649 return outCalib
651 def debugRatios(self, stepname, ratios, i, j, coeff=0.0, valid=False):
652 """Utility function to examine the final CT ratio set.
654 Parameters
655 ----------
656 stepname : `str`
657 State of processing to view.
658 ratios : `dict` of `dict` of `np.ndarray`
659 Array of measured CT ratios, indexed by source/victim
660 amplifier.
661 i : `str`
662 Index of the source amplifier.
663 j : `str`
664 Index of the target amplifier.
665 coeff : `float`, optional
666 Coefficient calculated to plot along with the simple mean.
667 valid : `bool`, optional
668 Validity to be added to the plot title.
669 """
670 frame = getDebugFrame(self._display, stepname)
671 if frame:
672 if i == j or ratios is None or len(ratios) < 1:
673 pass
675 ratioList = ratios[i][j]
676 if ratioList is None or len(ratioList) < 1:
677 pass
679 mean = np.mean(ratioList)
680 std = np.std(ratioList)
681 import matplotlib.pyplot as plt
682 figure = plt.figure(1)
683 figure.clear()
684 plt.hist(x=ratioList, bins=len(ratioList),
685 cumulative=True, color='b', density=True, histtype='step')
686 plt.xlabel("Measured pixel ratio")
687 plt.ylabel(f"CDF: n={len(ratioList)}")
688 plt.xlim(np.percentile(ratioList, [1.0, 99]))
689 plt.axvline(x=mean, color="k")
690 plt.axvline(x=coeff, color='g')
691 plt.axvline(x=(std / np.sqrt(len(ratioList))), color='r')
692 plt.axvline(x=-(std / np.sqrt(len(ratioList))), color='r')
693 plt.title(f"(Source {i} -> Target {j}) mean: {mean:.2g} coeff: {coeff:.2g} valid: {valid}")
694 figure.show()
696 prompt = "Press Enter to continue: "
697 while True:
698 ans = input(prompt).lower()
699 if ans in ("", "c",):
700 break
701 elif ans in ("pdb", "p",):
702 import pdb
703 pdb.set_trace()
704 plt.close()
707class MeasureCrosstalkConfig(Config):
708 extract = ConfigurableField(
709 target=CrosstalkExtractTask,
710 doc="Task to measure pixel ratios.",
711 )
712 solver = ConfigurableField(
713 target=CrosstalkSolveTask,
714 doc="Task to convert ratio lists to crosstalk coefficients.",
715 )
718class MeasureCrosstalkTask(pipeBase.CmdLineTask):
719 """Measure intra-detector crosstalk.
721 See also
722 --------
723 lsst.ip.isr.crosstalk.CrosstalkCalib
724 lsst.cp.pipe.measureCrosstalk.CrosstalkExtractTask
725 lsst.cp.pipe.measureCrosstalk.CrosstalkSolveTask
727 Notes
728 -----
729 The crosstalk this method measures assumes that when a bright
730 pixel is found in one detector amplifier, all other detector
731 amplifiers may see a signal change in the same pixel location
732 (relative to the readout amplifier) as these other pixels are read
733 out at the same time.
735 After processing each input exposure through a limited set of ISR
736 stages, bright unmasked pixels above the threshold are identified.
737 The potential CT signal is found by taking the ratio of the
738 appropriate background-subtracted pixel value on the other
739 amplifiers to the input value on the source amplifier. If the
740 source amplifier has a large number of bright pixels as well, the
741 background level may be elevated, leading to poor ratio
742 measurements.
744 The set of ratios found between each pair of amplifiers across all
745 input exposures is then gathered to produce the final CT
746 coefficients. The sigma-clipped mean and sigma are returned from
747 these sets of ratios, with the coefficient to supply to the ISR
748 CrosstalkTask() being the multiplicative inverse of these values.
750 This Task simply calls the pipetask versions of the measure
751 crosstalk code.
752 """
753 ConfigClass = MeasureCrosstalkConfig
754 _DefaultName = "measureCrosstalk"
756 # Let's use this instead of messing with parseAndRun.
757 RunnerClass = DataRefListRunner
759 def __init__(self, **kwargs):
760 super().__init__(**kwargs)
761 self.makeSubtask("extract")
762 self.makeSubtask("solver")
764 def runDataRef(self, dataRefList):
765 """Run extract task on each of inputs in the dataRef list, then pass
766 that to the solver task.
768 Parameters
769 ----------
770 dataRefList : `list` [`lsst.daf.peristence.ButlerDataRef`]
771 Data references for exposures for detectors to process.
773 Returns
774 -------
775 results : `lsst.pipe.base.Struct`
776 The results struct containing:
778 ``outputCrosstalk`` : `lsst.ip.isr.CrosstalkCalib`
779 Final crosstalk calibration.
780 ``outputProvenance`` : `lsst.ip.isr.IsrProvenance`
781 Provenance data for the new calibration.
783 Raises
784 ------
785 RuntimeError
786 Raised if multiple target detectors are supplied.
787 """
788 dataRef = dataRefList[0]
789 camera = dataRef.get("camera")
791 ratios = []
792 activeChip = None
793 for dataRef in dataRefList:
794 exposure = dataRef.get("postISRCCD")
795 if activeChip:
796 if exposure.getDetector().getName() != activeChip:
797 raise RuntimeError("Too many input detectors supplied!")
798 else:
799 activeChip = exposure.getDetector().getName()
801 self.extract.debugView("extract", exposure)
802 result = self.extract.run(exposure)
803 ratios.append(result.outputRatios)
805 for detIter, detector in enumerate(camera):
806 if detector.getName() == activeChip:
807 detectorId = detIter
808 outputDims = {'instrument': camera.getName(),
809 'detector': detectorId,
810 }
812 finalResults = self.solver.run(ratios, camera=camera, outputDims=outputDims)
813 dataRef.put(finalResults.outputCrosstalk, "crosstalk")
815 return finalResults