def plotCls(self,saveFile,keys=None,xlimits=None,ylimits=None,transform=True,showBinnedTheory=False,scaleX='linear',scaleY='linear'):
nsigma = 2.
binCenters = self.binner.getBinCenters()
if transform:
ylab = "$\ell C_{\ell}$"
mult = binCenters
multTh = 1.#binCenters*0.+1.
else:
ylab = "$C_{\ell}$"
mult = binCenters*0.+1.
multTh = 0.#binCenters*0.
pl = Plotter(labelX="$\ell$",labelY=ylab,scaleX=scaleX,scaleY=scaleY)
if keys is None: keys = self.datas.keys()
for key in keys:
dat = self.datas[key]
if dat['covmat'] is None:
#This is a theory curve
ells = np.array(range(len(dat['unbinned'])))
if dat['isFit']:
ls="--"
lw=1
else:
ls="-"
lw=2
base_line, = pl.add(ells,(multTh*(ells-1)+1.)*dat['unbinned'],label=dat['label'],lw=lw,ls=ls)
if dat['isFit']:
pl._ax.fill_between(ells,(multTh*(ells-1)+1.)*dat['unbinned']*(1.-nsigma*dat['amp'][1]/dat['amp'][0]),(multTh*(ells-1)+1.)*dat['unbinned']*(1.+nsigma*dat['amp'][1]/dat['amp'][0]),alpha=0.3, facecolor=base_line.get_color())
if showBinnedTheory:
pl.add(binCenters[:len(dat['binned'])],mult[:len(dat['binned'])]*dat['binned'],
ls='none',marker='x',mew=2,markersize=10,label=dat['label']+' binned')
else:
errs = np.sqrt(np.diagonal(dat['covmat']))
print dat['label']
pl.addErr(binCenters[:len(dat['binned'])],mult[:len(dat['binned'])]*dat['binned'],mult[:len(dat['binned'])]*errs,label=dat['label'],marker='o',elinewidth=2,markersize=10,mew=2,)
[i.set_linewidth(2.0) for i in pl._ax.spines.itervalues()]
pl._ax.tick_params(which='major',width=2)
pl._ax.tick_params(which='minor',width=2)
pl._ax.axhline(y=0.,ls='--')
if not(xlimits is None):
pl._ax.set_xlim(*xlimits)
else:
pl._ax.set_xlim(self.binner.bin_edges[0],self.binner.bin_edges[-1])
if not(ylimits is None): pl._ax.set_ylim(*ylimits)
pl.legendOn(loc='lower left',labsize=10)
pl.done(saveFile)
def fit(self,keyData,keyTheory,amplitudeRange=np.arange(0.1,2.0,0.01),debug=False,numbins=-1):
# evaluate likelihood on a 1d grid and fit to a gaussian
# store fit as new theory curve
width = amplitudeRange[1]-amplitudeRange[0]
Likelihood = lambda x: np.exp(-0.5*self.chisq(keyData,keyTheory,amp=x,numbins=numbins))
Likes = np.array([Likelihood(x) for x in amplitudeRange])
Likes = Likes / (Likes.sum()*width) #normalize
ampBest,ampErr = cfit(norm.pdf,amplitudeRange,Likes,p0=[1.0,0.5])[0]
if debug:
fitVals = np.array([norm.pdf(x,ampBest,ampErr) for x in amplitudeRange])
pl = Plotter()
pl.add(amplitudeRange,Likes,label="likes")
pl.add(amplitudeRange,fitVals,label="fit")
pl.legendOn()
pl.done("output/debug_coreFit.png")
fitKey = keyData+"_fitTo_"+keyTheory
self.datas[fitKey] = {}
self.datas[fitKey]['covmat'] = None
self.datas[fitKey]['binned'] = self.datas[keyTheory]['binned']*ampBest
self.datas[fitKey]['unbinned'] = self.datas[keyTheory]['unbinned']*ampBest
self.datas[fitKey]['label'] = keyData+" fit to "+keyTheory+" with amp "+'{0:.2f}'.format(ampBest)+"+-"+'{0:.2f}'.format(ampErr)
self.datas[fitKey]['amp']=(ampBest,ampErr)
self.datas[fitKey]['isFit'] = True
return fitKey
myCamb = CAMB("/astro/u/msyriac/software/cambRed/params_testbed.ini",seed=rank)
myCamb.setParam("accuracy_boost",1)
myCamb.setParam("redshift_file(2)","../../repos/cmb-lensing-projections/data/dndz/cmass_dndz.csv")
Hand = dndzHand(A,a,b,c)
norm = quad(Hand.dndz,0.,3.5)[0]
#print norm
distro = Hand.dndz(zlist)/norm
savemat = np.vstack((zlist,distro)).transpose()
redFile = "temp_dndz_"+str(rank)+"_.csv"
np.savetxt(redFile,savemat,delimiter=' ')
pl.add(zlist,distro)
outRoot = "dndzTest"+str(rank)
myCamb.setParam("output_root",outRoot)
myCamb.setParam("redshift_file(1)",redFile)
myCamb.call(suppress=False)
remove(redFile)
theoryFile = outRoot+"_scalCovCls.dat"
colnum = sn.getColNum(0,1,2)
norm="lsq"
transpower=[2.,0.5]
readCls = smartCls(theoryFile)
Cls = np.array(readCls.getCol(colnum=colnum,norm=norm,transpower=transpower))
ells = readCls.ells
fileList = glob.glob("output/"+derivRoot+"*.csv")
farr = np.loadtxt("output/"+derivRoot[:-5]+"fCls.csv",delimiter=',')
arrs = {}
for fileN in fileList:
lab = fileN[len("output/"+derivRoot):-4]
arrs[lab] = np.loadtxt(fileN,delimiter=',')
specList = ['TT','EE','BB','TE','KK','KT']
for spec in specList:
if spec=='BB': continue
pls = Plotter(scaleY='log',scaleX='log')
ind = specList.index(spec)
for lab in arrs:
arr = arrs[lab]
y = arr[:,ind]**2./farr[:,ind]**2.
if lab=='tau': ls = '--'
else: ls = "-"
pls.add(range(arr.shape[0]),y,label=lab,ls=ls)
pls.legendOn(loc='upper right',labsize=8)
pls._ax.set_xlim(20.,4000.)
pls.done("output/d"+spec+".png")
def main(argv):
iniFile = 'input/noise.ini'
config = ConfigParser()
config.read(iniFile)
mass = 1.E14
conc = 3.0
z = 1.0
#noiseT = 1.0
#beam = 5.0
#ellbeam = 7000.
Nclus = 1000.
arcupto = 10.
mss = []
#beams = np.arange(1.0,7.0,0.1)
beams = [float(argv[0])]
noiseT = float(argv[1])
xy = argv[2]
print beams
#sys.exit()
for beam in beams:
ellbeam = 7000
#ellbeam = int(np.sqrt(8.*np.log(2.)) / beam *60. * 180./np.pi)
print "Ellbeam, ", ellbeam
Nsupp = 10000.
px = 0.1
arc = 20.
#xy = 'TT'
bin_width = 10 #int(beam/px)
Nreals = 5000
Nbins = int(arcupto/bin_width)
scale = px
thetas = np.arange(bin_width*scale/2.,arcupto,scale*bin_width)
lensedClFile = "../cmb-lensing-projections/data/TheorySpectra/ell28k_highacc_lensedCls.dat"
unlensedClFile = "../cmb-lensing-projections/data/TheorySpectra/ell28k_highacc_scalCls.dat"
cmbells,cltt,clee,clbb,clte = Lens.loadCls(lensedClFile)
ucmbells,ucltt,uclee,uclte,dummy = Lens.loadCls(unlensedClFile)
uclbb = clbb.copy()[:len(ucmbells)]
uClsNow = [ucltt,uclee,uclbb,uclte]
uClsFid = [ucltt,uclee,uclbb,uclte]
lClsFid = [cltt,clee,clbb,clte]
template = "../DerivGen/data/order5_lensedCMB_T_beam_cutout_3.fits"
templateMap = liteMap.liteMapFromFits(template)
Lens.makeBinfile("../cmb-lensing-projections/data/bintemp.dat",first=2,last=9000,width=20)
lmin = 2.
lmax = 8000.
if xy=='mv':
NormGen = Lens.AL(templateMap,'TT',ucmbells,uClsNow,ucmbells,uClsFid,cmbells,lClsFid,lmax,lmax,gradCut=2000.)
NormGen.addWhiteNoise(noiseT,np.sqrt(2.)*noiseT,beam,(0,0,lmin,lmax),(lmin,lmax,lmin,lmax))
L1,Nl1,ph = NormGen.binnedNLkk("../cmb-lensing-projections/data/bintemp.dat",inverted=False,halo=True)
NormGen = Lens.AL(templateMap,'EB',ucmbells,uClsNow,ucmbells,uClsFid,cmbells,lClsFid,lmax,lmax,gradCut=2000.)
NormGen.addWhiteNoise(noiseT,np.sqrt(2.)*noiseT,beam,(0,0,lmin,lmax),(lmin,lmax,lmin,lmax))
L2,Nl2,ph = NormGen.binnedNLkk("../cmb-lensing-projections/data/bintemp.dat",inverted=False,halo=True)
assert np.all(L1==L2)
L = L1.copy()
Nl = 1./(1./Nl1+1./Nl2)
else:
NormGen = Lens.AL(templateMap,xy,ucmbells,uClsNow,ucmbells,uClsFid,cmbells,lClsFid,lmax,lmax,gradCut=2000.)
NormGen.addWhiteNoise(noiseT,np.sqrt(2.)*noiseT,beam,(0,0,lmin,lmax),(lmin,lmax,lmin,lmax))
L,Nl,ph = NormGen.binnedNLkk("../cmb-lensing-projections/data/bintemp.dat",inverted=False,halo=True)
pl = Plotter(scaleX='log',scaleY='log')
pl.add(L,Nl)
pl.done('stampNl.png')
#sys.exit()
rads = []
print "Making stamps to determine profile covmat..."
for i in range(Nreals):
#print i
lm = liteMap.makeEmptyCEATemplate(raSizeDeg=arc/60., decSizeDeg=arc/60.,pixScaleXarcmin = px, pixScaleYarcmin=px)
if i==0:
#print lm.data.shape
Npix = lm.data.shape[0]
lfilt = stepFunctionFilterFromLiteMap(lm,ellbeam)
kapmaker = kappaMaker(Cosmology(defaultLCDM),mass,conc,z,storeKap=False)
kapstamp,kaprad = kapmaker.getKappaAndProfile(Npix,scale=px,beam=None,bin_width=bin_width)
# pl = Plotter()
# pl.plot2d(kapstamp)
# pl.done('kappa.png')
# sys.exit()
lm.fillWithGaussianRandomField(L,Nl/Nsupp,bufferFactor = 1)
stamp = lm.data.copy()
stamp = stamp+kapstamp.copy()
stamp = np.nan_to_num(filterDataFromTemplate(stamp,lfilt))
prof = radial_data(stamp,annulus_width=bin_width).mean
#print prof
rads.append(prof)
if i%1000==0: print i
radmeans, covMean, cov, errMean,err,corrcoef = getStats(rads,Nreals)
thstamp = np.nan_to_num(filterDataFromTemplate(kapstamp,lfilt))
thprof = radial_data(thstamp,annulus_width=bin_width).mean
siginv = np.linalg.pinv(cov[:len(thetas),:len(thetas)])
#print siginv
#print radmeans[:len(thetas)]
b = np.dot(siginv,radmeans[:len(thetas)])
chisq = np.dot(radmeans[:len(thetas)],b)
print np.sqrt(chisq*Nclus/Nsupp)
#print radmeans
#print err
pl = Plotter()
pl.addErr(thetas,radmeans[:len(thetas)],yerr=err[:len(thetas)])
pl.add(thetas,kapmaker.kappa(thetas))
pl._ax.set_ylim(-0.01,0.25)
pl._ax.set_xlim(0.0,arcupto)
pl.done('profile.png')
pl = Plotter()
pl.plot2d(corrcoef)
pl.done('corrcoef.png')
pl = Plotter()
pl.plot2d(stamp)
pl.done('stamp.png')
amplitudeRange = np.arange(-1.,2.,0.01)
width = amplitudeRange[1]-amplitudeRange[0]
amplist = []
print "Fitting amplitudes..."
for i in range(Nreals):
prof = rads[i][:len(thetas)]
Likelihood = lambda x: np.exp(-0.5*fchisq(prof,siginv,thprof[:len(thetas)],amp=x))
Likes = np.array([Likelihood(x) for x in amplitudeRange])
Likes = Likes / (Likes.sum()*width) #normalize
ampBest,ampErr = cfit(norm.pdf,amplitudeRange,Likes,p0=[1.0,0.5])[0]
#print ampBest,ampErr
amplist.append(ampBest)
ms = plotstat( -1.,2.,0.01 , (np.array(amplist)) , "amps",fit=True,scale=np.sqrt(Nclus/Nsupp))
mss.append(ms)
pl = Plotter()
pl.add(beams,mss)
pl.done('beam.png')
np.savetxt("output/m1beamsms"+xy+argv[0]+"_noise"+str(noiseT)+".txt",np.vstack((beams,mss)).transpose())
def fitAuto(self,keyData,keyTheory,amplitudeRange=np.arange(0.1,2.0,0.01),constRange=np.arange(0.1,2.0,0.01),debug=False,store=False):
# evaluate likelihood on a 2d grid and fit to a gaussian
# store fit as new theory curve
width = amplitudeRange[1]-amplitudeRange[0]
height = constRange[1]-constRange[0]
Likelihood = lambda x,y: np.exp(-0.5*self.chisqAuto(keyData,keyTheory,amp=x,const=y))
#Likelihood = lambda x,y: -0.5*self.chisqAuto(keyData,keyTheory,amp=x,const=y)
Likes = np.array([[Likelihood(x,y) for x in amplitudeRange] for y in constRange])
ampLike = np.sum(Likes,axis=0)
constLike = np.sum(Likes,axis=1)
ampLike = ampLike / (ampLike.sum()*width) #normalize
constLike = constLike / (constLike.sum()*height) #normalize
ampBest,ampErr = cfit(norm.pdf,amplitudeRange,ampLike,p0=[amplitudeRange.mean(),0.1*amplitudeRange.mean()])[0]
constBest,constErr = cfit(norm.pdf,constRange,constLike,p0=[constRange.mean(),0.1*constRange.mean()])[0]
if debug:
pl = Plotter()
pl.plot2d(Likes)
pl.done("output/like2d.png")
pl = Plotter()
fitVals = np.array([norm.pdf(x,ampBest,ampErr) for x in amplitudeRange])
pl.add(amplitudeRange,ampLike,label="amplikes")
pl.add(amplitudeRange,fitVals,label="fit")
pl.legendOn()
pl.done("output/amplike1d.png")
pl = Plotter()
fitVals = np.array([norm.pdf(x,constBest,constErr) for x in constRange])
pl.add(constRange,constLike,label="constlikes")
pl.add(constRange,fitVals,label="fit")
pl.legendOn()
pl.done("output/constlike1d.png")
#sys.exit()
if not(store):
return constBest,constErr
else:
self.datas[keyData]['binned'] -= constBest
self.datas[keyData]['unbinned'] -= constBest
fitKey = keyData+"_fitTo_"+keyTheory
self.datas[fitKey] = {}
self.datas[fitKey]['covmat'] = None
self.datas[fitKey]['binned'] = self.datas[keyTheory]['binned']*ampBest
self.datas[fitKey]['unbinned'] = self.datas[keyTheory]['unbinned']*ampBest
self.datas[fitKey]['label'] = keyData+" fit to "+keyTheory+" with amp "+'{0:.2f}'.format(ampBest)+"+-"+'{0:.2f}'.format(ampErr)
self.datas[fitKey]['amp']=(ampBest,ampErr)
self.datas[fitKey]['const']=(constBest,constErr)
self.datas[fitKey]['isFit'] = True
return fitKey
zsource = 1.0
myInt.addDeltaNz('delta', zsource)
for i, zwidth in enumerate(np.arange(0.01, 0.1, 0.01)):
myInt.addStepNz('step' + str(i), zsource - zwidth / 2.,
zsource + zwidth / 2.)
print("getting cls..")
pl = Plotter(scaleY='log', scaleX='log')
ellrange = list(range(2, ellmax, 1))
myInt.generateCls(ellrange)
for i, tag in enumerate(sorted(myInt.kernels.keys())):
if tag == "cmb": continue
retcl = myInt.getCl("cmb", tag)
if tag == "delta":
compcl = retcl.copy()
lw = 2
ls = "--"
else:
lw = 1
ls = "-"
pl.add(ellrange, retcl, label=tag, ls=ls, lw=lw)
rat = (retcl / compcl)
ratio = (np.abs(rat[np.logical_and(ellrange > 100., ellrange < 2000.)] -
1.)).max() * 100.
print((tag, ratio, " %"))
pl.legendOn(loc='upper right', labsize=10)
pl.done("output/estcls.png")
print("getting cls..")
ellrange = list(range(2, ellmax, 1))
myInt.generateCls(ellrange)
truthCl = myInt.getCl("cmb", "cmb")
estCl1 = myInt.getCl("cmbDelta", "cmbDelta")
estCl2 = myInt.getCl("cmbStep1", "cmbStep1")
estCl3 = myInt.getCl("cmbStep2", "cmbStep2")
elapsedTime = time.time() - startTime
print(("Estimation took ", elapsedTime, " seconds."))
pl = Plotter(scaleY='log', scaleX='log')
cells = LF.theory.gCl("kk", ells)
pl.add(ellrange, truthCl, label="true", ls='-')
pl.add(ellrange, estCl1, label="delta", ls='-')
pl.add(ellrange, estCl2, label="step1", ls='-')
pl.add(ellrange, estCl3, label="step2", ls='-')
pl.add(ells, cells, label="CAMBkk", color='red', ls='--')
pl.legendOn(loc='upper right', labsize=10)
pl.done("output/estcls.png")
pl = Plotter()
for clNow, lab in zip([truthCl, estCl1, estCl2, estCl3],
["truth", "delta", "step 40", "step 1"]):
intmm = interp1d(ellrange, clNow, bounds_error=False, fill_value=0.)(ells)
pl.add(ells, intmm / LF.theory.gCl("kk", ells), label=lab)
pl.legendOn(loc='upper right', labsize=10)
pl._ax.set_ylim(0.9, 1.1)
print xy,beam
if files==[]:
print "skipping"
continue
print files[0]
noises = []
mss = []
for filen in files:
beam,ms = np.loadtxt(filen,unpack=True)
noise = float(filen[-7:-4])
noises.append(noise)
mss.append(ms)
print "last noise ", noises[-1]
#print mss[-1]
#pl.add(noises,mss,lw=3,label=xy+" "+str(beam) + " arcmin",ls='--',color=col)
pl.add(noises,np.array(mss)*0.01,lw=3,label=str(beam) + " arcmin",ls='-',color=col1)
pl._ax.set_xlim(1.,5.)
#pl._ax.set_ylim(0.,10.)
pl._ax.set_ylim(0.,4.*0.01)
pl.legendOn()
pl.done("beam.png")
myInt.generateCls(ellrange)
retclkks = myInt.getCl("cmb", "cmb")
retclkss = myInt.getCl("cmb", "s")
retclsss = myInt.getCl("s", "s")
retclsks = myInt.getCl("s", "cmb")
retclkgs = myInt.getCl("cmb", "g")
retclggs = myInt.getCl("g", "g")
retclgks = myInt.getCl("g", "cmb")
elapsedTime = time.time() - startTime
print(("Estimation took ", elapsedTime, " seconds."))
pl = Plotter(scaleY='log', scaleX='log')
cells = LF.theory.gCl("kk", ells)
pl.add(ellrange, retclkks, label="MMkk", color='red', ls='-')
pl.add(ells, cells, label="CAMBkk", color='red', ls='--')
cells = LF.theory.gCl("ks", ells)
pl.add(ellrange, retclkss, label="MMks", color='blue', ls='-')
pl.add(ellrange, retclsks, label="MMsk", color='blue', ls='-.', lw=2)
pl.add(ells, cells, label="CAMBks", color='blue', ls='--')
cells = LF.theory.gCl("ss", ells)
pl.add(ellrange, retclsss, label="MMss", color='green', ls='-')
pl.add(ells, cells, label="CAMBss", color='green', ls='--')
cells = LF.theory.gCl("kg", ells)
pl.add(ellrange, retclkgs, label="MMkg", color='purple', ls='-')
pl.add(ellrange, retclgks, label="MMgk", color='purple', ls='-.', lw=2)
pl.add(ells, cells, label="CAMBkg", color='purple', ls='--')
dummy = makeBinfile(tempBinfile,2.,4000.,100.,redundant=True)
clkkFile = "../actpLens/data/fidkk.dat"
clkk = np.loadtxt(clkkFile)
lkk = np.arange(2,len(clkk)+2)
N = 20
estcls = []
for i in range(N):
kappaMap,taperMap = getTaperedMap(lkk,clkk)
print((kappaMap.data.shape))
print((kappaMap.info()))
sys.exit()
lower, upper, center, bin_means = getBinnedPower(kappaMap,tempBinfile,taperMap)
estcls.append(bin_means)
print(i)
clmeans, covMean, cov, errMean,err,corrcoef = getStats(estcls,N)
pl = Plotter()
pl.add(lkk,lkk*clkk)
#pl.add(center,center*bin_means,ls="none",marker="x",color='red',markersize=8,mew=3)
pl.addErr(center,center*clmeans,yerr=center*errMean,ls="none",marker="o",color='red',markersize=8,mew=3)
pl._ax.set_xlim(0.,3500.)
pl.done("clpower.png")