def summarizeVisit(butler, *, exp=None, extendedSummary=False, **kwargs): from astroquery.simbad import Simbad import astropy.units as u from astropy.time import Time from astropy.coordinates import SkyCoord, EarthLocation, AltAz def _airMassFromrRawMd(md): auxTelLocation = EarthLocation(lat=-30.244639 * u.deg, lon=-70.749417 * u.deg, height=2663 * u.m) time = Time(md['DATE-OBS']) skyLocation = SkyCoord(md['RASTART'], md['DECSTART'], unit=u.deg) altAz = AltAz(obstime=time, location=auxTelLocation) observationAltAz = skyLocation.transform_to(altAz) return observationAltAz.secz.value items = ["OBJECT", "expTime", "FILTER", "imageType"] obj, expTime, filterCompound, imageType = butler.queryMetadata( 'raw', items, **kwargs)[0] filt, grating = filterCompound.split('~') rawMd = butler.get('raw_md', **kwargs) airmass = _airMassFromrRawMd(rawMd) print(f"Object name: {obj}") print(f"expTime: {expTime}s") print(f"imageType: {imageType}") print(f"Filter: {filt}") print(f"Grating: {grating}") print(f"Airmass: {airmass:.3f}") if imageType not in ['BIAS', 'FLAT', 'DARK']: simbadObj = Simbad.query_object(obj) if simbadObj is None: print(f"Failed to find {obj} in Simbad.") else: assert (len(simbadObj.as_array()) == 1) raStr = simbadObj[0]['RA'] decStr = simbadObj[0]['DEC'] skyLocation = SkyCoord(raStr, decStr, unit=(u.hourangle, u.degree), frame='icrs') raRad, decRad = skyLocation.ra.rad, skyLocation.dec.rad print(f"obj RA (str): {raStr}") print(f"obj DEC (str): {decStr}") print(f"obj RA (rad): {raRad:5f}") print(f"obj DEC (rad): {decRad:5f}") print(f"obj RA (deg): {raRad*180/math.pi:5f}") print(f"obj DEC (deg): {decRad*180/math.pi:5f}") if exp is not None: # calc source coords from exp wcs ra = geom.Angle(raRad) dec = geom.Angle(decRad) targetLocation = geom.SpherePoint(ra, dec) pixCoord = exp.getWcs().skyToPixel(targetLocation) print(exp.getWcs()) print(f"Source location: {pixCoord} using exp provided") else: # try to find one, but not too hard datasetTypes = ['calexp', 'quickLookExp', 'postISRCCD'] for datasetType in datasetTypes: wcs = None typeUsed = None try: wcs = butler.get(datasetType + '_wcs', **kwargs) typeUsed = datasetType break except butlerExcept.NoResults: pass if wcs is not None: ra = geom.Angle(raRad) dec = geom.Angle(decRad) targetLocation = geom.SpherePoint(ra, dec) pixCoord = wcs.skyToPixel(targetLocation) print(wcs) print(f"Source location: {pixCoord} using {typeUsed}") if extendedSummary: print('\n--- Extended Summary ---') ranIsr = False if exp is None: print("Running isr to compute image stats...") # catch all the ISR chat # logRedirection1 = LogRedirect(1, open(os.devnull, 'w')) # logRedirection2 = LogRedirect(2, open(os.devnull, 'w')) # import ipdb as pdb; pdb.set_trace() from lsst.ip.isr.isrTask import IsrTask isrConfig = IsrTask.ConfigClass() isrConfig.doLinearize = False isrConfig.doBias = False isrConfig.doFlat = False isrConfig.doDark = False isrConfig.doFringe = False isrConfig.doDefect = False isrConfig.doWrite = False isrTask = IsrTask(config=isrConfig) dataRef = butler.dataRef('raw', **kwargs) exp = isrTask.runDataRef(dataRef).exposure wcs = exp.getWcs() ranIsr = True # logRedirection1.finish() # end re-direct # logRedirection2.finish() # end re-direct print(wcs) if simbadObj and ranIsr: ra = geom.Angle(raRad) dec = geom.Angle(decRad) targetLocation = geom.SpherePoint(ra, dec) pixCoord = wcs.skyToPixel(targetLocation) print( f"Source location: {pixCoord} using postISR just-reconstructed wcs" ) print( f'\nImage stats from {"just-constructed" if ranIsr else "provided"} exp:\n' ) print(f'Image mean: {np.mean(exp.image.array):.2f}') print(f'Image median: {np.median(exp.image.array):.2f}') print(f'Image min: {np.min(exp.image.array):.2f}') print(f'Image max: {np.max(exp.image.array):.2f}') # TODO: quartiles/percentiles here # number of masked pixels, saturated pixels print() print(f'BAD pixels: {countPixels(exp.maskedImage, "BAD")}') print(f'SAT pixels: {countPixels(exp.maskedImage, "SAT")}') print(f'CR pixels: {countPixels(exp.maskedImage, "CR")}') print(f'INTRP pixels: {countPixels(exp.maskedImage, "INTRP")}') print(f'DETECTED pixels: {countPixels(exp.maskedImage, "DETECTED")}') # detector = exp.getDetector() visitInfo = exp.getInfo().getVisitInfo() rotAngle = visitInfo.getBoresightRotAngle() boresight = visitInfo.getBoresightRaDec() md = butler.get('raw_md', **kwargs) print("\n From VisitInfo:") print(f"boresight: {boresight}") print(f"rotAngle: {rotAngle}") print(f" → {rotAngle.asDegrees():.4f} deg") print("\n From raw_md:") print(f"ROTPA: {md['ROTPA']} deg") print(f" → {(md['ROTPA']*math.pi/180):.6f} rad")
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)