Coverage for python/lsst/cp/pipe/ptc/measurePtcGen2Task.py : 23%

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1# This file is part of cp_pipe.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
21#
22import numpy as np
24import lsst.pex.config as pexConfig
25import lsst.pipe.base as pipeBase
26from lsst.cp.pipe.utils import arrangeFlatsByExpTime
28from .photodiode import getBOTphotodiodeData
30from lsst.pipe.tasks.getRepositoryData import DataRefListRunner
31from lsst.cp.pipe.ptc.cpExtractPtcTask import PhotonTransferCurveExtractTask
32from lsst.cp.pipe.ptc.cpSolvePtcTask import PhotonTransferCurveSolveTask
35__all__ = ['MeasurePhotonTransferCurveTask', 'MeasurePhotonTransferCurveTaskConfig']
38class MeasurePhotonTransferCurveTaskConfig(pexConfig.Config):
39 extract = pexConfig.ConfigurableField(
40 target=PhotonTransferCurveExtractTask,
41 doc="Task to measure covariances from flats.",
42 )
43 solve = pexConfig.ConfigurableField(
44 target=PhotonTransferCurveSolveTask,
45 doc="Task to fit models to the measured covariances.",
46 )
47 ccdKey = pexConfig.Field(
48 dtype=str,
49 doc="The key by which to pull a detector from a dataId, e.g. 'ccd' or 'detector'.",
50 default='ccd',
51 )
52 doPhotodiode = pexConfig.Field(
53 dtype=bool,
54 doc="Apply a correction based on the photodiode readings if available?",
55 default=False,
56 )
57 photodiodeDataPath = pexConfig.Field(
58 dtype=str,
59 doc="Gen2 only: path to locate the data photodiode data files.",
60 default=""
61 )
64class MeasurePhotonTransferCurveTask(pipeBase.CmdLineTask):
65 """A class to calculate, fit, and plot a PTC from a set of flat pairs.
66 The Photon Transfer Curve (var(signal) vs mean(signal)) is a standard
67 tool used in astronomical detectors characterization (e.g., Janesick 2001,
68 Janesick 2007). If ptcFitType is "EXPAPPROXIMATION" or "POLYNOMIAL",
69 this task calculates the PTC from a series of pairs of flat-field images;
70 each pair taken at identical exposure times. The difference image of each
71 pair is formed to eliminate fixed pattern noise, and then the variance
72 of the difference image and the mean of the average image
73 are used to produce the PTC. An n-degree polynomial or the approximation
74 in Equation 16 of Astier+19 ("The Shape of the Photon Transfer Curve
75 of CCD sensors", arXiv:1905.08677) can be fitted to the PTC curve. These
76 models include parameters such as the gain (e/DN) and readout noise.
77 Linearizers to correct for signal-chain non-linearity are also calculated.
78 The `Linearizer` class, in general, can support per-amp linearizers, but
79 in this task this is not supported.
80 If ptcFitType is "FULLCOVARIANCE", the covariances of the difference
81 images are calculated via the DFT methods described in Astier+19 and the
82 variances for the PTC are given by the cov[0,0] elements at each signal
83 level. The full model in Equation 20 of Astier+19 is fit to the PTC
84 to get the gain and the noise.
86 Parameters
87 ----------
88 *args: `list`
89 Positional arguments passed to the Task constructor. None used at this
90 time.
91 **kwargs: `dict`
92 Keyword arguments passed on to the Task constructor. None used at this
93 time.
94 """
96 RunnerClass = DataRefListRunner
97 ConfigClass = MeasurePhotonTransferCurveTaskConfig
98 _DefaultName = "measurePhotonTransferCurve"
100 def __init__(self, *args, **kwargs):
101 super().__init__(**kwargs)
102 self.makeSubtask("extract")
103 self.makeSubtask("solve")
105 @pipeBase.timeMethod
106 def runDataRef(self, dataRefList):
107 """Run the Photon Transfer Curve (PTC) measurement task.
108 For a dataRef (which is each detector here),
109 and given a list of exposure pairs (postISR) at different exposure times,
110 measure the PTC.
112 Parameters
113 ----------
114 dataRefList : `list` [`lsst.daf.peristence.ButlerDataRef`]
115 Data references for exposures.
116 """
117 if len(dataRefList) < 2:
118 raise RuntimeError("Insufficient inputs to combine.")
120 # setup necessary objects
121 dataRef = dataRefList[0]
122 camera = dataRef.get('camera')
124 if len(set([dataRef.dataId[self.config.ccdKey] for dataRef in dataRefList])) > 1:
125 raise RuntimeError("Too many detectors supplied")
126 # Get exposure list.
127 expList = []
128 for dataRef in dataRefList:
129 try:
130 tempFlat = dataRef.get("postISRCCD")
131 except RuntimeError:
132 self.log.warn("postISR exposure could not be retrieved. Ignoring flat.")
133 continue
134 expList.append(tempFlat)
135 expIds = [exp.getInfo().getVisitInfo().getExposureId() for exp in expList]
137 # Create dictionary of exposures, keyed by exposure time
138 expDict = arrangeFlatsByExpTime(expList)
139 # Call the "extract" (measure flat covariances) and "solve" (fit covariances) subtasks
140 resultsExtract = self.extract.run(inputExp=expDict, inputDims=expIds)
141 resultsSolve = self.solve.run(resultsExtract.outputCovariances, camera=camera)
143 # Fill up the photodiode data, if found, that will be used by linearity task.
144 # Get expIdPairs from one of the amps
145 expIdsPairsList = []
146 ampNames = resultsSolve.outputPtcDataset.ampNames
147 for ampName in ampNames:
148 tempAmpName = ampName
149 if ampName not in resultsSolve.outputPtcDataset.badAmps:
150 break
151 for pair in resultsSolve.outputPtcDataset.inputExpIdPairs[tempAmpName]:
152 first, second = pair[0]
153 expIdsPairsList.append((first, second))
155 resultsSolve.outputPtcDataset = self._setBOTPhotocharge(dataRef, resultsSolve.outputPtcDataset,
156 expIdsPairsList)
157 self.log.info("Writing PTC data.")
158 dataRef.put(resultsSolve.outputPtcDataset, datasetType="photonTransferCurveDataset")
160 return
162 def _setBOTPhotocharge(self, dataRef, datasetPtc, expIdList):
163 """Set photoCharge attribute in PTC dataset
165 Parameters
166 ----------
167 dataRef : `lsst.daf.peristence.ButlerDataRef`
168 Data reference for exposurre for detector to process.
170 datasetPtc : `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
171 The dataset containing information such as the means, variances
172 and exposure times.
174 expIdList : `list`
175 List with exposure pairs Ids (one pair per list entry).
177 Returns
178 -------
179 datasetPtc: `lsst.ip.isr.ptcDataset.PhotonTransferCurveDataset`
180 This is the same dataset as the input parameter, however,
181 it has been modified to update the datasetPtc.photoCharge
182 attribute.
183 """
184 if self.config.doPhotodiode:
185 for (expId1, expId2) in expIdList:
186 charges = [-1, -1] # necessary to have a not-found value to keep lists in step
187 for i, expId in enumerate([expId1, expId2]):
188 # //1000 is a Gen2 only hack, working around the fact an
189 # exposure's ID is not the same as the expId in the
190 # registry. Currently expId is concatenated with the
191 # zero-padded detector ID. This will all go away in Gen3.
192 dataRef.dataId['expId'] = expId//1000
193 if self.config.photodiodeDataPath:
194 photodiodeData = getBOTphotodiodeData(dataRef, self.config.photodiodeDataPath)
195 else:
196 photodiodeData = getBOTphotodiodeData(dataRef)
197 if photodiodeData: # default path stored in function def to keep task clean
198 charges[i] = photodiodeData.getCharge()
199 else:
200 # full expId (not //1000) here, as that encodes the
201 # the detector number as so is fully qualifying
202 self.log.warn(f"No photodiode data found for {expId}")
204 for ampName in datasetPtc.ampNames:
205 datasetPtc.photoCharge[ampName].append((charges[0], charges[1]))
206 else:
207 # Can't be an empty list, as initialized, because astropy.Table won't allow it
208 # when saving as fits
209 for ampName in datasetPtc.ampNames:
210 datasetPtc.photoCharge[ampName] = np.repeat(np.nan, len(expIdList))
212 return datasetPtc