def testTicket2872(self):
"""Test that CoaddPsf.getAveragePosition() is always a position at which
we can call computeImage().
"""
cdelt = (0.2 * afwGeom.arcseconds).asDegrees()
wcs = afwImage.makeWcs(
afwCoord.IcrsCoord(afwGeom.Point2D(45.0, 45.0), afwGeom.degrees),
afwGeom.Point2D(50, 50), cdelt, 0.0, 0.0, cdelt)
kernel = measAlg.DoubleGaussianPsf(7, 7, 2.0).getKernel()
psf1 = measAlg.KernelPsf(kernel, afwGeom.Point2D(0, 50))
psf2 = measAlg.KernelPsf(kernel, afwGeom.Point2D(100, 50))
record1 = self.mycatalog.addNew()
record1.setPsf(psf1)
record1.setWcs(wcs)
record1.setD(self.weightKey, 1.0)
record1.setBBox(
afwGeom.Box2I(afwGeom.Point2I(-40, 0), afwGeom.Point2I(40, 100)))
record2 = self.mycatalog.addNew()
record2.setPsf(psf2)
record2.setWcs(wcs)
record2.setD(self.weightKey, 1.0)
record2.setBBox(
afwGeom.Box2I(afwGeom.Point2I(60, 0), afwGeom.Point2I(140, 100)))
coaddPsf = measAlg.CoaddPsf(self.mycatalog, wcs)
naiveAvgPos = afwGeom.Point2D(50, 50)
with self.assertRaises(pexExceptions.InvalidParameterError):
coaddPsf.computeKernelImage(naiveAvgPos)
# important test is that this doesn't throw:
coaddPsf.computeKernelImage()
def testTicket2872(self):
"""Test that CoaddPsf.getAveragePosition() is always a position at which
we can call computeImage().
"""
schema = afwTable.ExposureTable.makeMinimalSchema()
weightKey = schema.addField("weight",
type=float,
doc="photometric weight")
catalog = afwTable.ExposureCatalog(schema)
cdelt = (0.2 * afwGeom.arcseconds).asDegrees()
wcs = afwImage.makeWcs(
afwCoord.IcrsCoord(afwGeom.Point2D(45.0, 45.0), afwGeom.degrees),
afwGeom.Point2D(50, 50), cdelt, 0.0, 0.0, cdelt)
kernel = measAlg.DoubleGaussianPsf(7, 7, 2.0).getKernel()
psf1 = measAlg.KernelPsf(kernel, afwGeom.Point2D(0, 50))
psf2 = measAlg.KernelPsf(kernel, afwGeom.Point2D(100, 50))
record1 = catalog.addNew()
record1.setPsf(psf1)
record1.setWcs(wcs)
record1.setD(weightKey, 1.0)
record1.setBBox(
afwGeom.Box2I(afwGeom.Point2I(-40, 0), afwGeom.Point2I(40, 100)))
record2 = catalog.addNew()
record2.setPsf(psf2)
record2.setWcs(wcs)
record2.setD(weightKey, 1.0)
record2.setBBox(
afwGeom.Box2I(afwGeom.Point2I(60, 0), afwGeom.Point2I(140, 100)))
coaddPsf = measAlg.CoaddPsf(catalog, wcs)
naiveAvgPos = afwGeom.Point2D(50, 50)
self.assertRaises(pexExceptions.InvalidParameterError,
coaddPsf.computeKernelImage, naiveAvgPos)
# important test is that this doesn't throw:
coaddPsf.computeKernelImage()
def testTicket2872(self):
"""Test that CoaddPsf.getAveragePosition() is always a position at which
we can call computeImage().
"""
scale = 0.2 * lsst.geom.arcseconds
cdMatrix = afwGeom.makeCdMatrix(scale=scale)
wcs = afwGeom.makeSkyWcs(
crpix=lsst.geom.Point2D(50, 50),
crval=lsst.geom.SpherePoint(45.0, 45.0, lsst.geom.degrees),
cdMatrix=cdMatrix,
)
kernel = measAlg.DoubleGaussianPsf(7, 7, 2.0).getKernel()
psf1 = measAlg.KernelPsf(kernel, lsst.geom.Point2D(0, 50))
psf2 = measAlg.KernelPsf(kernel, lsst.geom.Point2D(100, 50))
record1 = self.mycatalog.addNew()
record1.setPsf(psf1)
record1.setWcs(wcs)
record1.setD(self.weightKey, 1.0)
record1.setBBox(
lsst.geom.Box2I(lsst.geom.Point2I(-40, 0),
lsst.geom.Point2I(40, 100)))
record2 = self.mycatalog.addNew()
record2.setPsf(psf2)
record2.setWcs(wcs)
record2.setD(self.weightKey, 1.0)
record2.setBBox(
lsst.geom.Box2I(lsst.geom.Point2I(60, 0),
lsst.geom.Point2I(140, 100)))
coaddPsf = measAlg.CoaddPsf(self.mycatalog, wcs)
naiveAvgPos = lsst.geom.Point2D(50, 50)
with self.assertRaises(pexExceptions.InvalidParameterError):
coaddPsf.computeKernelImage(naiveAvgPos)
# important test is that this doesn't throw:
coaddPsf.computeKernelImage(coaddPsf.getAveragePosition())
def performALZCExposureCorrection(templateExposure, exposure,
subtractedExposure, psfMatchingKernel, log):
kimg = alPsfMatchingKernelToArray(psfMatchingKernel, subtractedExposure)
# Compute the images' sigmas (sqrt of variance)
sig1 = templateExposure.getMaskedImage().getVariance().getArray()
sig2 = exposure.getMaskedImage().getVariance().getArray()
sig1squared, _, _, _ = computeClippedImageStats(sig1)
sig2squared, _, _, _ = computeClippedImageStats(sig2)
corrKernel = computeDecorrelationKernel(kimg, sig1squared, sig2squared)
# Eventually, use afwMath.convolve(), but for now just use scipy.
log.info("ALZC: Convolving.")
pci, _ = doConvolve(
subtractedExposure.getMaskedImage().getImage().getArray(), corrKernel)
subtractedExposure.getMaskedImage().getImage().getArray()[:, :] = pci
log.info("ALZC: Finished with convolution.")
# Compute the subtracted exposure's updated psf
psf = afwPsfToArray(subtractedExposure.getPsf(),
subtractedExposure) # .computeImage().getArray()
psfc = computeCorrectedDiffimPsf(corrKernel,
psf,
svar=sig1squared,
tvar=sig2squared)
psfcI = afwImage.ImageD(
subtractedExposure.getPsf().computeKernelImage().getBBox())
psfcI.getArray()[:, :] = psfc
psfcK = afwMath.FixedKernel(psfcI)
psfNew = measAlg.KernelPsf(psfcK)
subtractedExposure.setPsf(psfNew)
return subtractedExposure, corrKernel
def testKernelPsf(self):
"""Test creating a Psf from a Kernel"""
x,y = 10.4999, 10.4999
ksize = 15
sigma1 = 1
#
# Make a PSF from that kernel
#
kPsf = measAlg.KernelPsf(afwMath.AnalyticKernel(ksize, ksize,
afwMath.GaussianFunction2D(sigma1, sigma1)))
kIm = kPsf.computeImage(afwGeom.Point2D(x, y))
#
# And now via the dgPsf model
#
dgPsf = measAlg.DoubleGaussianPsf(ksize, ksize, sigma1)
dgIm = dgPsf.computeImage(afwGeom.Point2D(x, y))
#
# Check that they're the same
#
diff = type(kIm)(kIm, True); diff -= dgIm
stats = afwMath.makeStatistics(diff, afwMath.MAX | afwMath.MIN)
self.assertAlmostEqual(stats.getValue(afwMath.MAX), 0.0, places=16)
self.assertAlmostEqual(stats.getValue(afwMath.MIN), 0.0, places=16)
if display:
mos = displayUtils.Mosaic()
mos.setBackground(-0.1)
ds9.mtv(mos.makeMosaic([kIm, dgIm, diff], mode="x"), frame=1)
def makeHSCExposure(self, galData, psfData, pixScale, variance):
ny, nx = galData.shape
exposure = afwImg.ExposureF(nx, ny)
exposure.getMaskedImage().getImage().getArray()[:, :] = galData
exposure.getMaskedImage().getVariance().getArray()[:, :] = variance
#Set the PSF
ngridPsf = psfData.shape[0]
psfLsst = afwImg.ImageF(ngridPsf, ngridPsf)
psfLsst.getArray()[:, :] = psfData
psfLsst = psfLsst.convertD()
kernel = afwMath.FixedKernel(psfLsst)
kernelPSF = meaAlg.KernelPsf(kernel)
exposure.setPsf(kernelPSF)
#prepare the wcs
#Rotation
cdelt = (pixScale * afwGeom.arcseconds)
CD = afwGeom.makeCdMatrix(cdelt, afwGeom.Angle(0.)) #no rotation
#wcs
crval = afwGeom.SpherePoint(afwGeom.Angle(0., afwGeom.degrees),
afwGeom.Angle(0., afwGeom.degrees))
#crval = afwCoord.IcrsCoord(0.*afwGeom.degrees, 0.*afwGeom.degrees) # hscpipe6
crpix = afwGeom.Point2D(0.0, 0.0)
dataWcs = afwGeom.makeSkyWcs(crpix, crval, CD)
exposure.setWcs(dataWcs)
#prepare the frc
dataCalib = afwImg.makePhotoCalibFromCalibZeroPoint(63095734448.0194)
exposure.setPhotoCalib(dataCalib)
return exposure
def makeExposure(imgArray, psfArray, imgVariance):
"""! Convert an image numpy.array and corresponding PSF numpy.array into an exposure.
Add the (constant) variance plane equal to `imgVariance`.
@param imgArray 2-d numpy.array containing the image
@param psfArray 2-d numpy.array containing the PSF image
@param imgVariance variance of input image
@return a new exposure containing the image, PSF and desired variance plane
"""
# All this code to convert the template image array/psf array into an exposure.
bbox = geom.Box2I(
geom.Point2I(0, 0),
geom.Point2I(imgArray.shape[1] - 1, imgArray.shape[0] - 1))
im1ex = afwImage.ExposureD(bbox)
im1ex.getMaskedImage().getImage().getArray()[:, :] = imgArray
im1ex.getMaskedImage().getVariance().getArray()[:, :] = imgVariance
psfBox = geom.Box2I(geom.Point2I(-12, -12),
geom.Point2I(12, 12)) # a 25x25 pixel psf
psf = afwImage.ImageD(psfBox)
psfBox.shift(geom.Extent2I(size[0] // 2, size[1] // 2))
im1_psf_sub = psfArray[psfBox.getMinX():psfBox.getMaxX() + 1,
psfBox.getMinY():psfBox.getMaxY() + 1]
psf.getArray()[:, :] = im1_psf_sub
psfK = afwMath.FixedKernel(psf)
psfNew = measAlg.KernelPsf(psfK)
im1ex.setPsf(psfNew)
wcs = makeWcs()
im1ex.setWcs(wcs)
return im1ex
def makeExposure(imgArray, psfArray, imgVariance):
"""Convert an image and corresponding PSF into an exposure.
Set the (constant) variance plane equal to ``imgVariance``.
Parameters
----------
imgArray : `numpy.ndarray`
2D array containing the image.
psfArray : `numpy.ndarray`
2D array containing the PSF image.
imgVariance : `float` or `numpy.ndarray`
Set the variance plane to this value. If an array, must be broadcastable to ``imgArray.shape``.
Returns
-------
im1ex : `lsst.afw.image.Exposure`
The new exposure.
"""
# All this code to convert the template image array/psf array into an exposure.
bbox = geom.Box2I(geom.Point2I(0, 0), geom.Point2I(imgArray.shape[1] - 1, imgArray.shape[0] - 1))
im1ex = afwImage.ExposureD(bbox)
im1ex.image.array[:, :] = imgArray
im1ex.variance.array[:, :] = imgVariance
psfBox = geom.Box2I(geom.Point2I(-12, -12), geom.Point2I(12, 12)) # a 25x25 pixel psf
psf = afwImage.ImageD(psfBox)
psfBox.shift(geom.Extent2I(-(-size[0]//2), -(-size[1]//2))) # -N//2 != -(N//2) for odd numbers
im1_psf_sub = psfArray[psfBox.getMinY():psfBox.getMaxY() + 1, psfBox.getMinX():psfBox.getMaxX() + 1]
psf.getArray()[:, :] = im1_psf_sub
psfK = afwMath.FixedKernel(psf)
psfNew = measAlg.KernelPsf(psfK)
im1ex.setPsf(psfNew)
wcs = makeWcs()
im1ex.setWcs(wcs)
return im1ex
def doALdecorrelation(alTaskResult,
sig1squared=None,
sig2squared=None,
preConvKernel=None):
kimg = alPsfMatchingKernelToArray(alTaskResult.psfMatchingKernel,
alTaskResult.subtractedExposure)
if preConvKernel is not None and kimg.shape[0] < preConvKernel.shape[0]:
# This is likely brittle and may only work if both kernels are odd-shaped.
#kimg[np.abs(kimg) < 1e-4] = np.sign(kimg)[np.abs(kimg) < 1e-4] * 1e-8
#kimg -= kimg[0, 0]
padSize0 = preConvKernel.shape[0] // 2 - kimg.shape[0] // 2
padSize1 = preConvKernel.shape[1] // 2 - kimg.shape[1] // 2
kimg = np.pad(kimg, ((padSize0, padSize0), (padSize1, padSize1)),
mode='constant',
constant_values=0)
#kimg /= kimg.sum()
#preConvKernel = preConvKernel[padSize0:-padSize0, padSize1:-padSize1]
if sig1squared is None:
sig1squared = computeVarianceMean(im1)
if sig2squared is None:
sig2squared = computeVarianceMean(im2)
pck = computeDecorrelationKernel(kimg,
sig1squared,
sig2squared,
preConvKernel=preConvKernel,
delta=0.)
#return kimg, preConvKernel, pck
diffim, _ = doConvolve(alTaskResult.subtractedExposure,
pck,
use_scipy=False)
# For some reason, border areas of img and variance planes can become infinite. Fix it.
img = diffim.getMaskedImage().getImage().getArray()
img[~np.isfinite(img)] = np.nan
img = diffim.getMaskedImage().getVariance().getArray()
img[~np.isfinite(img)] = np.nan
# TBD: also need to update the mask as it is not (apparently) set correctly.
psf = afwPsfToArray(alTaskResult.subtractedExposure.getPsf(),
img=alTaskResult.subtractedExposure)
# NOTE! Need to compute the updated PSF including preConvKernel !!! This doesn't do it:
psfc = computeCorrectedDiffimPsf(kimg,
psf,
tvar=sig1squared,
svar=sig2squared)
psfcI = afwImage.ImageD(psfc.shape[0], psfc.shape[1])
psfcI.getArray()[:, :] = psfc
psfcK = afwMath.FixedKernel(psfcI)
psfNew = measAlg.KernelPsf(psfcK)
diffim.setPsf(psfNew)
alTaskResult.decorrelatedDiffim = diffim
alTaskResult.preConvKernel = preConvKernel
alTaskResult.decorrelationKernel = pck
alTaskResult.kappaImg = kimg
return alTaskResult
def _setNewPsf(self, exposure, psfArr):
"""Utility method to set an exposure's PSF when provided as a 2-d numpy.array
"""
psfI = afwImage.ImageD(psfArr.shape[0], psfArr.shape[1])
psfI.getArray()[:, :] = psfArr
psfK = afwMath.FixedKernel(psfI)
psfNew = measAlg.KernelPsf(psfK)
exposure.setPsf(psfNew)
return exposure
def makePsf(size, sigma1, mult1, sigma2, mult2):
"""
make a Gaussian with one or two components. Always square of dimensions size x size
"""
array0 = makeGaussianArray(size, sigma1)
array0 *= mult1
array1 = makeGaussianArray(size, sigma2)
array1 *= mult2
kernel = lsst.afw.math.FixedKernel(lsst.afw.image.ImageD(array0 + array1))
return measAlg.KernelPsf(kernel)
def runMeasurement(self, algorithmName, imageid, x, y, v):
"""Run the measurement algorithm on an image"""
# load the test image
imgFile = os.path.join(self.dataDir, "image.%d.fits" % imageid)
img = afwImage.ImageF(imgFile)
img -= self.bkgd
nx, ny = img.getWidth(), img.getHeight()
msk = afwImage.Mask(geom.Extent2I(nx, ny), 0x0)
var = afwImage.ImageF(geom.Extent2I(nx, ny), v)
mimg = afwImage.MaskedImageF(img, msk, var)
msk.getArray()[:] = np.where(np.fabs(img.getArray()) < 1.0e-8, msk.getPlaneBitMask("BAD"), 0)
# Put it in a bigger image, in case it matters
big = afwImage.MaskedImageF(self.offset + mimg.getDimensions())
big.getImage().set(0)
big.getMask().set(0)
big.getVariance().set(v)
subBig = afwImage.MaskedImageF(big, geom.Box2I(big.getXY0() + self.offset, mimg.getDimensions()))
subBig <<= mimg
mimg = big
mimg.setXY0(self.xy0)
exposure = afwImage.makeExposure(mimg)
cdMatrix = np.array([1.0/(2.53*3600.0), 0.0, 0.0, 1.0/(2.53*3600.0)])
cdMatrix.shape = (2, 2)
exposure.setWcs(afwGeom.makeSkyWcs(crpix=geom.Point2D(1.0, 1.0),
crval=geom.SpherePoint(0, 0, geom.degrees),
cdMatrix=cdMatrix))
# load the corresponding test psf
psfFile = os.path.join(self.dataDir, "psf.%d.fits" % imageid)
psfImg = afwImage.ImageD(psfFile)
psfImg -= self.bkgd
kernel = afwMath.FixedKernel(psfImg)
kernelPsf = algorithms.KernelPsf(kernel)
exposure.setPsf(kernelPsf)
# perform the shape measurement
msConfig = base.SingleFrameMeasurementConfig()
alg = base.SingleFramePlugin.registry[algorithmName].PluginClass.AlgClass
control = base.SingleFramePlugin.registry[algorithmName].PluginClass.ConfigClass().makeControl()
msConfig.algorithms.names = [algorithmName]
# Note: It is essential to remove the floating point part of the position for the
# Algorithm._apply. Otherwise, when the PSF is realised it will have been warped
# to account for the sub-pixel offset and we won't get *exactly* this PSF.
plugin, table = makePluginAndCat(alg, algorithmName, control, centroid="centroid")
center = geom.Point2D(int(x), int(y)) + geom.Extent2D(self.offset + geom.Extent2I(self.xy0))
source = table.makeRecord()
source.set("centroid_x", center.getX())
source.set("centroid_y", center.getY())
source.setFootprint(afwDetection.Footprint(afwGeom.SpanSet(exposure.getBBox(afwImage.PARENT))))
plugin.measure(source, exposure)
return source
def createImageAndKernel(sigma, psfSize, image):
function = afwMath.GaussianFunction2D(sigma, sigma)
kernel = afwMath.AnalyticKernel(psfSize, psfSize, function)
psf = measAlg.KernelPsf(kernel)
cim = afwImage.ImageF(image.getDimensions())
afwMath.convolve(cim, image, kernel, True)
# Trim off the border pixels
bbox = kernel.shrinkBBox(cim.getBBox(afwImage.LOCAL))
cim = afwImage.ImageF(cim, bbox, afwImage.LOCAL)
cim.setXY0(0, 0)
return cim, psf
def _growPsf(exp, extraPix=(2, 3)):
bbox = exp.getBBox()
center = ((bbox.getBeginX() + bbox.getEndX()) // 2., (bbox.getBeginY() + bbox.getEndY()) // 2.)
center = geom.Point2D(center[0], center[1])
kern = exp.getPsf().computeKernelImage(center).convertF()
kernSize = kern.getDimensions()
paddedKern = afwImage.ImageF(kernSize[0] + extraPix[0], kernSize[1] + extraPix[1])
bboxToPlace = geom.Box2I(geom.Point2I((kernSize[0] + extraPix[0] - kern.getWidth()) // 2,
(kernSize[1] + extraPix[1] - kern.getHeight()) // 2),
kern.getDimensions())
paddedKern.assign(kern, bboxToPlace)
fixedKern = afwMath.FixedKernel(paddedKern.convertD())
psfNew = measAlg.KernelPsf(fixedKern, center)
exp.setPsf(psfNew)
return exp
def makeKernelPsfFromArray(A):
"""Create a non spatially varying PSF from a `numpy.ndarray`.
Parameters
----------
A : `numpy.ndarray`
2D array to use as the new psf image. The pixels are copied.
Returns
-------
psfNew : `lsst.meas.algorithms.KernelPsf`
The constructed PSF.
"""
psfImg = afwImage.ImageD(A.astype(np.float64, copy=True), deep=False)
psfNew = measAlg.KernelPsf(afwMath.FixedKernel(psfImg))
return psfNew
def getCoaddPsf(self, exposure):
import lsst.afw.table as afwTable
import lsst.afw.image as afwImage
import lsst.afw.math as afwMath
import lsst.afw.geom as afwGeom
import lsst.meas.algorithms as measAlg
schema = afwTable.ExposureTable.makeMinimalSchema()
schema.addField("weight", type="D", doc="Coadd weight")
mycatalog = afwTable.ExposureCatalog(schema)
wcsref = exposure.getWcs()
extentX = int(exposure.getWidth() * 0.05)
extentY = int(exposure.getHeight() * 0.05)
ind = 0
for x in np.linspace(extentX, exposure.getWidth() - extentX, 10):
for y in np.linspace(extentY, exposure.getHeight() - extentY, 10):
x = int(x)
y = int(y)
image = self.getImage(x, y)
psf = afwImage.ImageD(image.shape[0], image.shape[1])
psf.getArray()[:, :] = image
psfK = afwMath.FixedKernel(psf)
psf = measAlg.KernelPsf(psfK)
record = mycatalog.getTable().makeRecord()
record.setPsf(psf)
record.setWcs(wcsref)
bbox = afwGeom.Box2I(
afwGeom.Point2I(
int(np.floor(x - extentX)) - 5,
int(np.floor(y - extentY)) - 5),
afwGeom.Point2I(
int(np.floor(x + extentX)) + 5,
int(np.floor(y + extentY)) + 5))
record.setBBox(bbox)
record['weight'] = 1.0
record['id'] = ind
ind += 1
mycatalog.append(record)
# create the coaddpsf
psf = measAlg.CoaddPsf(mycatalog, wcsref, 'weight')
return psf
def testKernelPsf(self):
"""Test creating a Psf from a Kernel.
"""
x, y = 10.4999, 10.4999
ksize = 15
sigma1 = 1
#
# Make a PSF from that kernel
#
kPsf = measAlg.KernelPsf(
afwMath.AnalyticKernel(ksize, ksize,
afwMath.GaussianFunction2D(sigma1, sigma1)))
kIm = kPsf.computeImage(lsst.geom.Point2D(x, y))
#
# And now via the dgPsf model
#
dgPsf = measAlg.DoubleGaussianPsf(ksize, ksize, sigma1)
dgIm = dgPsf.computeImage(lsst.geom.Point2D(x, y))
#
# Check that they're the same
#
diff = type(kIm)(kIm, True)
diff -= dgIm
stats = afwMath.makeStatistics(diff, afwMath.MAX | afwMath.MIN)
self.assertAlmostEqual(stats.getValue(afwMath.MAX), 0.0, places=16)
self.assertAlmostEqual(stats.getValue(afwMath.MIN), 0.0, places=16)
for pad in [-2, 4, 0]:
resizedKPsf = kPsf.resized(ksize + pad, ksize + pad)
self.assertEqual(resizedKPsf.computeBBox().getDimensions(),
lsst.geom.Extent2I(ksize + pad, ksize + pad))
self.assertEqual(resizedKPsf.getKernel().getKernelParameters(),
kPsf.getKernel().getKernelParameters())
self._compareKernelImages(kPsf, resizedKPsf)
if display:
mos = afwDisplay.utils.Mosaic()
mos.setBackground(-0.1)
afwDisplay.Display(frame=1).mtv(mos.makeMosaic([kIm, dgIm, diff],
mode="x"),
title=self._testMethodName +
": mosaic")
def makeLsstExposure(galData, psfData, pixScale, variance):
"""
make an LSST exposure object
Parameters:
galData (ndarray): array of galaxy image
psfData (ndarray): array of PSF image
pixScale (float): pixel scale
variance (float): noise variance
Returns:
exposure: LSST exposure object
"""
if not with_lsst:
raise ImportError('Do not have lsstpipe!')
ny, nx = galData.shape
exposure = afwImg.ExposureF(nx, ny)
exposure.getMaskedImage().getImage().getArray()[:, :] = galData
exposure.getMaskedImage().getVariance().getArray()[:, :] = variance
#Set the PSF
ngridPsf = psfData.shape[0]
psfLsst = afwImg.ImageF(ngridPsf, ngridPsf)
psfLsst.getArray()[:, :] = psfData
psfLsst = psfLsst.convertD()
kernel = afwMath.FixedKernel(psfLsst)
kernelPSF = meaAlg.KernelPsf(kernel)
exposure.setPsf(kernelPSF)
#prepare the wcs
#Rotation
cdelt = (pixScale * afwGeom.arcseconds)
CD = afwGeom.makeCdMatrix(cdelt, afwGeom.Angle(0.)) #no rotation
#wcs
crval = afwGeom.SpherePoint(afwGeom.Angle(0., afwGeom.degrees),
afwGeom.Angle(0., afwGeom.degrees))
#crval = afwCoord.IcrsCoord(0.*afwGeom.degrees, 0.*afwGeom.degrees) # hscpipe6
crpix = afwGeom.Point2D(0.0, 0.0)
dataWcs = afwGeom.makeSkyWcs(crpix, crval, CD)
exposure.setWcs(dataWcs)
#prepare the frc
dataCalib = afwImg.makePhotoCalibFromCalibZeroPoint(63095734448.0194)
exposure.setPhotoCalib(dataCalib)
return exposure
def performALZCExposureCorrection(templateExposure, exposure,
subtractedExposure, psfMatchingKernel, log):
import lsst.afw.image as afwImage
import lsst.meas.algorithms as measAlg
import lsst.afw.math as afwMath
spatialKernel = psfMatchingKernel
kimg = afwImage.ImageD(spatialKernel.getDimensions())
bbox = subtractedExposure.getBBox()
xcen = (bbox.getBeginX() + bbox.getEndX()) / 2.
ycen = (bbox.getBeginY() + bbox.getEndY()) / 2.
spatialKernel.computeImage(kimg, True, xcen, ycen)
# Compute the images' sigmas (sqrt of variance)
sig1 = templateExposure.getMaskedImage().getVariance().getArray()
sig2 = exposure.getMaskedImage().getVariance().getArray()
sig1squared, _ = computeClippedImageStats(sig1)
sig2squared, _ = computeClippedImageStats(sig2)
sig1 = np.sqrt(sig1squared)
sig2 = np.sqrt(sig2squared)
corrKernel = computeCorrectionKernelALZC(kimg.getArray(),
sig1=sig1,
sig2=sig2)
# Eventually, use afwMath.convolve(), but for now just use scipy.
log.info("ALZC: Convolving.")
pci, _ = doConvolve(
subtractedExposure.getMaskedImage().getImage().getArray(), corrKernel)
subtractedExposure.getMaskedImage().getImage().getArray()[:, :] = pci
log.info("ALZC: Finished with convolution.")
# Compute the subtracted exposure's updated psf
psf = subtractedExposure.getPsf().computeImage().getArray()
psfc = computeCorrectedDiffimPsfALZC(corrKernel, psf, sig1=sig1, sig2=sig2)
psfcI = afwImage.ImageD(
subtractedExposure.getPsf().computeImage().getBBox())
psfcI.getArray()[:, :] = psfc
psfcK = afwMath.FixedKernel(psfcI)
psfNew = measAlg.KernelPsf(psfcK)
subtractedExposure.setPsf(psfNew)
return subtractedExposure, corrKernel
def asAfwExposure(self):
import lsst.afw.image as afwImage
import lsst.afw.math as afwMath
import lsst.afw.geom as afwGeom
import lsst.meas.algorithms as measAlg
bbox = afwGeom.Box2I(
afwGeom.Point2I(0, 0),
afwGeom.Point2I(self.im.shape[0] - 1, self.im.shape[1] - 1))
im1ex = afwImage.ExposureF(bbox)
im1ex.getMaskedImage().getImage().getArray()[:, :] = self.im
im1ex.getMaskedImage().getVariance().getArray()[:, :] = self.var
psfShape = self.psf.shape[0] // 2
psfBox = afwGeom.Box2I(afwGeom.Point2I(-psfShape, -psfShape),
afwGeom.Point2I(psfShape, psfShape))
psf = afwImage.ImageD(psfBox)
psf.getArray()[:, :] = self.psf
psfK = afwMath.FixedKernel(psf)
psfNew = measAlg.KernelPsf(psfK)
im1ex.setPsf(psfNew)
wcs = makeWcs(naxis1=self.im.shape[0], naxis2=self.im.shape[1])
im1ex.setWcs(wcs)
return im1ex
def run(self,
subExposure,
expandedSubExposure,
fullBBox,
template,
science,
alTaskResult=None,
psfMatchingKernel=None,
preConvKernel=None,
returnDiffimPsf=False,
**kwargs):
"""Perform decorrelation operation on `subExposure`, using
`expandedSubExposure` to allow for invalid edge pixels arising from
convolutions.
This method performs A&L decorrelation on `subExposure` using
local measures for image variances and PSF. `subExposure` is a
sub-exposure of the non-decorrelated A&L diffim. It also
requires the corresponding sub-exposures of the template
(`template`) and science (`science`) exposures.
Parameters
----------
subExposure : afw.Exposure
the sub-exposure of the diffim
expandedSubExposure : afw.Exposure
the expanded sub-exposure upon which to operate
fullBBox : afwGeom.BoundingBox
the bounding box of the original exposure
template : afw.Exposure
the corresponding sub-exposure of the template exposure
science : afw.Exposure
the corresponding sub-exposure of the science exposure
alTaskResult : pipeBase.Struct
the result of A&L image differencing on `science` and
`template`, importantly containing the resulting
`psfMatchingKernel`. Can be `None`, only if
`psfMatchingKernel` is not `None`.
psfMatchingKernel : Alternative parameter for passing the
A&L `psfMatchingKernel` directly.
kwargs :
additional keyword arguments propagated from
`ImageMapReduceTask.run`.
Returns
-------
A `pipeBase.Struct containing the result of the `subExposure`
processing, labelled 'subExposure'. It also returns the
'decorrelationKernel', although that currently is not used.
Notes
-----
This `run` method accepts parameters identical to those of
`ImageMapperSubtask.run`, since it is called from the
`ImageMapperTask`. See that class for more information.
"""
templateExposure = template # input template
scienceExposure = science # input science image
if alTaskResult is None and psfMatchingKernel is None:
raise ValueError(
'Both alTaskResult and psfMatchingKernel cannot be None')
psfMatchingKernel = alTaskResult.psfMatchingKernel if alTaskResult is not None else psfMatchingKernel
# subExp and expandedSubExp are subimages of the (un-decorrelated) diffim!
# So here we compute corresponding subimages of templateExposure and scienceExposure
subExp2 = scienceExposure.Factory(scienceExposure,
expandedSubExposure.getBBox())
subExp1 = templateExposure.Factory(templateExposure,
expandedSubExposure.getBBox())
# Prevent too much log INFO verbosity from DecorrelateALKernelTask.run
#logLevel = self.log.getLevel()
#self.log.setLevel(lsst.log.WARN)
#res = ipDiffim.DecorrelateALKernelTask.run(self, subExp2, subExp1, expandedSubExposure,
# psfMatchingKernel)
svar = ipDiffim.DecorrelateALKernelTask.computeVarianceMean(
self, subExp2)
tvar = ipDiffim.DecorrelateALKernelTask.computeVarianceMean(
self, subExp1)
kimg = afwImage.ImageD(psfMatchingKernel.getDimensions())
bbox = subExposure.getBBox()
xcen = (bbox.getBeginX() + bbox.getEndX()) / 2.
ycen = (bbox.getBeginY() + bbox.getEndY()) / 2.
psfMatchingKernel.computeImage(kimg, True, xcen, ycen)
kernel = ipDiffim.DecorrelateALKernelTask._computeDecorrelationKernel(
kappa=kimg.getArray(), svar=svar, tvar=tvar)
if not returnDiffimPsf:
kernelImg = afwImage.ImageD(kernel.shape[0], kernel.shape[1])
kernelImg.getArray()[:, :] = kernel
kern = afwMath.FixedKernel(kernelImg)
maxloc = np.unravel_index(np.argmax(kernel), kernel.shape)
kern.setCtrX(maxloc[0])
kern.setCtrY(maxloc[1])
else: # Compute the subtracted exposure's updated psf
psf = subExposure.getPsf().computeImage(afwGeom.Point2D(
xcen, ycen)).getArray()
psfc = ipDiffim.DecorrelateALKernelTask.computeCorrectedDiffimPsf(
kernel, psf, svar=svar, tvar=tvar)
psfcI = afwImage.ImageD(psfc.shape[0], psfc.shape[1])
psfcI.getArray()[:, :] = psfc
kern = afwMath.FixedKernel(psfcI)
psf = measAlg.KernelPsf(kern)
out = pipeBase.Struct(psf=psf, bbox=subExposure.getBBox())
return out
def arrayToAfwPsf(array):
psfcK = arrayToAfwKernel(array)
psfNew = measAlg.KernelPsf(psfcK)
return psfNew
def run(self, exposure, templateExposure, subtractedExposure, psfMatchingKernel,
preConvKernel=None, xcen=None, ycen=None, svar=None, tvar=None):
"""Perform decorrelation of an image difference exposure.
Decorrelates the diffim due to the convolution of the templateExposure with the
A&L PSF matching kernel. Currently can accept a spatially varying matching kernel but in
this case it simply uses a static kernel from the center of the exposure. The decorrelation
is described in [DMTN-021, Equation 1](http://dmtn-021.lsst.io/#equation-1), where
`exposure` is I_1; templateExposure is I_2; `subtractedExposure` is D(k);
`psfMatchingKernel` is kappa; and svar and tvar are their respective
variances (see below).
Parameters
----------
exposure : `lsst.afw.image.Exposure`
The original science exposure (before `preConvKernel` applied) used for PSF matching.
templateExposure : `lsst.afw.image.Exposure`
The original template exposure (before matched to the science exposure
by `psfMatchingKernel`) warped into the science exposure dimensions. Always the PSF of the
`templateExposure` should be matched to the PSF of `exposure`, see notes below.
subtractedExposure :
the subtracted exposure produced by
`ip_diffim.ImagePsfMatchTask.subtractExposures()`. The `subtractedExposure` must
inherit its PSF from `exposure`, see notes below.
psfMatchingKernel :
An (optionally spatially-varying) PSF matching kernel produced
by `ip_diffim.ImagePsfMatchTask.subtractExposures()`
preConvKernel :
if not None, then the `exposure` was pre-convolved with this kernel
xcen : `float`, optional
X-pixel coordinate to use for computing constant matching kernel to use
If `None` (default), then use the center of the image.
ycen : `float`, optional
Y-pixel coordinate to use for computing constant matching kernel to use
If `None` (default), then use the center of the image.
svar : `float`, optional
Image variance for science image
If `None` (default) then compute the variance over the entire input science image.
tvar : `float`, optional
Image variance for template image
If `None` (default) then compute the variance over the entire input template image.
Returns
-------
result : `lsst.pipe.base.Struct`
- ``correctedExposure`` : the decorrelated diffim
Notes
-----
The `subtractedExposure` is NOT updated. The returned `correctedExposure` has an updated but
spatially fixed PSF. It is calculated as the center of image PSF corrected by the center of
image matching kernel.
In this task, it is _always_ the `templateExposure` that was matched to the `exposure`
by `psfMatchingKernel`. Swap arguments accordingly if actually the science exposure was matched
to a co-added template. In this case, tvar > svar typically occurs.
The `templateExposure` and `exposure` image dimensions must be the same.
Here we currently convert a spatially-varying matching kernel into a constant kernel,
just by computing it at the center of the image (tickets DM-6243, DM-6244).
We are also using a constant accross-the-image measure of sigma (sqrt(variance)) to compute
the decorrelation kernel.
TODO DM-23857 As part of the spatially varying correction implementation
consider whether returning a Struct is still necessary.
"""
spatialKernel = psfMatchingKernel
kimg = afwImage.ImageD(spatialKernel.getDimensions())
bbox = subtractedExposure.getBBox()
if xcen is None:
xcen = (bbox.getBeginX() + bbox.getEndX()) / 2.
if ycen is None:
ycen = (bbox.getBeginY() + bbox.getEndY()) / 2.
self.log.info("Using matching kernel computed at (%d, %d)", xcen, ycen)
spatialKernel.computeImage(kimg, True, xcen, ycen)
if svar is None:
svar = self.computeVarianceMean(exposure)
if tvar is None:
tvar = self.computeVarianceMean(templateExposure)
self.log.info("Variance (science, template): (%f, %f)", svar, tvar)
# Should not happen unless entire image has been masked, which could happen
# if this is a small subimage of the main exposure. In this case, just return a full NaN
# exposure
if np.isnan(svar) or np.isnan(tvar):
# Double check that one of the exposures is all NaNs
if (np.all(np.isnan(exposure.image.array))
or np.all(np.isnan(templateExposure.image.array))):
self.log.warn('Template or science image is entirely NaNs: skipping decorrelation.')
outExposure = subtractedExposure.clone()
return pipeBase.Struct(correctedExposure=outExposure, )
# The maximal correction value converges to sqrt(tvar/svar).
# Correction divergence warning if the correction exceeds 4 orders of magnitude.
tOverSVar = tvar/svar
if tOverSVar > 1e8:
self.log.warn("Diverging correction: science image variance is much smaller than template"
f", tvar/svar:{tOverSVar:.2e}")
oldVarMean = self.computeVarianceMean(subtractedExposure)
self.log.info("Variance (uncorrected diffim): %f", oldVarMean)
if preConvKernel is not None:
self.log.info('Using a pre-convolution kernel as part of decorrelation correction.')
kimg2 = afwImage.ImageD(preConvKernel.getDimensions())
preConvKernel.computeImage(kimg2, False)
pckArr = kimg2.array
kArr = kimg.array
diffExpArr = subtractedExposure.image.array
psfImg = subtractedExposure.getPsf().computeKernelImage(geom.Point2D(xcen, ycen))
psfDim = psfImg.getDimensions()
psfArr = psfImg.array
# Determine the common shape
if preConvKernel is None:
self.computeCommonShape(kArr.shape, psfArr.shape, diffExpArr.shape)
corrft = self.computeCorrection(kArr, svar, tvar)
else:
self.computeCommonShape(pckArr.shape, kArr.shape,
psfArr.shape, diffExpArr.shape)
corrft = self.computeCorrection(kArr, svar, tvar, preConvArr=pckArr)
diffExpArr = self.computeCorrectedImage(corrft, diffExpArr)
corrPsfArr = self.computeCorrectedDiffimPsf(corrft, psfArr)
psfcI = afwImage.ImageD(psfDim)
psfcI.array = corrPsfArr
psfcK = afwMath.FixedKernel(psfcI)
psfNew = measAlg.KernelPsf(psfcK)
correctedExposure = subtractedExposure.clone()
correctedExposure.image.array[...] = diffExpArr # Allow for numpy type casting
# The subtracted exposure variance plane is already correlated, we cannot propagate
# it through another convolution; instead we need to use the uncorrelated originals
# The whitening should scale it to svar + tvar on average
varImg = correctedExposure.variance.array
# Allow for numpy type casting
varImg[...] = exposure.variance.array + templateExposure.variance.array
correctedExposure.setPsf(psfNew)
newVarMean = self.computeVarianceMean(correctedExposure)
self.log.info(f"Variance (corrected diffim): {newVarMean:.2e}")
# TODO DM-23857 As part of the spatially varying correction implementation
# consider whether returning a Struct is still necessary.
return pipeBase.Struct(correctedExposure=correctedExposure, )
def run(self,
exposure,
templateExposure,
subtractedExposure,
psfMatchingKernel,
xcen=None,
ycen=None,
svar=None,
tvar=None):
"""! Perform decorrelation of an image difference exposure.
Decorrelates the diffim due to the convolution of the templateExposure with the
A&L PSF matching kernel. Currently can accept a spatially varying matching kernel but in
this case it simply uses a static kernel from the center of the exposure. The decorrelation
is described in [DMTN-021, Equation 1](http://dmtn-021.lsst.io/#equation-1), where
`exposure` is I_1; templateExposure is I_2; `subtractedExposure` is D(k);
`psfMatchingKernel` is kappa; and svar and tvar are their respective
variances (see below).
@param[in] exposure the science afwImage.Exposure used for PSF matching
@param[in] templateExposure the template afwImage.Exposure used for PSF matching
@param[in] subtractedExposure the subtracted exposure produced by
`ip_diffim.ImagePsfMatchTask.subtractExposures()`
@param[in] psfMatchingKernel an (optionally spatially-varying) PSF matching kernel produced
by `ip_diffim.ImagePsfMatchTask.subtractExposures()`
@param[in] xcen X-pixel coordinate to use for computing constant matching kernel to use
If `None` (default), then use the center of the image.
@param[in] ycen Y-pixel coordinate to use for computing constant matching kernel to use
If `None` (default), then use the center of the image.
@param[in] svar image variance for science image
If `None` (default) then compute the variance over the entire input science image.
@param[in] tvar image variance for template image
If `None` (default) then compute the variance over the entire input template image.
@return a `pipeBase.Struct` containing:
* `correctedExposure`: the decorrelated diffim
* `correctionKernel`: the decorrelation correction kernel (which may be ignored)
@note The `subtractedExposure` is NOT updated
@note The returned `correctedExposure` has an updated PSF as well.
@note Here we currently convert a spatially-varying matching kernel into a constant kernel,
just by computing it at the center of the image (tickets DM-6243, DM-6244).
@note We are also using a constant accross-the-image measure of sigma (sqrt(variance)) to compute
the decorrelation kernel.
@note Still TBD (ticket DM-6580): understand whether the convolution is correctly modifying
the variance plane of the new subtractedExposure.
"""
self.log.info("Starting.")
kimg = None
spatialKernel = psfMatchingKernel
kimg = afwImage.ImageD(spatialKernel.getDimensions())
bbox = subtractedExposure.getBBox()
if xcen is None:
xcen = (bbox.getBeginX() + bbox.getEndX()) / 2.
if ycen is None:
ycen = (bbox.getBeginY() + bbox.getEndY()) / 2.
self.log.info("Using matching kernel computed at (%d, %d)" %
(xcen, ycen))
spatialKernel.computeImage(kimg, True, xcen, ycen)
if False: # debug code to save spatially varying kernel for analysis
import pickle
import gzip
pickle.dump(spatialKernel, gzip.GzipFile('spatialKernel.p.gz',
'wb'))
if svar is None:
svar = self.computeVarianceMean(exposure)
self.log.info("Variance (science): %f" % svar)
if tvar is None:
tvar = self.computeVarianceMean(templateExposure)
self.log.info("Variance (template): %f" % tvar)
var = self.computeVarianceMean(subtractedExposure)
self.log.info("Variance (uncorrected diffim): %f" % var)
corrKernel = DecorrelateALKernelTask._computeDecorrelationKernel(
kimg.getArray(), svar, tvar)
self.log.info("Convolving.")
correctedExposure, corrKern = DecorrelateALKernelTask._doConvolve(
subtractedExposure, corrKernel)
self.log.info("Updating correctedExposure and its PSF.")
# Compute the subtracted exposure's updated psf
psf = subtractedExposure.getPsf().computeImage().getArray()
psfc = DecorrelateALKernelTask.computeCorrectedDiffimPsf(corrKernel,
psf,
svar=svar,
tvar=tvar)
psfcI = afwImage.ImageD(psfc.shape[0], psfc.shape[1])
psfcI.getArray()[:, :] = psfc
psfcK = afwMath.FixedKernel(psfcI)
psfNew = measAlg.KernelPsf(psfcK)
correctedExposure.setPsf(psfNew)
self.log.info("Complete.")
var = self.computeVarianceMean(correctedExposure)
self.log.info("Variance (corrected diffim): %f" % var)
return pipeBase.Struct(correctedExposure=correctedExposure,
correctionKernel=corrKern)
def makeBiaxialGaussianPsf(sizex, sizey, sigma1, sigma2, theta):
kernel = afwMath.AnalyticKernel(
sizex, sizey, afwMath.GaussianFunction2D(sigma1, sigma2, theta))
return measAlg.KernelPsf(kernel)
tot_images[filter_name].addNoise(noise)
tot_images[filter_name].write('%s/image_%s.fits' %
(output_dir, filter_name))
psf_bounds = galsim.BoundsI(0, 41, 0, 41)
psf_image = galsim.ImageF(psf_bounds, scale=scale)
psf.drawImage(image=psf_image)
psf_image.write('%s/psf_image.fits' % output_dir)
# Read in PSF
lsst_psf_image = afwImage.ImageF('%s/psf_image.fits' % output_dir)
bbox = afwGeom.Box2I(afwGeom.Point2I(0, 0), afwGeom.Extent2I(41, 41))
lsst_psf_image = lsst_psf_image[bbox].convertD()
lsst_psf_image = afwMath.offsetImage(lsst_psf_image, -0.5, -0.5)
kernel = afwMath.FixedKernel(lsst_psf_image)
kernelPsf = measAlg.KernelPsf(kernel)
# Exposure setup
wcs = afwImage.makeWcs(
afwCoord.Coord(0. * afwGeom.degrees, 0. * afwGeom.degrees),
afwGeom.Point2D(0.0, 0.0), 0.168 * 3600, 0.0, 0.0, 0.168 * 3600)
calib = afwImage.Calib()
calib.setFluxMag0(1e12)
# Config and task setup
measure_config = SingleFrameMeasurementTask.ConfigClass()
measure_config.load(
'/tigress/rea3/lsst/DM-8059/obs_subaru/config/apertures.py')
measure_config.load('/tigress/rea3/lsst/DM-8059/obs_subaru/config/kron.py')
measure_config.plugins.names |= [
def run(self, exposure, templateExposure, subtractedExposure, psfMatchingKernel,
preConvKernel=None, xcen=None, ycen=None, svar=None, tvar=None):
"""Perform decorrelation of an image difference exposure.
Decorrelates the diffim due to the convolution of the templateExposure with the
A&L PSF matching kernel. Currently can accept a spatially varying matching kernel but in
this case it simply uses a static kernel from the center of the exposure. The decorrelation
is described in [DMTN-021, Equation 1](http://dmtn-021.lsst.io/#equation-1), where
`exposure` is I_1; templateExposure is I_2; `subtractedExposure` is D(k);
`psfMatchingKernel` is kappa; and svar and tvar are their respective
variances (see below).
Parameters
----------
exposure : `lsst.afw.image.Exposure`
The science afwImage.Exposure used for PSF matching
templateExposure : `lsst.afw.image.Exposure`
The template exposure used for PSF matching
subtractedExposure :
the subtracted exposure produced by
`ip_diffim.ImagePsfMatchTask.subtractExposures()`
psfMatchingKernel :
An (optionally spatially-varying) PSF matching kernel produced
by `ip_diffim.ImagePsfMatchTask.subtractExposures()`
preConvKernel :
if not None, then the `exposure` was pre-convolved with this kernel
xcen : `float`, optional
X-pixel coordinate to use for computing constant matching kernel to use
If `None` (default), then use the center of the image.
ycen : `float`, optional
Y-pixel coordinate to use for computing constant matching kernel to use
If `None` (default), then use the center of the image.
svar : `float`, optional
image variance for science image
If `None` (default) then compute the variance over the entire input science image.
tvar : `float`, optional
Image variance for template image
If `None` (default) then compute the variance over the entire input template image.
Returns
-------
result : `Struct`
a `lsst.pipe.base.Struct` containing:
- ``correctedExposure`` : the decorrelated diffim
- ``correctionKernel`` : the decorrelation correction kernel (which may be ignored)
Notes
-----
The `subtractedExposure` is NOT updated
The returned `correctedExposure` has an updated PSF as well.
Here we currently convert a spatially-varying matching kernel into a constant kernel,
just by computing it at the center of the image (tickets DM-6243, DM-6244).
We are also using a constant accross-the-image measure of sigma (sqrt(variance)) to compute
the decorrelation kernel.
Still TBD (ticket DM-6580): understand whether the convolution is correctly modifying
the variance plane of the new subtractedExposure.
"""
spatialKernel = psfMatchingKernel
kimg = afwImage.ImageD(spatialKernel.getDimensions())
bbox = subtractedExposure.getBBox()
if xcen is None:
xcen = (bbox.getBeginX() + bbox.getEndX()) / 2.
if ycen is None:
ycen = (bbox.getBeginY() + bbox.getEndY()) / 2.
self.log.info("Using matching kernel computed at (%d, %d)", xcen, ycen)
spatialKernel.computeImage(kimg, True, xcen, ycen)
if svar is None:
svar = self.computeVarianceMean(exposure)
if tvar is None:
tvar = self.computeVarianceMean(templateExposure)
self.log.info("Variance (science, template): (%f, %f)", svar, tvar)
# Should not happen unless entire image has been masked, which could happen
# if this is a small subimage of the main exposure. In this case, just return a full NaN
# exposure
if np.isnan(svar) or np.isnan(tvar):
# Double check that one of the exposures is all NaNs
if (np.all(np.isnan(exposure.getMaskedImage().getImage().getArray())) or
np.all(np.isnan(templateExposure.getMaskedImage().getImage().getArray()))):
self.log.warn('Template or science image is entirely NaNs: skipping decorrelation.')
outExposure = subtractedExposure.clone()
return pipeBase.Struct(correctedExposure=outExposure, correctionKernel=None)
var = self.computeVarianceMean(subtractedExposure)
self.log.info("Variance (uncorrected diffim): %f", var)
pck = None
if preConvKernel is not None:
self.log.info('Using a pre-convolution kernel as part of decorrelation.')
kimg2 = afwImage.ImageD(preConvKernel.getDimensions())
preConvKernel.computeImage(kimg2, False)
pck = kimg2.getArray()
corrKernel = DecorrelateALKernelTask._computeDecorrelationKernel(kimg.getArray(), svar, tvar,
pck)
correctedExposure, corrKern = DecorrelateALKernelTask._doConvolve(subtractedExposure, corrKernel)
# Compute the subtracted exposure's updated psf
psf = subtractedExposure.getPsf().computeKernelImage(afwGeom.Point2D(xcen, ycen)).getArray()
psfc = DecorrelateALKernelTask.computeCorrectedDiffimPsf(corrKernel, psf, svar=svar, tvar=tvar)
psfcI = afwImage.ImageD(psfc.shape[0], psfc.shape[1])
psfcI.getArray()[:, :] = psfc
psfcK = afwMath.FixedKernel(psfcI)
psfNew = measAlg.KernelPsf(psfcK)
correctedExposure.setPsf(psfNew)
var = self.computeVarianceMean(correctedExposure)
self.log.info("Variance (corrected diffim): %f", var)
return pipeBase.Struct(correctedExposure=correctedExposure, correctionKernel=corrKern)