def testGood(self):
conf = CalibrateConfig()
conf.validate()
conf.doPhotoCal = False
conf.validate()
conf.doAstrometry = False
conf.validate()
def _checkDoRefcats(self, doAstrometry, doPhotoCal, ids):
"""Test whether run is called with the correct arguments.
In the case of `CalibrateTask`, the inputs should not depend on the
task configuration.
Parameters
----------
doAstrometry, doPhotoCal : `bool`
Values of the config flags of the same name.
ids : `dict` [`str`]
A mapping from the input dataset type to the data ID of the
dataset to process.
"""
config = CalibrateConfig()
config.doWriteMatches = False # no real output to write
config.doAstrometry = doAstrometry
config.doPhotoCal = doPhotoCal
config.connections.photoRefCat = "cal_ref_cat"
config.connections.astromRefCat = "cal_ref_cat"
task = CalibrateTask(config=config)
quantumId = ids["exposure"]
quantum = testUtils.makeQuantum(task, self.butler, quantumId, ids)
run = testUtils.runTestQuantum(task, self.butler, quantum)
run.assert_called_once()
self.assertEqual(run.call_args[0], ())
# Some arguments unprintable because we don't have a full environment
# So just check which ones were passed in
self.assertEqual(
run.call_args[1].keys(),
{"exposure", "exposureIdInfo", "background", "icSourceCat"})
def testGood(self):
conf = CalibrateConfig()
conf.validate()
conf.doPhotoCal = False
conf.validate()
conf.doAstrometry = False
conf.validate()
def processCCDs(image):
from lsst.pipe.tasks.calibrate import CalibrateTask, CalibrateConfig
from lsst.pipe.tasks.characterizeImage import CharacterizeImageTask
calibRes = None
# init tasks
charImage = CharacterizeImageTask()
calibrateConfig = CalibrateConfig(doPhotoCal=False,
doAstrometry=False,
doDeblend=False)
calibrateTask = CalibrateTask(config=calibrateConfig)
try:
# characterize image
charRes = charImage.characterize(image,
exposureIdInfo=None,
background=None)
# calibrate image
calibRes = calibrateTask.calibrate(charRes.exposure,
exposureIdInfo=None,
background=charRes.background,
icSourceCat=None)
except Exception as e:
print "failed to calibrate the image"
print str(e)
return calibRes
def testIsSinglePrimaryFlag(self):
"""Tests detect_isPrimary column gets added when run, and that sources
labelled as detect_isPrimary are not sky sources and have no children.
"""
calibConfig = CalibrateConfig()
calibConfig.doAstrometry = False
calibConfig.doPhotoCal = False
calibTask = CalibrateTask(config=calibConfig)
calibResults = calibTask.run(self.charImResults.exposure)
outputCat = calibResults.outputCat
self.assertTrue("detect_isPrimary" in outputCat.schema.getNames())
# make sure all sky sources are flagged as not primary
self.assertEqual(
sum((outputCat["detect_isPrimary"]) & (outputCat["sky_source"])),
0)
# make sure all parent sources are flagged as not primary
self.assertEqual(
sum((outputCat["detect_isPrimary"])
& (outputCat["deblend_nChild"] > 0)), 0)
with self.assertRaises(KeyError):
outputCat.getSchema().find("detect_isDelendedModelPrimary")
def testIsPrimaryFlag(self):
"""Tests detect_isPrimary column gets added when run, and that sources
labelled as detect_isPrimary are not sky sources and have no children.
"""
charImConfig = CharacterizeImageConfig()
charImTask = CharacterizeImageTask(config=charImConfig)
charImResults = charImTask.run(self.exposure)
calibConfig = CalibrateConfig()
calibConfig.doAstrometry = False
calibConfig.doPhotoCal = False
calibTask = CalibrateTask(config=calibConfig)
calibResults = calibTask.run(charImResults.exposure)
outputCat = calibResults.outputCat
self.assertTrue("detect_isPrimary" in outputCat.schema.getNames())
# make sure all sky sources are flagged as not primary
self.assertEqual(
sum((outputCat["detect_isPrimary"]) & (outputCat["sky_source"])),
0)
# make sure all parent sources are flagged as not primary
self.assertEqual(
sum((outputCat["detect_isPrimary"])
& (outputCat["deblend_nChild"] > 0)), 0)
def _checkSkySourceColumnExistence(self, doSkySources):
"""Implements sky_source column checking.
Parameters
----------
doSkySource : `bool`
Value of the config flag determining whether to insert sky sources.
"""
charImConfig = CharacterizeImageConfig()
charImConfig.measurePsf.psfDeterminer = 'piff'
charImConfig.measurePsf.psfDeterminer['piff'].spatialOrder = 0
charImTask = CharacterizeImageTask(config=charImConfig)
charImResults = charImTask.run(self.exposure)
calibConfig = CalibrateConfig()
calibConfig.doAstrometry = False
calibConfig.doPhotoCal = False
calibConfig.doSkySources = doSkySources
calibTask = CalibrateTask(config=calibConfig)
calibResults = calibTask.run(charImResults.exposure)
if doSkySources:
self.assertTrue('sky_source' in calibResults.outputCat.schema.getNames())
else:
self.assertFalse('sky_source' in calibResults.outputCat.schema.getNames())
########################################
####### Setup LSST begins
########################################
visit=289697
ccdnum = 1
HOME_PATH = os.path.expanduser("~")
butler = dafPersist.Butler(HOME_PATH + '/lsst_data/raw')
exposure = butler.get("instcal", visit=visit, ccdnum=ccdnum, filter='g', immediate=True)
mask = exposure.getMaskedImage().getMask().getArray() #TODO: move this matrix to SciDB
variance = exposure.getMaskedImage().getVariance().getArray() #TODO: move this matrix to SciDB
butler = dafPersist.Butler(HOME_PATH + '/lsst_data/raw')
filename = HOME_PATH + "/lsst_data/raw/crblasted0289697/instcal0289697.1.fits"
fitsHeader = afwImage.readMetadata(filename)
wcs = afwImage.makeWcs(fitsHeader)
charImage = CharacterizeImageTask()
calibrateConfig = CalibrateConfig(doPhotoCal=False, doAstrometry=False)
calibrateTask = CalibrateTask(config=calibrateConfig)
newSkyMapConfig = skymap.discreteSkyMap.DiscreteSkyMapConfig(projection='STG',
decList=[-4.9325280994132905],
patchInnerDimensions=[2000, 2000],
radiusList=[4.488775723429071],
pixelScale=0.333, rotation=0.0, patchBorder=100,
raList=[154.10660740464786], tractOverlap=0.0)
hits_skymap = skymap.discreteSkyMap.DiscreteSkyMap(config=newSkyMapConfig)
tract = hits_skymap[0]
sys.stderr.write("=====> DFZ 3/24/2017: mask.shape = " + str(mask.shape) + "\n")
########################################
####### Setup LSST ends
########################################
def main():
# try out one exposure
#visits = ["0288935","0288976"] #,"0289893","0289913","0289931","0289614","0289818","0289820", "0289850","0289851","0289871","0289892", "0288935","0288976","0289016","0289056","0289161","0289202","0289243","0289284","0289368","0289409","0289450","0289493","0289573","0289656"]
visits = ["0288976", "0288935"]
ccds = []
exit(0)
for i in range(1, 61):
ccds.append(i)
filterName = 'g'
DATA_PATH = "/root/extra_home/lsst_data/"
#spathprefix = "/home/dongfang/download/lsst_data/"
spathprefix = DATA_PATH + "raw/"
#calexpsloc = "/home/dongfang/download/lsst_data/calexps/"
calexpsloc = DATA_PATH + "calexps/"
#coaddloc = "/home/dongfang/download/lsst_data/coadds/"
coaddloc = DATA_PATH + "coadds/"
#mergecoaddloc = "/home/dongfang/download/lsst_data/merge/"
mergecoaddloc = DATA_PATH + "merge/"
# Characterize Image
charImageConfig = CharacterizeImageConfig()
charImage = CharacterizeImageTask()
calibrateConfig = CalibrateConfig(doPhotoCal=False, doAstrometry=False)
calibrateTask = CalibrateTask(config=calibrateConfig)
makeCTEConfig = MakeCoaddTempExpConfig()
makeCTE = MakeCoaddTempExpTask(config=makeCTEConfig)
newSkyMapConfig = skymap.discreteSkyMap.DiscreteSkyMapConfig(
projection='STG',
decList=[-4.9325280994132905],
patchInnerDimensions=[2000, 2000],
radiusList=[4.488775723429071],
pixelScale=0.333,
rotation=0.0,
patchBorder=100,
raList=[154.10660740464786],
tractOverlap=0.0)
hits_skymap = skymap.discreteSkyMap.DiscreteSkyMap(config=newSkyMapConfig)
tract = hits_skymap[0]
coaddTempDict = {}
calibResDict = {}
f = open("log.txt", 'wb')
start = datetime.datetime.now()
#process CCDs to create calexps.
for v in visits:
for ccd in ccds:
visit = int(v)
filename = "instcal" + v + "." + str(ccd) + ".fits"
calexpfn = calexpsloc + v + "/" + filename
source = spathprefix + v + "/" + filename
exposure = afwImg.ExposureF(source)
try:
# Characterize Image
charRes = charImage.characterize(exposure,
exposureIdInfo=None,
background=None)
except:
f.write("DFZ DEBUG at charRes: errors in visit " + v +
", ccd " + str(ccd) + "\n")
try:
# Caliberate Image
calibRes = calibrateTask.calibrate(
charRes.exposure,
exposureIdInfo=None,
background=charRes.background,
icSourceCat=None)
except:
f.write("DFZ DEBUG at calibRes: errors in visit " + v +
", ccd " + str(ccd) + "\n")
try:
#write out calexps
calibRes.exposure.writeFits(calexpfn)
#calbresDict.append((v,ccd),calibRes)
except:
f.write("DFZ DEBUG at calibRes.exposure: errors in visit " +
v + ", ccd " + str(ccd) + "\n")
end = datetime.datetime.now()
d = end - start
f.write("time for creating calexps: ")
f.write(str(d.total_seconds()))
f.write("\n")
#time for creating co-add tempexps.
start = datetime.datetime.now()
# map calexps to patch-ids
visit = visits[0]
ccdsPerPatch = []
for ccd in ccds:
filename = "instcal" + visit + "." + str(ccd) + ".fits"
source = calexpsloc + visit + "/" + filename
exposure = afwImg.ExposureF(source)
bbox = exposure.getBBox()
wcs = exposure.getWcs()
corners = bbox.getCorners()
xIndexMax, yIndexMax = tract.findPatch(
wcs.pixelToSky(corners[0][0], corners[0][1])).getIndex()
xIndexMin, yIndexMin = tract.findPatch(
wcs.pixelToSky(corners[2][0], corners[2][1])).getIndex()
yy = range(yIndexMin, yIndexMax + 1)
xx = range(xIndexMin, xIndexMax + 1)
for yIdx in yy:
for xIdx in xx:
ccdsPerPatch.append((ccd, (xIdx, yIdx)))
print len(ccdsPerPatch)
#import cPickle
#cPickle.dump(open("ccdsinpatch.p",'wb'),ccdsPerPatch)
# import cPickle
# f = open("ccdsInPatch.p",'wb')
# cPickle.dump(ccdsInPatch,f)
#import cPickle
#ccdsInPatch = cPickle.load(open("ccdsInPatch.p",'rb'))
df = pd.DataFrame(ccdsPerPatch)
dfgby = df.groupby(1)
makeCTEConfig = MakeCoaddTempExpConfig()
makeCTE = MakeCoaddTempExpTask(config=makeCTEConfig)
coaddTempExpDict = {}
for visit in visits:
for a in dfgby.indices:
coaddTempExpDict[a] = {}
xInd = a[0]
yInd = a[1]
skyInfo = getSkyInfo(hits_skymap, xInd, yInd)
v = int(visit)
coaddTempExp = afwImage.ExposureF(skyInfo.bbox, skyInfo.wcs)
coaddTempExp.getMaskedImage().set(
numpy.nan, afwImage.MaskU.getPlaneBitMask("NO_DATA"),
numpy.inf)
totGoodPix = 0
didSetMetadata = False
modelPsf = makeCTEConfig.modelPsf.apply(
) if makeCTEConfig.doPsfMatch else None
setInputRecorder = False
for b in dfgby.get_group(a)[0].ravel():
print a
print b
if not setInputRecorder:
ccdsinPatch = len(dfgby.get_group(a)[0].ravel())
try:
inputRecorder = makeCTE.inputRecorder.makeCoaddTempExpRecorder(
v, ccdsinPatch)
except:
f.write("DFZ DEBUG at inputRecorder\n")
setInputRecorder = True
numGoodPix = 0
ccd = b
filename = "instcal" + visit + "." + str(ccd) + ".fits"
source = calexpsloc + visit + "/" + filename
calExp = afwImg.ExposureF(source)
ccdId = calExp.getId()
warpedCcdExp = makeCTE.warpAndPsfMatch.run(
calExp,
modelPsf=modelPsf,
wcs=skyInfo.wcs,
maxBBox=skyInfo.bbox).exposure
if didSetMetadata:
mimg = calExp.getMaskedImage()
mimg *= (coaddTempExp.getCalib().getFluxMag0()[0] /
calExp.getCalib().getFluxMag0()[0])
del mimg
numGoodPix = coaddUtils.copyGoodPixels(
coaddTempExp.getMaskedImage(),
warpedCcdExp.getMaskedImage(), makeCTE.getBadPixelMask())
totGoodPix += numGoodPix
if numGoodPix > 0 and not didSetMetadata:
coaddTempExp.setCalib(warpedCcdExp.getCalib())
coaddTempExp.setFilter(warpedCcdExp.getFilter())
didSetMetadata = True
inputRecorder.addCalExp(calExp, ccdId, numGoodPix)
##### End loop over ccds here:
inputRecorder.finish(coaddTempExp, totGoodPix)
if totGoodPix > 0 and didSetMetadata:
coaddTempExp.setPsf(
modelPsf if makeCTEConfig.doPsfMatch else CoaddPsf(
inputRecorder.coaddInputs.ccds, skyInfo.wcs))
coaddTempExpDict[a][v] = coaddTempExp
coaddfilename = coaddloc + visit + "/" + "instcal" + visit + "." + str(
xInd) + "_" + str(yInd) + ".fits"
coaddTempExp.writeFits(coaddfilename)
end = datetime.datetime.now()
d = end - start
f.write("time for creating co-add tempexps:\n ")
f.write(str(d.total_seconds()))
f.write("\n")
#DFZ: stop here
exit(0)
start = datetime.datetime.now()
config = AssembleCoaddConfig()
assembleTask = AssembleCoaddTask(config=config)
mergcoadds = {}
for a in dfgby.indices:
ccdsinPatch = len(dfgby.get_group(a)[0].ravel())
xInd = a[0]
yInd = a[1]
imageScalerRes = prepareInputs(coaddTempExpDict[a].values(),
coaddTempExpDict[a].keys(),
assembleTask)
mask = None
doClip = False
if mask is None:
mask = assembleTask.getBadPixelMask()
statsCtrl = afwMath.StatisticsControl()
statsCtrl.setNumSigmaClip(assembleTask.config.sigmaClip)
statsCtrl.setNumIter(assembleTask.config.clipIter)
statsCtrl.setAndMask(mask)
statsCtrl.setNanSafe(True)
statsCtrl.setWeighted(True)
statsCtrl.setCalcErrorFromInputVariance(True)
for plane, threshold in assembleTask.config.maskPropagationThresholds.items(
):
bit = afwImage.MaskU.getMaskPlane(plane)
statsCtrl.setMaskPropagationThreshold(bit, threshold)
if doClip:
statsFlags = afwMath.MEANCLIP
else:
statsFlags = afwMath.MEAN
coaddExposure = afwImage.ExposureF(skyInfo.bbox, skyInfo.wcs)
coaddExposure.setCalib(assembleTask.scaleZeroPoint.getCalib())
coaddExposure.getInfo().setCoaddInputs(
assembleTask.inputRecorder.makeCoaddInputs())
#remember to set metadata if you want any hope of running detection and measurement on this coadd:
#self.assembleMetadata(coaddExposure, tempExpRefList, weightList)
#most important thing is the psf
coaddExposure.setFilter(coaddTempExpDict[a].values()[0].getFilter())
coaddInputs = coaddExposure.getInfo().getCoaddInputs()
for tempExp, weight in zip(coaddTempExpDict[a].values(),
imageScalerRes.weightList):
assembleTask.inputRecorder.addVisitToCoadd(coaddInputs, tempExp,
weight)
#takes numCcds as argument
coaddInputs.ccds.reserve(ccdsinPatch)
coaddInputs.visits.reserve(len(imageScalerRes.dataIdList))
psf = measAlg.CoaddPsf(coaddInputs.ccds, coaddExposure.getWcs())
coaddExposure.setPsf(psf)
maskedImageList = afwImage.vectorMaskedImageF()
coaddMaskedImage = coaddExposure.getMaskedImage()
for dataId, imageScaler, exposure in zip(
imageScalerRes.dataIdList, imageScalerRes.imageScalerList,
coaddTempExpDict[a].values()):
print dataId, imageScaler, exposure
maskedImage = exposure.getMaskedImage()
imageScaler.scaleMaskedImage(maskedImage)
maskedImageList.append(maskedImage)
maskedImage = afwMath.statisticsStack(maskedImageList, statsFlags,
statsCtrl,
imageScalerRes.weightList)
coaddMaskedImage.assign(maskedImage, skyInfo.bbox)
coaddUtils.setCoaddEdgeBits(coaddMaskedImage.getMask(),
coaddMaskedImage.getVariance())
# write out Coadd!
mergefilename = mergecoaddloc + str(xInd) + "_" + str(yInd) + ".fits"
mergcoadds[a] = coaddExposure
coaddExposure.writeFits(mergefilename)
end = datetime.datetime.now()
d = end - start
f.write("time for creating merged co-adds:\n ")
f.write(str(d.total_seconds()))
f.write("\n")
start = datetime.datetime.now()
config = DetectCoaddSourcesConfig()
detectCoaddSources = DetectCoaddSourcesTask(config=config)
for a in dfgby.indices:
# Detect on Coadd
exp = mergcoadds[a]
detRes = detectCoaddSources.runDetection(exp, idFactory=None)
end = datetime.datetime.now()
d = end - start
f.write("time for detecting sources:\n ")
f.write(str(d.total_seconds()))
f.close()
def testBad(self):
conf = CalibrateConfig()
with self.assertRaises(Exception):
conf.invalidField = True
def testBad(self):
conf = CalibrateConfig()
with self.assertRaises(Exception):
conf.invalidField = True
