def run(display=False):
exposure = loadData()
schema = afwTable.SourceTable.makeMinimalSchema()
#
# Create the detection and measurement Tasks
#
config = SourceDetectionTask.ConfigClass()
config.reEstimateBackground = False
detectionTask = SourceDetectionTask(config=config, schema=schema)
config = SingleFrameMeasurementTask.ConfigClass()
# Use the minimum set of plugins required.
config.plugins.names.clear()
for plugin in ["base_SdssCentroid", "base_SdssShape", "base_CircularApertureFlux", "base_PixelFlags"]:
config.plugins.names.add(plugin)
config.plugins["base_CircularApertureFlux"].radii = [7.0]
config.slots.psfFlux = "base_CircularApertureFlux_7_0" # Use of the PSF flux is hardcoded in secondMomentStarSelector
measureTask = SingleFrameMeasurementTask(schema, config=config)
#
# Create the measurePsf task
#
config = MeasurePsfTask.ConfigClass()
psfDeterminer = config.psfDeterminer.apply()
psfDeterminer.config.sizeCellX = 128
psfDeterminer.config.sizeCellY = 128
psfDeterminer.config.spatialOrder = 1
psfDeterminer.config.nEigenComponents = 3
measurePsfTask = MeasurePsfTask(config=config, schema=schema)
#
# Create the output table
#
tab = afwTable.SourceTable.make(schema)
#
# Process the data
#
sources = detectionTask.run(tab, exposure, sigma=2).sources
measureTask.measure(exposure, sources)
result = measurePsfTask.run(exposure, sources)
psf = result.psf
cellSet = result.cellSet
if display: # display on ds9 (see also --debug argparse option)
frame = 1
ds9.mtv(exposure, frame=frame)
with ds9.Buffering():
for s in sources:
xy = s.getCentroid()
ds9.dot('+', *xy, frame=frame)
if s.get("calib.psf.candidate"):
ds9.dot('x', *xy, ctype=ds9.YELLOW, frame=frame)
if s.get("calib.psf.used"):
ds9.dot('o', *xy, size=4, ctype=ds9.RED, frame=frame)
def test1(self):
#exposure = afwImage.ExposureF('mini-v85408556-fr-R23-S11.fits')
#exposure = afwImage.ExposureF('../afwdata/ImSim/calexp/v85408556-fr/R23/S11.fits')
#bb = afwGeom.Box2I(afwGeom.Point2I(0,0), afwGeom.Point2I(511,511))
#exposure = afwImage.ExposureF('data/goodSeeingCoadd/r/3/113,0/coadd-r-3-113,0.fits', 0, bb)
#exposure.writeFits('mini-r-3-113,0.fits')
fn = os.path.join(os.path.dirname(__file__), 'data', 'mini-r-3-113,0.fits.gz')
print 'Reading image', fn
exposure = afwImage.ExposureF(fn)
exposure.setPsf(afwDetection.GaussianPsf(15, 15, 3))
schema = afwTable.SourceTable.makeMinimalSchema()
idFactory = afwTable.IdFactory.makeSimple()
dconf = measAlg.SourceDetectionConfig()
dconf.reEstimateBackground = False
dconf.includeThresholdMultiplier = 5.
mconf = SingleFrameMeasurementConfig()
aconf = ANetAstrometryConfig()
aconf.forceKnownWcs = True
det = measAlg.SourceDetectionTask(schema=schema, config=dconf)
meas = SingleFrameMeasurementTask(schema, config=mconf)
astrom = ANetAstrometryTask(schema, config=aconf, name='astrom')
astrom.log.setThreshold(pexLog.Log.DEBUG)
inwcs = exposure.getWcs()
print 'inwcs:', inwcs
instr = inwcs.getFitsMetadata().toString()
print 'inwcs:', instr
table = afwTable.SourceTable.make(schema, idFactory)
sources = det.makeSourceCatalog(table, exposure, sigma=1).sources
meas.measure(exposure, sources)
for dosip in [False, True]:
aconf.solver.calculateSip = dosip
ast = astrom.run(sourceCat=sources, exposure=exposure)
outwcs = exposure.getWcs()
outstr = outwcs.getFitsMetadata().toString()
if dosip is False:
self.assertEqual(inwcs, outwcs)
self.assertEqual(instr, outstr)
print 'inwcs:', instr
print 'outwcs:', outstr
print len(ast.matches), 'matches'
self.assertTrue(len(ast.matches) > 10)
def test1(self):
fn = os.path.join(os.path.dirname(__file__), 'data', 'mini-r-3-113,0.fits.gz')
print('Reading image', fn)
exposure = afwImage.ExposureF(fn)
exposure.setPsf(afwDetection.GaussianPsf(15, 15, 3))
schema = afwTable.SourceTable.makeMinimalSchema()
idFactory = afwTable.IdFactory.makeSimple()
dconf = measAlg.SourceDetectionConfig()
dconf.reEstimateBackground = False
dconf.includeThresholdMultiplier = 5.
mconf = SingleFrameMeasurementConfig()
aconf = ANetAstrometryConfig()
aconf.forceKnownWcs = True
det = measAlg.SourceDetectionTask(schema=schema, config=dconf)
meas = SingleFrameMeasurementTask(schema, config=mconf)
astrom = ANetAstrometryTask(schema, config=aconf, name='astrom')
astrom.log.setLevel(astrom.log.TRACE)
inwcs = exposure.getWcs()
print('inwcs:', inwcs)
instr = inwcs.getFitsMetadata().toString()
print('inwcs:', instr)
table = afwTable.SourceTable.make(schema, idFactory)
sources = det.makeSourceCatalog(table, exposure, sigma=1).sources
meas.measure(sources, exposure)
for dosip in [False, True]:
aconf.solver.calculateSip = dosip
ast = astrom.run(sourceCat=sources, exposure=exposure)
outwcs = exposure.getWcs()
outstr = outwcs.getFitsMetadata().toString()
if not dosip:
self.assertEqual(inwcs, outwcs)
self.assertEqual(instr, outstr)
print('inwcs:', instr)
print('outwcs:', outstr)
print(len(ast.matches), 'matches')
self.assertGreater(len(ast.matches), 10)
def run(config, inputFiles, weightFiles=None, varianceFiles=None,
returnCalibSources=False, display=False, verbose=False):
#
# Create the tasks
#
schema = afwTable.SourceTable.makeMinimalSchema()
algMetadata = dafBase.PropertyList()
calibrateTask = CalibrateTask(config=config.calibrate)
sourceDetectionTask = SourceDetectionTask(config=config.detection, schema=schema)
if config.doDeblend:
if SourceDeblendTask:
sourceDeblendTask = SourceDeblendTask(config=config.deblend, schema=schema)
else:
print >> sys.stderr, "Failed to import lsst.meas.deblender; setting doDeblend = False"
config.doDeblend = False
sourceMeasurementTask = SingleFrameMeasurementTask(config=config.measurement,
schema=schema, algMetadata=algMetadata)
exposureDict = {}; calibSourcesDict = {}; sourcesDict = {}
for inputFile, weightFile, varianceFile in zip(inputFiles, weightFiles, varianceFiles):
#
# Create the output table
#
tab = afwTable.SourceTable.make(schema)
#
# read the data
#
if verbose:
print "Reading %s" % inputFile
exposure = makeExposure(inputFile, weightFile, varianceFile,
config.badPixelValue, config.variance, verbose)
#
# process the data
#
calibSources = None # sources used to calibrate the frame (photom, astrom, psf)
if config.doCalibrate:
result = calibrateTask.run(exposure)
exposure, sources = result.exposure, result.sources
if returnCalibSources:
calibSources = sources
else:
if not exposure.getPsf():
calibrateTask.installInitialPsf(exposure)
if config.edgeRolloff.applyModel:
if verbose:
print "Adding edge rolloff distortion to the exposure WCS"
addEdgeRolloffDistortion(exposure, config.edgeRolloff)
exposureDict[inputFile] = exposure
calibSourcesDict[inputFile] = calibSources
result = sourceDetectionTask.run(tab, exposure)
sources = result.sources
sourcesDict[inputFile] = sources
if config.doDeblend:
sourceDeblendTask.run(exposure, sources, exposure.getPsf())
sourceMeasurementTask.measure(exposure, sources)
if verbose:
print "Detected %d objects" % len(sources)
if display: # display on ds9 (see also --debug argparse option)
if algMetadata.exists("base_CircularApertureFlux_radii"):
radii = algMetadata.get("base_CircularApertureFlux_radii")
else:
radii = None
frame = 1
ds9.mtv(exposure, title=os.path.split(inputFile)[1], frame=frame)
with ds9.Buffering():
for s in sources:
xy = s.getCentroid()
ds9.dot('+', *xy, ctype=ds9.CYAN if s.get("flags_negative") else ds9.GREEN, frame=frame)
ds9.dot(s.getShape(), *xy, ctype=ds9.RED, frame=frame)
if radii:
for radius in radii:
ds9.dot('o', *xy, size=radius, ctype=ds9.YELLOW, frame=frame)
return exposureDict, calibSourcesDict, sourcesDict
def run(config,
inputFiles,
weightFiles=None,
varianceFiles=None,
returnCalibSources=False,
displayResults=[],
verbose=False):
#
# Create the tasks
#
schema = afwTable.SourceTable.makeMinimalSchema()
algMetadata = dafBase.PropertyList()
isrTask = IsrTask(config=config.isr)
charImageTask = CharacterizeImageTask(None, config=config.charImage)
sourceDetectionTask = SourceDetectionTask(config=config.detection,
schema=schema)
if config.doDeblend:
if SourceDeblendTask:
sourceDeblendTask = SourceDeblendTask(config=config.deblend,
schema=schema)
else:
print >> sys.stderr, "Failed to import lsst.meas.deblender; setting doDeblend = False"
config.doDeblend = False
sourceMeasurementTask = SingleFrameMeasurementTask(
schema=schema, config=config.measurement, algMetadata=algMetadata)
keysToCopy = []
for key in [
charImageTask.measurePsf.reservedKey,
charImageTask.measurePsf.usedKey,
]:
keysToCopy.append(
(schema.addField(charImageTask.schema.find(key).field), key))
exposureDict = {}
calibSourcesDict = {}
sourcesDict = {}
for inputFile, weightFile, varianceFile in zip(inputFiles, weightFiles,
varianceFiles):
#
# Create the output table
#
tab = afwTable.SourceTable.make(schema)
#
# read the data
#
if verbose:
print "Reading %s" % inputFile
exposure = makeExposure(inputFile, weightFile, varianceFile,
config.badPixelValue, config.variance)
#
if config.interpPlanes:
import lsst.ip.isr as ipIsr
defects = ipIsr.getDefectListFromMask(exposure.getMaskedImage(),
config.interpPlanes,
growFootprints=0)
isrTask.run(exposure, defects=defects)
#
# process the data
#
if config.doCalibrate:
result = charImageTask.characterize(exposure)
exposure, calibSources = result.exposure, result.sourceCat
else:
calibSources = None
if not exposure.getPsf():
charImageTask.installSimplePsf.run(exposure)
exposureDict[inputFile] = exposure
calibSourcesDict[
inputFile] = calibSources if returnCalibSources else None
result = sourceDetectionTask.run(tab, exposure)
sources = result.sources
sourcesDict[inputFile] = sources
if config.doDeblend:
sourceDeblendTask.run(exposure, sources)
sourceMeasurementTask.measure(exposure, sources)
if verbose:
print "Detected %d objects" % len(sources)
propagatePsfFlags(keysToCopy, calibSources, sources)
if displayResults: # display results of processing (see also --debug argparse option)
showApertures = "showApertures".upper() in displayResults
showPSFs = "showPSFs".upper() in displayResults
showShapes = "showShapes".upper() in displayResults
display = afwDisplay.getDisplay(frame=1)
if algMetadata.exists("base_CircularApertureFlux_radii"):
radii = algMetadata.get("base_CircularApertureFlux_radii")
else:
radii = []
display.mtv(exposure, title=os.path.split(inputFile)[1])
with display.Buffering():
for s in sources:
xy = s.getCentroid()
display.dot('+',
*xy,
ctype=afwDisplay.CYAN if
s.get("flags_negative") else afwDisplay.GREEN)
if showPSFs and (s.get("calib_psfUsed")
or s.get("calib_psfReserved")):
display.dot(
'o',
*xy,
size=10,
ctype=afwDisplay.GREEN
if s.get("calib_psfUsed") else afwDisplay.YELLOW)
if showShapes:
display.dot(s.getShape(), *xy, ctype=afwDisplay.RED)
if showApertures:
for radius in radii:
display.dot('o',
*xy,
size=radius,
ctype=afwDisplay.YELLOW)
return exposureDict, calibSourcesDict, sourcesDict
def run(config, inputFiles, weightFiles=None, varianceFiles=None,
returnCalibSources=False, displayResults=[], verbose=False):
#
# Create the tasks
#
schema = afwTable.SourceTable.makeMinimalSchema()
algMetadata = dafBase.PropertyList()
isrTask = IsrTask(config=config.isr)
calibrateTask = CalibrateTask(config=config.calibrate)
sourceDetectionTask = SourceDetectionTask(config=config.detection, schema=schema)
if config.doDeblend:
if SourceDeblendTask:
sourceDeblendTask = SourceDeblendTask(config=config.deblend, schema=schema)
else:
print >> sys.stderr, "Failed to import lsst.meas.deblender; setting doDeblend = False"
config.doDeblend = False
sourceMeasurementTask = SingleFrameMeasurementTask(config=config.measurement,
schema=schema, algMetadata=algMetadata)
sourceMeasurementTask.config.doApplyApCorr = 'yes'
#
# Add fields needed to identify stars while calibrating
#
keysToCopy = [(schema.addField(afwTable.Field["Flag"]("calib_detected",
"Source was detected by calibrate")), None)]
for key in calibrateTask.getCalibKeys():
keysToCopy.append((schema.addField(calibrateTask.schema.find(key).field), key))
exposureDict = {}; calibSourcesDict = {}; sourcesDict = {}
for inputFile, weightFile, varianceFile in zip(inputFiles, weightFiles, varianceFiles):
#
# Create the output table
#
tab = afwTable.SourceTable.make(schema)
#
# read the data
#
if verbose:
print "Reading %s" % inputFile
exposure = makeExposure(inputFile, weightFile, varianceFile,
config.badPixelValue, config.variance)
#
if config.interpPlanes:
import lsst.ip.isr as ipIsr
defects = ipIsr.getDefectListFromMask(exposure.getMaskedImage(), config.interpPlanes,
growFootprints=0)
isrTask.run(exposure, defects=defects)
#
# process the data
#
if config.doCalibrate:
result = calibrateTask.run(exposure)
exposure, calibSources = result.exposure, result.sources
else:
calibSources = None
if not exposure.getPsf():
calibrateTask.installInitialPsf(exposure)
exposureDict[inputFile] = exposure
calibSourcesDict[inputFile] = calibSources if returnCalibSources else None
result = sourceDetectionTask.run(tab, exposure)
sources = result.sources
sourcesDict[inputFile] = sources
if config.doDeblend:
sourceDeblendTask.run(exposure, sources, exposure.getPsf())
sourceMeasurementTask.measure(exposure, sources)
if verbose:
print "Detected %d objects" % len(sources)
propagateCalibFlags(keysToCopy, calibSources, sources)
if displayResults: # display results of processing (see also --debug argparse option)
showApertures = "showApertures".upper() in displayResults
showShapes = "showShapes".upper() in displayResults
display = afwDisplay.getDisplay(frame=1)
if algMetadata.exists("base_CircularApertureFlux_radii"):
radii = algMetadata.get("base_CircularApertureFlux_radii")
else:
radii = []
display.mtv(exposure, title=os.path.split(inputFile)[1])
with display.Buffering():
for s in sources:
xy = s.getCentroid()
display.dot('+', *xy,
ctype=afwDisplay.CYAN if s.get("flags_negative") else afwDisplay.GREEN)
if showShapes:
display.dot(s.getShape(), *xy, ctype=afwDisplay.RED)
if showApertures:
for radius in radii:
display.dot('o', *xy, size=radius, ctype=afwDisplay.YELLOW)
return exposureDict, calibSourcesDict, sourcesDict
def run(display=False):
exposure = loadData()
schema = afwTable.SourceTable.makeMinimalSchema()
#
# Create the detection and measurement Tasks
#
config = SourceDetectionTask.ConfigClass()
config.reEstimateBackground = False
detectionTask = SourceDetectionTask(config=config, schema=schema)
config = SingleFrameMeasurementTask.ConfigClass()
# Use the minimum set of plugins required.
config.plugins.names.clear()
for plugin in [
"base_SdssCentroid",
"base_SdssShape",
"base_CircularApertureFlux",
"base_PixelFlags",
"base_GaussianFlux",
]:
config.plugins.names.add(plugin)
config.plugins["base_CircularApertureFlux"].radii = [7.0, 12.0]
# Use of the PSF flux is hardcoded in secondMomentStarSelector
config.slots.psfFlux = "base_CircularApertureFlux_7_0"
measureTask = SingleFrameMeasurementTask(schema, config=config)
#
# Create the measurePsf task
#
config = MeasurePsfTask.ConfigClass()
psfDeterminer = config.psfDeterminer.apply()
psfDeterminer.config.sizeCellX = 128
psfDeterminer.config.sizeCellY = 128
psfDeterminer.config.spatialOrder = 1
psfDeterminer.config.nEigenComponents = 3
measurePsfTask = MeasurePsfTask(config=config, schema=schema)
#
# Create the output table
#
tab = afwTable.SourceTable.make(schema)
#
# Process the data
#
sources = detectionTask.run(tab, exposure, sigma=2).sources
measureTask.measure(sources, exposure)
result = measurePsfTask.run(exposure, sources)
print("psf=", result.psf)
if display:
frame = 1
disp = afwDisplay.Display(
frame=frame) # see also --debug argparse option
disp.mtv(exposure)
with disp.Buffering():
for s in sources:
xy = s.getCentroid()
disp.dot('+', *xy)
if s.get("calib_psf_candidate"):
disp.dot('x', *xy, ctype=afwDisplay.YELLOW)
if s.get("calib_psf_used"):
disp.dot('o', *xy, size=4, ctype=afwDisplay.RED)
