def ISR(self, fixCRs = True): """Run the ISR stage, removing CRs and patching bad columns""" mi = self.exposure.getMaskedImage() mi.getMask().set(0) # XXX # # Fix defects # # Mask known bad pixels # badPixels = measAlg.defects.policyToBadRegionList(os.path.join(eups.productDir("meas_algorithms"), "examples", "BadPixels.paf")) # did someone lie about the origin of the maskedImage? If so, adjust bad pixel list if self.XY0.getX() != mi.getX0() or self.XY0.getY() != mi.getY0(): dx = self.XY0.getX() - mi.getX0() dy = self.XY0.getY() - mi.getY0() for bp in badPixels: bp.shift(-dx, -dy) measAlg.interpolateOverDefects(mi, self.psf, badPixels) # # Subtract background # bctrl = afwMath.BackgroundControl("LINEAR"); bctrl.setNxSample(int(mi.getWidth()/256) + 1); bctrl.setNySample(int(mi.getHeight()/256) + 1); backobj = afwMath.makeBackground(mi.getImage(), bctrl) img = mi.getImage(); img -= backobj.getImageF(); del img # # Remove CRs # if fixCRs: crConfig = measAlg.FindCosmicRaysConfig() crs = measAlg.findCosmicRays(mi, self.psf, 0, pexConfig.makePolicy(crConfig)) if self.display: ds9.mtv(mi, frame = 0, lowOrderBits = True)
def testDetection(self): """Test CR detection.""" # # Subtract background # bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE) bctrl.setNxSample(int(self.mi.getWidth() / 256) + 1) bctrl.setNySample(int(self.mi.getHeight() / 256) + 1) bctrl.getStatisticsControl().setNumSigmaClip(3.0) bctrl.getStatisticsControl().setNumIter(2) im = self.mi.getImage() try: backobj = afwMath.makeBackground(im, bctrl) except Exception as e: print(e, file=sys.stderr) bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT) backobj = afwMath.makeBackground(im, bctrl) im -= backobj.getImageF() if display: frame = 0 disp = afwDisplay.Display(frame=frame) disp.mtv(self.mi, title=self._testMethodName + ": Raw") # raw frame if self.mi.getWidth() > 256: disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) # # Mask known bad pixels # measAlgorithmsDir = lsst.utils.getPackageDir('meas_algorithms') badPixels = defects.policyToBadRegionList( os.path.join(measAlgorithmsDir, "policy", "BadPixels.paf")) # did someone lie about the origin of the maskedImage? If so, adjust bad pixel list if self.XY0.getX() != self.mi.getX0() or self.XY0.getY( ) != self.mi.getY0(): dx = self.XY0.getX() - self.mi.getX0() dy = self.XY0.getY() - self.mi.getY0() for bp in badPixels: bp.shift(-dx, -dy) algorithms.interpolateOverDefects(self.mi, self.psf, badPixels) stats = afwMath.makeStatistics(self.mi.getImage(), afwMath.MEANCLIP | afwMath.STDEVCLIP) background = stats.getValue(afwMath.MEANCLIP) crConfig = algorithms.FindCosmicRaysConfig() crs = algorithms.findCosmicRays(self.mi, self.psf, background, pexConfig.makePolicy(crConfig)) if display: frame += 1 disp = afwDisplay.Display(frame=frame) disp.mtv(self.mi, title=self._testMethodName + ": CRs removed") if self.mi.getWidth() > 256: disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) print("Detected %d CRs" % len(crs)) if display and False: for cr in crs: bbox = cr.getBBox() bbox.shift( lsst.geom.ExtentI(-self.mi.getX0(), -self.mi.getY0())) disp.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5), (bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5), (bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5), (bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5), (bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)]) if self.nCR is not None: self.assertEqual(len(crs), self.nCR)
def testDetection(self): crConfig = algorithms.FindCosmicRaysConfig() crs = algorithms.findCosmicRays(self.mi, self.psf, 0.0, pexConfig.makePolicy(crConfig)) self.assertEqual(len(crs), 0, "Found %d CRs in empty image" % len(crs))
def testDetection(self): """Test CR detection.""" # # Subtract background # bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE) bctrl.setNxSample(int(self.mi.getWidth() / 256) + 1) bctrl.setNySample(int(self.mi.getHeight() / 256) + 1) bctrl.getStatisticsControl().setNumSigmaClip(3.0) bctrl.getStatisticsControl().setNumIter(2) im = self.mi.getImage() try: backobj = afwMath.makeBackground(im, bctrl) except Exception as e: print(e, file=sys.stderr) bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT) backobj = afwMath.makeBackground(im, bctrl) im -= backobj.getImageF() if display: frame = 0 disp = afwDisplay.Display(frame=frame) disp.mtv(self.mi, title=self._testMethodName + ": Raw") # raw frame if self.mi.getWidth() > 256: disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) # # Mask known bad pixels # badPixels = testUtils.makeDefectList() algorithms.interpolateOverDefects(self.mi, self.psf, badPixels) stats = afwMath.makeStatistics(self.mi.getImage(), afwMath.MEANCLIP | afwMath.STDEVCLIP) background = stats.getValue(afwMath.MEANCLIP) crConfig = algorithms.FindCosmicRaysConfig() crs = algorithms.findCosmicRays(self.mi, self.psf, background, pexConfig.makePropertySet(crConfig)) if display: frame += 1 disp = afwDisplay.Display(frame=frame) disp.mtv(self.mi, title=self._testMethodName + ": CRs removed") if self.mi.getWidth() > 256: disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) print("Detected %d CRs" % len(crs)) if display and False: for cr in crs: bbox = cr.getBBox() bbox.shift( lsst.geom.ExtentI(-self.mi.getX0(), -self.mi.getY0())) disp.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5), (bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5), (bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5), (bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5), (bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)]) if self.nCR is not None: self.assertEqual(len(crs), self.nCR)
def testDetection(self): """Test object detection""" # # Fix defects # # Mask known bad pixels # measAlgorithmsDir = lsst.utils.getPackageDir('meas_algorithms') badPixels = defects.policyToBadRegionList(os.path.join(measAlgorithmsDir, "policy/BadPixels.paf")) # did someone lie about the origin of the maskedImage? If so, adjust bad pixel list if self.XY0.getX() != self.mi.getX0() or self.XY0.getY() != self.mi.getY0(): dx = self.XY0.getX() - self.mi.getX0() dy = self.XY0.getY() - self.mi.getY0() for bp in badPixels: bp.shift(-dx, -dy) algorithms.interpolateOverDefects(self.mi, self.psf, badPixels) # # Subtract background # bgGridSize = 64 # was 256 ... but that gives only one region and the spline breaks bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE) bctrl.setNxSample(int(self.mi.getWidth()/bgGridSize) + 1) bctrl.setNySample(int(self.mi.getHeight()/bgGridSize) + 1) backobj = afwMath.makeBackground(self.mi.getImage(), bctrl) self.mi.getImage()[:] -= backobj.getImageF() # # Remove CRs # crConfig = algorithms.FindCosmicRaysConfig() algorithms.findCosmicRays(self.mi, self.psf, 0, pexConfig.makePolicy(crConfig)) # # We do a pretty good job of interpolating, so don't propagagate the convolved CR/INTRP bits # (we'll keep them for the original CR/INTRP pixels) # savedMask = self.mi.getMask().Factory(self.mi.getMask(), True) saveBits = savedMask.getPlaneBitMask("CR") | \ savedMask.getPlaneBitMask("BAD") | \ savedMask.getPlaneBitMask("INTRP") # Bits to not convolve savedMask &= saveBits msk = self.mi.getMask() msk &= ~saveBits # Clear the saved bits del msk # # Smooth image # psf = algorithms.DoubleGaussianPsf(15, 15, self.FWHM/(2*math.sqrt(2*math.log(2)))) cnvImage = self.mi.Factory(self.mi.getBBox()) kernel = psf.getKernel() afwMath.convolve(cnvImage, self.mi, kernel, afwMath.ConvolutionControl()) msk = cnvImage.getMask() msk |= savedMask # restore the saved bits del msk threshold = afwDetection.Threshold(3, afwDetection.Threshold.STDEV) # # Only search the part of the frame that was PSF-smoothed # llc = lsst.geom.PointI(psf.getKernel().getWidth()//2, psf.getKernel().getHeight()//2) urc = lsst.geom.PointI(cnvImage.getWidth() - llc[0] - 1, cnvImage.getHeight() - llc[1] - 1) middle = cnvImage.Factory(cnvImage, lsst.geom.BoxI(llc, urc), afwImage.LOCAL) ds = afwDetection.FootprintSet(middle, threshold, "DETECTED") del middle # # Reinstate the saved (e.g. BAD) (and also the DETECTED | EDGE) bits in the unsmoothed image # savedMask[:] = cnvImage.getMask() msk = self.mi.getMask() msk |= savedMask del msk del savedMask if display: disp = afwDisplay.Display(frame=2) disp.mtv(self.mi, title=self._testMethodName + ": image") afwDisplay.Display(frame=3).mtv(cnvImage, title=self._testMethodName + ": cnvImage") # # Time to actually measure # schema = afwTable.SourceTable.makeMinimalSchema() sfm_config = measBase.SingleFrameMeasurementConfig() sfm_config.plugins = ["base_SdssCentroid", "base_CircularApertureFlux", "base_PsfFlux", "base_SdssShape", "base_GaussianFlux", "base_PixelFlags"] sfm_config.slots.centroid = "base_SdssCentroid" sfm_config.slots.shape = "base_SdssShape" sfm_config.slots.psfFlux = "base_PsfFlux" sfm_config.slots.gaussianFlux = None sfm_config.slots.apFlux = "base_CircularApertureFlux_3_0" sfm_config.slots.modelFlux = "base_GaussianFlux" sfm_config.slots.calibFlux = None sfm_config.plugins["base_SdssShape"].maxShift = 10.0 sfm_config.plugins["base_CircularApertureFlux"].radii = [3.0] task = measBase.SingleFrameMeasurementTask(schema, config=sfm_config) measCat = afwTable.SourceCatalog(schema) # detect the sources and run with the measurement task ds.makeSources(measCat) self.exposure.setPsf(self.psf) task.run(measCat, self.exposure) self.assertGreater(len(measCat), 0) for source in measCat: if source.get("base_PixelFlags_flag_edge"): continue if display: disp.dot("+", source.getX(), source.getY())
class CosmicRayTestCase(unittest.TestCase): """A test case for Cosmic Ray detection""" def setUp(self): self.FWHM = 5 # pixels self.psf = algorithms.DoubleGaussianPsf( 29, 29, self.FWHM / (2 * sqrt(2 * log(2)))) self.mi = afwImage.MaskedImageF(imageFile) self.XY0 = afwGeom.PointI(0, 0) # origin of the subimage we use if imageFile == imageFile0: if True: # use full image, trimmed to data section self.XY0 = afwGeom.PointI(32, 2) self.mi = self.mi.Factory( self.mi, afwGeom.BoxI(self.XY0, afwGeom.PointI(2079, 4609)), afwImage.LOCAL) self.mi.setXY0(afwGeom.PointI(0, 0)) self.nCR = 1076 # number of CRs we should detect else: # use sub-image if True: self.XY0 = afwGeom.PointI(824, 140) self.nCR = 10 else: self.XY0 = afwGeom.PointI(280, 2750) self.nCR = 2 self.mi = self.mi.Factory( self.mi, afwGeom.BoxI(self.XY0, afwGeom.ExtentI(256, 256), afwImage.LOCAL)) self.mi.setXY0(afwGeom.PointI(0, 0)) else: self.nCR = None self.mi.getMask().addMaskPlane("DETECTED") def tearDown(self): del self.mi del self.psf def testDetection(self): """Test CR detection""" # # Subtract background # bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE) bctrl.setNxSample(int(self.mi.getWidth() / 256) + 1) bctrl.setNySample(int(self.mi.getHeight() / 256) + 1) bctrl.getStatisticsControl().setNumSigmaClip(3.0) bctrl.getStatisticsControl().setNumIter(2) im = self.mi.getImage() try: backobj = afwMath.makeBackground(im, bctrl) except Exception, e: print >> sys.stderr, e, bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT) backobj = afwMath.makeBackground(im, bctrl) im -= backobj.getImageF() if display: frame = 0 ds9.mtv(self.mi, frame=frame, title="Raw") # raw frame if self.mi.getWidth() > 256: ds9.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) # # Mask known bad pixels # badPixels = defects.policyToBadRegionList( os.path.join(os.environ["MEAS_ALGORITHMS_DIR"], "policy", "BadPixels.paf")) # did someone lie about the origin of the maskedImage? If so, adjust bad pixel list if self.XY0.getX() != self.mi.getX0() or self.XY0.getY( ) != self.mi.getY0(): dx = self.XY0.getX() - self.mi.getX0() dy = self.XY0.getY() - self.mi.getY0() for bp in badPixels: bp.shift(-dx, -dy) algorithms.interpolateOverDefects(self.mi, self.psf, badPixels) stats = afwMath.makeStatistics(self.mi.getImage(), afwMath.MEANCLIP | afwMath.STDEVCLIP) background = stats.getValue(afwMath.MEANCLIP) crConfig = algorithms.FindCosmicRaysConfig() crs = algorithms.findCosmicRays(self.mi, self.psf, background, pexConfig.makePolicy(crConfig)) if display: ds9.mtv(self.mi, frame=frame + 1, title="CRs removed") if self.mi.getWidth() > 256: ds9.pan(944 - self.mi.getX0(), 260 - self.mi.getY0()) print "Detected %d CRs" % len(crs) if display and False: for cr in crs: bbox = cr.getBBox() bbox.shift(afwGeom.ExtentI(-self.mi.getX0(), -self.mi.getY0())) ds9.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5), (bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5), (bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5), (bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5), (bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)], frame=frame + 1) if self.nCR is not None: self.assertEqual(len(crs), self.nCR)