def run(self, matchLists, filterName, wcsList, butler):
if self.config.applyColorTerms:
ct = self.config.colorterms.selectColorTerm(filterName)
else:
ct = None
# Convert matchLists to meas_mosaic specific format
mlVisit = dict()
for ccdId in matchLists:
if matchLists[ccdId] is None:
continue
visit, ccd = self.decodeCcdExposureId(ccdId)
if visit not in mlVisit:
mlVisit[visit] = list()
matches = [m for m in matchLists[ccdId] if m[0] is not None]
keys = self.getKeys(matches[0][1].schema)
matches = self.selectMatches(matches, keys)
matches = self.selectStars(matches)
# Apply color term
if ct is not None and len(matches) != 0:
refSchema = matches[0][0].schema
key_p = refSchema.find(ct.primary).key
key_s = refSchema.find(ct.secondary).key
key_f = refSchema.find("flux").key
refFlux1 = numpy.array([m[0].get(key_p) for m in matches])
refFlux2 = numpy.array([m[0].get(key_s) for m in matches])
refMag1 = -2.5 * numpy.log10(refFlux1)
refMag2 = -2.5 * numpy.log10(refFlux2)
refMag = ct.transformMags(refMag1, refMag2)
refFlux = numpy.power(10.0, -0.4 * refMag)
matches = [
self.setCatFlux(m, f, key_f)
for m, f in zip(matches, refFlux) if f == f
]
for m in matches:
if m[0] is not None and m[1] is not None:
match = (measMosaic.Source(m[0], wcsList[ccdId]),
measMosaic.Source(m[1]))
match[1].setExp(visit)
match[1].setChip(ccd)
mlVisit[visit].append(match)
matchList = []
for visit in mlVisit:
matchList.append(mlVisit[visit])
rootMat = measMosaic.kdtreeMat(matchList)
allMat = rootMat.mergeMat()
# Read CCD information
ccdSet = {}
for ccdId in matchLists:
if matchLists[ccdId] is None:
continue
visit, ccd = self.decodeCcdExposureId(ccdId)
if ccd not in ccdSet:
ccdDev = cameraGeomUtils.findCcd(butler.mapper.camera,
cameraGeom.Id(int(ccd)))
ccdSet[ccd] = ccdDev
# meas_mosaic specific wcs information
wcsDic = {}
for ccdId in wcsList:
visit, ccd = self.decodeCcdExposureId(ccdId)
if visit not in wcsDic and wcsList[ccdId] is not None:
wcs = wcsList[ccdId]
ccdDev = ccdSet[ccd]
offset = afwGeom.Extent2D(ccdDev.getCenter().getPixels(
ccdDev.getPixelSize()))
wcsDic[visit] = wcs.copyAtShiftedPixelOrigin(offset)
# meas_mosaic specific object list
matchVec = measMosaic.obsVecFromSourceGroup(allMat, wcsDic, ccdSet)
sourceVec = []
# Apply Jocabian correction calculated from wcs
for m in matchVec:
wcs = wcsList[m.iexp * 200 + m.ichip]
m.mag -= 2.5 * math.log10(
measMosaic.computeJacobian(wcs, afwGeom.Point2D(m.x, m.y)))
fluxFitOrder = self.config.fluxFitOrder
absolute = True
chebyshev = True
commonFluxCorr = False
solveCcdScale = True
ffpSet = {}
for visit in wcsDic:
ffp = measMosaic.FluxFitParams(fluxFitOrder, absolute, chebyshev)
u_max, v_max = self.getExtent(matchVec)
ffp.u_max = (math.floor(u_max / 10.) + 1) * 10
ffp.v_max = (math.floor(v_max / 10.) + 1) * 10
ffpSet[visit] = ffp
fexp = {}
fchip = {}
matchVec, sourceVec, wcsDic, ccdSet, fexp, fchip, ffpSet = measMosaic.fluxFit(
absolute, commonFluxCorr, matchVec, len(matchVec), sourceVec,
len(sourceVec), wcsDic, ccdSet, fexp, fchip, ffpSet, solveCcdScale)
self.writeFcr(butler, list(matchLists.keys()), ccdSet, filterName,
fexp, fchip, ffpSet)
return (1.0 / fexp[list(fexp.keys())[0]])
def run(self, dataRefList, tractInfo, ct=None, debug=False, diagDir=".",
diagnostics=False, snapshots=False, numCoresForReadSource=1, readTimeout=9999, verbose=False):
self.log.info(str(self.config))
self.outputDir = os.path.join(diagDir, "%04d" % tractInfo.getId())
if ((diagnostics or snapshots) and not os.path.isdir(self.outputDir)):
os.makedirs(self.outputDir)
if self.config.nBrightest != 0:
self.log.fatal("Config paremeter nBrightest is deprecated.")
self.log.fatal("Please use cellSize and nStarPerCell.")
self.log.fatal("Exiting ...")
return []
dataRefListOverlapWithTract, dataRefListToUse = self.checkOverlapWithTract(tractInfo, dataRefList)
sourceSet, matchList, dataRefListUsed = self.readCatalog(dataRefListToUse, ct, numCoresForReadSource,
readTimeout, verbose)
if not matchList:
raise RuntimeError("No reference source matches found")
dataRefListToOutput = list(set(dataRefListUsed) & set(dataRefListOverlapWithTract))
ccdSet = self.readCcd(dataRefListUsed)
if debug:
for ccd in ccdSet.values():
self.log.info(str(ccd.getId().getSerial()) + " " +
str(ccd.getCenter().getPixels(ccd.getPixelSize())) + " " +
str(ccd.getOrientation().getYaw()))
wcsDic = self.readWcs(dataRefListUsed, ccdSet)
self.removeNonExistCcd(dataRefListUsed, ccdSet)
if debug:
for iexp, wcs in wcsDic.items():
self.log.info(str(iexp) + " " + str(wcs.getPixelOrigin()) + " " +
str(wcs.getSkyOrigin().getPosition(afwGeom.degrees)))
self.log.info("frameIds : " + str(list(wcsDic.keys())))
self.log.info("ccdIds : " + str(list(ccdSet.keys())))
d_lim = afwGeom.Angle(self.config.radXMatch, afwGeom.arcseconds)
if debug:
self.log.info("d_lim : %f" % d_lim)
allMat, allSource =self.mergeCatalog(sourceSet, matchList, ccdSet, d_lim)
self.log.info("Flag suspect objects")
measMosaic.flagSuspect(allMat, allSource, wcsDic)
if self.config.clipSourcesOutsideTract:
tractBBox = afwGeom.Box2D(tractInfo.getBBox())
tractWcs = tractInfo.getWcs()
allSourceClipped = [ss for ss in allSource if tractBBox.contains(tractWcs.skyToPixel(ss[0].getSky()))]
self.log.info("Num of allSources: %d" % (len(allSource)))
self.log.info("Num of clipped allSources: %d" % (len(allSourceClipped)))
allSource = allSourceClipped
self.log.info("Make obsVec")
nmatch = len(allMat)
nsource = len(allSource)
matchVec = measMosaic.obsVecFromSourceGroup(allMat, wcsDic, ccdSet)
sourceVec = measMosaic.obsVecFromSourceGroup(allSource, wcsDic, ccdSet)
self.log.info("Solve mosaic ...")
order = self.config.fittingOrder
internal = self.config.internalFitting
solveCcd = self.config.solveCcd
allowRotation = self.config.allowRotation
fluxFitOrder = self.config.fluxFitOrder
chebyshev = self.config.chebyshev
absolute = self.config.fluxFitAbsolute
solveCcdScale = self.config.fluxFitSolveCcd
catRMS = self.config.catRMS
if not internal:
sourceVec = []
if debug:
self.log.info("order : %d" % order)
self.log.info("internal : %r" % internal)
self.log.info("solveCcd : %r " % solveCcd)
self.log.info("allowRotation : %r" % allowRotation)
if self.config.doSolveWcs:
if internal:
coeffSet, matchVec, sourceVec, wcsDic, ccdSet = measMosaic.solveMosaic_CCD(order, nmatch, nsource,
matchVec, sourceVec,
wcsDic, ccdSet,
solveCcd, allowRotation,
verbose, catRMS,
snapshots, self.outputDir)
else:
coeffSet, matchVec, wcsDic, ccdSet = measMosaic.solveMosaic_CCD_shot(order, nmatch, matchVec,
wcsDic, ccdSet,
solveCcd, allowRotation,
verbose, catRMS,
snapshots, self.outputDir)
self.matchVec = matchVec
self.sourceVec = sourceVec
self.wcsDic = wcsDic
self.ccdSet = ccdSet
self.coeffSet = coeffSet
self.writeNewWcs(dataRefListToOutput)
if diagnostics:
self.outputDiagWcs()
for m in matchVec:
coeff = coeffSet[m.iexp]
scale = coeff.pixelScale()
m.mag -= 2.5*math.log10(coeff.detJ(m.u, m.v)/scale**2)
if len(sourceVec) != 0:
for s in sourceVec:
coeff = coeffSet[s.iexp]
scale = coeff.pixelScale()
s.mag -= 2.5*math.log10(coeff.detJ(s.u, s.v)/scale**2)
else:
wcsAll = dict()
for dataRef in dataRefListUsed:
frameId = "%07d-%03d" % (dataRef.dataId["visit"], dataRef.dataId["ccd"])
md = dataRef.get("calexp_md")
wcsAll[frameId] = afwGeom.makeSkyWcs(md)
del md
for m in matchVec:
wcs = wcsAll["%07d-%03d" % (m.iexp, m.ichip)]
m.mag -= 2.5*math.log10(measMosaic.computeJacobian(wcs, afwGeom.Point2D(m.x, m.y)))
if len(sourceVec) != 0:
for s in sourceVec:
wcs = wcsAll["%07d-%03d" % (s.iexp, s.ichip)]
s.mag -= 2.5*math.log10(measMosaic.computeJacobian(wcs, afwGeom.Point2D(s.x, s.y)))
del wcsAll
if self.config.doSolveFlux:
ffpSet = {}
for visit in wcsDic:
ffp = measMosaic.FluxFitParams(fluxFitOrder, absolute, chebyshev)
u_max, v_max = mosaicUtils.getExtent(matchVec)
ffp.u_max = (math.floor(u_max/10.0) + 1)*10
ffp.v_max = (math.floor(v_max/10.0) + 1)*10
ffpSet[visit] = ffp
fexp = {}
fchip = {}
matchVec, sourceVec, wcsDic, ccdSet, fexp, fchip, ffpSet = measMosaic.fluxFit(absolute, self.config.commonFluxCorr, matchVec, len(matchVec), sourceVec, len(sourceVec), wcsDic, ccdSet, fexp, fchip, ffpSet, solveCcdScale)
self.ffpSet = ffpSet
self.fexp = fexp
self.fchip = fchip
self.writeFcr(dataRefListToOutput)
if diagnostics:
self.outputDiagFlux()
if diagnostics and self.config.doSolveWcs and self.config.doSolveFlux:
if len(sourceVec) != 0:
mosaicUtils.writeCatalog(coeffSet, ffpSet, fexp, fchip, matchVec, sourceVec,
os.path.join(self.outputDir, "catalog.fits"))
return list(wcsDic.keys())
def mosaic(self,
dataRefList,
tractInfo,
ct=None,
debug=False,
diagDir=".",
diagnostics=False,
snapshots=False,
numCoresForReadSource=1,
readTimeout=9999,
verbose=False):
self.log.info(str(self.config))
self.outputDir = os.path.join(diagDir, "%04d" % tractInfo.getId())
if ((diagnostics or snapshots) and not os.path.isdir(self.outputDir)):
os.makedirs(self.outputDir)
if self.config.nBrightest != 0:
self.log.fatal("Config paremeter nBrightest is deprecated.")
self.log.fatal("Please use cellSize and nStarPerCell.")
self.log.fatal("Exiting ...")
return []
dataRefListOverlapWithTract, dataRefListToUse = self.checkOverlapWithTract(
tractInfo, dataRefList)
sourceSet, matchList, dataRefListUsed = self.readCatalog(
dataRefListToUse, ct, numCoresForReadSource, readTimeout, verbose)
dataRefListToOutput = list(
set(dataRefListUsed) & set(dataRefListOverlapWithTract))
ccdSet = self.readCcd(dataRefListUsed)
if debug:
for ccd in ccdSet.values():
self.log.info(
str(ccd.getId().getSerial()) + " " +
str(ccd.getCenter().getPixels(ccd.getPixelSize())) + " " +
str(ccd.getOrientation().getYaw()))
wcsDic = self.readWcs(dataRefListUsed, ccdSet)
self.removeNonExistCcd(dataRefListUsed, ccdSet)
if debug:
for iexp, wcs in wcsDic.items():
self.log.info(
str(iexp) + " " + str(wcs.getPixelOrigin()) + " " +
str(wcs.getSkyOrigin().getPosition(afwGeom.degrees)))
self.log.info("frameIds : " + str(list(wcsDic.keys())))
self.log.info("ccdIds : " + str(list(ccdSet.keys())))
d_lim = afwGeom.Angle(self.config.radXMatch, afwGeom.arcseconds)
if debug:
self.log.info("d_lim : %f" % d_lim)
allMat, allSource = self.mergeCatalog(sourceSet, matchList, ccdSet,
d_lim)
self.log.info("Flag suspect objects")
measMosaic.flagSuspect(allMat, allSource, wcsDic)
if self.config.clipSourcesOutsideTract:
tractBBox = afwGeom.Box2D(tractInfo.getBBox())
tractWcs = tractInfo.getWcs()
allSourceClipped = [
ss for ss in allSource
if tractBBox.contains(tractWcs.skyToPixel(ss[0].getSky()))
]
self.log.info("Num of allSources: %d" % (len(allSource)))
self.log.info("Num of clipped allSources: %d" %
(len(allSourceClipped)))
allSource = allSourceClipped
self.log.info("Make obsVec")
nmatch = len(allMat)
nsource = len(allSource)
matchVec = measMosaic.obsVecFromSourceGroup(allMat, wcsDic, ccdSet)
sourceVec = measMosaic.obsVecFromSourceGroup(allSource, wcsDic, ccdSet)
self.log.info("Solve mosaic ...")
order = self.config.fittingOrder
internal = self.config.internalFitting
solveCcd = self.config.solveCcd
allowRotation = self.config.allowRotation
fluxFitOrder = self.config.fluxFitOrder
chebyshev = self.config.chebyshev
absolute = self.config.fluxFitAbsolute
solveCcdScale = self.config.fluxFitSolveCcd
catRMS = self.config.catRMS
if not internal:
sourceVec = []
if debug:
self.log.info("order : %d" % order)
self.log.info("internal : %r" % internal)
self.log.info("solveCcd : %r " % solveCcd)
self.log.info("allowRotation : %r" % allowRotation)
if self.config.doSolveWcs:
if internal:
coeffSet, matchVec, sourceVec, wcsDic, ccdSet = measMosaic.solveMosaic_CCD(
order, nmatch, nsource, matchVec, sourceVec, wcsDic,
ccdSet, solveCcd, allowRotation, verbose, catRMS,
snapshots, self.outputDir)
else:
coeffSet, matchVec, wcsDic, ccdSet = measMosaic.solveMosaic_CCD_shot(
order, nmatch, matchVec, wcsDic, ccdSet, solveCcd,
allowRotation, verbose, catRMS, snapshots, self.outputDir)
self.matchVec = matchVec
self.sourceVec = sourceVec
self.wcsDic = wcsDic
self.ccdSet = ccdSet
self.coeffSet = coeffSet
self.writeNewWcs(dataRefListToOutput)
if diagnostics:
self.outputDiagWcs()
for m in matchVec:
coeff = coeffSet[m.iexp]
scale = coeff.pixelScale()
m.mag -= 2.5 * math.log10(coeff.detJ(m.u, m.v) / scale**2)
if len(sourceVec) != 0:
for s in sourceVec:
coeff = coeffSet[s.iexp]
scale = coeff.pixelScale()
s.mag -= 2.5 * math.log10(coeff.detJ(s.u, s.v) / scale**2)
else:
wcsAll = dict()
for dataRef in dataRefListUsed:
frameId = "%07d-%03d" % (dataRef.dataId["visit"],
dataRef.dataId["ccd"])
md = dataRef.get("calexp_md")
wcsAll[frameId] = afwGeom.makeSkyWcs(md)
del md
for m in matchVec:
wcs = wcsAll["%07d-%03d" % (m.iexp, m.ichip)]
m.mag -= 2.5 * math.log10(
measMosaic.computeJacobian(wcs, afwGeom.Point2D(m.x, m.y)))
if len(sourceVec) != 0:
for s in sourceVec:
wcs = wcsAll["%07d-%03d" % (s.iexp, s.ichip)]
s.mag -= 2.5 * math.log10(
measMosaic.computeJacobian(wcs,
afwGeom.Point2D(s.x, s.y)))
del wcsAll
if self.config.doSolveFlux:
ffpSet = {}
for visit in wcsDic:
ffp = measMosaic.FluxFitParams(fluxFitOrder, absolute,
chebyshev)
u_max, v_max = mosaicUtils.getExtent(matchVec)
ffp.u_max = (math.floor(u_max / 10.0) + 1) * 10
ffp.v_max = (math.floor(v_max / 10.0) + 1) * 10
ffpSet[visit] = ffp
fexp = {}
fchip = {}
matchVec, sourceVec, wcsDic, ccdSet, fexp, fchip, ffpSet = measMosaic.fluxFit(
absolute, self.config.commonFluxCorr, matchVec, len(matchVec),
sourceVec, len(sourceVec), wcsDic, ccdSet, fexp, fchip, ffpSet,
solveCcdScale)
self.ffpSet = ffpSet
self.fexp = fexp
self.fchip = fchip
self.writeFcr(dataRefListToOutput)
if diagnostics:
self.outputDiagFlux()
if diagnostics and self.config.doSolveWcs and self.config.doSolveFlux:
if len(sourceVec) != 0:
mosaicUtils.writeCatalog(
coeffSet, ffpSet, fexp, fchip, matchVec, sourceVec,
os.path.join(self.outputDir, "catalog.fits"))
return list(wcsDic.keys())
def run(self, matchLists, filterName, wcsList, butler):
if self.config.applyColorTerms:
ct = self.config.colorterms.selectColorTerm(filterName)
else:
ct = None
# Convert matchLists to meas_mosaic specific format
mlVisit = dict()
for ccdId in matchLists:
if matchLists[ccdId] is None:
continue
visit, ccd = self.decodeCcdExposureId(ccdId)
if visit not in mlVisit:
mlVisit[visit] = list()
matches = [m for m in matchLists[ccdId] if m[0] is not None]
keys = self.getKeys(matches[0][1].schema)
matches = self.selectMatches(matches, keys)
matches = self.selectStars(matches)
# Apply color term
if ct is not None and len(matches) != 0:
refSchema = matches[0][0].schema
key_p = refSchema.find(ct.primary).key
key_s = refSchema.find(ct.secondary).key
key_f = refSchema.find("flux").key
refFlux1 = numpy.array([m[0].get(key_p) for m in matches])
refFlux2 = numpy.array([m[0].get(key_s) for m in matches])
refMag1 = -2.5*numpy.log10(refFlux1)
refMag2 = -2.5*numpy.log10(refFlux2)
refMag = ct.transformMags(refMag1, refMag2)
refFlux = numpy.power(10.0, -0.4*refMag)
matches = [self.setCatFlux(m, f, key_f) for m, f in zip(matches, refFlux) if f == f]
for m in matches:
if m[0] is not None and m[1] is not None:
match = (measMosaic.Source(m[0], wcsList[ccdId]), measMosaic.Source(m[1]))
match[1].setExp(visit)
match[1].setChip(ccd)
mlVisit[visit].append(match)
matchList = []
for visit in mlVisit:
matchList.append(mlVisit[visit])
rootMat = measMosaic.kdtreeMat(matchList)
allMat = rootMat.mergeMat()
# Read CCD information
ccdSet = {}
for ccdId in matchLists:
if matchLists[ccdId] is None:
continue
visit, ccd = self.decodeCcdExposureId(ccdId)
if ccd not in ccdSet:
ccdDev = cameraGeomUtils.findCcd(butler.mapper.camera, cameraGeom.Id(int(ccd)))
ccdSet[ccd] = ccdDev
# meas_mosaic specific wcs information
wcsDic = {}
for ccdId in wcsList:
visit, ccd = self.decodeCcdExposureId(ccdId)
if visit not in wcsDic and wcsList[ccdId] is not None:
wcs = wcsList[ccdId]
ccdDev = ccdSet[ccd]
offset = afwGeom.Extent2D(ccdDev.getCenter().getPixels(ccdDev.getPixelSize()))
wcsDic[visit] = wcs.copyAtShiftedPixelOrigin(offset)
# meas_mosaic specific object list
matchVec = measMosaic.obsVecFromSourceGroup(allMat, wcsDic, ccdSet)
sourceVec = []
# Apply Jocabian correction calculated from wcs
for m in matchVec:
wcs = wcsList[m.iexp*200+m.ichip]
m.mag -= 2.5*math.log10(measMosaic.computeJacobian(wcs, afwGeom.Point2D(m.x, m.y)))
fluxFitOrder = self.config.fluxFitOrder
absolute = True
chebyshev = True
commonFluxCorr = False
solveCcdScale = True
ffpSet = {}
for visit in wcsDic:
ffp = measMosaic.FluxFitParams(fluxFitOrder, absolute, chebyshev)
u_max, v_max = self.getExtent(matchVec)
ffp.u_max = (math.floor(u_max / 10.) + 1) * 10
ffp.v_max = (math.floor(v_max / 10.) + 1) * 10
ffpSet[visit] = ffp
fexp = {}
fchip = {}
matchVec, sourceVec, wcsDic, ccdSet, fexp, fchip, ffpSet = measMosaic.fluxFit(absolute, commonFluxCorr, matchVec, len(matchVec), sourceVec, len(sourceVec), wcsDic, ccdSet, fexp, fchip, ffpSet, solveCcdScale)
self.writeFcr(butler, list(matchLists.keys()), ccdSet, filterName,
fexp, fchip, ffpSet)
return (1.0/fexp[list(fexp.keys())[0]])