def sfine2(mom,leps,thk=254,emax=3.4,minor=0,dofit=4,inorm=[1,1,1],doplot=False):
'''
dofit==1: fit only thickness, renorm parameters fixed
minor: minim. value of refer. spectrum to include point in chi2
'''
import profit
inipars=[thk]+inorm
enxz=enx[enx<emax]
def zres(pars):
model1=profit.plate(enxz,[leps,epssi[enx<emax]],pars[:1])
dif=0
for i in range(len(mom)):
dsel=(mom[i]>0)*(enx<emax)
if minor>0: dsel*=nor[i]>minor
dif+=((mom[i][dsel]*pars[i+1]-model1[dsel[enx<emax]])**2*nor[i][dsel]).sum()*wnor[i]
return dif
from scipy import optimize as op
if dofit==1:
fitpars=op.fmin(lambda p:zres(list(p)+inipars[1:]),inipars[:1],disp=0)
qpars=inipars[1:]
else:
fitpars=op.fmin(zres,inipars,disp=0)
qpars=fitpars[1:]
if doplot:
from matplotlib import plot as pl
model1=profit.plate(enxz,[leps,epssi[enx<emax]],fitpars[:1])
pl.plot(enxz,model1)
for i in range(len(mom)):
m=mom[i]
pl.plot(enx[(m>0)*(enx<emax)],m[(m>0)*(enx<emax)]*qpars[i],'rgm'[i])
if dofit==1:
return fitpars,zres(list(fitpars)+inipars[1:])
else:
return fitpars,zres(fitpars)
def zres(pars):
model1=profit.plate(enxz,[leps,epssi[enx<emax]],pars[:1])
dif=0
for i in range(len(mom)):
dsel=(mom[i]>0)*(enx<emax)
if minor>0: dsel*=nor[i]>minor
dif+=((mom[i][dsel]*pars[i+1]-model1[dsel[enx<emax]])**2*nor[i][dsel]).sum()*wnor[i]
return dif
def calc_ellips_plate(freq,epsil,wid=[],ang=60,conv=1,rep=0,corr=None):
'''calculates ellipsometric angles for given layers'''
from numpy import arctan,arctan2,abs
from profit import plate,reflect
if conv: conv=180./pi
if len(wid)==0: #bulk material
zz=reflect(epsil[0],ang=ang,polar='p',rep=0)
zz/=reflect(epsil[0],ang=ang,polar='s',rep=0)
else:
if ang<0:
fr=plate(freq,epsil,wid,ang=ang,rep=-1)
zz=friter([f[:,0] for f in fr[0]],fr[1],fr[2])/friter([f[:,1] for f in fr[0]],fr[1],fr[2])
else:
zz=plate(freq,epsil,wid,ang=ang,rep=0,polar='p')
zz/=plate(freq,epsil,wid,ang=ang,rep=0,polar='s')
if rep==-2: return zz
out=arctan(abs(zz))*conv,-arctan2(zz.imag,zz.real)*conv
if corr=='pos':
out[1][out[1]<-90]+=360.
if rep==1: return out[0]+1j*out[1]
else: return out
def measure(self,npix=None,**kwargs):
from numpy.random import normal
from math import sqrt
if self.config==None:
print("You must config first!")
return
if 'noise' in kwargs: noise=float(kwargs['noise'])
else: noise=getattr(self.config,'Noise',0.05)
noise/=sqrt(self.config.m_NrAverages)
rep=normal(size=self.pixtable.shape,scale=noise)
mater=None
if 'mater' in kwargs: mater=kwargs['mater']
elif hasattr(self.config,'Material') and self.config.Material.decode('ascii')!='simu': mater=self.config.Material.decode('ascii')
else: mater=rc.simu_mater
#print('using |'+str(mater)+'|')
if mater!=None:
if type(mater)==list:
for m in mater:
if not m in self.data:
if m in rc.eps_ext:
from profit import dielect
self.data[m]=dielect(self.pixtable,rc.eps_ext[m][0],rc.eps_ext[m][1])
elif m in rc.mod_ext:
from numpy import polyval
self.data[m]=polyval(rc.mod_ext[m],self.pixtable)**2
print('calculating diel. '+m)
if len(mater)-len(rc.simu_layer) in [0,1]:
from profit import plate
wid=rc.simu_layer
if hasattr(rc,'simu_layer_fluc'): wid=[wid[i]*normal(1,rc.simu_layer_fluc[i]) for i in range(len(wid))]
rep+=plate(self.pixtable,[self.data[m] for m in mater],wid)
else:
if not mater in self.data:
if mater in rc.mod_ext:
from numpy import polyval
self.data[mater]=polyval(rc.mod_ext[mater],self.pixtable)**2
else:
from spectra import dbload
if type(mater)==bytes: dbname=mater.decode('ascii')
else: dbname=mater
if dbname in rc.eps_trans: dbname=rc.eps_trans[dbname]
try:
inp=dbload(dbname,self.pixtable)
except:
print('cannot load material '+dbname)
return rep
#for i in range(len(inp)):
self.data[mater]=inp[1]
if len(self.data)>0:
from profit import reflect
rep+=reflect(self.data[mater])#,self.data[mater[1]])
rep*=self.config.m_IntegrationTime
return rep
def reconstruct(x,y8,points=None,di=10,re_ord=2,n_subs=3.46,thick=2000.,im_ini=0,im_ind=-1):
if points==None: points=range(5*di,len(x)-5*di,5*di)
res=spectra.extrema(y8,x,poly=-1,msplit='sort',extsel=half_anal_width,loud=0)
mis=[((array(o[1:])+array(o[:-1]))/2.,(array(o[1:])-array(o[:-1]))) for o in res]
from extra import polyfit as rob_fit
n_pr=array([rob_fit(m[0],1/(spectra.ev2um*m[1]*2.*thick/1000.),re_ord,clip=1,lim=1.1) for m in mis])
n_re=polyval(n_pr.mean()/r_[re_ord+1:0.:-1.],x) #real part from oscillations
moo=[im_ini]
from scipy import optimize
for i in points:
muf=lambda z:sum((y8[i-di:i+di]-profit.plate(x[i-di:i+di],[(n_re[i-di:i+di]+1j*z)**2,n_subs**2],[thick]))**2)
moo.append(optimize.fmin(muf,moo[im_ind])[0])
return n_pr,moo
def test_prepare(wrange,w2=1000,norm=620,j=0):
global sig_limit,dt
import profit
tsig=sig_limit
sig_limit=0
epsil=profit.dielect(px,spectra.lor_si_low[0],spectra.lor_si_low[1])
oxide=polyval(spectra.cau_sio2,px)
if (dt==None) or (len(wrange)!=len(dt)): dt=[profit.plate(px,[epsil,oxide,epsil],[w1,w2]) for w1 in wrange]
out=[]
for a in range(len(wrange)):
if anal(a,j,rep=2)[2]>2: out.append([mids,(norm/pers)])
sig_limit=tsig
return out
def extra_test(wid1=1300,wid2=300,step=0.002,isel=1,levabs=0.1,prec=False):
global bins,refe,mall,dall,zzall,nomal,epsil
if bins==None:
bins=r_[1:3:step]
if epsil==None:
epsil=dielect(bins,spectra.lor_si_low2[0],spectra.lor_si_low2[1])
mall=sqrt(epsil.real+1j*levabs).real*bins
dall=(mall[2:]-mall[:-2])/(bins[2:]-bins[:-2])
oxide=polyval(spectra.cau_sio2,bins)
dd=plate(bins,[epsil.real+1j*levabs,oxide,epsil],[wid1,wid2])
if prec:
aall=spectra.extrema(dd,bins,poly=-1,msplit='fine',extsel=5)
a2=array([sum(bins<a) for a in aall[isel]])
dp=array(aall[isel])[1:]-array(aall[isel])[:-1]
else:
aall=spectra.extrema(dd)
a2=array(aall[isel])
dp=bins[a2][1:]-bins[a2][:-1]
b2=(a2[1:]+a2[:-1])/2
return bins[b2],dp,dall[b2-1]
def bump(w2=310,w1=1500,vl=None,slim=[2.2,2.6],rep=1,min_dis=0.015,loud=0,fit_wid=2):
global counter
if vl==None:
oxide=polyval(spectra.cau_sio2,px)
epsil=profit.dielect(px,spectra.lor_si_low[0],spectra.lor_si_low[1])
vl=profit.plate(px,[epsil,oxide,epsil],[w1,w2])
a,b=spectra.extrema(vl)
if len(a)<len(b):a,b=b,a
if a[0]>b[0]:
sh=sum(b<a[0])
b=b[sh:]
elif a[1]<b[0]:
sh=sum(a<b[0])
a=a[sh-1:]
if a[-1]<b[-1]:
sh=sum(b>a[-1])
b=b[:-sh]
elif a[-2]>b[-1]:
sh=sum(a>b[-1])
a=a[:-sh+1]
assert len(b)==len(a)-1
m2=concatenate([(px[b]+px[a][:-1])/2.,(px[b]+px[a][1:])/2.])
n2=concatenate([(vl[b]-vl[a][:-1])/2.,(vl[b]-vl[a][1:])/2.])
s2=argsort(m2)
n2=n2[s2]
m2=m2[s2]
sel=n2>min_dis
m2=m2[sel]
n2=n2[sel]
if rep==0: return m2,n2
sel=(m2>slim[0])*(m2<slim[1])
if sum(sel)<2*fit_wid:
return 0,0
i1=argmin(n2[sel])
s=(m2[sel][i1]+m2[sel][i1+1])/2.
j1=i1>fit_wid and i1-fit_wid or None
j2=i1+fit_wid+1
counter+=1
k,l=polyfit(m2[sel][j1:j2],(n2[sel]*sign(m2[sel]-s))[j1:j2],1)
chi2=sum((polyval([k,l],m2[sel][j1:j2])-(n2[sel]*sign(m2[sel]-s))[j1:j2])**2)
return -l/k,chi2