def sourceTableToCandidateList(sourceTable,
templateExposure,
scienceExposure,
kConfig,
dConfig,
log,
basisList,
doBuild=False):
"""Takes an input list of Sources, and turns them into
KernelCandidates for fitting of the Psf-matching kernel."""
kernelSize = basisList[0].getWidth()
footprintList = sourceToFootprintList(list(sourceTable), templateExposure,
scienceExposure, kernelSize, dConfig,
log)
candList = []
if doBuild and not basisList:
doBuild = False
else:
policy = pexConfig.makePolicy(kConfig)
visitor = diffimLib.BuildSingleKernelVisitorF(basisList, policy)
policy = pexConfig.makePolicy(kConfig)
for cand in footprintList:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateExposure.getMaskedImage(), bbox)
smi = afwImage.MaskedImageF(scienceExposure.getMaskedImage(), bbox)
kCand = diffimLib.makeKernelCandidate(cand['source'], tmi, smi, policy)
if doBuild:
visitor.processCandidate(kCand)
kCand.setStatus(afwMath.SpatialCellCandidate.UNKNOWN)
candList.append(kCand)
return candList
def sourceTableToCandidateList(sourceTable, templateExposure, scienceExposure, kConfig, dConfig, log,
basisList, doBuild=False):
"""Takes an input list of Sources, and turns them into
KernelCandidates for fitting of the Psf-matching kernel."""
kernelSize = basisList[0].getWidth()
footprintList = sourceToFootprintList(list(sourceTable), templateExposure, scienceExposure,
kernelSize, dConfig, log)
candList = []
if doBuild and not basisList:
doBuild = False
else:
policy = pexConfig.makePolicy(kConfig)
visitor = diffimLib.BuildSingleKernelVisitorF(basisList, policy)
policy = pexConfig.makePolicy(kConfig)
for cand in footprintList:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateExposure.getMaskedImage(), bbox)
smi = afwImage.MaskedImageF(scienceExposure.getMaskedImage(), bbox)
kCand = diffimLib.makeKernelCandidate(cand['source'], tmi, smi, policy)
if doBuild:
visitor.processCandidate(kCand)
kCand.setStatus(afwMath.SpatialCellCandidate.UNKNOWN)
candList.append(kCand)
return candList
def sourceTableToCandidateList(sourceTable,
templateExposure,
scienceExposure,
kConfig,
dConfig,
log,
basisList,
doBuild=False):
"""Convert a list of Sources into KernelCandidates.
The KernelCandidates are used for fitting the Psf-matching kernel.
Parameters
----------
sourceTable : TODO: DM-17458
TODO: DM-17458
templateExposure : TODO: DM-17458
TODO: DM-17458
scienceExposure : TODO: DM-17458
TODO: DM-17458
kConfig : TODO: DM-17458
TODO: DM-17458
dConfig : TODO: DM-17458
TODO: DM-17458
log : TODO: DM-17458
TODO: DM-17458
basisList : TODO: DM-17458
TODO: DM-17458
doBuild : `bool`, optional
TODO: DM-17458
Returns
-------
TODO: DM-17458
TODO: DM-17458
"""
kernelSize = basisList[0].getWidth()
footprintList = sourceToFootprintList(list(sourceTable), templateExposure,
scienceExposure, kernelSize, dConfig,
log)
candList = []
if doBuild and not basisList:
doBuild = False
else:
policy = pexConfig.makePolicy(kConfig)
visitor = diffimLib.BuildSingleKernelVisitorF(basisList, policy)
policy = pexConfig.makePolicy(kConfig)
for cand in footprintList:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateExposure.getMaskedImage(), bbox)
smi = afwImage.MaskedImageF(scienceExposure.getMaskedImage(), bbox)
kCand = diffimLib.makeKernelCandidate(cand['source'], tmi, smi, policy)
if doBuild:
visitor.processCandidate(kCand)
kCand.setStatus(afwMath.SpatialCellCandidate.UNKNOWN)
candList.append(kCand)
return candList
def testConvertPolicy(self):
with self.assertWarns(FutureWarning):
pol = pexConfig.makePolicy(self.simple)
self.assertFalse(pol.exists("i"))
self.assertEqual(pol.get("f"), self.simple.f)
self.assertEqual(pol.get("b"), self.simple.b)
self.assertEqual(pol.get("c"), self.simple.c)
self.assertEqual(pol.getArray("ll"), list(self.simple.ll))
with self.assertWarns(FutureWarning):
pol = pexConfig.makePolicy(self.comp)
self.assertEqual(pol.get("c.f"), self.comp.c.f)
def sourceTableToCandidateList(sourceTable, templateExposure, scienceExposure, kConfig, dConfig, log,
basisList, doBuild=False):
"""Convert a list of Sources into KernelCandidates.
The KernelCandidates are used for fitting the Psf-matching kernel.
Parameters
----------
sourceTable : TODO: DM-17458
TODO: DM-17458
templateExposure : TODO: DM-17458
TODO: DM-17458
scienceExposure : TODO: DM-17458
TODO: DM-17458
kConfig : TODO: DM-17458
TODO: DM-17458
dConfig : TODO: DM-17458
TODO: DM-17458
log : TODO: DM-17458
TODO: DM-17458
basisList : TODO: DM-17458
TODO: DM-17458
doBuild : `bool`, optional
TODO: DM-17458
Returns
-------
TODO: DM-17458
TODO: DM-17458
"""
kernelSize = basisList[0].getWidth()
footprintList = sourceToFootprintList(list(sourceTable), templateExposure, scienceExposure,
kernelSize, dConfig, log)
candList = []
if doBuild and not basisList:
doBuild = False
else:
policy = pexConfig.makePolicy(kConfig)
visitor = diffimLib.BuildSingleKernelVisitorF(basisList, policy)
policy = pexConfig.makePolicy(kConfig)
for cand in footprintList:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateExposure.getMaskedImage(), bbox)
smi = afwImage.MaskedImageF(scienceExposure.getMaskedImage(), bbox)
kCand = diffimLib.makeKernelCandidate(cand['source'], tmi, smi, policy)
if doBuild:
visitor.processCandidate(kCand)
kCand.setStatus(afwMath.SpatialCellCandidate.UNKNOWN)
candList.append(kCand)
return candList
def setUp(self):
self.configAL = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configAL.kernel.name = "AL"
self.subconfigAL = self.configAL.kernel.active
self.configDF = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configDF.kernel.name = "DF"
self.subconfigDF = self.configDF.kernel.active
self.policyAL = pexConfig.makePolicy(self.subconfigAL)
self.policyDF = pexConfig.makePolicy(self.subconfigDF)
self.kSize = self.policyAL.getInt("kernelSize")
def setUp(self):
self.configAL = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configAL.kernel.name = "AL"
self.subconfigAL = self.configAL.kernel.active
self.configDF = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configDF.kernel.name = "DF"
self.subconfigDF = self.configDF.kernel.active
self.policyAL = pexConfig.makePolicy(self.subconfigAL)
self.policyDF = pexConfig.makePolicy(self.subconfigDF)
self.kSize = self.policyAL.getInt("kernelSize")
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "DF"
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.kList = ipDiffim.makeKernelBasisList(self.subconfig)
def setUp(self):
schema = afwTable.SourceTable.makeMinimalSchema()
afwTable.Point2DKey.addFields(schema, "Centroid", "input centroid",
"pixels")
schema.addField("PsfFlux_flux", type=float)
schema.addField("PsfFlux_fluxSigma", type=float)
schema.addField("PsfFlux_flag", type="Flag")
self.table = afwTable.SourceTable.make(schema)
self.table.definePsfFlux("PsfFlux")
self.table.defineCentroid("Centroid")
self.ss = afwTable.SourceCatalog(self.table)
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "DF"
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.policy.set('fitForBackground',
True) # we are testing known background recovery here
self.policy.set('checkConditionNumber', False) # just in case
self.policy.set("useRegularization", False)
# known input images
try:
self.defDataDir = lsst.utils.getPackageDir('afwdata')
except Exception:
self.defDataDir = None
if self.defDataDir:
defSciencePath = os.path.join(self.defDataDir, "DC3a-Sim", "sci",
"v26-e0", "v26-e0-c011-a10.sci.fits")
defTemplatePath = os.path.join(self.defDataDir, "DC3a-Sim", "sci",
"v5-e0", "v5-e0-c011-a10.sci.fits")
scienceExposure = afwImage.ExposureF(defSciencePath)
templateExposure = afwImage.ExposureF(defTemplatePath)
# set XY0 = 0
scienceExposure.getMaskedImage().setXY0(afwGeom.Point2I(0, 0))
templateExposure.getMaskedImage().setXY0(afwGeom.Point2I(0, 0))
# do the warping first so we don't have any masked pixels in the postage stamps
warper = afwMath.Warper.fromConfig(self.subconfig.warpingConfig)
templateExposure = warper.warpExposure(
scienceExposure.getWcs(),
templateExposure,
destBBox=scienceExposure.getBBox())
# Change xy0
# Nice star at position 276, 717
# And should be at index 40, 40
# No masked pixels in this one
self.x02 = 276
self.y02 = 717
size = 40
bbox2 = afwGeom.Box2I(
afwGeom.Point2I(self.x02 - size, self.y02 - size),
afwGeom.Point2I(self.x02 + size, self.y02 + size))
self.scienceImage2 = afwImage.ExposureF(scienceExposure, bbox2,
afwImage.LOCAL)
self.templateExposure2 = afwImage.ExposureF(
templateExposure, bbox2, afwImage.LOCAL)
def testGetCollection(self):
# NOTE - you need to subtract off background from the image
# you run detection on. Here it is the template.
bgConfig = self.subconfig.afwBackgroundConfig
diffimTools.backgroundSubtract(bgConfig, [
self.templateImage,
])
detConfig = self.subconfig.detectionConfig
maskPlane = detConfig.badMaskPlanes[0]
maskVal = afwImage.Mask.getPlaneBitMask(maskPlane)
kcDetect = ipDiffim.KernelCandidateDetectionF(
pexConfig.makePolicy(detConfig))
kcDetect.apply(self.templateImage, self.scienceImage)
fpList1 = kcDetect.getFootprints()
self.assertNotEqual(len(fpList1), 0)
for fp in fpList1:
bbox = fp.getBBox()
tmi = afwImage.MaskedImageF(self.templateImage,
bbox,
origin=afwImage.LOCAL)
smi = afwImage.MaskedImageF(self.scienceImage,
bbox,
origin=afwImage.LOCAL)
tmask = tmi.getMask()
smask = smi.getMask()
for j in range(tmask.getHeight()):
for i in range(tmask.getWidth()):
# No masked pixels in either image
self.assertEqual(tmask.get(i, j), 0)
self.assertEqual(smask.get(i, j), 0)
# add a masked pixel to the template image and make sure you don't get it
afwImage.MaskedImageF(self.templateImage,
fpList1[0].getBBox(),
origin=afwImage.LOCAL).getMask().set(
tmask.getWidth() // 2,
tmask.getHeight() // 2, maskVal)
kcDetect.apply(self.templateImage, self.scienceImage)
fpList2 = kcDetect.getFootprints()
self.assertEqual(len(fpList2), (len(fpList1) - 1))
# add a masked pixel to the science image and make sure you don't get it
afwImage.MaskedImageF(self.scienceImage,
fpList1[1].getBBox(),
origin=afwImage.LOCAL).getMask().set(
smask.getWidth() // 2,
smask.getHeight() // 2, maskVal)
afwImage.MaskedImageF(self.scienceImage,
fpList1[2].getBBox(),
origin=afwImage.LOCAL).getMask().set(
smask.getWidth() // 2,
smask.getHeight() // 2, maskVal)
kcDetect.apply(self.templateImage, self.scienceImage)
fpList3 = kcDetect.getFootprints()
self.assertEqual(len(fpList3), (len(fpList1) - 3))
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "DF"
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.kList = ipDiffim.makeKernelBasisList(self.subconfig)
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "AL"
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.size = 51
def __init__(self, *args, **kwargs):
"""Create the psf-matching Task
Parameters
----------
*args
Arguments to be passed to ``lsst.pipe.base.task.Task.__init__``
**kwargs
Keyword arguments to be passed to ``lsst.pipe.base.task.Task.__init__``
Notes
-----
The initialization sets the Psf-matching kernel configuration using the value of
self.config.kernel.active. If the kernel is requested with regularization to moderate
the bias/variance tradeoff, currently only used when a delta function kernel basis
is provided, it creates a regularization matrix stored as member variable
self.hMat.
"""
pipeBase.Task.__init__(self, *args, **kwargs)
self.kConfig = self.config.kernel.active
if 'useRegularization' in self.kConfig:
self.useRegularization = self.kConfig.useRegularization
else:
self.useRegularization = False
if self.useRegularization:
self.hMat = diffimLib.makeRegularizationMatrix(
pexConfig.makePolicy(self.kConfig))
def cosmicray(exp, config, display=False):
bg = 0.0 # We background-subtracted, right?
crList = measAlg.findCosmicRays(exp.getMaskedImage(), exp.getPsf(), bg, makePolicy(config), True)
if crList is None:
print "No CRs found"
return
mask = exp.getMaskedImage().getMask()
crBit = mask.getPlaneBitMask("CR")
afwDet.setMaskFromFootprintList(mask, crList, crBit)
num = len(crList)
print "Found %d CRs" % num
if display:
frame = 2
import lsst.afw.display.ds9 as ds9
import lsst.afw.display.utils as displayUtils
ds9.mtv(exp, title="Exposure with CRs")
with ds9.Buffering():
for cr in crList:
displayUtils.drawBBox(cr.getBBox(), borderWidth=0.55)
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.kSize = self.policy.getInt('kernelSize')
# gaussian reference kernel
self.gSize = self.kSize
self.gaussFunction = afwMath.GaussianFunction2D(2, 3)
self.gaussKernel = afwMath.AnalyticKernel(self.gSize, self.gSize,
self.gaussFunction)
# known input images
try:
self.defDataDir = lsst.utils.getPackageDir('afwdata')
except Exception:
self.defDataDir = None
if self.defDataDir:
defImagePath = os.path.join(self.defDataDir, "DC3a-Sim", "sci",
"v5-e0", "v5-e0-c011-a00.sci.fits")
self.templateImage = afwImage.MaskedImageF(defImagePath)
self.scienceImage = self.templateImage.Factory(
self.templateImage.getDimensions())
afwMath.convolve(self.scienceImage, self.templateImage,
self.gaussKernel, False)
def __init__(self, *args, **kwargs):
"""Create the psf-matching Task
Parameters
----------
*args
Arguments to be passed to ``lsst.pipe.base.task.Task.__init__``
**kwargs
Keyword arguments to be passed to ``lsst.pipe.base.task.Task.__init__``
Notes
-----
The initialization sets the Psf-matching kernel configuration using the value of
self.config.kernel.active. If the kernel is requested with regularization to moderate
the bias/variance tradeoff, currently only used when a delta function kernel basis
is provided, it creates a regularization matrix stored as member variable
self.hMat.
"""
pipeBase.Task.__init__(self, *args, **kwargs)
self.kConfig = self.config.kernel.active
if 'useRegularization' in self.kConfig:
self.useRegularization = self.kConfig.useRegularization
else:
self.useRegularization = False
if self.useRegularization:
self.hMat = diffimLib.makeRegularizationMatrix(pexConfig.makePolicy(self.kConfig))
def stats(self, cid, diffim, core=5):
policy = pexConfig.makePolicy(self.config)
dStats = ipDiffim.ImageStatisticsF(policy)
dStats.apply(diffim)
logger.debug("Candidate %d : Residuals all (%d px): %.3f +/- %.3f",
cid, dStats.getNpix(), dStats.getMean(), dStats.getRms())
dStats.apply(diffim, core)
logger.debug("Candidate %d : Residuals core (%d px): %.3f +/- %.3f",
cid, dStats.getNpix(), dStats.getMean(), dStats.getRms())
def cosmicRay(self, exposure, keepCRs=None):
"""Mask cosmic rays
\param[in,out] exposure Exposure to process
\param[in] keepCRs Don't interpolate over the CR pixels (defer to pex_config if None)
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayCR = lsstDebug.Info(__name__).displayCR
assert exposure, "No exposure provided"
psf = exposure.getPsf()
assert psf, "No psf provided"
# Blow away old mask
try:
mask = exposure.getMaskedImage().getMask()
crBit = mask.getMaskPlane("CR")
mask.clearMaskPlane(crBit)
except Exception:
pass
mi = exposure.getMaskedImage()
bg = afwMath.makeStatistics(mi, afwMath.MEDIAN).getValue()
if keepCRs is None:
keepCRs = self.config.cosmicray.keepCRs
try:
crs = measAlg.findCosmicRays(mi, psf, bg, pexConfig.makePolicy(self.config.cosmicray), keepCRs)
except Exception:
if display:
import lsst.afw.display.ds9 as ds9
ds9.mtv(exposure, title="Failed CR")
raise
num = 0
if crs is not None:
mask = mi.getMask()
crBit = mask.getPlaneBitMask("CR")
afwDet.setMaskFromFootprintList(mask, crs, crBit)
num = len(crs)
if display and displayCR:
import lsst.afw.display.ds9 as ds9
import lsst.afw.display.utils as displayUtils
ds9.incrDefaultFrame()
ds9.mtv(exposure, title="Post-CR")
with ds9.Buffering():
for cr in crs:
displayUtils.drawBBox(cr.getBBox(), borderWidth=0.55)
self.log.info("Identified %s cosmic rays." % (num,))
def testConvert(self):
pol = pexConfig.makePolicy(self.simple)
self.assertEqual(pol.exists("i"), False)
self.assertEqual(pol.get("f"), self.simple.f)
self.assertEqual(pol.get("b"), self.simple.b)
self.assertEqual(pol.get("c"), self.simple.c)
self.assertEqual(pol.getArray("ll"), list(self.simple.ll))
ps = pexConfig.makePropertySet(self.simple)
self.assertEqual(ps.exists("i"), False)
self.assertEqual(ps.getScalar("f"), self.simple.f)
self.assertEqual(ps.getScalar("b"), self.simple.b)
self.assertEqual(ps.getScalar("c"), self.simple.c)
self.assertEqual(list(ps.getArray("ll")), list(self.simple.ll))
pol = pexConfig.makePolicy(self.comp)
self.assertEqual(pol.get("c.f"), self.comp.c.f)
ps = pexConfig.makePropertySet(self.comp)
self.assertEqual(ps.getScalar("c.f"), self.comp.c.f)
def setUp(self):
schema = afwTable.SourceTable.makeMinimalSchema()
afwTable.Point2DKey.addFields(schema, "Centroid", "input centroid", "pixels")
schema.addField("PsfFlux_flux", type=float)
schema.addField("PsfFlux_fluxSigma", type=float)
schema.addField("PsfFlux_flag", type="Flag")
self.table = afwTable.SourceTable.make(schema)
self.table.definePsfFlux("PsfFlux")
self.table.defineCentroid("Centroid")
self.ss = afwTable.SourceCatalog(self.table)
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "DF"
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.policy.set('fitForBackground', True) # we are testing known background recovery here
self.policy.set('checkConditionNumber', False) # just in case
self.policy.set("useRegularization", False)
# known input images
try:
self.defDataDir = lsst.utils.getPackageDir('afwdata')
except Exception:
self.defDataDir = None
if self.defDataDir:
defSciencePath = os.path.join(self.defDataDir, "DC3a-Sim", "sci", "v26-e0",
"v26-e0-c011-a10.sci.fits")
defTemplatePath = os.path.join(self.defDataDir, "DC3a-Sim", "sci", "v5-e0",
"v5-e0-c011-a10.sci.fits")
scienceExposure = afwImage.ExposureF(defSciencePath)
templateExposure = afwImage.ExposureF(defTemplatePath)
# set XY0 = 0
scienceExposure.getMaskedImage().setXY0(afwGeom.Point2I(0, 0))
templateExposure.getMaskedImage().setXY0(afwGeom.Point2I(0, 0))
# do the warping first so we don't have any masked pixels in the postage stamps
warper = afwMath.Warper.fromConfig(self.subconfig.warpingConfig)
templateExposure = warper.warpExposure(scienceExposure.getWcs(), templateExposure,
destBBox = scienceExposure.getBBox())
# Change xy0
# Nice star at position 276, 717
# And should be at index 40, 40
# No masked pixels in this one
self.x02 = 276
self.y02 = 717
size = 40
bbox2 = afwGeom.Box2I(afwGeom.Point2I(self.x02 - size, self.y02 - size),
afwGeom.Point2I(self.x02 + size, self.y02 + size))
self.scienceImage2 = afwImage.ExposureF(scienceExposure, bbox2, afwImage.LOCAL)
self.templateExposure2 = afwImage.ExposureF(templateExposure, bbox2, afwImage.LOCAL)
def cosmicRay(self, exposure, keepCRs=None):
"""Mask cosmic rays
@param[in,out] exposure Exposure to process
@param keepCRs Don't interpolate over the CR pixels (defer to pex_config if None)
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayCR = lsstDebug.Info(__name__).displayCR
assert exposure, "No exposure provided"
psf = exposure.getPsf()
assert psf, "No psf provided"
# Blow away old mask
try:
mask = exposure.getMaskedImage().getMask()
crBit = mask.getMaskPlane("CR")
mask.clearMaskPlane(crBit)
except Exception:
pass
exposure0 = exposure # initial value of exposure
binSize = self.config.cosmicray.background.binSize
nx, ny = exposure.getWidth()/binSize, exposure.getHeight()/binSize
if nx*ny <= 1:
bg = afwMath.makeStatistics(exposure.getMaskedImage(), afwMath.MEDIAN).getValue()
bkgd = None
else:
exposure = exposure.Factory(exposure, True)
bkgd, exposure = measAlg.estimateBackground(exposure, self.config.cosmicray.background,
subtract=True)
bg = 0.0
if keepCRs is None:
keepCRs = self.config.cosmicray.keepCRs
try:
crs = measAlg.findCosmicRays(exposure.getMaskedImage(),
psf, bg, pexConfig.makePolicy(self.config.cosmicray), keepCRs)
if bkgd:
# Add back background image
img = exposure.getMaskedImage().getImage()
img += bkgd.getImageF()
del img
# Replace original image with CR subtracted image
mimg = exposure0.getMaskedImage()
mimg <<= exposure.getMaskedImage()
del mimg
except Exception, e:
if display:
import lsst.afw.display.ds9 as ds9
ds9.mtv(exposure0, title="Failed CR")
raise
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "DF"
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.policy.set("useRegularization", False)
self.policy.set("checkConditionNumber", False) # I am making shady kernels by hand
self.policy.set("useCoreStats", False) # I am making off-center resids
self.kList = ipDiffim.makeKernelBasisList(self.subconfig)
self.size = 51
def _buildCellSet(self, templateMaskedImage, scienceMaskedImage,
candidateList):
"""Build a SpatialCellSet for use with the solve method.
Parameters
----------
templateMaskedImage : `lsst.afw.image.MaskedImage`
MaskedImage to PSF-matched to scienceMaskedImage
scienceMaskedImage : `lsst.afw.image.MaskedImage`
Reference MaskedImage
candidateList : `list`
A list of footprints/maskedImages for kernel candidates;
- Currently supported: list of Footprints or measAlg.PsfCandidateF
Returns
-------
kernelCellSet : `lsst.afw.math.SpatialCellSet`
a SpatialCellSet for use with self._solve
"""
if not candidateList:
raise RuntimeError(
"Candidate list must be populated by makeCandidateList")
sizeCellX, sizeCellY = self._adaptCellSize(candidateList)
# Object to store the KernelCandidates for spatial modeling
kernelCellSet = afwMath.SpatialCellSet(templateMaskedImage.getBBox(),
sizeCellX, sizeCellY)
policy = pexConfig.makePolicy(self.kConfig)
# Place candidates within the spatial grid
for cand in candidateList:
if isinstance(cand, afwDetect.Footprint):
bbox = cand.getBBox()
else:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateMaskedImage, bbox)
smi = afwImage.MaskedImageF(scienceMaskedImage, bbox)
if not isinstance(cand, afwDetect.Footprint):
if 'source' in cand:
cand = cand['source']
xPos = cand.getCentroid()[0]
yPos = cand.getCentroid()[1]
cand = diffimLib.makeKernelCandidate(xPos, yPos, tmi, smi, policy)
self.log.debug("Candidate %d at %f, %f", cand.getId(),
cand.getXCenter(), cand.getYCenter())
kernelCellSet.insertCandidate(cand)
return kernelCellSet
def __call__(self, kernelCellSet, log):
d1, d2, d3 = self.psfMatchConfig.alardDegGauss
bicArray = {}
for d1i in range(1, d1 + 1):
for d2i in range(1, d2 + 1):
for d3i in range(1, d3 + 1):
dList = [d1i, d2i, d3i]
bicConfig = type(self.psfMatchConfig)(self.psfMatchConfig,
alardDegGauss=dList)
kList = makeKernelBasisList(bicConfig, self.psfFwhmPixTc,
self.psfFwhmPixTnc)
k = len(kList)
visitor = diffimLib.BuildSingleKernelVisitorF(
kList, pexConfig.makePolicy(bicConfig))
visitor.setSkipBuilt(False)
kernelCellSet.visitCandidates(visitor,
bicConfig.nStarPerCell)
for cell in kernelCellSet.getCellList():
for cand in cell.begin(
False): # False = include bad candidates
if cand.getStatus(
) != afwMath.SpatialCellCandidate.GOOD:
continue
diffIm = cand.getDifferenceImage(
diffimLib.KernelCandidateF.RECENT)
bbox = cand.getKernel(
diffimLib.KernelCandidateF.RECENT).shrinkBBox(
diffIm.getBBox(afwImage.LOCAL))
diffIm = type(diffIm)(diffIm, bbox, True)
chi2 = diffIm.getImage().getArray(
)**2 / diffIm.getVariance().getArray()
n = chi2.shape[0] * chi2.shape[1]
bic = np.sum(chi2) + k * np.log(n)
if cand.getId() not in bicArray:
bicArray[cand.getId()] = {}
bicArray[cand.getId()][(d1i, d2i, d3i)] = bic
bestConfigs = []
for candId in bicArray:
cconfig, cvals = list(bicArray[candId].keys()), list(
bicArray[candId].values())
idx = np.argsort(cvals)
bestConfig = cconfig[idx[0]]
bestConfigs.append(bestConfig)
counter = Counter(bestConfigs).most_common(3)
log.info(
"B.I.C. prefers basis complexity %s %d times; %s %d times; %s %d times",
counter[0][0], counter[0][1], counter[1][0], counter[1][1],
counter[2][0], counter[2][1])
return counter[0][0], counter[1][0], counter[2][0]
def _buildCellSet(self, templateMaskedImage, scienceMaskedImage, candidateList):
"""Build a SpatialCellSet for use with the solve method.
Parameters
----------
templateMaskedImage : `lsst.afw.image.MaskedImage`
MaskedImage to PSF-matched to scienceMaskedImage
scienceMaskedImage : `lsst.afw.image.MaskedImage`
Reference MaskedImage
candidateList : `list`
A list of footprints/maskedImages for kernel candidates;
- Currently supported: list of Footprints or measAlg.PsfCandidateF
Returns
-------
kernelCellSet : `lsst.afw.math.SpatialCellSet`
a SpatialCellSet for use with self._solve
"""
if not candidateList:
raise RuntimeError("Candidate list must be populated by makeCandidateList")
sizeCellX, sizeCellY = self._adaptCellSize(candidateList)
# Object to store the KernelCandidates for spatial modeling
kernelCellSet = afwMath.SpatialCellSet(templateMaskedImage.getBBox(),
sizeCellX, sizeCellY)
policy = pexConfig.makePolicy(self.kConfig)
# Place candidates within the spatial grid
for cand in candidateList:
if isinstance(cand, afwDetect.Footprint):
bbox = cand.getBBox()
else:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateMaskedImage, bbox)
smi = afwImage.MaskedImageF(scienceMaskedImage, bbox)
if not isinstance(cand, afwDetect.Footprint):
if 'source' in cand:
cand = cand['source']
xPos = cand.getCentroid()[0]
yPos = cand.getCentroid()[1]
cand = diffimLib.makeKernelCandidate(xPos, yPos, tmi, smi, policy)
self.log.debug("Candidate %d at %f, %f", cand.getId(), cand.getXCenter(), cand.getYCenter())
kernelCellSet.insertCandidate(cand)
return kernelCellSet
def testGetCollection(self):
if not self.defDataDir:
print >> sys.stderr, "Warning: afwdata is not set up; not running KernelCandidateDetection.py"
return
# NOTE - you need to subtract off background from the image
# you run detection on. Here it is the template.
bgConfig = self.subconfig.afwBackgroundConfig
diffimTools.backgroundSubtract(bgConfig, [self.templateImage,])
detConfig = self.subconfig.detectionConfig
maskPlane = detConfig.badMaskPlanes[0]
maskVal = afwImage.MaskU.getPlaneBitMask(maskPlane)
kcDetect = ipDiffim.KernelCandidateDetectionF(pexConfig.makePolicy(detConfig))
kcDetect.apply(self.templateImage, self.scienceImage)
fpList1 = kcDetect.getFootprints()
self.assertTrue(len(fpList1) != 0)
for fp in fpList1:
bbox = fp.getBBox()
tmi = afwImage.MaskedImageF(self.templateImage, bbox, afwImage.LOCAL)
smi = afwImage.MaskedImageF(self.scienceImage, bbox, afwImage.LOCAL)
tmask = tmi.getMask()
smask = smi.getMask()
for j in range(tmask.getHeight()):
for i in range(tmask.getWidth()):
# No masked pixels in either image
self.assertEqual(tmask.get(i, j), 0)
self.assertEqual(smask.get(i, j), 0)
# add a masked pixel to the template image and make sure you don't get it
afwImage.MaskedImageF(self.templateImage, fpList1[0].getBBox(), afwImage.LOCAL).getMask().set(
tmask.getWidth()//2, tmask.getHeight()//2, maskVal)
kcDetect.apply(self.templateImage, self.scienceImage)
fpList2 = kcDetect.getFootprints()
self.assertTrue(len(fpList2) == (len(fpList1)-1))
# add a masked pixel to the science image and make sure you don't get it
afwImage.MaskedImageF(self.scienceImage, fpList1[1].getBBox(), afwImage.LOCAL).getMask().set(
smask.getWidth()//2, smask.getHeight()//2, maskVal)
afwImage.MaskedImageF(self.scienceImage, fpList1[2].getBBox(), afwImage.LOCAL).getMask().set(
smask.getWidth()//2, smask.getHeight()//2, maskVal)
kcDetect.apply(self.templateImage, self.scienceImage)
fpList3 = kcDetect.getFootprints()
self.assertTrue(len(fpList3) == (len(fpList1)-3))
def jackknifeResample(self, psfmatch, results):
kernel = results.psfMatchingKernel
bg = results.backgroundModel
cellSet = results.kernelCellSet
goodList = []
for cell in cellSet.getCellList():
print
for cand in cell.begin(False):
cand = ipDiffim.cast_KernelCandidateF(cand)
if cand.getStatus() == afwMath.SpatialCellCandidate.GOOD:
goodList.append(cand.getId())
else:
# This is so that UNKNOWNs are not processed
cand.setStatus(afwMath.SpatialCellCandidate.BAD)
nStarPerCell = self.config.nStarPerCell
policy = pexConfig.makePolicy(self.config)
for idx in range(len(goodList)):
cid = goodList[idx]
print # clear the screen
pexLog.Trace("lsst.ip.diffim.JackknifeResampleKernel", 1,
"Removing candidate %d" % (cid))
cand = self.setStatus(cellSet, cid, afwMath.SpatialCellCandidate.BAD)
# From _solve
regionBBox = cellSet.getBBox()
spatialkv = ipDiffim.BuildSpatialKernelVisitorF(kernel.getKernelList(), regionBBox, policy)
cellSet.visitCandidates(spatialkv, nStarPerCell)
spatialkv.solveLinearEquation()
jkKernel, jkBg = spatialkv.getSolutionPair()
#jkResults = psfmatch._solve(cellSet, kernel.getKernelList())
#jkKernel = jkResults[1]
#jkBg = jkResults[2]
# lots of windows
# self.assess(cand, kernel, bg, jkKernel, jkBg, 6*idx+1)
# only 6 windows
self.assess(cand, kernel, bg, jkKernel, jkBg, 1)
self.setStatus(cellSet, cid, afwMath.SpatialCellCandidate.GOOD)
def cosmicray(exp, config, display=False):
bg = 0.0 # We background-subtracted, right?
crList = measAlg.findCosmicRays(exp.getMaskedImage(), exp.getPsf(), bg, makePolicy(config), True)
if crList is None:
print "No CRs found"
return
mask = exp.getMaskedImage().getMask()
crBit = mask.getPlaneBitMask("CR")
afwDet.setMaskFromFootprintList(mask, crList, crBit)
num = len(crList)
print "Found %d CRs" % num
if display:
frame = 2
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.subconfig = self.config.kernel.active
self.policy = pexConfig.makePolicy(self.subconfig)
self.kSize = self.policy.getInt('kernelSize')
# gaussian reference kernel
self.gSize = self.kSize
self.gaussFunction = afwMath.GaussianFunction2D(2, 3)
self.gaussKernel = afwMath.AnalyticKernel(self.gSize, self.gSize, self.gaussFunction)
if defDataDir:
defImagePath = os.path.join(defDataDir, "DC3a-Sim", "sci", "v5-e0",
"v5-e0-c011-a00.sci.fits")
self.templateImage = afwImage.MaskedImageF(defImagePath)
self.scienceImage = self.templateImage.Factory(self.templateImage.getDimensions())
afwMath.convolve(self.scienceImage, self.templateImage, self.gaussKernel, False)
def testGetCollection(self):
# NOTE - you need to subtract off background from the image
# you run detection on. Here it is the template.
bgConfig = self.subconfig.afwBackgroundConfig
diffimTools.backgroundSubtract(bgConfig, [self.templateImage, ])
detConfig = self.subconfig.detectionConfig
maskPlane = detConfig.badMaskPlanes[0]
maskVal = afwImage.Mask.getPlaneBitMask(maskPlane)
kcDetect = ipDiffim.KernelCandidateDetectionF(pexConfig.makePolicy(detConfig))
kcDetect.apply(self.templateImage, self.scienceImage)
fpList1 = kcDetect.getFootprints()
self.assertNotEqual(len(fpList1), 0)
for fp in fpList1:
bbox = fp.getBBox()
tmi = afwImage.MaskedImageF(self.templateImage, bbox, origin=afwImage.LOCAL)
smi = afwImage.MaskedImageF(self.scienceImage, bbox, origin=afwImage.LOCAL)
tmask = tmi.getMask()
smask = smi.getMask()
for j in range(tmask.getHeight()):
for i in range(tmask.getWidth()):
# No masked pixels in either image
self.assertEqual(tmask[i, j, afwImage.LOCAL], 0)
self.assertEqual(smask[i, j, afwImage.LOCAL], 0)
# add a masked pixel to the template image and make sure you don't get it
tp = afwGeom.Point2I(tmask.getWidth()//2, tmask.getHeight()//2)
self.templateImage.mask[fpList1[0].getBBox(), afwImage.LOCAL][tp, afwImage.LOCAL] = maskVal
kcDetect.apply(self.templateImage, self.scienceImage)
fpList2 = kcDetect.getFootprints()
self.assertEqual(len(fpList2), (len(fpList1)-1))
# add a masked pixel to the science image and make sure you don't get it
sp = afwGeom.Point2I(smask.getWidth()//2, smask.getHeight()//2)
self.scienceImage.mask[fpList1[1].getBBox(), afwImage.LOCAL][sp, afwImage.LOCAL] = maskVal
self.scienceImage.mask[fpList1[2].getBBox(), afwImage.LOCAL][sp, afwImage.LOCAL] = maskVal
kcDetect.apply(self.templateImage, self.scienceImage)
fpList3 = kcDetect.getFootprints()
self.assertEqual(len(fpList3), (len(fpList1)-3))
def __call__(self, kernelCellSet, log):
d1, d2, d3 = self.psfMatchConfig.alardDegGauss
bicArray = {}
for d1i in range(1, d1 + 1):
for d2i in range(1, d2 + 1):
for d3i in range(1, d3 + 1):
dList = [d1i, d2i, d3i]
bicConfig = type(self.psfMatchConfig)(self.psfMatchConfig, alardDegGauss=dList)
kList = makeKernelBasisList(bicConfig, self.psfFwhmPixTc, self.psfFwhmPixTnc)
k = len(kList)
visitor = diffimLib.BuildSingleKernelVisitorF(kList, pexConfig.makePolicy(bicConfig))
visitor.setSkipBuilt(False)
kernelCellSet.visitCandidates(visitor, bicConfig.nStarPerCell)
for cell in kernelCellSet.getCellList():
for cand in cell.begin(False): # False = include bad candidates
if cand.getStatus() != afwMath.SpatialCellCandidate.GOOD:
continue
diffIm = cand.getDifferenceImage(diffimLib.KernelCandidateF.RECENT)
bbox = cand.getKernel(diffimLib.KernelCandidateF.RECENT).shrinkBBox(
diffIm.getBBox(afwImage.LOCAL))
diffIm = type(diffIm)(diffIm, bbox, True)
chi2 = diffIm.getImage().getArray()**2/diffIm.getVariance().getArray()
n = chi2.shape[0]*chi2.shape[1]
bic = np.sum(chi2) + k*np.log(n)
if cand.getId() not in bicArray:
bicArray[cand.getId()] = {}
bicArray[cand.getId()][(d1i, d2i, d3i)] = bic
bestConfigs = []
for candId in bicArray:
cconfig, cvals = list(bicArray[candId].keys()), list(bicArray[candId].values())
idx = np.argsort(cvals)
bestConfig = cconfig[idx[0]]
bestConfigs.append(bestConfig)
counter = Counter(bestConfigs).most_common(3)
log.info("B.I.C. prefers basis complexity %s %d times; %s %d times; %s %d times",
counter[0][0], counter[0][1],
counter[1][0], counter[1][1],
counter[2][0], counter[2][1])
return counter[0][0], counter[1][0], counter[2][0]
def _buildCellSet(self, templateMaskedImage, scienceMaskedImage,
candidateList):
"""!Build a SpatialCellSet for use with the solve method
@param templateMaskedImage: MaskedImage to PSF-matched to scienceMaskedImage
@param scienceMaskedImage: reference MaskedImage
@param candidateList: a list of footprints/maskedImages for kernel candidates;
if None then source detection is run.
- Currently supported: list of Footprints or measAlg.PsfCandidateF
@return kernelCellSet: a SpatialCellSet for use with self._solve
"""
if not candidateList:
raise RuntimeError(
"Candidate list must be populated by makeCandidateList")
sizeCellX, sizeCellY = self._adaptCellSize(candidateList)
# Object to store the KernelCandidates for spatial modeling
kernelCellSet = afwMath.SpatialCellSet(templateMaskedImage.getBBox(),
sizeCellX, sizeCellY)
policy = pexConfig.makePolicy(self.kConfig)
# Place candidates within the spatial grid
for cand in candidateList:
bbox = cand['footprint'].getBBox()
tmi = afwImage.MaskedImageF(templateMaskedImage, bbox)
smi = afwImage.MaskedImageF(scienceMaskedImage, bbox)
cand = diffimLib.makeKernelCandidate(cand['source'], tmi, smi,
policy)
self.log.logdebug(
"Candidate %d at %f, %f" %
(cand.getId(), cand.getXCenter(), cand.getYCenter()))
kernelCellSet.insertCandidate(cand)
return kernelCellSet
def setUp(self):
self.configAL = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configAL.kernel.name = "AL"
self.subconfigAL = self.configAL.kernel.active
self.configDF = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configDF.kernel.name = "DF"
self.subconfigDF = self.configDF.kernel.active
self.configDFr = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configDFr.kernel.name = "DF"
self.subconfigDFr = self.configDFr.kernel.active
self.subconfigDF.useRegularization = False
self.subconfigDFr.useRegularization = True
self.subconfigDFr.lambdaValue = 1000.0
self.subconfigAL.fitForBackground = fitForBackground
self.subconfigDF.fitForBackground = fitForBackground
self.subconfigDFr.fitForBackground = fitForBackground
self.subconfigAL.constantVarianceWeighting = constantVarianceWeighting
self.subconfigDF.constantVarianceWeighting = constantVarianceWeighting
self.subconfigDFr.constantVarianceWeighting = constantVarianceWeighting
self.kListAL = ipDiffim.makeKernelBasisList(self.subconfigAL)
self.kListDF = ipDiffim.makeKernelBasisList(self.subconfigDF)
self.kListDFr = ipDiffim.makeKernelBasisList(self.subconfigDFr)
self.hMatDFr = ipDiffim.makeRegularizationMatrix(
pexConfig.makePolicy(self.subconfigDFr))
self.bskvAL = ipDiffim.BuildSingleKernelVisitorF(
self.kListAL, pexConfig.makePolicy(self.subconfigAL))
self.bskvDF = ipDiffim.BuildSingleKernelVisitorF(
self.kListDF, pexConfig.makePolicy(self.subconfigDF))
self.bskvDFr = ipDiffim.BuildSingleKernelVisitorF(
self.kListDFr, pexConfig.makePolicy(self.subconfigDF),
self.hMatDFr)
defSciencePath = globals()['defSciencePath']
defTemplatePath = globals()['defTemplatePath']
if defSciencePath and defTemplatePath:
self.scienceExposure = afwImage.ExposureF(defSciencePath)
self.templateExposure = afwImage.ExposureF(defTemplatePath)
else:
defDataDir = lsst.utils.getPackageDir('afwdata')
defSciencePath = os.path.join(defDataDir, "DC3a-Sim", "sci",
"v26-e0", "v26-e0-c011-a00.sci")
defTemplatePath = os.path.join(defDataDir, "DC3a-Sim", "sci",
"v5-e0", "v5-e0-c011-a00.sci")
self.scienceExposure = afwImage.ExposureF(defSciencePath)
self.templateExposure = afwImage.ExposureF(defTemplatePath)
warper = afwMath.Warper.fromConfig(self.subconfigAL.warpingConfig)
self.templateExposure = warper.warpExposure(
self.scienceExposure.getWcs(),
self.templateExposure,
destBBox=self.scienceExposure.getBBox())
# image statistics
self.dStats = ipDiffim.ImageStatisticsF()
#
tmi = self.templateExposure.getMaskedImage()
smi = self.scienceExposure.getMaskedImage()
# Object detection
detConfig = self.subconfigAL.detectionConfig
detPolicy = pexConfig.makePolicy(detConfig)
detPolicy.set("detThreshold", 50.)
detPolicy.set("detThresholdType", "stdev")
detPolicy.set("detOnTemplate", False)
kcDetect = ipDiffim.KernelCandidateDetectionF(detPolicy)
kcDetect.apply(tmi, smi)
self.footprints = kcDetect.getFootprints()
configDFr = ipDiffim.ImagePsfMatchTask.ConfigClass()
configDFr.kernel.name = "DF"
subconfigDFr = configDFr.kernel.active
subconfigDF.useRegularization = False
subconfigDFr.useRegularization = True
for param in [["spatialKernelOrder", 0], ["spatialBgOrder", 0],
["usePcaForSpatialKernel", True], ["fitForBackground", True]]:
exec("subconfigAL.%s = %s" % (param[0], param[1]))
exec("subconfigDF.%s = %s" % (param[0], param[1]))
exec("subconfigDFr.%s = %s" % (param[0], param[1]))
detConfig = subconfigAL.detectionConfig
kcDetect = ipDiffim.KernelCandidateDetectionF(pexConfig.makePolicy(detConfig))
kcDetect.apply(templateMaskedImage, scienceMaskedImage)
footprints = kcDetect.getFootprints()
# delta function
psfmatch1 = ipDiffim.ImagePsfMatchTask(config=configDF)
results1 = psfmatch1.run(templateMaskedImage,
scienceMaskedImage,
"subtractMaskedImages",
candidateList=footprints)
diffim1 = results1.subtractedImage
spatialKernel1 = results1.psfMatchingKernel
spatialBg1 = results1.backgroundModel
kernelCellSet1 = results1.kernelCellSet
# alard lupton
def makeFakeKernelSet(sizeCell=128, nCell=3,
deltaFunctionCounts=1.e4, tGaussianWidth=1.0,
addNoise=True, bgValue=100., display=False):
"""Generate test template and science images with sources.
Parameters
----------
sizeCell : `int`, optional
Size of the square spatial cells in pixels.
nCell : `int`, optional
Number of adjacent spatial cells in both direction in both images.
deltaFunctionCounts : `float`, optional
Flux value for the template image sources.
tGaussianWidth : `float`, optional
Sigma of the generated Gaussian PSF sources in the template image.
addNoise : `bool`, optional
If `True`, Poisson noise is added to both the generated template
and science images.
bgValue : `float`, optional
Background level to be added to the generated science image.
display : `bool`, optional
If `True` displays the generated template and science images by
`lsst.afw.display.Display`.
Notes
-----
- The generated images consist of adjacent ``nCell x nCell`` cells, each
of pixel size ``sizeCell x sizeCell``.
- The sources in the science image are generated by convolving the
template by ``sKernel``. ``sKernel`` is a spatial `LinearCombinationKernel`
of hard wired kernel bases functions. The linear combination has first
order polynomial spatial dependence with polynomial parameters from ``fakeCoeffs()``.
- The template image sources are generated in the center of each spatial
cell from one pixel, set to `deltaFunctionCounts` counts, then convolved
by a 2D Gaussian with sigma of `tGaussianWidth` along each axis.
- The sources are also returned in ``kernelCellSet`` each source is "detected"
exactly at the center of a cell.
Returns
-------
tMi : `lsst.afw.image.MaskedImage`
Generated template image.
sMi : `lsst.afw.image.MaskedImage`
Generated science image.
sKernel : `lsst.afw.math.LinearCombinationKernel`
The spatial kernel used to generate the sources in the science image.
kernelCellSet : `lsst.afw.math.SpatialCellSet`
Cell grid of `lsst.afw.math.SpatialCell` instances, containing
`lsst.ip.diffim.KernelCandidate` instances around all the generated sources
in the science image.
configFake : `lsst.ip.diffim.ImagePsfMatchConfig`
Config instance used in the image generation.
"""
from . import imagePsfMatch
configFake = imagePsfMatch.ImagePsfMatchConfig()
configFake.kernel.name = "AL"
subconfigFake = configFake.kernel.active
subconfigFake.alardNGauss = 1
subconfigFake.alardSigGauss = [2.5, ]
subconfigFake.alardDegGauss = [2, ]
subconfigFake.sizeCellX = sizeCell
subconfigFake.sizeCellY = sizeCell
subconfigFake.spatialKernelOrder = 1
subconfigFake.spatialModelType = "polynomial"
subconfigFake.singleKernelClipping = False # variance is a hack
subconfigFake.spatialKernelClipping = False # variance is a hack
if bgValue > 0.0:
subconfigFake.fitForBackground = True
policyFake = pexConfig.makePolicy(subconfigFake)
basisList = makeKernelBasisList(subconfigFake)
kSize = subconfigFake.kernelSize
# This sets the final extent of each convolved delta function
gaussKernelWidth = sizeCell//2
# This sets the scale over which pixels are correlated in the
# spatial convolution; should be at least as big as the kernel you
# are trying to fit for
spatialKernelWidth = kSize
# Number of bad pixels due to convolutions
border = (gaussKernelWidth + spatialKernelWidth)//2
# Make a fake image with a matrix of delta functions
totalSize = nCell*sizeCell + 2*border
tim = afwImage.ImageF(afwGeom.Extent2I(totalSize, totalSize))
for x in range(nCell):
for y in range(nCell):
tim[x*sizeCell + sizeCell//2 + border - 1,
y*sizeCell + sizeCell//2 + border - 1,
afwImage.LOCAL] = deltaFunctionCounts
# Turn this into stars with a narrow width; conserve counts
gaussFunction = afwMath.GaussianFunction2D(tGaussianWidth, tGaussianWidth)
gaussKernel = afwMath.AnalyticKernel(gaussKernelWidth, gaussKernelWidth, gaussFunction)
cim = afwImage.ImageF(tim.getDimensions())
afwMath.convolve(cim, tim, gaussKernel, True)
tim = cim
# Trim off border pixels
bbox = gaussKernel.shrinkBBox(tim.getBBox(afwImage.LOCAL))
tim = afwImage.ImageF(tim, bbox, afwImage.LOCAL)
# Now make a science image which is this convolved with some
# spatial function. Use input basis list.
polyFunc = afwMath.PolynomialFunction2D(1)
kCoeffs = fakeCoeffs()
nToUse = min(len(kCoeffs), len(basisList))
# Make the full convolved science image
sKernel = afwMath.LinearCombinationKernel(basisList[:nToUse], polyFunc)
sKernel.setSpatialParameters(kCoeffs[:nToUse])
sim = afwImage.ImageF(tim.getDimensions())
afwMath.convolve(sim, tim, sKernel, True)
# Get the good subregion
bbox = sKernel.shrinkBBox(sim.getBBox(afwImage.LOCAL))
# Add background
sim += bgValue
# Watch out for negative values
tim += 2*np.abs(np.min(tim.getArray()))
# Add noise?
if addNoise:
sim = makePoissonNoiseImage(sim)
tim = makePoissonNoiseImage(tim)
# And turn into MaskedImages
sim = afwImage.ImageF(sim, bbox, afwImage.LOCAL)
svar = afwImage.ImageF(sim, True)
smask = afwImage.Mask(sim.getDimensions())
smask.set(0x0)
sMi = afwImage.MaskedImageF(sim, smask, svar)
tim = afwImage.ImageF(tim, bbox, afwImage.LOCAL)
tvar = afwImage.ImageF(tim, True)
tmask = afwImage.Mask(tim.getDimensions())
tmask.set(0x0)
tMi = afwImage.MaskedImageF(tim, tmask, tvar)
if display:
import lsst.afw.display as afwDisplay
afwDisplay.Display(frame=1).mtv(tMi)
afwDisplay.Display(frame=2).mtv(sMi)
# Finally, make a kernelSet from these 2 images
kernelCellSet = afwMath.SpatialCellSet(afwGeom.Box2I(afwGeom.Point2I(0, 0),
afwGeom.Extent2I(sizeCell*nCell,
sizeCell*nCell)),
sizeCell,
sizeCell)
stampHalfWidth = 2*kSize
for x in range(nCell):
for y in range(nCell):
xCoord = x*sizeCell + sizeCell//2
yCoord = y*sizeCell + sizeCell//2
p0 = afwGeom.Point2I(xCoord - stampHalfWidth,
yCoord - stampHalfWidth)
p1 = afwGeom.Point2I(xCoord + stampHalfWidth,
yCoord + stampHalfWidth)
bbox = afwGeom.Box2I(p0, p1)
tsi = afwImage.MaskedImageF(tMi, bbox, origin=afwImage.LOCAL)
ssi = afwImage.MaskedImageF(sMi, bbox, origin=afwImage.LOCAL)
kc = diffimLib.makeKernelCandidate(xCoord, yCoord, tsi, ssi, policyFake)
kernelCellSet.insertCandidate(kc)
tMi.setXY0(0, 0)
sMi.setXY0(0, 0)
return tMi, sMi, sKernel, kernelCellSet, configFake
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):
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))
for switch in ['A', 'B', 'C']:
if switch == 'A':
# AL
config = subconfigAL
elif switch == 'B':
# AL with ~320 bases
config = subconfigAL
config.alardDegGauss = (15, 10, 5)
elif switch == 'C':
config = subconfigDF
config.useRegularization = False
kList = ipDiffim.makeKernelBasisList(config)
policy = pexConfig.makePolicy(config)
bskv = ipDiffim.BuildSingleKernelVisitorF(kList, policy)
# TEST 1
tmi, smi = makeTest1(doAddNoise)
kc = ipDiffim.makeKernelCandidate(0.0, 0.0, tmi, smi, policy)
bskv.processCandidate(kc)
kernel = kc.getKernel(ipDiffim.KernelCandidateF.ORIG)
kimage = afwImage.ImageD(kernel.getDimensions())
kernel.computeImage(kimage, False)
diffim = kc.getDifferenceImage(ipDiffim.KernelCandidateF.ORIG)
afwDisplay.Display(frame=fnum).mtv(tmi)
fnum += 1
afwDisplay.Display(frame=fnum).mtv(smi)
def _buildCellSet(self, exposure, referencePsfModel):
"""!Build a SpatialCellSet for use with the solve method
@param exposure: The science exposure that will be convolved; must contain a Psf
@param referencePsfModel: Psf model to match to
@return
-kernelCellSet: a SpatialCellSet to be used by self._solve
-referencePsfModel: Validated and/or modified reference model used to populate the SpatialCellSet
If the reference Psf model and science Psf model have different dimensions,
adjust the referencePsfModel (the model to which the exposure PSF will be matched)
to match that of the science Psf. If the science Psf dimensions vary across the image,
as is common with a WarpedPsf, either pad or clip (depending on config.padPsf)
the dimensions to be constant.
"""
scienceBBox = exposure.getBBox()
sciencePsfModel = exposure.getPsf()
dimenR = referencePsfModel.getLocalKernel().getDimensions()
psfWidth, psfHeight = dimenR
regionSizeX, regionSizeY = scienceBBox.getDimensions()
scienceX0, scienceY0 = scienceBBox.getMin()
sizeCellX = self.kConfig.sizeCellX
sizeCellY = self.kConfig.sizeCellY
kernelCellSet = afwMath.SpatialCellSet(
afwGeom.Box2I(afwGeom.Point2I(scienceX0, scienceY0),
afwGeom.Extent2I(regionSizeX, regionSizeY)),
sizeCellX, sizeCellY
)
nCellX = regionSizeX//sizeCellX
nCellY = regionSizeY//sizeCellY
if nCellX == 0 or nCellY == 0:
raise ValueError("Exposure dimensions=%s and sizeCell=(%s, %s). Insufficient area to match" %
(scienceBBox.getDimensions(), sizeCellX, sizeCellY))
# Survey the PSF dimensions of the Spatial Cell Set
# to identify the minimum enclosed or maximum bounding square BBox.
widthList = []
heightList = []
for row in range(nCellY):
posY = sizeCellY*row + sizeCellY//2 + scienceY0
for col in range(nCellX):
posX = sizeCellX*col + sizeCellX//2 + scienceX0
widthS, heightS = sciencePsfModel.computeBBox(afwGeom.Point2D(posX, posY)).getDimensions()
widthList.append(widthS)
heightList.append(heightS)
psfSize = max(max(heightList), max(widthList))
if self.config.doAutoPadPsf:
minPsfSize = nextOddInteger(self.kConfig.kernelSize*self.config.autoPadPsfTo)
paddingPix = max(0, minPsfSize - psfSize)
else:
if self.config.padPsfBy % 2 != 0:
raise ValueError("Config padPsfBy (%i pixels) must be even number." %
self.config.padPsfBy)
paddingPix = self.config.padPsfBy
if paddingPix > 0:
self.log.info("Padding Science PSF from (%s, %s) to (%s, %s) pixels" %
(psfSize, psfSize, paddingPix + psfSize, paddingPix + psfSize))
psfSize += paddingPix
# Check that PSF is larger than the matching kernel
maxKernelSize = psfSize - 1
if maxKernelSize % 2 == 0:
maxKernelSize -= 1
if self.kConfig.kernelSize > maxKernelSize:
message = """
Kernel size (%d) too big to match Psfs of size %d.
Please reconfigure by setting one of the following:
1) kernel size to <= %d
2) doAutoPadPsf=True
3) padPsfBy to >= %s
""" % (self.kConfig.kernelSize, psfSize,
maxKernelSize, self.kConfig.kernelSize - maxKernelSize)
raise ValueError(message)
dimenS = afwGeom.Extent2I(psfSize, psfSize)
if (dimenR != dimenS):
try:
referencePsfModel = referencePsfModel.resized(psfSize, psfSize)
self.log.info("Adjusted dimensions of reference PSF model from %s to %s" % (dimenR, dimenS))
except Exception as e:
self.log.warn("Zero padding or clipping the reference PSF model of type %s and dimensions %s"
" to the science Psf dimensions %s because: %s",
referencePsfModel.__class__.__name__, dimenR, dimenS, e)
dimenR = dimenS
policy = pexConfig.makePolicy(self.kConfig)
for row in range(nCellY):
# place at center of cell
posY = sizeCellY * row + sizeCellY//2 + scienceY0
for col in range(nCellX):
# place at center of cell
posX = sizeCellX * col + sizeCellX//2 + scienceX0
log.log("TRACE4." + self.log.getName(), log.DEBUG,
"Creating Psf candidate at %.1f %.1f", posX, posY)
# reference kernel image, at location of science subimage
referenceMI = self._makePsfMaskedImage(referencePsfModel, posX, posY, dimensions=dimenR)
# kernel image we are going to convolve
scienceMI = self._makePsfMaskedImage(sciencePsfModel, posX, posY, dimensions=dimenR)
# The image to convolve is the science image, to the reference Psf.
kc = diffimLib.makeKernelCandidate(posX, posY, scienceMI, referenceMI, policy)
kernelCellSet.insertCandidate(kc)
import lsstDebug
display = lsstDebug.Info(__name__).display
displaySpatialCells = lsstDebug.Info(__name__).displaySpatialCells
maskTransparency = lsstDebug.Info(__name__).maskTransparency
if not maskTransparency:
maskTransparency = 0
if display:
ds9.setMaskTransparency(maskTransparency)
if display and displaySpatialCells:
diUtils.showKernelSpatialCells(exposure.getMaskedImage(), kernelCellSet,
symb="o", ctype=ds9.CYAN, ctypeUnused=ds9.YELLOW, ctypeBad=ds9.RED,
size=4, frame=lsstDebug.frame, title="Image to be convolved")
lsstDebug.frame += 1
return pipeBase.Struct(kernelCellSet=kernelCellSet,
referencePsfModel=referencePsfModel,
)
def setUp(self):
self.configAL = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configAL.kernel.name = "AL"
self.subconfigAL = self.configAL.kernel.active
self.configDF = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configDF.kernel.name = "DF"
self.subconfigDF = self.configDF.kernel.active
self.configDFr = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.configDFr.kernel.name = "DF"
self.subconfigDFr = self.configDFr.kernel.active
self.subconfigDF.useRegularization = False
self.subconfigDFr.useRegularization = True
self.subconfigDFr.lambdaValue = 1000.0
self.subconfigAL.fitForBackground = fitForBackground
self.subconfigDF.fitForBackground = fitForBackground
self.subconfigDFr.fitForBackground = fitForBackground
self.subconfigAL.constantVarianceWeighting = constantVarianceWeighting
self.subconfigDF.constantVarianceWeighting = constantVarianceWeighting
self.subconfigDFr.constantVarianceWeighting = constantVarianceWeighting
self.kListAL = ipDiffim.makeKernelBasisList(self.subconfigAL)
self.kListDF = ipDiffim.makeKernelBasisList(self.subconfigDF)
self.kListDFr = ipDiffim.makeKernelBasisList(self.subconfigDFr)
self.hMatDFr = ipDiffim.makeRegularizationMatrix(pexConfig.makePolicy(self.subconfigDFr))
self.bskvAL = ipDiffim.BuildSingleKernelVisitorF(self.kListAL, pexConfig.makePolicy(self.subconfigAL))
self.bskvDF = ipDiffim.BuildSingleKernelVisitorF(self.kListDF, pexConfig.makePolicy(self.subconfigDF))
self.bskvDFr = ipDiffim.BuildSingleKernelVisitorF(self.kListDFr,
pexConfig.makePolicy(self.subconfigDF),
self.hMatDFr)
defSciencePath = globals()['defSciencePath']
defTemplatePath = globals()['defTemplatePath']
if defSciencePath and defTemplatePath:
self.scienceExposure = afwImage.ExposureF(defSciencePath)
self.templateExposure = afwImage.ExposureF(defTemplatePath)
else:
defDataDir = lsst.utils.getPackageDir('afwdata')
defSciencePath = os.path.join(defDataDir, "DC3a-Sim", "sci", "v26-e0",
"v26-e0-c011-a00.sci.fits")
defTemplatePath = os.path.join(defDataDir, "DC3a-Sim", "sci", "v5-e0",
"v5-e0-c011-a00.sci.fits")
self.scienceExposure = afwImage.ExposureF(defSciencePath)
self.templateExposure = afwImage.ExposureF(defTemplatePath)
warper = afwMath.Warper.fromConfig(self.subconfigAL.warpingConfig)
self.templateExposure = warper.warpExposure(self.scienceExposure.getWcs(), self.templateExposure,
destBBox=self.scienceExposure.getBBox())
#
tmi = self.templateExposure.getMaskedImage()
smi = self.scienceExposure.getMaskedImage()
# Object detection
detConfig = self.subconfigAL.detectionConfig
detPolicy = pexConfig.makePolicy(detConfig)
detPolicy.set("detThreshold", 50.)
detPolicy.set("detThresholdType", "stdev")
detPolicy.set("detOnTemplate", False)
kcDetect = ipDiffim.KernelCandidateDetectionF(detPolicy)
kcDetect.apply(tmi, smi)
self.footprints = kcDetect.getFootprints()
def applyVisitor(self, invert=False, xloc=397, yloc=580):
print('# %.2f %.2f' % (xloc, yloc))
imsize = int(3 * self.subconfigAL.kernelSize)
# chop out a region around a known object
bbox = afwGeom.Box2I(afwGeom.Point2I(xloc - imsize//2,
yloc - imsize//2),
afwGeom.Point2I(xloc + imsize//2,
yloc + imsize//2))
# sometimes the box goes off the image; no big deal...
try:
if invert:
tmi = afwImage.MaskedImageF(self.scienceExposure.getMaskedImage(), bbox,
origin=afwImage.LOCAL)
smi = afwImage.MaskedImageF(self.templateExposure.getMaskedImage(), bbox,
orign=afwImage.LOCAL)
else:
smi = afwImage.MaskedImageF(self.scienceExposure.getMaskedImage(), bbox,
origin=afwImage.LOCAL)
tmi = afwImage.MaskedImageF(self.templateExposure.getMaskedImage(), bbox,
origin=afwImage.LOCAL)
except Exception:
return None
#
###
#
# delta function kernel
resultsDF = self.apply(pexConfig.makePolicy(self.subconfigDF), self.bskvDF, xloc, yloc, tmi, smi)
kSumDF, bgDF, dmeanDF, dstdDF, vmeanDF, kImageOutDF, diffImDF, kcDF, dStats = resultsDF
kcDF.getKernelSolution(ipDiffim.KernelCandidateF.RECENT).getConditionNumber(
ipDiffim.KernelSolution.EIGENVALUE)
kcDF.getKernelSolution(ipDiffim.KernelCandidateF.RECENT).getConditionNumber(
ipDiffim.KernelSolution.SVD)
print('DF Diffim residuals : %.2f +/- %.2f; %.2f, %.2f; %.2f %.2f, %.2f' % (dStats.getMean(),
dStats.getRms(),
kSumDF, bgDF,
dmeanDF, dstdDF, vmeanDF))
if display:
afwDisplay.Display(frame=1).mtv(tmi) # ds9 switches frame 0 and 1 for some reason
afwDisplay.Display(frame=0).mtv(smi)
afwDisplay.Display(frame=2).mtv(kImageOutDF)
afwDisplay.Display(frame=3).mtv(diffImDF)
if writefits:
tmi.writeFits('t')
smi.writeFits('s')
kImageOutDF.writeFits('kDF.fits')
diffImDF.writeFits('dDF')
#
###
#
# regularized delta function kernel
resultsDFr = self.apply(pexConfig.makePolicy(self.subconfigDFr), self.bskvDFr, xloc, yloc, tmi, smi)
kSumDFr, bgDFr, dmeanDFr, dstdDFr, vmeanDFr, kImageOutDFr, diffImDFr, kcDFr, dStats = resultsDFr
kcDFr.getKernelSolution(ipDiffim.KernelCandidateF.RECENT).getConditionNumber(
ipDiffim.KernelSolution.EIGENVALUE)
kcDFr.getKernelSolution(ipDiffim.KernelCandidateF.RECENT).getConditionNumber(
ipDiffim.KernelSolution.SVD)
print('DFr Diffim residuals : %.2f +/- %.2f; %.2f, %.2f; %.2f %.2f, %.2f' %
(dStats.getMean(), dStats.getRms(), kSumDFr, bgDFr, dmeanDFr, dstdDFr, vmeanDFr))
if display:
afwDisplay.Display(frame=4).mtv(tmi)
afwDisplay.Display(frame=5).mtv(smi)
afwDisplay.Display(frame=6).mtv(kImageOutDFr)
afwDisplay.Display(frame=7).mtv(diffImDFr)
if writefits:
kImageOutDFr.writeFits('kDFr.fits')
diffImDFr.writeFits('dDFr')
#
###
#
# alard-lupton kernel
resultsAL = self.apply(pexConfig.makePolicy(self.subconfigAL), self.bskvAL, xloc, yloc, tmi, smi)
kSumAL, bgAL, dmeanAL, dstdAL, vmeanAL, kImageOutAL, diffImAL, kcAL, dStats = resultsAL
kcAL.getKernelSolution(ipDiffim.KernelCandidateF.RECENT).getConditionNumber(
ipDiffim.KernelSolution.EIGENVALUE)
kcAL.getKernelSolution(ipDiffim.KernelCandidateF.RECENT).getConditionNumber(
ipDiffim.KernelSolution.SVD)
print('AL Diffim residuals : %.2f +/- %.2f; %.2f, %.2f; %.2f %.2f, %.2f' % (dStats.getMean(),
dStats.getRms(),
kSumAL, bgAL,
dmeanAL, dstdAL, vmeanAL))
# outputs
if display:
afwDisplay.Display(frame=8).mtv(tmi)
afwDisplay.Display(frame=9).mtv(smi)
afwDisplay.Display(frame=10).mtv(kImageOutAL)
afwDisplay.Display(frame=11).mtv(diffImAL)
if writefits:
kImageOutAL.writeFits('kAL.fits')
diffImAL.writeFits('dAL')
input('Next: ')
def cosmicRay(self, exposure, keepCRs=None):
"""Mask cosmic rays
@param[in,out] exposure Exposure to process
@param[in] keepCRs Don't interpolate over the CR pixels (defer to pex_config if None)
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayCR = lsstDebug.Info(__name__).displayCR
assert exposure, "No exposure provided"
psf = exposure.getPsf()
assert psf, "No psf provided"
# Blow away old mask
try:
mask = exposure.getMaskedImage().getMask()
crBit = mask.getMaskPlane("CR")
mask.clearMaskPlane(crBit)
except Exception:
pass
exposure0 = exposure # initial value of exposure
binSize = self.config.cosmicray.background.binSize
nx, ny = exposure.getWidth() / binSize, exposure.getHeight() / binSize
# Treat constant background as a special case to avoid the extra complexity in calling
# measAlg.SubtractBackgroundTask().
if nx * ny <= 1:
medianBg = afwMath.makeStatistics(exposure.getMaskedImage(),
afwMath.MEDIAN).getValue()
modelBg = None
else:
# make a deep copy of the exposure before subtracting its background,
# because this routine is only allowed to modify the exposure by setting mask planes
# and interpolating over defects, not changing the background level
exposure = exposure.Factory(exposure, True)
subtractBackgroundTask = measAlg.SubtractBackgroundTask(
config=self.config.cosmicray.background)
modelBg = subtractBackgroundTask.run(exposure).background
medianBg = 0.0
if keepCRs is None:
keepCRs = self.config.cosmicray.keepCRs
try:
crs = measAlg.findCosmicRays(
exposure.getMaskedImage(), psf, medianBg,
pexConfig.makePolicy(self.config.cosmicray), keepCRs)
if modelBg:
# Add back background image
img = exposure.getMaskedImage()
img += modelBg.getImageF()
del img
# Replace original image with CR subtracted image
exposure0.setMaskedImage(exposure.getMaskedImage())
except Exception:
if display:
afwDisplay.Display().mtv(exposure0, title="Failed CR")
raise
num = 0
if crs is not None:
mask = exposure0.getMaskedImage().getMask()
crBit = mask.getPlaneBitMask("CR")
afwDet.setMaskFromFootprintList(mask, crs, crBit)
num = len(crs)
if display and displayCR:
disp = afwDisplay.Display()
disp.incrDefaultFrame()
disp.mtv(exposure0, title="Post-CR")
with disp.Buffering():
for cr in crs:
afwDisplay.utils.drawBBox(cr.getBBox(),
borderWidth=0.55)
self.log.info("Identified %s cosmic rays." % (num, ))
def makeFakeKernelSet(sizeCell=128,
nCell=3,
deltaFunctionCounts=1.e4,
tGaussianWidth=1.0,
addNoise=True,
bgValue=100.,
display=False):
"""Generate test template and science images with sources.
Parameters
----------
sizeCell : `int`, optional
Size of the square spatial cells in pixels.
nCell : `int`, optional
Number of adjacent spatial cells in both direction in both images.
deltaFunctionCounts : `float`, optional
Flux value for the template image sources.
tGaussianWidth : `float`, optional
Sigma of the generated Gaussian PSF sources in the template image.
addNoise : `bool`, optional
If `True`, Poisson noise is added to both the generated template
and science images.
bgValue : `float`, optional
Background level to be added to the generated science image.
display : `bool`, optional
If `True` displays the generated template and science images by
`lsst.afw.display.Display`.
Notes
-----
- The generated images consist of adjacent ``nCell x nCell`` cells, each
of pixel size ``sizeCell x sizeCell``.
- The sources in the science image are generated by convolving the
template by ``sKernel``. ``sKernel`` is a spatial `LinearCombinationKernel`
of hard wired kernel bases functions. The linear combination has first
order polynomial spatial dependence with polynomial parameters from ``fakeCoeffs()``.
- The template image sources are generated in the center of each spatial
cell from one pixel, set to `deltaFunctionCounts` counts, then convolved
by a 2D Gaussian with sigma of `tGaussianWidth` along each axis.
- The sources are also returned in ``kernelCellSet`` each source is "detected"
exactly at the center of a cell.
Returns
-------
tMi : `lsst.afw.image.MaskedImage`
Generated template image.
sMi : `lsst.afw.image.MaskedImage`
Generated science image.
sKernel : `lsst.afw.math.LinearCombinationKernel`
The spatial kernel used to generate the sources in the science image.
kernelCellSet : `lsst.afw.math.SpatialCellSet`
Cell grid of `lsst.afw.math.SpatialCell` instances, containing
`lsst.ip.diffim.KernelCandidate` instances around all the generated sources
in the science image.
configFake : `lsst.ip.diffim.ImagePsfMatchConfig`
Config instance used in the image generation.
"""
from . import imagePsfMatch
configFake = imagePsfMatch.ImagePsfMatchConfig()
configFake.kernel.name = "AL"
subconfigFake = configFake.kernel.active
subconfigFake.alardNGauss = 1
subconfigFake.alardSigGauss = [
2.5,
]
subconfigFake.alardDegGauss = [
2,
]
subconfigFake.sizeCellX = sizeCell
subconfigFake.sizeCellY = sizeCell
subconfigFake.spatialKernelOrder = 1
subconfigFake.spatialModelType = "polynomial"
subconfigFake.singleKernelClipping = False # variance is a hack
subconfigFake.spatialKernelClipping = False # variance is a hack
if bgValue > 0.0:
subconfigFake.fitForBackground = True
policyFake = pexConfig.makePolicy(subconfigFake)
basisList = makeKernelBasisList(subconfigFake)
kSize = subconfigFake.kernelSize
# This sets the final extent of each convolved delta function
gaussKernelWidth = sizeCell // 2
# This sets the scale over which pixels are correlated in the
# spatial convolution; should be at least as big as the kernel you
# are trying to fit for
spatialKernelWidth = kSize
# Number of bad pixels due to convolutions
border = (gaussKernelWidth + spatialKernelWidth) // 2
# Make a fake image with a matrix of delta functions
totalSize = nCell * sizeCell + 2 * border
tim = afwImage.ImageF(afwGeom.Extent2I(totalSize, totalSize))
for x in range(nCell):
for y in range(nCell):
tim[x * sizeCell + sizeCell // 2 + border - 1,
y * sizeCell + sizeCell // 2 + border - 1,
afwImage.LOCAL] = deltaFunctionCounts
# Turn this into stars with a narrow width; conserve counts
gaussFunction = afwMath.GaussianFunction2D(tGaussianWidth, tGaussianWidth)
gaussKernel = afwMath.AnalyticKernel(gaussKernelWidth, gaussKernelWidth,
gaussFunction)
cim = afwImage.ImageF(tim.getDimensions())
afwMath.convolve(cim, tim, gaussKernel, True)
tim = cim
# Trim off border pixels
bbox = gaussKernel.shrinkBBox(tim.getBBox(afwImage.LOCAL))
tim = afwImage.ImageF(tim, bbox, afwImage.LOCAL)
# Now make a science image which is this convolved with some
# spatial function. Use input basis list.
polyFunc = afwMath.PolynomialFunction2D(1)
kCoeffs = fakeCoeffs()
nToUse = min(len(kCoeffs), len(basisList))
# Make the full convolved science image
sKernel = afwMath.LinearCombinationKernel(basisList[:nToUse], polyFunc)
sKernel.setSpatialParameters(kCoeffs[:nToUse])
sim = afwImage.ImageF(tim.getDimensions())
afwMath.convolve(sim, tim, sKernel, True)
# Get the good subregion
bbox = sKernel.shrinkBBox(sim.getBBox(afwImage.LOCAL))
# Add background
sim += bgValue
# Watch out for negative values
tim += 2 * np.abs(np.min(tim.getArray()))
# Add noise?
if addNoise:
sim = makePoissonNoiseImage(sim)
tim = makePoissonNoiseImage(tim)
# And turn into MaskedImages
sim = afwImage.ImageF(sim, bbox, afwImage.LOCAL)
svar = afwImage.ImageF(sim, True)
smask = afwImage.Mask(sim.getDimensions())
smask.set(0x0)
sMi = afwImage.MaskedImageF(sim, smask, svar)
tim = afwImage.ImageF(tim, bbox, afwImage.LOCAL)
tvar = afwImage.ImageF(tim, True)
tmask = afwImage.Mask(tim.getDimensions())
tmask.set(0x0)
tMi = afwImage.MaskedImageF(tim, tmask, tvar)
if display:
import lsst.afw.display as afwDisplay
afwDisplay.Display(frame=1).mtv(tMi)
afwDisplay.Display(frame=2).mtv(sMi)
# Finally, make a kernelSet from these 2 images
kernelCellSet = afwMath.SpatialCellSet(
afwGeom.Box2I(afwGeom.Point2I(0, 0),
afwGeom.Extent2I(sizeCell * nCell, sizeCell * nCell)),
sizeCell, sizeCell)
stampHalfWidth = 2 * kSize
for x in range(nCell):
for y in range(nCell):
xCoord = x * sizeCell + sizeCell // 2
yCoord = y * sizeCell + sizeCell // 2
p0 = afwGeom.Point2I(xCoord - stampHalfWidth,
yCoord - stampHalfWidth)
p1 = afwGeom.Point2I(xCoord + stampHalfWidth,
yCoord + stampHalfWidth)
bbox = afwGeom.Box2I(p0, p1)
tsi = afwImage.MaskedImageF(tMi, bbox, origin=afwImage.LOCAL)
ssi = afwImage.MaskedImageF(sMi, bbox, origin=afwImage.LOCAL)
kc = diffimLib.makeKernelCandidate(xCoord, yCoord, tsi, ssi,
policyFake)
kernelCellSet.insertCandidate(kc)
tMi.setXY0(0, 0)
sMi.setXY0(0, 0)
return tMi, sMi, sKernel, kernelCellSet, configFake
def applyVisitor(self, invert=False, xloc=397, yloc=580):
print('# %.2f %.2f' % (xloc, yloc))
imsize = int(3 * self.subconfig1.kernelSize)
# chop out a region around a known object
bbox = afwGeom.Box2I(
afwGeom.Point2I(xloc - imsize // 2, yloc - imsize // 2),
afwGeom.Point2I(xloc + imsize // 2, yloc + imsize // 2))
# sometimes the box goes off the image; no big deal...
try:
if invert:
tmi = afwImage.MaskedImageF(
self.scienceExposure.getMaskedImage(),
bbox,
origin=afwImage.LOCAL)
smi = afwImage.MaskedImageF(
self.templateExposure.getMaskedImage(),
bbox,
origin=afwImage.LOCAL)
else:
smi = afwImage.MaskedImageF(
self.scienceExposure.getMaskedImage(),
bbox,
origin=afwImage.LOCAL)
tmi = afwImage.MaskedImageF(
self.templateExposure.getMaskedImage(),
bbox,
origin=afwImage.LOCAL)
except Exception:
return None
# delta function kernel
logger.debug('DF run')
results1 = self.apply(pexConfig.makePolicy(self.subconfig1),
self.bskv1, xloc, yloc, tmi, smi)
kSum1, bg1, dmean1, dstd1, vmean1, kImageOut1, diffIm1, kc1, dStats1 = results1
res = 'DF residuals : %.3f +/- %.3f; %.2f, %.2f; %.2f %.2f, %.2f' % (
dStats1.getMean(), dStats1.getRms(), kSum1, bg1, dmean1, dstd1,
vmean1)
logger.debug(res)
if display:
afwDisplay.Display(frame=1).mtv(
tmi, title="Template image") # ds9 switches frame 0 and 1
afwDisplay.Display(frame=0).mtv(smi, title="Sciencte image")
afwDisplay.Display(frame=2).mtv(kImageOut1,
title="Kernal image: 1")
afwDisplay.Display(frame=3).mtv(diffIm1,
title="Difference image: 1")
if writefits:
tmi.writeFits('t.fits')
smi.writeFits('s.fits')
kImageOut1.writeFits('k1.fits')
diffIm1.writeFits('d1.fits')
# regularized delta function kernel
logger.debug('DFrC5 run')
results2 = self.apply(pexConfig.makePolicy(self.subconfig2),
self.bskv2, xloc, yloc, tmi, smi)
kSum2, bg2, dmean2, dstd2, vmean2, kImageOut2, diffIm2, kc2, dStats2 = results2
res = 'DFrC5 residuals : %.3f +/- %.3f; %.2f, %.2f; %.2f %.2f, %.2f' % (
dStats2.getMean(), dStats2.getRms(), kSum2, bg2, dmean2, dstd2,
vmean2)
logger.debug(res)
if display:
afwDisplay.Display(frame=4).mtv(tmi, title="Template image")
afwDisplay.Display(frame=5).mtv(smi, title="Science image")
afwDisplay.Display(frame=6).mtv(kImageOut2,
title="Kernal image: 2")
afwDisplay.Display(frame=7).mtv(diffIm2,
title="Difference image: 2")
if writefits:
kImageOut2.writeFits('k2.fits')
diffIm2.writeFits('d2')
# regularized delta function kernel
logger.debug('DFrC9 run')
results3 = self.apply(pexConfig.makePolicy(self.subconfig3),
self.bskv3, xloc, yloc, tmi, smi)
kSum3, bg3, dmean3, dstd3, vmean3, kImageOut3, diffIm3, kc3, dStats3 = results3
res = 'DFrC9 residuals : %.3f +/- %.3f; %.2f, %.2f; %.2f %.2f, %.2f' % (
dStats3.getMean(), dStats3.getRms(), kSum3, bg3, dmean3, dstd3,
vmean3)
logger.debug(res)
if display:
afwDisplay.Display(frame=8).mtv(tmi)
afwDisplay.Display(frame=9).mtv(smi)
afwDisplay.Display(frame=10).mtv(kImageOut3)
afwDisplay.Display(frame=11).mtv(diffIm3)
if writefits:
kImageOut2.writeFits('k3.fits')
diffIm2.writeFits('d3')
# regularized delta function kernel
logger.debug('DFrF12 run')
results4 = self.apply(pexConfig.makePolicy(self.subconfig4),
self.bskv4, xloc, yloc, tmi, smi)
kSum4, bg4, dmean4, dstd4, vmean4, kImageOut4, diffIm4, kc4, dStats4 = results4
res = 'DFrF12 residuals : %.3f +/- %.3f; %.2f, %.2f; %.2f %.2f, %.2f' % (
dStats4.getMean(), dStats4.getRms(), kSum4, bg4, dmean4, dstd4,
vmean4)
logger.debug(res)
if display:
afwDisplay.Display(frame=12).mtv(tmi)
afwDisplay.Display(frame=13).mtv(smi)
afwDisplay.Display(frame=14).mtv(kImageOut4)
afwDisplay.Display(frame=15).mtv(diffIm4)
if writefits:
kImageOut2.writeFits('k4.fits')
diffIm2.writeFits('d4')
input('Next: ')
def setUp(self, CFHT=True):
lambdaValue = 1.0
self.config1 = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config1.kernel.name = "DF"
self.subconfig1 = self.config1.kernel.active
self.config2 = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config2.kernel.name = "DF"
self.subconfig2 = self.config2.kernel.active
self.config3 = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config3.kernel.name = "DF"
self.subconfig3 = self.config3.kernel.active
self.config4 = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config4.kernel.name = "DF"
self.subconfig4 = self.config4.kernel.active
self.subconfig1.useRegularization = False
self.subconfig2.useRegularization = True
self.subconfig2.lambdaType = "absolute"
self.subconfig2.lambdaValue = lambdaValue
self.subconfig2.regularizationType = "centralDifference"
self.subconfig2.centralRegularizationStencil = 5
self.subconfig3.useRegularization = True
self.subconfig3.lambdaType = "absolute"
self.subconfig3.lambdaValue = lambdaValue
self.subconfig3.regularizationType = "centralDifference"
self.subconfig3.centralRegularizationStencil = 9
self.subconfig4.useRegularization = True
self.subconfig4.lambdaType = "absolute"
self.subconfig4.lambdaValue = lambdaValue
self.subconfig4.regularizationType = "forwardDifference"
self.subconfig4.forwardRegularizationOrders = [1, 2]
self.kList1 = ipDiffim.makeKernelBasisList(self.subconfig1)
self.bskv1 = ipDiffim.BuildSingleKernelVisitorF(
self.kList1, pexConfig.makePolicy(self.subconfig1))
self.kList2 = ipDiffim.makeKernelBasisList(self.subconfig2)
self.hMat2 = ipDiffim.makeRegularizationMatrix(
pexConfig.makePolicy(self.subconfig2))
self.bskv2 = ipDiffim.BuildSingleKernelVisitorF(
self.kList2, pexConfig.makePolicy(self.subconfig2), self.hMat2)
self.kList3 = ipDiffim.makeKernelBasisList(self.subconfig3)
self.hMat3 = ipDiffim.makeRegularizationMatrix(
pexConfig.makePolicy(self.subconfig3))
self.bskv3 = ipDiffim.BuildSingleKernelVisitorF(
self.kList3, pexConfig.makePolicy(self.subconfig3), self.hMat3)
self.kList4 = ipDiffim.makeKernelBasisList(self.subconfig4)
self.hMat4 = ipDiffim.makeRegularizationMatrix(
pexConfig.makePolicy(self.subconfig4))
self.bskv4 = ipDiffim.BuildSingleKernelVisitorF(
self.kList4, pexConfig.makePolicy(self.subconfig4), self.hMat4)
# known input images
defDataDir = lsst.utils.getPackageDir('afwdata')
if CFHT:
defSciencePath = os.path.join(defDataDir, 'CFHT', 'D4',
CFHTTORUN + '.fits')
defTemplatePath = os.path.join(defDataDir, 'CFHT', 'D4',
CFHTTORUN + '_tmpl.fits')
# no need to remap
self.scienceExposure = afwImage.ExposureF(defSciencePath)
self.templateExposure = afwImage.ExposureF(defTemplatePath)
else:
defSciencePath = os.path.join(defDataDir, "DC3a-Sim", "sci",
"v26-e0", "v26-e0-c011-a00.sci")
defTemplatePath = os.path.join(defDataDir, "DC3a-Sim", "sci",
"v5-e0", "v5-e0-c011-a00.sci")
self.scienceExposure = afwImage.ExposureF(defSciencePath)
self.templateExposure = afwImage.ExposureF(defTemplatePath)
warper = afwMath.Warper.fromConfig(self.subconfig1.warpingConfig)
self.templateExposure = warper.warpExposure(
self.scienceExposure.getWcs(),
self.templateExposure,
destBBox=self.scienceExposure.getBBox())
diffimTools.backgroundSubtract(self.subconfig1.afwBackgroundConfig, [
self.scienceExposure.getMaskedImage(),
self.templateExposure.getMaskedImage()
])
#
tmi = self.templateExposure.getMaskedImage()
smi = self.scienceExposure.getMaskedImage()
detConfig = self.subconfig1.detectionConfig
detPolicy = pexConfig.makePolicy(detConfig)
detPolicy.set("detThreshold", 50.)
detPolicy.set("detOnTemplate", False)
kcDetect = ipDiffim.KernelCandidateDetectionF(detPolicy)
kcDetect.apply(tmi, smi)
self.footprints = kcDetect.getFootprints()
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())
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.subconfig = self.config.kernel["DF"]
self.policy = pexConfig.makePolicy(self.subconfig)
def setUp(self):
self.config = ipDiffim.ImagePsfMatchTask.ConfigClass()
self.config.kernel.name = "AL"
self.subconfig = self.config.kernel.active
# Test was put together before the min size went to 21
self.subconfig.kernelSize = 19
self.subconfig.scaleByFwhm = False
self.subconfig.fitForBackground = True
self.subconfig.spatialModelType = "polynomial"
self.policy = pexConfig.makePolicy(self.subconfig)
self.smi = afwImage.MaskedImageF('tests/compareToHotpants/scienceMI.fits')
self.tmi = afwImage.MaskedImageF('tests/compareToHotpants/templateMI.fits')
self.smi.setXY0(0, 0)
self.tmi.setXY0(0, 0)
# Run detection
# detConfig = self.subconfig.detectionConfig
# Note here regarding detConfig:
#
# If I set detThresholdType = "pixel_stdev", I get slightly
# different centroids than if I use "stdev". These different
# centroids screw up the testing since hotpants was hardcoded to
# use the "stdev" centroids. For completeness these are:
#
# 32 32
# 96 32
# 160 32
# 96 95
# 31 96
# 160 96
# 96 160
# 160 160
# 32 160
# As of Winter2013, KernelCandidateDetectionF does not return
# these exact centroids anymore, so I need to hardcode them
# in.
self.footprints = []
for xc, yc in [(32, 32), (96, 32), (160, 32),
(96, 95), (31, 96), (160, 96),
(96, 160), (160, 160), (32, 160)]:
self.footprints.append(afwDet.Footprint(afwGeom.SpanSet(
afwGeom.Box2I(afwGeom.Point2I(xc, yc),
afwGeom.Extent2I(1, 1)))))
# Make a basis list that hotpants has been run with
nGauss = 1
sGauss = [3.]
dGauss = [3]
self.subconfig.alardNGauss = nGauss
self.subconfig.alardSigGauss = sGauss
self.subconfig.alardDegGauss = dGauss
basisList0 = ipDiffim.makeKernelBasisList(self.subconfig)
# HP does things in a different order, and with different normalization, so reorder list
order = [0, 2, 5, 9, 1, 4, 8, 3, 7, 6]
scaling = [1.000000e+00,
8.866037e-02,
1.218095e+01,
5.099318e-03,
8.866037e-02,
4.179772e-02,
1.138120e-02,
1.218095e+01,
1.138120e-02,
5.099318e-03]
self.basisList = []
for i in range(len(order)):
im = afwImage.ImageD(basisList0[order[i]].getDimensions())
basisList0[order[i]].computeImage(im, False)
im /= scaling[i]
# im.writeFits('k%d.fits' % (i))
k = afwMath.FixedKernel(im)
self.basisList.append(k)
# And a place to put candidates
self.kernelCellSet = afwMath.SpatialCellSet(afwGeom.Box2I(afwGeom.Point2I(0, 0),
afwGeom.Extent2I(self.smi.getWidth(),
self.smi.getHeight())),
self.policy.getInt("sizeCellX"),
self.policy.getInt("sizeCellY"))
# There are some -1 factors that come from differences in how
# convolution is done. Some resulting convovled images end up
# being a factor of -1 different, therefore the coefficients
# need to be a factor of -1 different as well.
self.parity = [1, -1, 1, -1, -1, 1, -1, 1, -1, -1, 1]
for switch in ['A', 'B', 'C']:
if switch == 'A':
# Default Alard Lupton
config = subconfigAL
elif switch == 'B':
# Add more AL bases (typically 4 3 2)
config = subconfigAL
config.alardDegGauss = (8, 6, 4)
elif switch == 'C':
# Delta function
config = subconfigDF
config.useRegularization = False
kList = ipDiffim.makeKernelBasisList(config)
policy = pexConfig.makePolicy(config)
bskv = ipDiffim.BuildSingleKernelVisitorF(kList, policy)
# TEST 1
tmi, smi = makeTest1(doAddNoise)
kc = ipDiffim.makeKernelCandidate(0.0, 0.0, tmi, smi, policy)
bskv.processCandidate(kc)
kernel = kc.getKernel(ipDiffim.KernelCandidateF.ORIG)
kimage = afwImage.ImageD(kernel.getDimensions())
kernel.computeImage(kimage, False)
diffim = kc.getDifferenceImage(ipDiffim.KernelCandidateF.ORIG)
ds9.mtv(tmi, frame=fnum)
fnum += 1
ds9.mtv(smi, frame=fnum)
def _buildCellSet(self, exposure, referencePsfModel):
"""!Build a SpatialCellSet for use with the solve method
@param exposure: The science exposure that will be convolved; must contain a Psf
@param referencePsfModel: Psf model to match to
@return kernelCellSet: a SpatialCellSet to be used by self._solve
Raise a RuntimeError if the reference Psf model and science Psf model have different dimensions
"""
scienceBBox = exposure.getBBox()
sciencePsfModel = exposure.getPsf()
# The Psf base class does not support getKernel() in general, as there are some Psf
# classes for which this is not meaningful.
# Many Psfs we use in practice are KernelPsfs, and this algorithm will work fine for them,
# but someday it should probably be modified to support arbitrary Psfs.
referencePsfModel = measAlg.KernelPsf.swigConvert(referencePsfModel)
sciencePsfModel = measAlg.KernelPsf.swigConvert(sciencePsfModel)
if referencePsfModel is None or sciencePsfModel is None:
raise RuntimeError("ERROR: Psf matching is only implemented for KernelPsfs")
if (referencePsfModel.getKernel().getDimensions() != sciencePsfModel.getKernel().getDimensions()):
pexLog.Trace(self.log.getName(), 1,
"ERROR: Dimensions of reference Psf and science Psf different; exiting")
raise RuntimeError, "ERROR: Dimensions of reference Psf and science Psf different; exiting"
psfWidth, psfHeight = referencePsfModel.getKernel().getDimensions()
maxKernelSize = min(psfWidth, psfHeight) - 1
if maxKernelSize % 2 == 0:
maxKernelSize -= 1
if self.kConfig.kernelSize > maxKernelSize:
raise ValueError, "Kernel size (%d) too big to match Psfs of size %d; reduce to at least %d" % (
self.kConfig.kernelSize, psfWidth, maxKernelSize)
# Infer spatial order of Psf model!
#
# Infer from the number of spatial parameters.
# (O + 1) * (O + 2) / 2 = N
# O^2 + 3 * O + 2 * (1 - N) = 0
#
# Roots are [-3 +/- sqrt(9 - 8 * (1 - N))] / 2
#
nParameters = sciencePsfModel.getKernel().getNSpatialParameters()
root = num.sqrt(9 - 8 * (1 - nParameters))
if (root != root // 1): # We know its an integer solution
pexLog.Trace(self.log.getName(), 3, "Problem inferring spatial order of image's Psf")
else:
order = (root - 3) / 2
if (order != order // 1):
pexLog.Trace(self.log.getName(), 3, "Problem inferring spatial order of image's Psf")
else:
pexLog.Trace(self.log.getName(), 2, "Spatial order of Psf = %d; matching kernel order = %d" % (
order, self.kConfig.spatialKernelOrder))
regionSizeX, regionSizeY = scienceBBox.getDimensions()
scienceX0, scienceY0 = scienceBBox.getMin()
sizeCellX = self.kConfig.sizeCellX
sizeCellY = self.kConfig.sizeCellY
kernelCellSet = afwMath.SpatialCellSet(
afwGeom.Box2I(afwGeom.Point2I(scienceX0, scienceY0),
afwGeom.Extent2I(regionSizeX, regionSizeY)),
sizeCellX, sizeCellY
)
nCellX = regionSizeX // sizeCellX
nCellY = regionSizeY // sizeCellY
dimenR = referencePsfModel.getKernel().getDimensions()
dimenS = sciencePsfModel.getKernel().getDimensions()
policy = pexConfig.makePolicy(self.kConfig)
for row in range(nCellY):
# place at center of cell
posY = sizeCellY * row + sizeCellY // 2 + scienceY0
for col in range(nCellX):
# place at center of cell
posX = sizeCellX * col + sizeCellX // 2 + scienceX0
pexLog.Trace(self.log.getName(), 5, "Creating Psf candidate at %.1f %.1f" % (posX, posY))
# reference kernel image, at location of science subimage
kernelImageR = referencePsfModel.computeImage(afwGeom.Point2D(posX, posY)).convertF()
kernelMaskR = afwImage.MaskU(dimenR)
kernelMaskR.set(0)
kernelVarR = afwImage.ImageF(dimenR)
kernelVarR.set(1.0)
referenceMI = afwImage.MaskedImageF(kernelImageR, kernelMaskR, kernelVarR)
# kernel image we are going to convolve
kernelImageS = sciencePsfModel.computeImage(afwGeom.Point2D(posX, posY)).convertF()
kernelMaskS = afwImage.MaskU(dimenS)
kernelMaskS.set(0)
kernelVarS = afwImage.ImageF(dimenS)
kernelVarS.set(1.0)
scienceMI = afwImage.MaskedImageF(kernelImageS, kernelMaskS, kernelVarS)
# The image to convolve is the science image, to the reference Psf.
kc = diffimLib.makeKernelCandidate(posX, posY, scienceMI, referenceMI, policy)
kernelCellSet.insertCandidate(kc)
import lsstDebug
display = lsstDebug.Info(__name__).display
displaySpatialCells = lsstDebug.Info(__name__).displaySpatialCells
maskTransparency = lsstDebug.Info(__name__).maskTransparency
if not maskTransparency:
maskTransparency = 0
if display:
ds9.setMaskTransparency(maskTransparency)
if display and displaySpatialCells:
diUtils.showKernelSpatialCells(exposure.getMaskedImage(), kernelCellSet,
symb="o", ctype=ds9.CYAN, ctypeUnused=ds9.YELLOW, ctypeBad=ds9.RED,
size=4, frame=lsstDebug.frame, title="Image to be convolved")
lsstDebug.frame += 1
return kernelCellSet
def sizeMagnitudeStarSelectorFactory(config):
return SizeMagnitudeStarSelector(pexConfig.makePolicy(config))
def cosmicRay(self, exposure, keepCRs=None):
"""Mask cosmic rays
\param[in,out] exposure Exposure to process
\param[in] keepCRs Don't interpolate over the CR pixels (defer to pex_config if None)
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayCR = lsstDebug.Info(__name__).displayCR
assert exposure, "No exposure provided"
psf = exposure.getPsf()
assert psf, "No psf provided"
# Blow away old mask
try:
mask = exposure.getMaskedImage().getMask()
crBit = mask.getMaskPlane("CR")
mask.clearMaskPlane(crBit)
except Exception:
pass
exposure0 = exposure # initial value of exposure
binSize = self.config.cosmicray.background.binSize
nx, ny = exposure.getWidth()/binSize, exposure.getHeight()/binSize
# Treat constant background as a special case to avoid the extra complexity in calling
# measAlg.SubtractBackgroundTask().
if nx*ny <= 1:
medianBg = afwMath.makeStatistics(exposure.getMaskedImage(), afwMath.MEDIAN).getValue()
modelBg = None
else:
# make a deep copy of the exposure before subtracting its background,
# because this routine is only allowed to modify the exposure by setting mask planes
# and interpolating over defects, not changing the background level
exposure = exposure.Factory(exposure, True)
subtractBackgroundTask = measAlg.SubtractBackgroundTask(config=self.config.cosmicray.background)
modelBg = subtractBackgroundTask.run(exposure).background
medianBg = 0.0
if keepCRs is None:
keepCRs = self.config.cosmicray.keepCRs
try:
crs = measAlg.findCosmicRays(exposure.getMaskedImage(), psf, medianBg,
pexConfig.makePolicy(self.config.cosmicray), keepCRs)
if modelBg:
# Add back background image
img = exposure.getMaskedImage()
img += modelBg.getImageF()
del img
# Replace original image with CR subtracted image
exposure0.setMaskedImage(exposure.getMaskedImage())
except Exception:
if display:
import lsst.afw.display.ds9 as ds9
ds9.mtv(exposure0, title="Failed CR")
raise
num = 0
if crs is not None:
mask = exposure0.getMaskedImage().getMask()
crBit = mask.getPlaneBitMask("CR")
afwDet.setMaskFromFootprintList(mask, crs, crBit)
num = len(crs)
if display and displayCR:
import lsst.afw.display.ds9 as ds9
import lsst.afw.display.utils as displayUtils
ds9.incrDefaultFrame()
ds9.mtv(exposure0, title="Post-CR")
with ds9.Buffering():
for cr in crs:
displayUtils.drawBBox(cr.getBBox(), borderWidth=0.55)
self.log.info("Identified %s cosmic rays." % (num,))
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)
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)