def testStretch(self):
"""Test playing with the lookup table"""
ds9.show()
ds9.scale("linear", "zscale")
def determinePsf(self,
exposure,
psfCandidateList,
metadata=None,
flagKey=None):
"""!Determine a PCA PSF model for an exposure given a list of PSF candidates
\param[in] exposure exposure containing the psf candidates (lsst.afw.image.Exposure)
\param[in] psfCandidateList a sequence of PSF candidates (each an lsst.meas.algorithms.PsfCandidate);
typically obtained by detecting sources and then running them through a star selector
\param[in,out] metadata a home for interesting tidbits of information
\param[in] flagKey schema key used to mark sources actually used in PSF determination
\return a list of
- psf: the measured PSF, an lsst.meas.algorithms.PcaPsf
- cellSet: an lsst.afw.math.SpatialCellSet containing the PSF candidates
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayExposure = lsstDebug.Info(
__name__).displayExposure # display the Exposure + spatialCells
displayPsfCandidates = lsstDebug.Info(
__name__).displayPsfCandidates # show the viable candidates
displayIterations = lsstDebug.Info(
__name__).displayIterations # display on each PSF iteration
displayPsfComponents = lsstDebug.Info(
__name__).displayPsfComponents # show the PCA components
displayResiduals = lsstDebug.Info(
__name__).displayResiduals # show residuals
displayPsfMosaic = lsstDebug.Info(
__name__).displayPsfMosaic # show mosaic of reconstructed PSF(x,y)
# match Kernel amplitudes for spatial plots
matchKernelAmplitudes = lsstDebug.Info(__name__).matchKernelAmplitudes
# Keep matplotlib alive post mortem
keepMatplotlibPlots = lsstDebug.Info(__name__).keepMatplotlibPlots
displayPsfSpatialModel = lsstDebug.Info(
__name__).displayPsfSpatialModel # Plot spatial model?
showBadCandidates = lsstDebug.Info(
__name__).showBadCandidates # Include bad candidates
# Normalize residuals by object amplitude
normalizeResiduals = lsstDebug.Info(__name__).normalizeResiduals
pause = lsstDebug.Info(
__name__).pause # Prompt user after each iteration?
if display > 1:
pause = True
mi = exposure.getMaskedImage()
if len(psfCandidateList) == 0:
raise RuntimeError("No PSF candidates supplied.")
# construct and populate a spatial cell set
bbox = mi.getBBox()
psfCellSet = afwMath.SpatialCellSet(bbox, self.config.sizeCellX,
self.config.sizeCellY)
sizes = []
for i, psfCandidate in enumerate(psfCandidateList):
if psfCandidate.getSource().getPsfFluxFlag(): # bad measurement
continue
try:
psfCellSet.insertCandidate(psfCandidate)
except Exception as e:
self.log.debug("Skipping PSF candidate %d of %d: %s", i,
len(psfCandidateList), e)
continue
source = psfCandidate.getSource()
quad = afwEll.Quadrupole(source.getIxx(), source.getIyy(),
source.getIxy())
axes = afwEll.Axes(quad)
sizes.append(axes.getA())
if len(sizes) == 0:
raise RuntimeError("No usable PSF candidates supplied")
nEigenComponents = self.config.nEigenComponents # initial version
if self.config.kernelSize >= 15:
self.log.warn(
"WARNING: NOT scaling kernelSize by stellar quadrupole moment "
+
"because config.kernelSize=%s >= 15; using config.kernelSize as as the width, instead",
self.config.kernelSize)
actualKernelSize = int(self.config.kernelSize)
else:
medSize = numpy.median(sizes)
actualKernelSize = 2 * int(self.config.kernelSize *
math.sqrt(medSize) + 0.5) + 1
if actualKernelSize < self.config.kernelSizeMin:
actualKernelSize = self.config.kernelSizeMin
if actualKernelSize > self.config.kernelSizeMax:
actualKernelSize = self.config.kernelSizeMax
if display:
print("Median size=%s" % (medSize, ))
self.log.trace("Kernel size=%s", actualKernelSize)
# Set size of image returned around candidate
psfCandidateList[0].setHeight(actualKernelSize)
psfCandidateList[0].setWidth(actualKernelSize)
if self.config.doRejectBlends:
# Remove blended candidates completely
blendedCandidates = [
] # Candidates to remove; can't do it while iterating
for cell, cand in candidatesIter(psfCellSet, False):
if len(cand.getSource().getFootprint().getPeaks()) > 1:
blendedCandidates.append((cell, cand))
continue
if display:
print("Removing %d blended Psf candidates" %
len(blendedCandidates))
for cell, cand in blendedCandidates:
cell.removeCandidate(cand)
if sum(1 for cand in candidatesIter(psfCellSet, False)) == 0:
raise RuntimeError("All PSF candidates removed as blends")
if display:
frame = 0
if displayExposure:
ds9.mtv(exposure, frame=frame, title="psf determination")
maUtils.showPsfSpatialCells(exposure,
psfCellSet,
self.config.nStarPerCell,
symb="o",
ctype=ds9.CYAN,
ctypeUnused=ds9.YELLOW,
size=4,
frame=frame)
#
# Do a PCA decomposition of those PSF candidates
#
reply = "y" # used in interactive mode
for iterNum in range(self.config.nIterForPsf):
if display and displayPsfCandidates: # Show a mosaic of usable PSF candidates
#
import lsst.afw.display.utils as displayUtils
stamps = []
for cell in psfCellSet.getCellList():
for cand in cell.begin(not showBadCandidates
): # maybe include bad candidates
try:
im = cand.getMaskedImage()
chi2 = cand.getChi2()
if chi2 > 1e100:
chi2 = numpy.nan
stamps.append(
(im, "%d%s" %
(maUtils.splitId(cand.getSource().getId(),
True)["objId"], chi2),
cand.getStatus()))
except Exception as e:
continue
if len(stamps) == 0:
print(
"WARNING: No PSF candidates to show; try setting showBadCandidates=True"
)
else:
mos = displayUtils.Mosaic()
for im, label, status in stamps:
im = type(im)(im, True)
try:
im /= afwMath.makeStatistics(
im, afwMath.MAX).getValue()
except NotImplementedError:
pass
mos.append(
im, label, ds9.GREEN
if status == afwMath.SpatialCellCandidate.GOOD else
ds9.YELLOW if status ==
afwMath.SpatialCellCandidate.UNKNOWN else ds9.RED)
mos.makeMosaic(frame=8, title="Psf Candidates")
# Re-fit until we don't have any candidates with naughty chi^2 values influencing the fit
cleanChi2 = False # Any naughty (negative/NAN) chi^2 values?
while not cleanChi2:
cleanChi2 = True
#
# First, estimate the PSF
#
psf, eigenValues, nEigenComponents, fitChi2 = \
self._fitPsf(exposure, psfCellSet, actualKernelSize, nEigenComponents)
#
# In clipping, allow all candidates to be innocent until proven guilty on this iteration.
# Throw out any prima facie guilty candidates (naughty chi^2 values)
#
for cell in psfCellSet.getCellList():
awfulCandidates = []
for cand in cell.begin(False): # include bad candidates
cand.setStatus(afwMath.SpatialCellCandidate.UNKNOWN
) # until proven guilty
rchi2 = cand.getChi2()
if not numpy.isfinite(rchi2) or rchi2 <= 0:
# Guilty prima facie
awfulCandidates.append(cand)
cleanChi2 = False
self.log.debug("chi^2=%s; id=%s", cand.getChi2(),
cand.getSource().getId())
for cand in awfulCandidates:
if display:
print("Removing bad candidate: id=%d, chi^2=%f" % \
(cand.getSource().getId(), cand.getChi2()))
cell.removeCandidate(cand)
#
# Clip out bad fits based on reduced chi^2
#
badCandidates = list()
for cell in psfCellSet.getCellList():
for cand in cell.begin(False): # include bad candidates
rchi2 = cand.getChi2(
) # reduced chi^2 when fitting PSF to candidate
assert rchi2 > 0
if rchi2 > self.config.reducedChi2ForPsfCandidates:
badCandidates.append(cand)
badCandidates.sort(key=lambda x: x.getChi2(), reverse=True)
numBad = numCandidatesToReject(len(badCandidates), iterNum,
self.config.nIterForPsf)
for i, c in zip(range(numBad), badCandidates):
if display:
chi2 = c.getChi2()
if chi2 > 1e100:
chi2 = numpy.nan
print("Chi^2 clipping %-4d %.2g" %
(c.getSource().getId(), chi2))
c.setStatus(afwMath.SpatialCellCandidate.BAD)
#
# Clip out bad fits based on spatial fitting.
#
# This appears to be better at getting rid of sources that have a single dominant kernel component
# (other than the zeroth; e.g., a nearby contaminant) because the surrounding sources (which help
# set the spatial model) don't contain that kernel component, and so the spatial modeling
# downweights the component.
#
residuals = list()
candidates = list()
kernel = psf.getKernel()
noSpatialKernel = psf.getKernel()
for cell in psfCellSet.getCellList():
for cand in cell.begin(False):
candCenter = afwGeom.PointD(cand.getXCenter(),
cand.getYCenter())
try:
im = cand.getMaskedImage(kernel.getWidth(),
kernel.getHeight())
except Exception as e:
continue
fit = fitKernelParamsToImage(noSpatialKernel, im,
candCenter)
params = fit[0]
kernels = fit[1]
amp = 0.0
for p, k in zip(params, kernels):
amp += p * k.getSum()
predict = [
kernel.getSpatialFunction(k)(candCenter.getX(),
candCenter.getY())
for k in range(kernel.getNKernelParameters())
]
#print cand.getSource().getId(), [a / amp for a in params], predict
residuals.append(
[a / amp - p for a, p in zip(params, predict)])
candidates.append(cand)
residuals = numpy.array(residuals)
for k in range(kernel.getNKernelParameters()):
if False:
# Straight standard deviation
mean = residuals[:, k].mean()
rms = residuals[:, k].std()
elif False:
# Using interquartile range
sr = numpy.sort(residuals[:, k])
mean = sr[int(0.5*len(sr))] if len(sr) % 2 else \
0.5 * (sr[int(0.5*len(sr))] + sr[int(0.5*len(sr))+1])
rms = 0.74 * (sr[int(0.75 * len(sr))] -
sr[int(0.25 * len(sr))])
else:
stats = afwMath.makeStatistics(
residuals[:, k], afwMath.MEANCLIP | afwMath.STDEVCLIP)
mean = stats.getValue(afwMath.MEANCLIP)
rms = stats.getValue(afwMath.STDEVCLIP)
rms = max(
1.0e-4,
rms) # Don't trust RMS below this due to numerical issues
if display:
print("Mean for component %d is %f" % (k, mean))
print("RMS for component %d is %f" % (k, rms))
badCandidates = list()
for i, cand in enumerate(candidates):
if numpy.fabs(residuals[i, k] -
mean) > self.config.spatialReject * rms:
badCandidates.append(i)
badCandidates.sort(
key=lambda x: numpy.fabs(residuals[x, k] - mean),
reverse=True)
numBad = numCandidatesToReject(len(badCandidates), iterNum,
self.config.nIterForPsf)
for i, c in zip(range(min(len(badCandidates), numBad)),
badCandidates):
cand = candidates[c]
if display:
print("Spatial clipping %d (%f,%f) based on %d: %f vs %f" % \
(cand.getSource().getId(), cand.getXCenter(), cand.getYCenter(), k,
residuals[badCandidates[i], k], self.config.spatialReject * rms))
cand.setStatus(afwMath.SpatialCellCandidate.BAD)
#
# Display results
#
if display and displayIterations:
if displayExposure:
if iterNum > 0:
ds9.erase(frame=frame)
maUtils.showPsfSpatialCells(exposure,
psfCellSet,
self.config.nStarPerCell,
showChi2=True,
symb="o",
size=8,
frame=frame,
ctype=ds9.YELLOW,
ctypeBad=ds9.RED,
ctypeUnused=ds9.MAGENTA)
if self.config.nStarPerCellSpatialFit != self.config.nStarPerCell:
maUtils.showPsfSpatialCells(
exposure,
psfCellSet,
self.config.nStarPerCellSpatialFit,
symb="o",
size=10,
frame=frame,
ctype=ds9.YELLOW,
ctypeBad=ds9.RED)
if displayResiduals:
while True:
try:
maUtils.showPsfCandidates(
exposure,
psfCellSet,
psf=psf,
frame=4,
normalize=normalizeResiduals,
showBadCandidates=showBadCandidates)
maUtils.showPsfCandidates(
exposure,
psfCellSet,
psf=psf,
frame=5,
normalize=normalizeResiduals,
showBadCandidates=showBadCandidates,
variance=True)
except:
if not showBadCandidates:
showBadCandidates = True
continue
break
if displayPsfComponents:
maUtils.showPsf(psf, eigenValues, frame=6)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure,
psf,
frame=7,
showFwhm=True)
ds9.scale('linear', 0, 1, frame=7)
if displayPsfSpatialModel:
maUtils.plotPsfSpatialModel(
exposure,
psf,
psfCellSet,
showBadCandidates=True,
matchKernelAmplitudes=matchKernelAmplitudes,
keepPlots=keepMatplotlibPlots)
if pause:
while True:
try:
reply = input(
"Next iteration? [ynchpqQs] ").strip()
except EOFError:
reply = "n"
reply = reply.split()
if reply:
reply, args = reply[0], reply[1:]
else:
reply = ""
if reply in ("", "c", "h", "n", "p", "q", "Q", "s",
"y"):
if reply == "c":
pause = False
elif reply == "h":
print("c[ontinue without prompting] h[elp] n[o] p[db] q[uit displaying] " \
"s[ave fileName] y[es]")
continue
elif reply == "p":
import pdb
pdb.set_trace()
elif reply == "q":
display = False
elif reply == "Q":
sys.exit(1)
elif reply == "s":
fileName = args.pop(0)
if not fileName:
print("Please provide a filename")
continue
print("Saving to %s" % fileName)
maUtils.saveSpatialCellSet(psfCellSet,
fileName=fileName)
continue
break
else:
print("Unrecognised response: %s" % reply,
file=sys.stderr)
if reply == "n":
break
# One last time, to take advantage of the last iteration
psf, eigenValues, nEigenComponents, fitChi2 = \
self._fitPsf(exposure, psfCellSet, actualKernelSize, nEigenComponents)
#
# Display code for debugging
#
if display and reply != "n":
if displayExposure:
maUtils.showPsfSpatialCells(exposure,
psfCellSet,
self.config.nStarPerCell,
showChi2=True,
symb="o",
ctype=ds9.YELLOW,
ctypeBad=ds9.RED,
size=8,
frame=frame)
if self.config.nStarPerCellSpatialFit != self.config.nStarPerCell:
maUtils.showPsfSpatialCells(
exposure,
psfCellSet,
self.config.nStarPerCellSpatialFit,
symb="o",
ctype=ds9.YELLOW,
ctypeBad=ds9.RED,
size=10,
frame=frame)
if displayResiduals:
maUtils.showPsfCandidates(
exposure,
psfCellSet,
psf=psf,
frame=4,
normalize=normalizeResiduals,
showBadCandidates=showBadCandidates)
if displayPsfComponents:
maUtils.showPsf(psf, eigenValues, frame=6)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure, psf, frame=7, showFwhm=True)
ds9.scale("linear", 0, 1, frame=7)
if displayPsfSpatialModel:
maUtils.plotPsfSpatialModel(
exposure,
psf,
psfCellSet,
showBadCandidates=True,
matchKernelAmplitudes=matchKernelAmplitudes,
keepPlots=keepMatplotlibPlots)
#
# Generate some QA information
#
# Count PSF stars
#
numGoodStars = 0
numAvailStars = 0
avgX = 0.0
avgY = 0.0
for cell in psfCellSet.getCellList():
for cand in cell.begin(False): # don't ignore BAD stars
numAvailStars += 1
for cand in cell.begin(True): # do ignore BAD stars
src = cand.getSource()
if flagKey is not None:
src.set(flagKey, True)
avgX += src.getX()
avgY += src.getY()
numGoodStars += 1
avgX /= numGoodStars
avgY /= numGoodStars
if metadata is not None:
metadata.set("spatialFitChi2", fitChi2)
metadata.set("numGoodStars", numGoodStars)
metadata.set("numAvailStars", numAvailStars)
metadata.set("avgX", avgX)
metadata.set("avgY", avgY)
psf = PcaPsf(psf.getKernel(), afwGeom.Point2D(avgX, avgY))
return psf, psfCellSet
action="store_true",
help="Load debug.py?",
default=False)
parser.add_argument('--ds9',
action="store_true",
help="Display the result?",
default=False)
parser.add_argument('--write',
'-w',
action="store_true",
help="Write the result?",
default=False)
args = parser.parse_args()
if args.debug:
try:
import debug
except ImportError as e:
print(e, file=sys.stderr)
exposure = runIsr()
if args.ds9:
im = exposure.getMaskedImage().getImage()
im_median = numpy.median(im.getArray())
ds9.mtv(im)
ds9.scale(min=im_median * 0.90, max=im_median * 1.1, type='SQRT')
if args.write:
exposure.writeFits("postISRCCD.fits")
flatExposure = exampleUtils.makeFlat(GRADIENT)
rawExposure = exampleUtils.makeRaw(DARKVAL, OSCAN, GRADIENT, EXPTIME)
output = isrTask.run(rawExposure, dark=darkExposure, flat=flatExposure)
return output.exposure
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Demonstrate the use of IsrTask")
parser.add_argument('--debug', '-d', action="store_true", help="Load debug.py?", default=False)
parser.add_argument('--ds9', action="store_true", help="Display the result?", default=False)
parser.add_argument('--write', '-w', action="store_true", help="Write the result?", default=False)
args = parser.parse_args()
if args.debug:
try:
import debug
except ImportError as e:
print >> sys.stderr, e
exposure = runIsr()
if args.ds9:
im = exposure.getMaskedImage().getImage()
im_median = numpy.median(im.getArray())
ds9.mtv(im)
ds9.scale(min=im_median*0.90, max=im_median*1.1, type='SQRT')
if args.write:
exposure.writeFits("postISRCCD.fits")
showBadCandidates=showBadCandidates)
maUtils.showPsfCandidates(exposure, psfCellSet, psf=psf, frame=5,
normalize=normalizeResiduals,
showBadCandidates=showBadCandidates,
variance=True)
except:
if not showBadCandidates:
showBadCandidates = True
continue
break
if displayPsfComponents:
maUtils.showPsf(psf, eigenValues, frame=6)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure, psf, frame=7, showFwhm=True)
ds9.scale('linear', 0, 1, frame=7)
if displayPsfSpatialModel:
maUtils.plotPsfSpatialModel(exposure, psf, psfCellSet, showBadCandidates=True,
matchKernelAmplitudes=matchKernelAmplitudes,
keepPlots=keepMatplotlibPlots)
if pause:
while True:
try:
reply = raw_input("Next iteration? [ynchpqQs] ").strip()
except EOFError:
reply = "n"
reply = reply.split()
if reply:
reply, args = reply[0], reply[1:]
def run(self, exposure, sources, expId=0, matches=None):
"""!Measure the PSF
\param[in,out] exposure Exposure to process; measured PSF will be added.
\param[in,out] sources Measured sources on exposure; flag fields will be set marking
stars chosen by the star selector and the PSF determiner if a schema
was passed to the task constructor.
\param[in] expId Exposure id used for generating random seed.
\param[in] matches A list of lsst.afw.table.ReferenceMatch objects
(\em i.e. of lsst.afw.table.Match
with \c first being of type lsst.afw.table.SimpleRecord and \c second
type lsst.afw.table.SourceRecord --- the reference object and detected
object respectively) as returned by \em e.g. the AstrometryTask.
Used by star selectors that choose to refer to an external catalog.
\return a pipe.base.Struct with fields:
- psf: The measured PSF (also set in the input exposure)
- cellSet: an lsst.afw.math.SpatialCellSet containing the PSF candidates
as returned by the psf determiner.
"""
self.log.info("Measuring PSF")
import lsstDebug
display = lsstDebug.Info(__name__).display
displayExposure = lsstDebug.Info(
__name__).displayExposure # display the Exposure + spatialCells
displayPsfMosaic = lsstDebug.Info(
__name__).displayPsfMosaic # show mosaic of reconstructed PSF(x,y)
displayPsfCandidates = lsstDebug.Info(
__name__).displayPsfCandidates # show mosaic of candidates
displayResiduals = lsstDebug.Info(
__name__).displayResiduals # show residuals
showBadCandidates = lsstDebug.Info(
__name__).showBadCandidates # include bad candidates
normalizeResiduals = lsstDebug.Info(
__name__).normalizeResiduals # normalise residuals by object peak
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
# Run star selector
#
selectionResult = self.starSelector.run(exposure=exposure,
sourceCat=sources,
matches=matches)
reserveResult = self.reserve.run(selectionResult.starCat, expId=expId)
psfCandidateList = [
cand for cand, use in zip(selectionResult.psfCandidates,
reserveResult.use) if use
]
if psfCandidateList and self.candidateKey is not None:
for cand in psfCandidateList:
source = cand.getSource()
source.set(self.candidateKey, True)
self.log.info("PSF star selector found %d candidates" %
len(psfCandidateList))
if display:
frame = display
if displayExposure:
ds9.mtv(exposure, frame=frame, title="psf determination")
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
# Determine PSF
#
psf, cellSet = self.psfDeterminer.determinePsf(exposure,
psfCandidateList,
self.metadata,
flagKey=self.usedKey)
self.log.info("PSF determination using %d/%d stars." %
(self.metadata.get("numGoodStars"),
self.metadata.get("numAvailStars")))
exposure.setPsf(psf)
if display:
frame = display
if displayExposure:
showPsfSpatialCells(exposure,
cellSet,
showBadCandidates,
frame=frame)
frame += 1
if displayPsfCandidates: # Show a mosaic of PSF candidates
plotPsfCandidates(cellSet, showBadCandidates, frame)
frame += 1
if displayResiduals:
frame = plotResiduals(exposure,
cellSet,
showBadCandidates=showBadCandidates,
normalizeResiduals=normalizeResiduals,
frame=frame)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure,
psf,
frame=frame,
showFwhm=True)
ds9.scale(0, 1, "linear", frame=frame)
frame += 1
return pipeBase.Struct(
psf=psf,
cellSet=cellSet,
)
def run(self, exposure, sources, expId=0, matches=None):
"""!Measure the PSF
\param[in,out] exposure Exposure to process; measured PSF will be added.
\param[in,out] sources Measured sources on exposure; flag fields will be set marking
stars chosen by the star selector and the PSF determiner if a schema
was passed to the task constructor.
\param[in] expId Exposure id used for generating random seed.
\param[in] matches A list of lsst.afw.table.ReferenceMatch objects
(\em i.e. of lsst.afw.table.Match
with \c first being of type lsst.afw.table.SimpleRecord and \c second
type lsst.afw.table.SourceRecord --- the reference object and detected
object respectively) as returned by \em e.g. the AstrometryTask.
Used by star selectors that choose to refer to an external catalog.
\return a pipe.base.Struct with fields:
- psf: The measured PSF (also set in the input exposure)
- cellSet: an lsst.afw.math.SpatialCellSet containing the PSF candidates
as returned by the psf determiner.
"""
self.log.info("Measuring PSF")
import lsstDebug
display = lsstDebug.Info(__name__).display
displayExposure = lsstDebug.Info(__name__).displayExposure # display the Exposure + spatialCells
displayPsfMosaic = lsstDebug.Info(__name__).displayPsfMosaic # show mosaic of reconstructed PSF(x,y)
displayPsfCandidates = lsstDebug.Info(__name__).displayPsfCandidates # show mosaic of candidates
displayResiduals = lsstDebug.Info(__name__).displayResiduals # show residuals
showBadCandidates = lsstDebug.Info(__name__).showBadCandidates # include bad candidates
normalizeResiduals = lsstDebug.Info(__name__).normalizeResiduals # normalise residuals by object peak
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
# Run star selector
#
psfCandidateList = self.starSelector.run(exposure=exposure, sourceCat=sources,
matches=matches).psfCandidates
reserveList = []
if self.config.reserveFraction > 0 :
random.seed(self.config.reserveSeed*expId)
reserveList = random.sample(psfCandidateList,
int((self.config.reserveFraction)*len(psfCandidateList)))
for cand in reserveList:
psfCandidateList.remove(cand)
if reserveList and self.reservedKey is not None:
for cand in reserveList:
source = cand.getSource()
source.set(self.reservedKey,True)
if psfCandidateList and self.candidateKey is not None:
for cand in psfCandidateList:
source = cand.getSource()
source.set(self.candidateKey, True)
self.log.info("PSF star selector found %d candidates" % len(psfCandidateList))
if self.config.reserveFraction > 0 :
self.log.info("Reserved %d candidates from the fitting" % len(reserveList))
if display:
frame = display
if displayExposure:
ds9.mtv(exposure, frame=frame, title="psf determination")
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
# Determine PSF
#
psf, cellSet = self.psfDeterminer.determinePsf(exposure, psfCandidateList, self.metadata,
flagKey=self.usedKey)
self.log.info("PSF determination using %d/%d stars." %
(self.metadata.get("numGoodStars"), self.metadata.get("numAvailStars")))
exposure.setPsf(psf)
if display:
frame = display
if displayExposure:
showPsfSpatialCells(exposure, cellSet, showBadCandidates, frame=frame)
frame += 1
if displayPsfCandidates: # Show a mosaic of PSF candidates
plotPsfCandidates(cellSet, showBadCandidates, frame)
frame += 1
if displayResiduals:
frame = plotResiduals(exposure, cellSet,
showBadCandidates=showBadCandidates,
normalizeResiduals=normalizeResiduals,
frame=frame)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure, psf, frame=frame, showFwhm=True)
ds9.scale(0, 1, "linear", frame=frame)
frame += 1
return pipeBase.Struct(
psf = psf,
cellSet = cellSet,
)
def runDataRef(self, sensorRef):
self.log.info("Performing ISR on sensor %s" % (sensorRef.dataId))
ccdExposure = sensorRef.get('raw')
if self.config.removePcCards: # Remove any PC00N00M cards in the header
raw_md = sensorRef.get("raw_md")
nPc = 0
for i in (
1,
2,
):
for j in (
1,
2,
):
k = "PC%03d%03d" % (i, j)
for md in (raw_md, ccdExposure.getMetadata()):
if md.exists(k):
md.remove(k)
nPc += 1
if nPc:
self.log.info("Recreating Wcs after stripping PC00n00m" %
(sensorRef.dataId))
ccdExposure.setWcs(afwImage.makeWcs(raw_md))
ccdExposure = self.convertIntToFloat(ccdExposure)
ccd = ccdExposure.getDetector()
# Read in defects to check for any dead amplifiers (entire amp is within defect region)
defects = sensorRef.get("defects", immediate=True)
for amp in ccd:
# Check if entire amp region is defined as defect (need to use amp.getBBox() for correct
# comparison with current defects definition.
badAmp = bool(
sum([v.getBBox().contains(amp.getBBox()) for v in defects]))
# In the case of bad amp, we will set mask to "BAD" (here use amp.getRawBBox() for correct
# association with pixels in current ccdExposure).
if badAmp:
dataView = afwImage.MaskedImageF(ccdExposure.getMaskedImage(),
amp.getRawBBox(),
afwImage.PARENT)
maskView = dataView.getMask()
maskView |= maskView.getPlaneBitMask("BAD")
del maskView
self.measureOverscan(ccdExposure, amp)
if self.config.doSaturation and not badAmp:
self.saturationDetection(ccdExposure, amp)
if self.config.doSuspect and not badAmp:
self.suspectDetection(ccdExposure, amp)
ampMask = afwImage.Mask(ccdExposure.getMaskedImage().getMask(),
amp.getRawDataBBox(), afwImage.PARENT)
maskVal = ampMask.getPlaneBitMask(
[self.config.saturatedMaskName, self.config.suspectMaskName])
if numpy.all(ampMask.getArray() & maskVal > 0):
badAmp = True
if self.config.doOverscan and not badAmp:
ampImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(),
amp.getRawDataBBox(),
afwImage.PARENT)
overscan = afwImage.MaskedImageF(
ccdExposure.getMaskedImage(),
amp.getRawHorizontalOverscanBBox(), afwImage.PARENT)
overscanArray = overscan.getImage().getArray()
median = numpy.ma.median(
numpy.ma.masked_where(overscan.getMask().getArray(),
overscanArray))
bad = numpy.where(
numpy.abs(overscanArray -
median) > self.config.overscanMaxDev)
overscan.getMask().getArray()[bad] = overscan.getMask(
).getPlaneBitMask("SAT")
statControl = afwMath.StatisticsControl()
statControl.setAndMask(
ccdExposure.getMaskedImage().getMask().getPlaneBitMask(
"SAT"))
lsstIsr.overscanCorrection(
ampMaskedImage=ampImage,
overscanImage=overscan,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
statControl=statControl,
)
ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
ccd = ccdExposure.getDetector()
if self.config.qa.doWriteOss:
sensorRef.put(ccdExposure, "ossImage")
if self.config.qa.doThumbnailOss:
self.writeThumbnail(sensorRef, "ossThumb", ccdExposure)
if self.config.doBias:
biasExposure = self.getIsrExposure(sensorRef, "bias")
self.biasCorrection(ccdExposure, biasExposure)
if self.config.doVariance:
for amp in ccd:
ampExposure = ccdExposure.Factory(ccdExposure, amp.getBBox(),
afwImage.PARENT)
self.updateVariance(ampExposure, amp)
if self.doLinearize(ccd):
# immediate=True required for functors and linearizers are functors; see ticket DM-6515
linearizer = sensorRef.get("linearizer", immediate=True)
linearizer(image=ccdExposure.getMaskedImage().getImage(),
detector=ccd,
log=self.log)
if self.config.doCrosstalk:
self.crosstalk.run(ccdExposure)
if self.config.doWidenSaturationTrails:
self.widenSaturationTrails(ccdExposure.getMaskedImage().getMask())
interpolationDone = False
darkExposure = self.getIsrExposure(
sensorRef, "dark") if self.config.doDark else None
flatExposure = self.getIsrExposure(
sensorRef, "flat") if self.config.doFlat else None
if self.config.doBrighterFatter:
# We need to apply flats and darks before we can interpolate, and we
# need to interpolate before we do B-F, but we do B-F without the
# flats and darks applied so we can work in units of electrons or holes.
# This context manager applies and then removes the darks and flats.
with self.flatContext(ccdExposure, flatExposure, darkExposure):
if self.config.doDefect:
self.maskAndInterpDefect(ccdExposure, defects)
if self.config.doSaturationInterpolation:
self.saturationInterpolation(ccdExposure)
self.maskAndInterpNan(ccdExposure)
interpolationDone = True
brighterFatterKernel = sensorRef.get('bfKernel')
self.brighterFatterCorrection(
ccdExposure,
brighterFatterKernel,
self.config.brighterFatterMaxIter,
self.config.brighterFatterThreshold,
self.config.brighterFatterApplyGain,
)
if self.config.doDark:
self.darkCorrection(ccdExposure, darkExposure)
if self.config.doStrayLight:
self.strayLight.run(sensorRef, ccdExposure)
if self.config.doFlat:
self.flatCorrection(ccdExposure,
flatExposure,
doTweakFlat=self.config.doTweakFlat)
if self.config.doDefect and not interpolationDone:
self.maskAndInterpDefect(ccdExposure, defects)
if self.config.doApplyGains:
self.applyGains(ccdExposure, self.config.normalizeGains)
if self.config.doSaturation and not interpolationDone:
self.saturationInterpolation(ccdExposure)
if self.config.doFringe:
self.fringe.runDataRef(ccdExposure, sensorRef)
if self.config.doSetBadRegions:
self.setBadRegions(ccdExposure)
if not interpolationDone or self.config.doNanInterpAfterFlat:
self.maskAndInterpNan(ccdExposure)
if self.config.qa.doWriteFlattened:
sensorRef.put(ccdExposure, "flattenedImage")
if self.config.qa.doThumbnailFlattened:
self.writeThumbnail(sensorRef, "flattenedThumb", ccdExposure)
self.measureBackground(ccdExposure)
if self.config.doGuider:
self.guider(ccdExposure)
self.roughZeroPoint(ccdExposure)
if self.config.doWriteVignettePolygon:
self.setValidPolygonIntersect(ccdExposure, self.vignettePolygon)
if self.config.doWrite:
sensorRef.put(ccdExposure, "postISRCCD")
if self._display:
im = ccdExposure.getMaskedImage().getImage()
im_median = float(numpy.median(im.getArray()))
ds9.mtv(im)
ds9.scale(min=im_median * 0.95, max=im_median * 1.15)
return Struct(exposure=ccdExposure)
showBadCandidates=showBadCandidates,
variance=True)
except:
if not showBadCandidates:
showBadCandidates = True
continue
break
if displayPsfComponents:
maUtils.showPsf(psf, eigenValues, frame=6)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure,
psf,
frame=7,
showFwhm=True)
ds9.scale('linear', 0, 1, frame=7)
if displayPsfSpatialModel:
maUtils.plotPsfSpatialModel(
exposure,
psf,
psfCellSet,
showBadCandidates=True,
matchKernelAmplitudes=matchKernelAmplitudes,
keepPlots=keepMatplotlibPlots)
if pause:
while True:
try:
reply = raw_input(
"Next iteration? [ynchpqQs] ").strip()
except EOFError:
def runDataRef(self, sensorRef):
self.log.log(self.log.INFO,
"Performing ISR on sensor %s" % (sensorRef.dataId))
ccdExposure = sensorRef.get('raw')
if self.config.removePcCards: # Remove any PC00N00M cards in the header
raw_md = sensorRef.get("raw_md")
nPc = 0
for i in (
1,
2,
):
for j in (
1,
2,
):
k = "PC%03d%03d" % (i, j)
for md in (raw_md, ccdExposure.getMetadata()):
if md.exists(k):
md.remove(k)
nPc += 1
if nPc:
self.log.log(
self.log.INFO, "Recreating Wcs after stripping PC00n00m" %
(sensorRef.dataId))
ccdExposure.setWcs(afwImage.makeWcs(raw_md))
ccdExposure = self.convertIntToFloat(ccdExposure)
ccd = ccdExposure.getDetector()
for amp in ccd:
self.measureOverscan(ccdExposure, amp)
if self.config.doSaturation:
self.saturationDetection(ccdExposure, amp)
if self.config.doOverscan:
ampImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(),
amp.getRawDataBBox(),
afwImage.PARENT)
overscan = afwImage.MaskedImageF(
ccdExposure.getMaskedImage(),
amp.getRawHorizontalOverscanBBox(), afwImage.PARENT)
overscanArray = overscan.getImage().getArray()
median = numpy.ma.median(
numpy.ma.masked_where(overscan.getMask().getArray(),
overscanArray))
bad = numpy.where(
numpy.abs(overscanArray -
median) > self.config.overscanMaxDev)
overscan.getMask().getArray()[bad] = overscan.getMask(
).getPlaneBitMask("SAT")
statControl = afwMath.StatisticsControl()
statControl.setAndMask(
ccdExposure.getMaskedImage().getMask().getPlaneBitMask(
"SAT"))
lsstIsr.overscanCorrection(
ampMaskedImage=ampImage,
overscanImage=overscan,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
statControl=statControl,
)
if self.config.doVariance:
# Ideally, this should be done after bias subtraction,
# but CCD assembly demands a variance plane
ampExposure = ccdExposure.Factory(ccdExposure,
amp.getRawDataBBox(),
afwImage.PARENT)
self.updateVariance(ampExposure, amp)
ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
ccd = ccdExposure.getDetector()
doRotateCalib = False # Rotate calib images for bias/dark/flat correction?
nQuarter = ccd.getOrientation().getNQuarter()
if nQuarter != 0:
doRotateCalib = True
if self.config.doDefect:
defects = sensorRef.get('defects', immediate=True)
self.maskAndInterpDefect(ccdExposure, defects)
if self.config.qa.doWriteOss:
sensorRef.put(ccdExposure, "ossImage")
if self.config.qa.doThumbnailOss:
self.writeThumbnail(sensorRef, "ossThumb", ccdExposure)
if self.config.doBias:
biasExposure = self.getIsrExposure(sensorRef, "bias")
if not doRotateCalib:
self.biasCorrection(ccdExposure, biasExposure)
else:
with self.rotated(ccdExposure) as exp:
self.biasCorrection(exp, biasExposure)
if self.config.doLinearize:
self.linearize(ccdExposure)
if self.config.doCrosstalk:
self.crosstalk.run(ccdExposure)
if self.config.doDark:
darkExposure = self.getIsrExposure(sensorRef, "dark")
if not doRotateCalib:
self.darkCorrection(ccdExposure, darkExposure)
else:
with self.rotated(ccdExposure) as exp:
self.darkCorrection(exp, darkExposure)
if self.config.doFlat:
flatExposure = self.getIsrExposure(sensorRef, "flat")
if not doRotateCalib:
self.flatCorrection(ccdExposure, flatExposure)
else:
with self.rotated(ccdExposure) as exp:
self.flatCorrection(exp, flatExposure)
if self.config.doApplyGains:
self.applyGains(ccdExposure, self.config.normalizeGains)
if self.config.doWidenSaturationTrails:
self.widenSaturationTrails(ccdExposure.getMaskedImage().getMask())
if self.config.doSaturation:
self.saturationInterpolation(ccdExposure)
if self.config.doFringe:
self.fringe.runDataRef(ccdExposure, sensorRef)
if self.config.doSetBadRegions:
self.setBadRegions(ccdExposure)
self.maskAndInterpNan(ccdExposure)
if self.config.qa.doWriteFlattened:
sensorRef.put(ccdExposure, "flattenedImage")
if self.config.qa.doThumbnailFlattened:
self.writeThumbnail(sensorRef, "flattenedThumb", ccdExposure)
self.measureBackground(ccdExposure)
if self.config.doGuider:
self.guider(ccdExposure)
self.roughZeroPoint(ccdExposure)
if self.config.doWriteVignettePolygon:
self.setValidPolygonIntersect(ccdExposure, self.vignettePolygon)
if self.config.doWrite:
sensorRef.put(ccdExposure, "postISRCCD")
if self._display:
im = ccdExposure.getMaskedImage().getImage()
im_median = float(numpy.median(im.getArray()))
ds9.mtv(im)
ds9.scale(min=im_median * 0.95, max=im_median * 1.15)
return Struct(exposure=ccdExposure)
def determinePsf(self,
exposure,
psfCandidateList,
metadata=None,
flagKey=None):
"""Determine a PSFEX PSF model for an exposure given a list of PSF candidates
@param[in] exposure: exposure containing the psf candidates (lsst.afw.image.Exposure)
@param[in] psfCandidateList: a sequence of PSF candidates (each an lsst.meas.algorithms.PsfCandidate);
typically obtained by detecting sources and then running them through a star selector
@param[in,out] metadata a home for interesting tidbits of information
@param[in] flagKey: schema key used to mark sources actually used in PSF determination
@return psf: a meas.extensions.psfex.PsfexPsf
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayExposure = display and \
lsstDebug.Info(__name__).displayExposure # display the Exposure + spatialCells
displayPsfComponents = display and \
lsstDebug.Info(__name__).displayPsfComponents # show the basis functions
showBadCandidates = display and \
lsstDebug.Info(__name__).showBadCandidates # Include bad candidates (meaningless, methinks)
displayResiduals = display and \
lsstDebug.Info(__name__).displayResiduals # show residuals
displayPsfMosaic = display and \
lsstDebug.Info(__name__).displayPsfMosaic # show mosaic of reconstructed PSF(x,y)
normalizeResiduals = lsstDebug.Info(__name__).normalizeResiduals
# Normalise residuals by object amplitude
mi = exposure.getMaskedImage()
nCand = len(psfCandidateList)
if nCand == 0:
raise RuntimeError("No PSF candidates supplied.")
#
# How big should our PSF models be?
#
if display: # only needed for debug plots
# construct and populate a spatial cell set
bbox = mi.getBBox(afwImage.PARENT)
psfCellSet = afwMath.SpatialCellSet(bbox, self.config.sizeCellX,
self.config.sizeCellY)
else:
psfCellSet = None
sizes = np.empty(nCand)
for i, psfCandidate in enumerate(psfCandidateList):
try:
if psfCellSet:
psfCellSet.insertCandidate(psfCandidate)
except Exception as e:
self.log.debug("Skipping PSF candidate %d of %d: %s", i,
len(psfCandidateList), e)
continue
source = psfCandidate.getSource()
quad = afwEll.Quadrupole(source.getIxx(), source.getIyy(),
source.getIxy())
rmsSize = quad.getTraceRadius()
sizes[i] = rmsSize
if self.config.kernelSize >= 15:
self.log.warn(
"NOT scaling kernelSize by stellar quadrupole moment, but using absolute value"
)
actualKernelSize = int(self.config.kernelSize)
else:
actualKernelSize = 2 * int(self.config.kernelSize *
np.sqrt(np.median(sizes)) + 0.5) + 1
if actualKernelSize < self.config.kernelSizeMin:
actualKernelSize = self.config.kernelSizeMin
if actualKernelSize > self.config.kernelSizeMax:
actualKernelSize = self.config.kernelSizeMax
if display:
rms = np.median(sizes)
print("Median PSF RMS size=%.2f pixels (\"FWHM\"=%.2f)" %
(rms, 2 * np.sqrt(2 * np.log(2)) * rms))
# If we manually set the resolution then we need the size in pixel units
pixKernelSize = actualKernelSize
if self.config.samplingSize > 0:
pixKernelSize = int(actualKernelSize * self.config.samplingSize)
if pixKernelSize % 2 == 0:
pixKernelSize += 1
self.log.trace("Psfex Kernel size=%.2f, Image Kernel Size=%.2f",
actualKernelSize, pixKernelSize)
psfCandidateList[0].setHeight(pixKernelSize)
psfCandidateList[0].setWidth(pixKernelSize)
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BEGIN PSFEX
#
# Insert the good candidates into the set
#
defaultsFile = os.path.join(os.environ["MEAS_EXTENSIONS_PSFEX_DIR"],
"config", "default-lsst.psfex")
args_md = dafBase.PropertySet()
args_md.set("BASIS_TYPE", str(self.config.psfexBasis))
args_md.set("PSFVAR_DEGREES", str(self.config.spatialOrder))
args_md.set("PSF_SIZE", str(actualKernelSize))
args_md.set("PSF_SAMPLING", str(self.config.samplingSize))
prefs = psfex.Prefs(defaultsFile, args_md)
prefs.setCommandLine([])
prefs.addCatalog("psfexPsfDeterminer")
prefs.use()
principalComponentExclusionFlag = bool(
bool(psfex.Context.REMOVEHIDDEN) if False else psfex.Context.
KEEPHIDDEN)
context = psfex.Context(prefs.getContextName(),
prefs.getContextGroup(), prefs.getGroupDeg(),
principalComponentExclusionFlag)
set = psfex.Set(context)
set.setVigSize(pixKernelSize, pixKernelSize)
set.setFwhm(2 * np.sqrt(2 * np.log(2)) * np.median(sizes))
set.setRecentroid(self.config.recentroid)
catindex, ext = 0, 0
backnoise2 = afwMath.makeStatistics(mi.getImage(),
afwMath.VARIANCECLIP).getValue()
ccd = exposure.getDetector()
if ccd:
gain = np.mean(np.array([a.getGain() for a in ccd]))
else:
gain = 1.0
self.log.warn("Setting gain to %g" % (gain, ))
contextvalp = []
for i, key in enumerate(context.getName()):
if context.getPcflag(i):
contextvalp.append(pcval[pc])
pc += 1
elif key[0] == ':':
try:
contextvalp.append(exposure.getMetadata().get(key[1:]))
except KeyError:
raise RuntimeError(
"*Error*: %s parameter not found in the header of %s" %
(key[1:], prefs.getContextName()))
else:
try:
contextvalp.append(
np.array([
psfCandidateList[_].getSource().get(key)
for _ in range(nCand)
]))
except KeyError:
raise RuntimeError("*Error*: %s parameter not found" %
(key, ))
set.setContextname(i, key)
if display:
frame = 0
if displayExposure:
ds9.mtv(exposure, frame=frame, title="psf determination")
badBits = mi.getMask().getPlaneBitMask(self.config.badMaskBits)
fluxName = prefs.getPhotfluxRkey()
fluxFlagName = "base_" + fluxName + "_flag"
xpos, ypos = [], []
for i, psfCandidate in enumerate(psfCandidateList):
source = psfCandidate.getSource()
xc, yc = source.getX(), source.getY()
try:
int(xc), int(yc)
except ValueError:
continue
try:
pstamp = psfCandidate.getMaskedImage().clone()
except Exception as e:
continue
if fluxFlagName in source.schema and source.get(fluxFlagName):
continue
flux = source.get(fluxName)
if flux < 0 or np.isnan(flux):
continue
# From this point, we're configuring the "sample" (PSFEx's version of a PSF candidate).
# Having created the sample, we must proceed to configure it, and then fini (finalize),
# or it will be malformed.
try:
sample = set.newSample()
sample.setCatindex(catindex)
sample.setExtindex(ext)
sample.setObjindex(i)
imArray = pstamp.getImage().getArray()
imArray[np.where(np.bitwise_and(pstamp.getMask().getArray(), badBits))] = \
-2*psfex.BIG
sample.setVig(imArray)
sample.setNorm(flux)
sample.setBacknoise2(backnoise2)
sample.setGain(gain)
sample.setX(xc)
sample.setY(yc)
sample.setFluxrad(sizes[i])
for j in range(set.getNcontext()):
sample.setContext(j, float(contextvalp[j][i]))
except Exception as e:
self.log.debug(
"Exception when processing sample at (%f,%f): %s", xc, yc,
e)
continue
else:
set.finiSample(sample)
xpos.append(xc) # for QA
ypos.append(yc)
if displayExposure:
with ds9.Buffering():
ds9.dot("o", xc, yc, ctype=ds9.CYAN, size=4, frame=frame)
if set.getNsample() == 0:
raise RuntimeError("No good PSF candidates to pass to PSFEx")
#---- Update min and max and then the scaling
for i in range(set.getNcontext()):
cmin = contextvalp[i].min()
cmax = contextvalp[i].max()
set.setContextScale(i, cmax - cmin)
set.setContextOffset(i, (cmin + cmax) / 2.0)
# Don't waste memory!
set.trimMemory()
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- END PSFEX
#
# Do a PSFEX decomposition of those PSF candidates
#
fields = []
field = psfex.Field("Unknown")
field.addExt(exposure.getWcs(), exposure.getWidth(),
exposure.getHeight(), set.getNsample())
field.finalize()
fields.append(field)
sets = []
sets.append(set)
psfex.makeit(fields, sets)
psfs = field.getPsfs()
# Flag which objects were actually used in psfex by
good_indices = []
for i in range(sets[0].getNsample()):
index = sets[0].getSample(i).getObjindex()
if index > -1:
good_indices.append(index)
if flagKey is not None:
for i, psfCandidate in enumerate(psfCandidateList):
source = psfCandidate.getSource()
if i in good_indices:
source.set(flagKey, True)
xpos = np.array(xpos)
ypos = np.array(ypos)
numGoodStars = len(good_indices)
avgX, avgY = np.mean(xpos), np.mean(ypos)
psf = psfex.PsfexPsf(psfs[0], afwGeom.Point2D(avgX, avgY))
if False and (displayResiduals or displayPsfMosaic):
ext = 0
frame = 1
diagnostics = True
catDir = "."
title = "psfexPsfDeterminer"
psfex.psfex.showPsf(psfs,
set,
ext, [(exposure.getWcs(), exposure.getWidth(),
exposure.getHeight())],
nspot=3,
trim=5,
frame=frame,
diagnostics=diagnostics,
outDir=catDir,
title=title)
#
# Display code for debugging
#
if display:
assert psfCellSet is not None
if displayExposure:
maUtils.showPsfSpatialCells(exposure,
psfCellSet,
showChi2=True,
symb="o",
ctype=ds9.YELLOW,
ctypeBad=ds9.RED,
size=8,
frame=frame)
if displayResiduals:
maUtils.showPsfCandidates(exposure,
psfCellSet,
psf=psf,
frame=4,
normalize=normalizeResiduals,
showBadCandidates=showBadCandidates)
if displayPsfComponents:
maUtils.showPsf(psf, frame=6)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure, psf, frame=7, showFwhm=True)
ds9.scale('linear', 0, 1, frame=7)
#
# Generate some QA information
#
# Count PSF stars
#
if metadata is not None:
metadata.set("spatialFitChi2", np.nan)
metadata.set("numAvailStars", nCand)
metadata.set("numGoodStars", numGoodStars)
metadata.set("avgX", avgX)
metadata.set("avgY", avgY)
psfCellSet = None
return psf, psfCellSet
def testStretch(self):
"""Test playing with the lookup table"""
ds9.show()
ds9.scale("linear", "zscale")
def runDataRef(self, sensorRef):
self.log.log(self.log.INFO, "Performing ISR on sensor %s" % (sensorRef.dataId))
ccdExposure = sensorRef.get('raw')
if self.config.removePcCards: # Remove any PC00N00M cards in the header
raw_md = sensorRef.get("raw_md")
nPc = 0
for i in (1, 2,):
for j in (1, 2,):
k = "PC%03d%03d" % (i, j)
for md in (raw_md, ccdExposure.getMetadata()):
if md.exists(k):
md.remove(k)
nPc += 1
if nPc:
self.log.log(self.log.INFO, "Recreating Wcs after stripping PC00n00m" % (sensorRef.dataId))
ccdExposure.setWcs(afwImage.makeWcs(raw_md))
ccdExposure = self.convertIntToFloat(ccdExposure)
ccd = ccdExposure.getDetector()
# Read in defects to check for any dead amplifiers (entire amp is within defect region)
defectsRaw = sensorRef.get("defects", immediate=True)
# Need to rotate defects bbox if we are dealing with a rotated ccd as they are defined assuming
# that (0, 0) is the lower-left corner (LLC). Rotation needs to be done in trimmed/assembled image
# dimensions as that is the frame for which the defects are defined. This is computed here as
# bboxTrimmed. Also need to accommodate even and odd number of 90deg rotations.
bboxTrimmed = afwGeom.Box2I()
for amp in ccd:
bboxTrimmed.include(amp.getBBox())
nQuarter = ccd.getOrientation().getNQuarter()
defects = []
if nQuarter != 0:
for v in defectsRaw:
rotBox = afwImage.imageLib.DefectBase(
afwCG.rotateBBoxBy90(v.getBBox(), 4 - nQuarter,
afwGeom.Extent2I(bboxTrimmed.getHeight(), bboxTrimmed.getHeight())))
# We have rotated about the center of a square with ccd height dimension on a side.
# rotateBBoxBy90 rotates CCW, so using 4 - nQuarter we are effectively rotating
# CW nQuarter turns. So, for nQuarter = 2 or 3, the rotated LLC will be shifted
# in x by width - height pixels wrt the LLC of the rotation square. Thus defects
# for all nQuarter > 1 ccds need to be shifted back in x by this amount.
if nQuarter > 1:
shiftBoxX0 = bboxTrimmed.getWidth() - bboxTrimmed.getHeight()
shiftBoxY0 = 0
rotBox.shift(afwGeom.Extent2I(shiftBoxX0, shiftBoxY0))
defects.append(rotBox)
else:
defects = defectsRaw
for amp in ccd:
# Check if entire amp region is defined as defect (need to use amp.getBBox() for correct
# comparison with current defects definition.
badAmp = bool(sum([v.getBBox().contains(amp.getBBox()) for v in defects]))
# In the case of bad amp, we will set mask to "BAD" (here use amp.getRawBBox() for correct
# association with pixels in current ccdExposure).
if badAmp:
dataView = afwImage.MaskedImageF(ccdExposure.getMaskedImage(), amp.getRawBBox(),
afwImage.PARENT)
maskView = dataView.getMask()
maskView |= maskView.getPlaneBitMask("BAD")
del maskView
self.measureOverscan(ccdExposure, amp)
if self.config.doSaturation and not badAmp:
self.saturationDetection(ccdExposure, amp)
if self.config.doOverscan and not badAmp:
ampImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(), amp.getRawDataBBox(),
afwImage.PARENT)
overscan = afwImage.MaskedImageF(ccdExposure.getMaskedImage(),
amp.getRawHorizontalOverscanBBox(), afwImage.PARENT)
overscanArray = overscan.getImage().getArray()
median = numpy.ma.median(numpy.ma.masked_where(overscan.getMask().getArray(), overscanArray))
bad = numpy.where(numpy.abs(overscanArray - median) > self.config.overscanMaxDev)
overscan.getMask().getArray()[bad] = overscan.getMask().getPlaneBitMask("SAT")
statControl = afwMath.StatisticsControl()
statControl.setAndMask(ccdExposure.getMaskedImage().getMask().getPlaneBitMask("SAT"))
lsstIsr.overscanCorrection(ampMaskedImage=ampImage, overscanImage=overscan,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
statControl=statControl,
)
if self.config.doVariance:
# Ideally, this should be done after bias subtraction,
# but CCD assembly demands a variance plane
ampExposure = ccdExposure.Factory(ccdExposure, amp.getRawDataBBox(), afwImage.PARENT)
self.updateVariance(ampExposure, amp)
ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
ccd = ccdExposure.getDetector()
doRotateCalib = False # Rotate calib images for bias/dark/flat correction?
if nQuarter != 0:
doRotateCalib = True
if self.config.doDefect:
self.maskAndInterpDefect(ccdExposure, defects)
if self.config.qa.doWriteOss:
sensorRef.put(ccdExposure, "ossImage")
if self.config.qa.doThumbnailOss:
self.writeThumbnail(sensorRef, "ossThumb", ccdExposure)
if self.config.doBias:
biasExposure = self.getIsrExposure(sensorRef, "bias")
if not doRotateCalib:
self.biasCorrection(ccdExposure, biasExposure)
else:
with self.rotated(ccdExposure) as exp:
self.biasCorrection(exp, biasExposure)
if self.config.doLinearize:
self.linearize(ccdExposure)
if self.config.doCrosstalk:
self.crosstalk.run(ccdExposure)
if self.config.doBrighterFatter:
brighterFatterKernel = sensorRef.get('bfKernel')
self.brighterFatterCorrection(ccdExposure, brighterFatterKernel,
self.config.brighterFatterMaxIter,
self.config.brighterFatterThreshold,
self.config.brighterFatterApplyGain,
)
if self.config.doDark:
darkExposure = self.getIsrExposure(sensorRef, "dark")
if not doRotateCalib:
self.darkCorrection(ccdExposure, darkExposure)
else:
with self.rotated(ccdExposure) as exp:
self.darkCorrection(exp, darkExposure)
if self.config.doFlat:
flatExposure = self.getIsrExposure(sensorRef, "flat")
if not doRotateCalib:
self.flatCorrection(ccdExposure, flatExposure)
else:
with self.rotated(ccdExposure) as exp:
self.flatCorrection(exp, flatExposure)
if self.config.doApplyGains:
self.applyGains(ccdExposure, self.config.normalizeGains)
if self.config.doWidenSaturationTrails:
self.widenSaturationTrails(ccdExposure.getMaskedImage().getMask())
if self.config.doSaturation:
self.saturationInterpolation(ccdExposure)
if self.config.doFringe:
self.fringe.runDataRef(ccdExposure, sensorRef)
if self.config.doSetBadRegions:
self.setBadRegions(ccdExposure)
self.maskAndInterpNan(ccdExposure)
if self.config.qa.doWriteFlattened:
sensorRef.put(ccdExposure, "flattenedImage")
if self.config.qa.doThumbnailFlattened:
self.writeThumbnail(sensorRef, "flattenedThumb", ccdExposure)
self.measureBackground(ccdExposure)
if self.config.doGuider:
self.guider(ccdExposure)
self.roughZeroPoint(ccdExposure)
if self.config.doWriteVignettePolygon:
self.setValidPolygonIntersect(ccdExposure, self.vignettePolygon)
if self.config.doWrite:
sensorRef.put(ccdExposure, "postISRCCD")
if self._display:
im = ccdExposure.getMaskedImage().getImage()
im_median = float(numpy.median(im.getArray()))
ds9.mtv(im)
ds9.scale(min=im_median*0.95, max=im_median*1.15)
return Struct(exposure=ccdExposure)
def runDataRef(self, sensorRef):
self.log.log(self.log.INFO, "Performing ISR on sensor %s" % (sensorRef.dataId))
ccdExposure = sensorRef.get("raw")
if self.config.removePcCards: # Remove any PC00N00M cards in the header
raw_md = sensorRef.get("raw_md")
nPc = 0
for i in (1, 2):
for j in (1, 2):
k = "PC%03d%03d" % (i, j)
for md in (raw_md, ccdExposure.getMetadata()):
if md.exists(k):
md.remove(k)
nPc += 1
if nPc:
self.log.log(self.log.INFO, "Recreating Wcs after stripping PC00n00m" % (sensorRef.dataId))
ccdExposure.setWcs(afwImage.makeWcs(raw_md))
ccdExposure = self.convertIntToFloat(ccdExposure)
ccd = ccdExposure.getDetector()
for amp in ccd:
self.measureOverscan(ccdExposure, amp)
if self.config.doSaturation:
self.saturationDetection(ccdExposure, amp)
if self.config.doOverscan:
ampImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(), amp.getRawDataBBox(), afwImage.PARENT)
overscan = afwImage.MaskedImageF(
ccdExposure.getMaskedImage(), amp.getRawHorizontalOverscanBBox(), afwImage.PARENT
)
overscanArray = overscan.getImage().getArray()
median = numpy.ma.median(numpy.ma.masked_where(overscan.getMask().getArray(), overscanArray))
bad = numpy.where(numpy.abs(overscanArray - median) > self.config.overscanMaxDev)
overscan.getMask().getArray()[bad] = overscan.getMask().getPlaneBitMask("SAT")
statControl = afwMath.StatisticsControl()
statControl.setAndMask(ccdExposure.getMaskedImage().getMask().getPlaneBitMask("SAT"))
lsstIsr.overscanCorrection(
ampMaskedImage=ampImage,
overscanImage=overscan,
fitType=self.config.overscanFitType,
order=self.config.overscanOrder,
collapseRej=self.config.overscanRej,
statControl=statControl,
)
if self.config.doVariance:
# Ideally, this should be done after bias subtraction,
# but CCD assembly demands a variance plane
ampExposure = ccdExposure.Factory(ccdExposure, amp.getRawDataBBox(), afwImage.PARENT)
self.updateVariance(ampExposure, amp)
ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
ccd = ccdExposure.getDetector()
doRotateCalib = False # Rotate calib images for bias/dark/flat correction?
nQuarter = ccd.getOrientation().getNQuarter()
if nQuarter != 0:
doRotateCalib = True
if self.config.doDefect:
defects = sensorRef.get("defects", immediate=True)
self.maskAndInterpDefect(ccdExposure, defects)
if self.config.qa.doWriteOss:
sensorRef.put(ccdExposure, "ossImage")
if self.config.qa.doThumbnailOss:
self.writeThumbnail(sensorRef, "ossThumb", ccdExposure)
if self.config.doBias:
biasExposure = self.getIsrExposure(sensorRef, "bias")
if not doRotateCalib:
self.biasCorrection(ccdExposure, biasExposure)
else:
with self.rotated(ccdExposure) as exp:
self.biasCorrection(exp, biasExposure)
if self.config.doLinearize:
self.linearize(ccdExposure)
if self.config.doCrosstalk:
self.crosstalk.run(ccdExposure)
if self.config.doDark:
darkExposure = self.getIsrExposure(sensorRef, "dark")
if not doRotateCalib:
self.darkCorrection(ccdExposure, darkExposure)
else:
with self.rotated(ccdExposure) as exp:
self.darkCorrection(exp, darkExposure)
if self.config.doFlat:
flatExposure = self.getIsrExposure(sensorRef, "flat")
if not doRotateCalib:
self.flatCorrection(ccdExposure, flatExposure)
else:
with self.rotated(ccdExposure) as exp:
self.flatCorrection(exp, flatExposure)
if self.config.doApplyGains:
self.applyGains(ccdExposure, self.config.normalizeGains)
if self.config.doWidenSaturationTrails:
self.widenSaturationTrails(ccdExposure.getMaskedImage().getMask())
if self.config.doSaturation:
self.saturationInterpolation(ccdExposure)
if self.config.doFringe:
self.fringe.runDataRef(ccdExposure, sensorRef)
if self.config.doSetBadRegions:
self.setBadRegions(ccdExposure)
self.maskAndInterpNan(ccdExposure)
if self.config.qa.doWriteFlattened:
sensorRef.put(ccdExposure, "flattenedImage")
if self.config.qa.doThumbnailFlattened:
self.writeThumbnail(sensorRef, "flattenedThumb", ccdExposure)
self.measureBackground(ccdExposure)
if self.config.doGuider:
self.guider(ccdExposure)
self.roughZeroPoint(ccdExposure)
if self.config.doWriteVignettePolygon:
self.setValidPolygonIntersect(ccdExposure, self.vignettePolygon)
if self.config.doWrite:
sensorRef.put(ccdExposure, "postISRCCD")
if self._display:
im = ccdExposure.getMaskedImage().getImage()
im_median = float(numpy.median(im.getArray()))
ds9.mtv(im)
ds9.scale(min=im_median * 0.95, max=im_median * 1.15)
return Struct(exposure=ccdExposure)
def determinePsf(self, exposure, psfCandidateList, metadata=None, flagKey=None):
"""Determine a PSFEX PSF model for an exposure given a list of PSF candidates
@param[in] exposure: exposure containing the psf candidates (lsst.afw.image.Exposure)
@param[in] psfCandidateList: a sequence of PSF candidates (each an lsst.meas.algorithms.PsfCandidate);
typically obtained by detecting sources and then running them through a star selector
@param[in,out] metadata a home for interesting tidbits of information
@param[in] flagKey: schema key used to mark sources actually used in PSF determination
@return psf: a meas.extensions.psfex.PsfexPsf
"""
import lsstDebug
display = lsstDebug.Info(__name__).display
displayExposure = display and \
lsstDebug.Info(__name__).displayExposure # display the Exposure + spatialCells
displayPsfComponents = display and \
lsstDebug.Info(__name__).displayPsfComponents # show the basis functions
showBadCandidates = display and \
lsstDebug.Info(__name__).showBadCandidates # Include bad candidates (meaningless, methinks)
displayResiduals = display and \
lsstDebug.Info(__name__).displayResiduals # show residuals
displayPsfMosaic = display and \
lsstDebug.Info(__name__).displayPsfMosaic # show mosaic of reconstructed PSF(x,y)
normalizeResiduals = lsstDebug.Info(__name__).normalizeResiduals
# Normalise residuals by object amplitude
mi = exposure.getMaskedImage()
nCand = len(psfCandidateList)
if nCand == 0:
raise RuntimeError("No PSF candidates supplied.")
#
# How big should our PSF models be?
#
if display: # only needed for debug plots
# construct and populate a spatial cell set
bbox = mi.getBBox(afwImage.PARENT)
psfCellSet = afwMath.SpatialCellSet(bbox, self.config.sizeCellX, self.config.sizeCellY)
else:
psfCellSet = None
sizes = np.empty(nCand)
for i, psfCandidate in enumerate(psfCandidateList):
try:
if psfCellSet:
psfCellSet.insertCandidate(psfCandidate)
except Exception as e:
self.log.debug("Skipping PSF candidate %d of %d: %s", i, len(psfCandidateList), e)
continue
source = psfCandidate.getSource()
quad = afwEll.Quadrupole(source.getIxx(), source.getIyy(), source.getIxy())
rmsSize = quad.getTraceRadius()
sizes[i] = rmsSize
if self.config.kernelSize >= 15:
self.log.warn("NOT scaling kernelSize by stellar quadrupole moment, but using absolute value")
actualKernelSize = int(self.config.kernelSize)
else:
actualKernelSize = 2 * int(self.config.kernelSize * np.sqrt(np.median(sizes)) + 0.5) + 1
if actualKernelSize < self.config.kernelSizeMin:
actualKernelSize = self.config.kernelSizeMin
if actualKernelSize > self.config.kernelSizeMax:
actualKernelSize = self.config.kernelSizeMax
if display:
rms = np.median(sizes)
print("Median PSF RMS size=%.2f pixels (\"FWHM\"=%.2f)" % (rms, 2*np.sqrt(2*np.log(2))*rms))
# If we manually set the resolution then we need the size in pixel units
pixKernelSize = actualKernelSize
if self.config.samplingSize > 0:
pixKernelSize = int(actualKernelSize*self.config.samplingSize)
if pixKernelSize % 2 == 0:
pixKernelSize += 1
self.log.trace("Psfex Kernel size=%.2f, Image Kernel Size=%.2f", actualKernelSize, pixKernelSize)
psfCandidateList[0].setHeight(pixKernelSize)
psfCandidateList[0].setWidth(pixKernelSize)
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BEGIN PSFEX
#
# Insert the good candidates into the set
#
defaultsFile = os.path.join(os.environ["MEAS_EXTENSIONS_PSFEX_DIR"], "config", "default-lsst.psfex")
args_md = dafBase.PropertySet()
args_md.set("PSFVAR_DEGREES", str(self.config.spatialOrder))
args_md.set("PSF_SIZE", str(actualKernelSize))
args_md.set("PSF_SAMPLING", str(self.config.samplingSize))
prefs = psfex.Prefs(defaultsFile, args_md)
prefs.setCommandLine([])
prefs.addCatalog("psfexPsfDeterminer")
prefs.use()
principalComponentExclusionFlag = bool(bool(psfex.Context.REMOVEHIDDEN)
if False else psfex.Context.KEEPHIDDEN)
context = psfex.Context(prefs.getContextName(), prefs.getContextGroup(),
prefs.getGroupDeg(), principalComponentExclusionFlag)
set = psfex.Set(context)
set.setVigSize(pixKernelSize, pixKernelSize)
set.setFwhm(2*np.sqrt(2*np.log(2))*np.median(sizes))
set.setRecentroid(self.config.recentroid)
catindex, ext = 0, 0
backnoise2 = afwMath.makeStatistics(mi.getImage(), afwMath.VARIANCECLIP).getValue()
ccd = exposure.getDetector()
if ccd:
gain = np.mean(np.array([a.getGain() for a in ccd]))
else:
gain = 1.0
self.log.warn("Setting gain to %g" % (gain,))
contextvalp = []
for i, key in enumerate(context.getName()):
if context.getPcflag(i):
contextvalp.append(pcval[pc])
pc += 1
elif key[0] == ':':
try:
contextvalp.append(exposure.getMetadata().get(key[1:]))
except KeyError:
raise RuntimeError("*Error*: %s parameter not found in the header of %s" %
(key[1:], prefs.getContextName()))
else:
try:
contextvalp.append(np.array([psfCandidateList[_].getSource().get(key)
for _ in range(nCand)]))
except KeyError:
raise RuntimeError("*Error*: %s parameter not found" % (key,))
set.setContextname(i, key)
if display:
frame = 0
if displayExposure:
ds9.mtv(exposure, frame=frame, title="psf determination")
badBits = mi.getMask().getPlaneBitMask(self.config.badMaskBits)
fluxName = prefs.getPhotfluxRkey()
fluxFlagName = "base_" + fluxName + "_flag"
xpos, ypos = [], []
for i, psfCandidate in enumerate(psfCandidateList):
source = psfCandidate.getSource()
xc, yc = source.getX(), source.getY()
try:
int(xc), int(yc)
except ValueError:
continue
try:
pstamp = psfCandidate.getMaskedImage().clone()
except Exception as e:
continue
if fluxFlagName in source.schema and source.get(fluxFlagName):
continue
flux = source.get(fluxName)
if flux < 0 or np.isnan(flux):
continue
# From this point, we're configuring the "sample" (PSFEx's version of a PSF candidate).
# Having created the sample, we must proceed to configure it, and then fini (finalize),
# or it will be malformed.
try:
sample = set.newSample()
sample.setCatindex(catindex)
sample.setExtindex(ext)
sample.setObjindex(i)
imArray = pstamp.getImage().getArray()
imArray[np.where(np.bitwise_and(pstamp.getMask().getArray(), badBits))] = \
-2*psfex.cvar.BIG
sample.setVig(imArray)
sample.setNorm(flux)
sample.setBacknoise2(backnoise2)
sample.setGain(gain)
sample.setX(xc)
sample.setY(yc)
sample.setFluxrad(sizes[i])
for j in range(set.getNcontext()):
sample.setContext(j, float(contextvalp[j][i]))
except Exception as e:
self.log.debug("Exception when processing sample at (%f,%f): %s", xc, yc, e)
continue
else:
set.finiSample(sample)
xpos.append(xc) # for QA
ypos.append(yc)
if displayExposure:
with ds9.Buffering():
ds9.dot("o", xc, yc, ctype=ds9.CYAN, size=4, frame=frame)
if set.getNsample() == 0:
raise RuntimeError("No good PSF candidates to pass to PSFEx")
#---- Update min and max and then the scaling
for i in range(set.getNcontext()):
cmin = contextvalp[i].min()
cmax = contextvalp[i].max()
set.setContextScale(i, cmax - cmin)
set.setContextOffset(i, (cmin + cmax)/2.0)
# Don't waste memory!
set.trimMemory()
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- END PSFEX
#
# Do a PSFEX decomposition of those PSF candidates
#
fields = psfex.vectorField()
field = psfex.Field("Unknown")
field.addExt(exposure.getWcs(), exposure.getWidth(), exposure.getHeight(), set.getNsample())
field.finalize()
fields.append(field)
sets = psfex.vectorSet()
sets.append(set)
psfex.makeit(fields, sets)
psfs = field.getPsfs()
# Flag which objects were actually used in psfex by
good_indices = []
for i in range(sets[0].getNsample()):
index = sets[0].getSample(i).getObjindex()
if index > -1:
good_indices.append(index)
if flagKey is not None:
for i, psfCandidate in enumerate(psfCandidateList):
source = psfCandidate.getSource()
if i in good_indices:
source.set(flagKey, True)
xpos = np.array(xpos)
ypos = np.array(ypos)
numGoodStars = len(good_indices)
avgX, avgY = np.mean(xpos), np.mean(ypos)
psf = psfex.PsfexPsf(psfs[0], afwGeom.Point2D(avgX, avgY))
if False and (displayResiduals or displayPsfMosaic):
ext = 0
frame = 1
diagnostics = True
catDir = "."
title = "psfexPsfDeterminer"
psfex.psfex.showPsf(psfs, set, ext,
[(exposure.getWcs(), exposure.getWidth(), exposure.getHeight())],
nspot=3, trim=5, frame=frame, diagnostics=diagnostics, outDir=catDir,
title=title)
#
# Display code for debugging
#
if display:
assert psfCellSet is not None
if displayExposure:
maUtils.showPsfSpatialCells(exposure, psfCellSet, showChi2=True,
symb="o", ctype=ds9.YELLOW, ctypeBad=ds9.RED, size=8, frame=frame)
if displayResiduals:
maUtils.showPsfCandidates(exposure, psfCellSet, psf=psf, frame=4,
normalize=normalizeResiduals,
showBadCandidates=showBadCandidates)
if displayPsfComponents:
maUtils.showPsf(psf, frame=6)
if displayPsfMosaic:
maUtils.showPsfMosaic(exposure, psf, frame=7, showFwhm=True)
ds9.scale('linear', 0, 1, frame=7)
#
# Generate some QA information
#
# Count PSF stars
#
if metadata is not None:
metadata.set("spatialFitChi2", np.nan)
metadata.set("numAvailStars", nCand)
metadata.set("numGoodStars", numGoodStars)
metadata.set("avgX", avgX)
metadata.set("avgY", avgY)
psfCellSet = None
return psf, psfCellSet