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IsrTask: add option to set variance from empirical read noise
The read noise is measured from the overscan. This might be useful when working on detectors whose read noise hasn't been measured, or drifts due to hardware tests.
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| Original file line number | Diff line number | Diff line change |
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| # | ||
| # LSST Data Management System | ||
| # Copyright 2018 LSST Corporation. | ||
| # | ||
| # This product includes software developed by the | ||
| # LSST Project (http://www.lsst.org/). | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the LSST License Statement and | ||
| # the GNU General Public License along with this program. If not, | ||
| # see <http://www.lsstcorp.org/LegalNotices/>. | ||
| # | ||
| import numpy as np | ||
| import unittest | ||
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| import lsst.utils.tests | ||
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| from lsst.daf.base import PropertyList | ||
| from lsst.afw.cameraGeom import Detector, SCIENCE, Orientation, TransformMap, CameraSys | ||
| from lsst.afw.table import AmpInfoCatalog, AmpInfoTable | ||
| from lsst.afw.geom import Point2I, Extent2I, Box2I, Extent2D | ||
| from lsst.afw.image import ExposureF, VisitInfo | ||
| from lsst.pipe.base import Struct | ||
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| from lsst.ip.isr.isrTask import IsrTask | ||
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| def makeAmplifier(catalog, name, bbox, rawImageBox, overscanBox, gain, readNoise, saturation): | ||
| amp = catalog.addNew() | ||
| amp.setName(name) | ||
| amp.setBBox(bbox) | ||
| amp.setRawDataBBox(rawImageBox) | ||
| amp.setRawHorizontalOverscanBBox(overscanBox) | ||
| amp.setHasRawInfo(True) | ||
| amp.setGain(gain) | ||
| amp.setReadNoise(readNoise) | ||
| amp.setSaturation(saturation) | ||
| amp.setSuspectLevel(np.nan) | ||
| return amp | ||
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| class EmpiricalVarianceTestCast(lsst.utils.tests.TestCase): | ||
| def setUp(self): | ||
| """Constructs a CCD with two amplifiers and prepares for ISR""" | ||
| np.random.seed(12345) | ||
| baseValue = 100.0 | ||
| gain = 1.0 | ||
| readNoise = 123456789.0 | ||
| saturation = 987654321.0 | ||
| height = 234 | ||
| imageSize = Extent2I(123, height) | ||
| overscanSize = Extent2I(16, height) | ||
| self.sigma = 1.234 | ||
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| # Set up the various regions | ||
| overscan1 = Box2I(Point2I(0, 0), overscanSize) | ||
| image1 = Box2I(Point2I(overscanSize[0], 0), imageSize) | ||
| image2 = Box2I(Point2I(overscanSize[0] + imageSize[0], 0), imageSize) | ||
| overscan2 = Box2I(Point2I(overscanSize[0] + 2*imageSize[0], 0), overscanSize) | ||
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| leftBox = Box2I(overscan1.getMin(), Extent2I(overscan1.getWidth() + image1.getWidth(), height)) | ||
| rightBox = Box2I(image2.getMin(), Extent2I(image2.getWidth() + overscan2.getWidth(), height)) | ||
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| target1 = Box2I(Point2I(0, 0), imageSize) | ||
| target2 = Box2I(Point2I(image1.getWidth(), 0), imageSize) | ||
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| # Set the pixels | ||
| exposure = ExposureF(Box2I(Point2I(0, 0), Extent2I(imageSize[0]*2 + overscanSize[0]*2, height))) | ||
| yy = np.arange(0, height, 1, dtype=np.float32) | ||
| leftImage = ExposureF(exposure, leftBox) | ||
| leftImage.image.array[:] = baseValue + yy[:, np.newaxis] | ||
| rightImage = ExposureF(exposure, rightBox) | ||
| rightImage.image.array[:] = baseValue - yy[:, np.newaxis] | ||
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| leftOverscan = ExposureF(exposure, overscan1) | ||
| leftOverscan.image.array += np.random.normal(0.0, self.sigma, leftOverscan.image.array.shape) | ||
| rightOverscan = ExposureF(exposure, overscan2) | ||
| rightOverscan.image.array += np.random.normal(0.0, self.sigma, leftOverscan.image.array.shape) | ||
| exposure.mask.array[:] = 0.0 | ||
| exposure.variance.array[:] = np.nan | ||
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| # Construct the detectors | ||
| amps = AmpInfoCatalog(AmpInfoTable.makeMinimalSchema()) | ||
| makeAmplifier(amps, "left", target1, image1, overscan1, gain, readNoise, saturation) | ||
| makeAmplifier(amps, "right", target2, image2, overscan2, gain, readNoise, saturation) | ||
| ccdBox = Box2I(Point2I(0, 0), Extent2I(image1.getWidth() + image2.getWidth(), height)) | ||
| ccd = Detector("detector", 1, SCIENCE, "det1", ccdBox, amps, Orientation(), Extent2D(1.0, 1.0), {}) | ||
| exposure.setDetector(ccd) | ||
| header = PropertyList() | ||
| header.add("EXPTIME", 0.0) | ||
| exposure.getInfo().setVisitInfo(VisitInfo(header)) | ||
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| self.exposure = exposure | ||
| self.config = IsrTask.ConfigClass() | ||
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| # Disable everything we don't care about | ||
| self.config.doBias = False | ||
| self.config.doDark = False | ||
| self.config.doFlat = False | ||
| self.config.doFringe = False | ||
| self.config.doDefect = False | ||
| self.config.doAddDistortionModel = False | ||
| self.config.doWrite = False | ||
| self.config.expectWcs = False | ||
| self.config.doLinearize = False | ||
| self.config.doCrosstalk = False | ||
| self.config.doBrighterFatter = False | ||
| self.config.doAttachTransmissionCurve = False | ||
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| # Set the things that match our test setup | ||
| self.config.overscanFitType = "CHEB" | ||
| self.config.overscanOrder = 1 | ||
| self.config.doEmpiricalReadNoise = True | ||
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| self.task = IsrTask(config=self.config) | ||
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| def tearDown(self): | ||
| del self.exposure | ||
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| def testEmpiricalVariance(self): | ||
| results = self.task.run(self.exposure) | ||
| exposure = results.exposure | ||
| self.assertFloatsEqual(exposure.mask.array, 0) | ||
| # Image is not exactly zero because the noise in the overscan (required to be able to set | ||
| # the empirical variance) leads to a slight misestimate in the polynomial fit. | ||
| self.assertFloatsAlmostEqual(exposure.image.array, 0.0, atol=5.0e-2) | ||
| self.assertFloatsAlmostEqual(exposure.variance.array, self.sigma**2, rtol=5.0e-2) | ||
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| class MemoryTester(lsst.utils.tests.MemoryTestCase): | ||
| pass | ||
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| def setup_module(module): | ||
| lsst.utils.tests.init() | ||
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| if __name__ == "__main__": | ||
| import sys | ||
| setup_module(sys.modules[__name__]) | ||
| unittest.main() |