def detectSources(exposure, threshold, psf=None):
"""Detect sources above positiveThreshold in the provided exposure returning the sourceList
"""
if not psf:
FWHM = 5
psf = algorithms.createPSF("DoubleGaussian", 15, 15, FWHM/(2*math.sqrt(2*math.log(2))))
#
# Subtract background
#
mi = exposure.getMaskedImage()
bctrl = afwMath.BackgroundControl(afwMath.NATURAL_SPLINE);
bctrl.setNxSample(int(mi.getWidth()/256) + 1);
bctrl.setNySample(int(mi.getHeight()/256) + 1);
backobj = afwMath.makeBackground(mi.getImage(), bctrl)
img = mi.getImage(); img -= backobj.getImageF(); del img
if display:
ds9.mtv(exposure)
ds = detectFootprints(exposure, threshold)
objects = ds.getFootprints()
#
# Time to actually measure
#
measPipelineDir = lsst.utils.getPackageDir('meas_pipeline')
moPolicy = policy.Policy.createPolicy(os.path.join(measPipelineDir,
"policy", "MeasureSources.paf"))
moPolicy = moPolicy.getPolicy("measureObjects")
measureSources = algorithms.makeMeasureSources(exposure, moPolicy, psf)
sourceList = afwDetection.SourceSet()
for i in range(len(objects)):
source = afwDetection.Source()
sourceList.append(source)
source.setId(i)
source.setFlagForDetection(source.getFlagForDetection() | algorithms.Flags.BINNED1);
try:
measureSources.apply(source, objects[i])
except Exception:
pass
if source.getFlagForDetection() & algorithms.Flags.EDGE:
continue
if display:
xc, yc = source.getXAstrom() - mi.getX0(), source.getYAstrom() - mi.getY0()
if False:
ds9.dot("%.1f %d" % (source.getPsfFlux(), source.getId()), xc, yc+1)
ds9.dot("+", xc, yc, size=1)
return sourceList
def detectSources(exposure, threshold, psf=None):
"""Detect sources above positiveThreshold in the provided exposure returning the sourceList
"""
if not psf:
FWHM = 5
psf = algorithms.createPSF("DoubleGaussian", 15, 15,
FWHM / (2 * math.sqrt(2 * math.log(2))))
#
# Subtract background
#
mi = exposure.getMaskedImage()
bctrl = afwMath.BackgroundControl(afwMath.NATURAL_SPLINE)
bctrl.setNxSample(int(mi.getWidth() / 256) + 1)
bctrl.setNySample(int(mi.getHeight() / 256) + 1)
backobj = afwMath.makeBackground(mi.getImage(), bctrl)
img = mi.getImage()
img -= backobj.getImageF()
del img
if display:
disp = afwDisplay.Display()
disp.mtv(exposure)
ds = detectFootprints(exposure, threshold)
objects = ds.getFootprints()
#
# Time to actually measure
#
measPipelineDir = lsst.utils.getPackageDir('meas_pipeline')
moPolicy = policy.Policy.createPolicy(
os.path.join(measPipelineDir, "policy", "MeasureSources.paf"))
moPolicy = moPolicy.getPolicy("measureObjects")
measureSources = algorithms.makeMeasureSources(exposure, moPolicy, psf)
sourceList = afwDetection.SourceSet()
for i in range(len(objects)):
source = afwDetection.Source()
sourceList.append(source)
source.setId(i)
source.setFlagForDetection(source.getFlagForDetection()
| algorithms.Flags.BINNED1)
try:
measureSources.apply(source, objects[i])
except Exception:
pass
if source.getFlagForDetection() & algorithms.Flags.EDGE:
continue
if display:
xc, yc = source.getXAstrom() - mi.getX0(), source.getYAstrom(
) - mi.getY0()
if False:
display.dot(
"%.1f %d" % (source.getPsfInstFlux(), source.getId()), xc,
yc + 1)
disp.dot("+", xc, yc, size=1)
return sourceList
def run2(self, exposure, defects=None, background=None):
assert exposure is not None, "No exposure provided"
print('creating fake PSF...')
psf, wcs = self.fakePsf(exposure)
print('wcs is', wcs)
if False:
import lsst.meas.utils.sourceDetection as muDetection
import lsst.meas.utils.sourceMeasurement as muMeasurement
# phot.py : detect()
print('Simulating detect()...')
policy = self.config['detect']
posSources, negSources = muDetection.detectSources(
exposure, psf, policy.getPolicy())
numPos = len(
posSources.getFootprints()) if posSources is not None else 0
numNeg = len(
negSources.getFootprints()) if negSources is not None else 0
print('found', numPos, 'pos and', numNeg, 'neg footprints')
footprintSet = posSources
# phot.py : measure()
print('Simulating measure()...')
policy = self.config['measure'].getPolicy()
footprints = []
num = len(footprintSet.getFootprints())
self.log.log(self.log.INFO,
"Measuring %d positive footprints" % num)
footprints.append([footprintSet.getFootprints(), False])
sources = muMeasurement.sourceMeasurement(exposure, psf,
footprints, policy)
print('sources:', sources)
for s in sources:
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(),
s.getIxx(), s.getIyy(), s.getIxy())
# sourceMeasurement():
import lsst.meas.algorithms as measAlg
import lsst.afw.detection as afwDetection
print('Simulating sourceMeasurement()...')
exposure.setPsf(psf)
measureSources = measAlg.makeMeasureSources(exposure, policy)
# print('ms policy', str(measureSources.getPolicy()))
# print('ms astrom:', measureSources.getMeasureAstrom())
# print('ms photom:', measureSources.getMeasurePhotom())
# print('ms shape:', measureSources.getMeasureShape())
F = footprints[0][0]
for i in range(len(F)):
# create a new source, and add it to the list, initialize ...
s = afwDetection.Source()
f = F[i]
print('measuring footprint', f)
measureSources.apply(s, f)
print('got', s)
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(),
s.getIxx(), s.getIyy(), s.getIxy())
print('initial photometry...')
sources, footprints = self.phot(exposure, psf)
# print('got sources', str(sources))
# print('got footprints', str(footprints))
# print('sources:', sources)
print('got sources:', len(sources))
for s in sources:
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(),
s.getIxx(), s.getIyy(), s.getIxy())
print('re-photometry...')
sources = self.rephot(exposure, footprints, psf)
# print('got sources', str(sources))
print('sources:', len(sources))
for s in sources:
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(),
s.getIxx(), s.getIyy(), s.getIxy())
return psf, sources, footprints
def run2(self, exposure, defects=None, background=None):
assert exposure is not None, "No exposure provided"
print('creating fake PSF...')
psf, wcs = self.fakePsf(exposure)
print('wcs is', wcs)
if False:
import lsst.meas.utils.sourceDetection as muDetection
import lsst.meas.utils.sourceMeasurement as muMeasurement
# phot.py : detect()
print('Simulating detect()...')
policy = self.config['detect']
posSources, negSources = muDetection.detectSources(exposure, psf, policy.getPolicy())
numPos = len(posSources.getFootprints()) if posSources is not None else 0
numNeg = len(negSources.getFootprints()) if negSources is not None else 0
print('found', numPos, 'pos and', numNeg, 'neg footprints')
footprintSet = posSources
# phot.py : measure()
print('Simulating measure()...')
policy = self.config['measure'].getPolicy()
footprints = []
num = len(footprintSet.getFootprints())
self.log.log(self.log.INFO, "Measuring %d positive footprints" % num)
footprints.append([footprintSet.getFootprints(), False])
sources = muMeasurement.sourceMeasurement(exposure, psf, footprints, policy)
print('sources:', sources)
for s in sources:
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(),
s.getIxx(), s.getIyy(), s.getIxy())
# sourceMeasurement():
import lsst.meas.algorithms as measAlg
import lsst.afw.detection as afwDetection
print('Simulating sourceMeasurement()...')
exposure.setPsf(psf)
measureSources = measAlg.makeMeasureSources(exposure, policy)
# print('ms policy', str(measureSources.getPolicy()))
# print('ms astrom:', measureSources.getMeasureAstrom())
# print('ms photom:', measureSources.getMeasurePhotom())
# print('ms shape:', measureSources.getMeasureShape())
F = footprints[0][0]
for i in range(len(F)):
# create a new source, and add it to the list, initialize ...
s = afwDetection.Source()
f = F[i]
print('measuring footprint', f)
measureSources.apply(s, f)
print('got', s)
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(),
s.getIxx(), s.getIyy(), s.getIxy())
print('initial photometry...')
sources, footprints = self.phot(exposure, psf)
# print('got sources', str(sources))
# print('got footprints', str(footprints))
# print('sources:', sources)
print('got sources:', len(sources))
for s in sources:
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(), s.getIxx(), s.getIyy(), s.getIxy())
print('re-photometry...')
sources = self.rephot(exposure, footprints, psf)
# print('got sources', str(sources))
print('sources:', len(sources))
for s in sources:
print(' ', s, s.getXAstrom(), s.getYAstrom(), s.getPsfFlux(), s.getIxx(), s.getIyy(), s.getIxy())
return psf, sources, footprints
def measure(self):
"""Detect and measure sources"""
mi = self.exposure.getMaskedImage()
#
# We do a pretty good job of interpolating, so don't propagagate the convolved CR/INTRP bits
# (we'll keep them for the original CR/INTRP pixels)
#
savedMask = mi.getMask().Factory(mi.getMask(), True)
saveBits = savedMask.getPlaneBitMask("CR") | \
savedMask.getPlaneBitMask("BAD") | \
savedMask.getPlaneBitMask("INTRP") # Bits to not convolve
savedMask &= saveBits
msk = mi.getMask(); msk &= ~saveBits; del msk # Clear the saved bits
#
# Smooth image
#
cnvImage = mi.Factory(mi.getBBox(afwImage.PARENT))
afwMath.convolve(cnvImage, mi, self.psf.getKernel(), afwMath.ConvolutionControl())
msk = cnvImage.getMask(); msk |= savedMask; del msk # restore the saved bits
threshold = afwDetection.Threshold(3, afwDetection.Threshold.STDEV)
#
# Only search the part of the frame that was PSF-smoothed
#
llc = afwGeom.PointI(self.psf.getKernel().getWidth()/2, self.psf.getKernel().getHeight()/2)
urc = afwGeom.PointI(cnvImage.getWidth() - 1, cnvImage.getHeight() - 1) - afwGeom.ExtentI(llc[0], llc[1]);
middle = cnvImage.Factory(cnvImage, afwGeom.BoxI(llc, urc), afwImage.LOCAL)
ds = afwDetection.FootprintSetF(middle, threshold, "DETECTED")
del middle
#
# ds only searched the middle but it belongs to the entire MaskedImage
#
ds.setRegion(mi.getBBox(afwImage.PARENT))
#
# We want to grow the detections into the edge by at least one pixel so that it sees the EDGE bit
#
grow, isotropic = 1, False
ds = afwDetection.FootprintSetF(ds, grow, isotropic)
ds.setMask(mi.getMask(), "DETECTED")
#
# Reinstate the saved (e.g. BAD) (and also the DETECTED | EDGE) bits in the unsmoothed image
#
savedMask <<= cnvImage.getMask()
msk = mi.getMask(); msk |= savedMask; del msk
del savedMask; savedMask = None
#msk = mi.getMask(); msk &= ~0x10; del msk # XXXX
if self.display:
ds9.mtv(mi, frame = 0, lowOrderBits = True)
ds9.mtv(cnvImage, frame = 1)
objects = ds.getFootprints()
#
# Time to actually measure
#
msPolicy = policy.Policy.createPolicy(policy.DefaultPolicyFile("meas_algorithms",
"examples/measureSources.paf"))
msPolicy = msPolicy.getPolicy("measureSources")
measureSources = measAlg.makeMeasureSources(self.exposure, msPolicy)
self.sourceList = afwDetection.SourceSet()
for i in range(len(objects)):
source = afwDetection.Source()
self.sourceList.append(source)
source.setId(i)
source.setFlagForDetection(source.getFlagForDetection() | measAlg.Flags.BINNED1);
try:
measureSources.apply(source, objects[i])
except Exception, e:
try:
print e
except Exception, ee:
print ee