def runIsr(self, doCrosstalk): """Run DecamCpIsrTask with or without crosstalk correction """ dataRef = self.butler.dataRef('raw', dataId=self.dataId) rawExposure = self.butler.get('raw', dataId=self.dataId) camera = dataRef.get('camera') config = getObsDecamConfig(IsrTask) config.doCrosstalk = doCrosstalk decamCpIsrTask = IsrTask(config=config) isrData = decamCpIsrTask.readIsrData(dataRef, rawExposure) isrResult = decamCpIsrTask.run(rawExposure, camera=camera, **isrData.getDict()) return isrResult
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 # 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) leftBox = Box2I(overscan1.getMin(), Extent2I(overscan1.getWidth() + image1.getWidth(), height)) rightBox = Box2I(image2.getMin(), Extent2I(image2.getWidth() + overscan2.getWidth(), height)) target1 = Box2I(Point2I(0, 0), imageSize) target2 = Box2I(Point2I(image1.getWidth(), 0), imageSize) # 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] 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 # 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)) self.exposure = exposure self.config = IsrTask.ConfigClass() # 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 # Set the things that match our test setup self.config.overscanFitType = "CHEB" self.config.overscanOrder = 1 self.config.doEmpiricalReadNoise = True self.task = IsrTask(config=self.config) def tearDown(self): del self.exposure def testEmpiricalVariance(self): results = self.task.run(self.exposure) postIsr = results.exposure self.assertFloatsEqual(postIsr.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(postIsr.image.array, 0.0, atol=5.0e-2) self.assertFloatsAlmostEqual(postIsr.variance.array, self.sigma**2, rtol=5.0e-2)
class IsrTaskUnTrimmedTestCases(lsst.utils.tests.TestCase): """Test IsrTask methods using untrimmed raw data. """ def setUp(self): self.config = IsrTaskConfig() self.config.qa = IsrQaConfig() self.task = IsrTask(config=self.config) self.mockConfig = isrMock.IsrMockConfig() self.mockConfig.isTrimmed = False self.doGenerateImage = True self.dataRef = isrMock.DataRefMock(config=self.mockConfig) self.camera = isrMock.IsrMock(config=self.mockConfig).getCamera() self.inputExp = isrMock.RawMock(config=self.mockConfig).run() self.amp = self.inputExp.getDetector()[0] self.mi = self.inputExp.getMaskedImage() def batchSetConfiguration(self, value): """Set the configuration state to a consistent value. Disable options we do not need as well. Parameters ---------- value : `bool` Value to switch common ISR configuration options to. """ self.config.qa.flatness.meshX = 20 self.config.qa.flatness.meshY = 20 self.config.doWrite = False self.config.doLinearize = False self.config.doCrosstalk = False self.config.doConvertIntToFloat = value self.config.doSaturation = value self.config.doSuspect = value self.config.doSetBadRegions = value self.config.doOverscan = value self.config.doBias = value self.config.doVariance = value self.config.doWidenSaturationTrails = value self.config.doBrighterFatter = value self.config.doDefect = value self.config.doSaturationInterpolation = value self.config.doDark = value self.config.doStrayLight = value self.config.doFlat = value self.config.doFringe = value self.config.doMeasureBackground = value self.config.doVignette = value self.config.doAttachTransmissionCurve = value self.config.doUseOpticsTransmission = value self.config.doUseFilterTransmission = value self.config.doUseSensorTransmission = value self.config.doUseAtmosphereTransmission = value self.config.qa.saveStats = value self.config.qa.doThumbnailOss = value self.config.qa.doThumbnailFlattened = value self.config.doApplyGains = not value self.config.doCameraSpecificMasking = value def validateIsrResults(self): """results should be a struct with components that are not None if included in the configuration file. Returns ------- results : `pipeBase.Struct` Results struct generated from the current ISR configuration. """ self.task = IsrTask(config=self.config) results = self.task.run( self.inputExp, camera=self.camera, bias=self.dataRef.get("bias"), dark=self.dataRef.get("dark"), flat=self.dataRef.get("flat"), bfKernel=self.dataRef.get("bfKernel"), defects=self.dataRef.get("defects"), fringes=Struct(fringes=self.dataRef.get("fringe"), seed=1234), opticsTransmission=self.dataRef.get("transmission_"), filterTransmission=self.dataRef.get("transmission_"), sensorTransmission=self.dataRef.get("transmission_"), atmosphereTransmission=self.dataRef.get("transmission_")) self.assertIsInstance(results, Struct) self.assertIsInstance(results.exposure, afwImage.Exposure) return results def test_overscanCorrection(self): """Expect that this should reduce the image variance with a full fit. The default fitType of MEDIAN will reduce the median value. This needs to operate on a RawMock() to have overscan data to use. The output types may be different when fitType != MEDIAN. """ statBefore = computeImageMedianAndStd( self.inputExp.image[self.amp.getRawDataBBox()]) oscanResults = self.task.overscanCorrection(self.inputExp, self.amp) self.assertIsInstance(oscanResults, Struct) self.assertIsInstance(oscanResults.imageFit, float) self.assertIsInstance(oscanResults.overscanFit, float) self.assertIsInstance(oscanResults.overscanImage, afwImage.MaskedImageF) statAfter = computeImageMedianAndStd( self.inputExp.image[self.amp.getRawDataBBox()]) self.assertLess(statAfter[0], statBefore[0]) def test_overscanCorrectionMedianPerRow(self): """Expect that this should reduce the image variance with a full fit. fitType of MEDIAN_PER_ROW will reduce the median value. This needs to operate on a RawMock() to have overscan data to use. The output types may be different when fitType != MEDIAN_PER_ROW. """ self.config.overscan.fitType = 'MEDIAN_PER_ROW' statBefore = computeImageMedianAndStd( self.inputExp.image[self.amp.getRawDataBBox()]) oscanResults = self.task.overscanCorrection(self.inputExp, self.amp) self.assertIsInstance(oscanResults, Struct) self.assertIsInstance(oscanResults.imageFit, afwImage.ImageF) self.assertIsInstance(oscanResults.overscanFit, afwImage.ImageF) self.assertIsInstance(oscanResults.overscanImage, afwImage.MaskedImageF) statAfter = computeImageMedianAndStd( self.inputExp.image[self.amp.getRawDataBBox()]) self.assertLess(statAfter[0], statBefore[0]) def test_runDataRef(self): """Expect a dataRef to be handled correctly. """ self.config.doLinearize = False self.config.doWrite = False self.task = IsrTask(config=self.config) results = self.task.runDataRef(self.dataRef) self.assertIsInstance(results, Struct) self.assertIsInstance(results.exposure, afwImage.Exposure) def test_run_allTrue(self): """Expect successful run with expected outputs when all non-exclusive configuration options are on. Output results should be tested more precisely by the individual function tests. """ self.batchSetConfiguration(True) self.validateIsrResults() def test_run_allFalse(self): """Expect successful run with expected outputs when all non-exclusive configuration options are off. Output results should be tested more precisely by the individual function tests. """ self.batchSetConfiguration(False) self.validateIsrResults() def test_failCases(self): """Expect failure with crosstalk enabled. Output results should be tested more precisely by the individual function tests. """ self.batchSetConfiguration(True) # This breaks it self.config.doCrosstalk = True with self.assertRaises(RuntimeError): self.validateIsrResults() def test_maskingCase_negativeVariance(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.doSaturation = False self.config.doWidenSaturationTrails = False self.config.doSaturationInterpolation = False self.config.doSuspect = False self.config.doSetBadRegions = False self.config.doDefect = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = True self.config.doInterpolate = False results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 40800) def test_maskingCase_noMasking(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.doSaturation = False self.config.doWidenSaturationTrails = False self.config.doSaturationInterpolation = False self.config.doSuspect = False self.config.doSetBadRegions = False self.config.doDefect = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = False self.config.doInterpolate = False results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0) def test_maskingCase_satMasking(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.saturation = 20000.0 self.config.doSaturation = True self.config.doWidenSaturationTrails = True self.config.doSaturationInterpolation = False self.config.doSuspect = False self.config.doSetBadRegions = False self.config.doDefect = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = False # These are mock images. results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0) def test_maskingCase_satMaskingAndInterp(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.saturation = 20000.0 self.config.doSaturation = True self.config.doWidenSaturationTrails = True self.config.doSaturationInterpolation = True self.config.doSuspect = False self.config.doSetBadRegions = False self.config.doDefect = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = False # These are mock images. results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0) def test_maskingCase_throughEdge(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.saturation = 20000.0 self.config.doSaturation = True self.config.doWidenSaturationTrails = True self.config.doSaturationInterpolation = True self.config.numEdgeSuspect = 5 self.config.doSuspect = True self.config.doSetBadRegions = False self.config.doDefect = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = False # These are mock images. results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0) def test_maskingCase_throughDefects(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.saturation = 20000.0 self.config.doSaturation = True self.config.doWidenSaturationTrails = True self.config.doSaturationInterpolation = True self.config.numEdgeSuspect = 5 self.config.doSuspect = True self.config.doDefect = True self.config.doSetBadRegions = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = False # These are mock images. results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 3940) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000) def test_maskingCase_throughDefectsAmpEdges(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.saturation = 20000.0 self.config.doSaturation = True self.config.doWidenSaturationTrails = True self.config.doSaturationInterpolation = True self.config.numEdgeSuspect = 5 self.config.doSuspect = True self.config.doDefect = True self.config.edgeMaskLevel = 'AMP' self.config.doSetBadRegions = False self.config.doBrighterFatter = False self.config.maskNegativeVariance = False # These are mock images. results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 11280) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000) def test_maskingCase_throughBad(self): """Test masking cases of configuration parameters. """ self.batchSetConfiguration(True) self.config.overscanFitType = "POLY" self.config.overscanOrder = 1 self.config.saturation = 20000.0 self.config.doSaturation = True self.config.doWidenSaturationTrails = True self.config.doSaturationInterpolation = True self.config.doSuspect = True self.config.doDefect = True self.config.doSetBadRegions = True self.config.doBrighterFatter = False self.config.maskNegativeVariance = False # These are mock images. results = self.validateIsrResults() self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000) self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0) self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)
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 # 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) leftBox = Box2I( overscan1.getMin(), Extent2I(overscan1.getWidth() + image1.getWidth(), height)) rightBox = Box2I( image2.getMin(), Extent2I(image2.getWidth() + overscan2.getWidth(), height)) target1 = Box2I(Point2I(0, 0), imageSize) target2 = Box2I(Point2I(image1.getWidth(), 0), imageSize) # 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] 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 # Construct the detectors amp1 = makeAmplifier("left", target1, image1, overscan1, gain, readNoise, saturation) amp2 = makeAmplifier("right", target2, image2, overscan2, gain, readNoise, saturation) ccdBox = Box2I(Point2I(0, 0), Extent2I(image1.getWidth() + image2.getWidth(), height)) camBuilder = cameraGeom.Camera.Builder("fakeCam") detBuilder = camBuilder.add("detector", 1) detBuilder.setSerial("det1") detBuilder.setBBox(ccdBox) detBuilder.setPixelSize(Extent2D(1.0, 1.0)) detBuilder.setOrientation(cameraGeom.Orientation()) detBuilder.append(amp1) detBuilder.append(amp2) cam = camBuilder.finish() exposure.setDetector(cam.get('detector')) header = PropertyList() header.add("EXPTIME", 0.0) exposure.getInfo().setVisitInfo(VisitInfo(header)) self.exposure = exposure self.config = IsrTask.ConfigClass() # 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.doWrite = False self.config.expectWcs = False self.config.doLinearize = False self.config.doCrosstalk = False self.config.doBrighterFatter = False self.config.doAttachTransmissionCurve = False self.config.doAssembleCcd = False self.config.doNanMasking = False self.config.doInterpolate = False self.config.maskNegativeVariance = False # This runs on mocks. # Set the things that match our test setup self.config.overscan.fitType = "CHEB" self.config.overscan.order = 1 self.config.doEmpiricalReadNoise = True self.task = IsrTask(config=self.config) def tearDown(self): del self.exposure def testEmpiricalVariance(self): results = self.task.run(self.exposure) postIsr = results.exposure self.assertFloatsEqual(postIsr.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(np.median(postIsr.image.array), 0.0, atol=5.0e-2) self.assertFloatsAlmostEqual(np.nanmedian(postIsr.variance.array), self.sigma**2, rtol=5.0e-2)
print("finished ingesting spots images") spots_butler = Butler(SPOTS_REPO_DIR) visits = [] my_metaData = spots_butler.queryMetadata('raw', ['visit', 'dateObs']) for item in my_metaData: visits.append(item[0]) byamp_results = [] byamp_corrected_results = [] for visit in visits: print("Getting exposure # %d"%visit) sys.stdout.flush() exposure = spots_butler.get('raw', dataId={'visit': visit, 'detector': DETECTOR}) # Perform the instrument signature removal (mainly assembling the CCD) isrTask = IsrTask(config=isrConfig) exposure_isr = isrTask.run(exposure).exposure # For now, we're applying the gain manually ccd = exposure_isr.getDetector() for do_bf_corr in [False, True]: exposure_copy=exposure_isr.clone() for amp in ccd: if spots_bbox.overlaps(amp.getBBox()): gain = gain_data[amp.getName()] img = exposure_copy.image sim = img.Factory(img, amp.getBBox()) sim *= gain print(amp.getName(), gain, amp.getBBox()) sys.stdout.flush() if do_bf_corr: brighterFatterCorrection(exposure_copy[amp.getBBox()],bf_kernel.kernel[amp.getName()],20,10,False) else: