def Bootratiofit2(fitfnc,fitfncratio,p0,p1,x,xr,ydata,yratio,bounds=None,bounds2=None):
"""Fitting the correlator first and then the ratio with two energy shifts"""
data = np.array([y.values for y in ydata])
yerr = bstd(data)
cv = np.diag(yerr**(-2))
nboot = np.shape(data)[1]
result = np.zeros((fitfnc.npar,nboot))
exppar = np.zeros((len(fitfncratio.q),nboot))
datar = np.array([y.values for y in yratio])
yerrr = bstd(datar)
cvr = np.diag(yerrr**(-2))
resultratio = np.zeros((fitfncratio.npar,nboot))
for iboot in range(nboot):
#Fit the correlator to get amplitudes and energies, and set the variables for the ratio fit
yboot=data[:,iboot]
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'gtol': 1e-9, 'maxcor': 20, 'maxls': 50, 'disp': False})
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='Nelder-Mead',options={'disp': False})
res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'disp': False})
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='BFGS',options={'disp': False})
#res = syopt.basinhopping(ff.chisqfn,p0,niter=5,stepsize=3,T=5,minimizer_kwargs={'args':(fitfnc.eval,x,yboot,cv),'method':'L-BFGS-B','bounds':bounds}, disp=False)
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='Nelder-Mead',options={'disp': False})
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='BFGS',options={'gtol': 1e-9, 'disp': False})
if res.x[3]<res.x[1]: sortres = np.array([*res.x[-2:],*res.x[:2]])
else: sortres = res.x.copy()
result[:,iboot]=sortres.copy()
fitfncratio.q = sortres.copy()
# fitfncratio.q[0] = sortres[0]
# fitfncratio.q[1] = sortres[2]
# fitfncratio.q[2] = sortres[3]-sortres[1]
# p1[0] = sortres[0]
# p1[2] = sortres[2]
#print(f"{p1=}")
exppar[:,iboot]=np.array([fitfncratio.q[0],fitfncratio.q[1],fitfncratio.q[2], fitfncratio.q[3]])
ybootr=datar[:,iboot]
#res2 = syopt.minimize(ff.chisqfn,p1,args=(fitfncratio.eval,xr,ybootr,cvr),method='L-BFGS-B',bounds=bounds2,options={'gtol': 1e-7, 'disp': False})
#res2 = syopt.minimize(ff.chisqfn,p1,args=(fitfncratio.eval,xr,ybootr,cvr),method='BFGS',options={'gtol': 1e-7, 'disp': False})
#res2 = syopt.minimize(ff.chisqfn,p1,args=(fitfncratio.eval,xr,ybootr,cvr),method='Nelder-Mead',options={'disp': False})
res2 = syopt.minimize(ff.chisqfn,p1,args=(fitfncratio.eval,xr,ybootr,cvr),method='L-BFGS-B',bounds=bounds2,options={'disp': False})
#print(f"{res2.x=}")
# if res2.x[3]<res2.x[1]: ratiores = np.array([*res2.x[-2:],*res2.x[:2]])
# else: ratiores = res2.x.copy()
# resultratio[:,iboot]=ratiores.copy()
resultratio[:,iboot] = res2.x.copy()
#print(f"{np.average(resultratio,axis=1)=}")
energies = np.array([result[2*i+1][:] for i in range(int(fitfnc.npar/2))])
energyshift = np.array([resultratio[2*i+1][:] for i in range(int(fitfncratio.npar/2))])
#energyshiftsort = np.sort(energyshift, axis=0)
BSen = []
BSen2 = []
for i in range(len(energies)):
BSen.append( BootStrap(len(energies[0]),68))
BSen[i].values = energies[i]
BSen[i].Stats()
BSen2.append(BootStrap(len(energyshift[0]),68))
BSen2[i].values = energyshift[i]
BSen2[i].Stats()
return result, exppar, resultratio, BSen, BSen2
def Bootratiofit(fitfnc,fitfncratio,p0,p1,x,ydata,yratio,bounds=None,bounds2=None):
"""Fitting the correlator first and then the ratio with two energy shifts"""
data = np.array([y.values for y in ydata])
yerr = bstd(data)
cv = np.diag(yerr**(-2))
nboot=np.shape(data)[1]
result=np.zeros((fitfnc.npar,nboot))
exppar=np.zeros((2,nboot))
datar = np.array([y.values for y in yratio])
yerrr = bstd(datar)
cvr = np.diag(yerrr**(-2))
resultratio=np.zeros((fitfncratio.npar,nboot))
for iboot in range(nboot):
#Fit the correlator to get amplitudes and energies, and set the variables for the ratio fit
yboot=data[:,iboot]
fitfnc.initparfnc(yboot)
res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'gtol': 1e-9, 'disp': False})
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='nelder-mead',options={'disp': False})
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='BFGS',bounds=bounds,options={'gtol': 1e-9, 'disp': False})
fitfncratio.q[0] = (res.x[2]/res.x[0])**(np.sign(res.x[3]-res.x[1]))
fitfncratio.q[1] = np.abs(res.x[3]-res.x[1])
#print(fitfncratio.q[1])
result[:,iboot]=res.x
exppar[:,iboot]=np.array([fitfncratio.q[0],fitfncratio.q[1]])
ybootr=datar[:,iboot]
fitfnc.initparfnc(ybootr)
res2 = syopt.minimize(ff.chisqfn,p1,args=(fitfncratio.eval,x,ybootr,cvr),method='L-BFGS-B',bounds=bounds2,options={'gtol': 1e-7, 'disp': False})
resultratio[:,iboot]=res2.x
energies = np.array([result[2*i+1][:] for i in range(int(fitfnc.npar/2))])
energiessort = np.sort(energies, axis=0)
energyshift = np.array([resultratio[i][:] for i in range(int(fitfncratio.npar))])
energyshiftsort = np.sort(energyshift, axis=0)
if np.any(energies != energiessort):
print("Energies Sorted")
BSen = []
BSen2 = []
for i in range(len(energiessort)):
BSen.append( BootStrap(len(energiessort[0]),68))
BSen[i].values = energiessort[i]
BSen[i].Stats()
BSen2.append(BootStrap(len(energiessort[0]),68))
BSen2[i].values = energyshiftsort[i]
BSen2[i].Stats()
return result, exppar, resultratio, BSen, BSen2
def ReadEvxptdump(file, par, boots, confs=0, times=64, number=0, bin=1):
# par should be 0 or 1 depending on whether the real or imaginary part is chosen (0=R,1=I)
# number defines which result you want, if there are multiple in the same file
f = open(file)
FF = []
for line in f:
strpln = line.rstrip()
if len(strpln) > 0:
if strpln[0] == "+" and strpln[1] == "E" and strpln[2] == "N":
tmp = f.readline()
tmp = f.readline()
tmp = f.readline().split()
times = int(tmp[5])
if strpln[0] == "+" and strpln[1] == "R" and strpln[
2] == "P" and int(strpln[4:6]) == number:
tmp = f.readline().split()
while tmp[0] != "nmeas":
tmp = f.readline().split()
confs = int(tmp[2])
G = zeros(shape=(confs, times, 2))
if strpln[0] == "+" and strpln[1] == "R" and strpln[
2] == "D" and int(strpln[4:6]) == number:
for iff in range(confs):
for nt in range(times):
tmp = f.readline().split()
G[iff, nt, 0] = tmp[1]
G[iff, nt, 1] = tmp[2]
f.close()
for j in range(times):
FF.append(BootStrap(boots, 68))
FF[-1].Import(G[:, j, par], bin=bin)
FF[-1].Stats()
return FF
def BootFitcomb3(chifunc,fitfnc,x1,x2,ydata,p0,bounds=None,time=False):
"""Fit to every bootstrap ensemble and use multiprocessing to split up the task over two processors"""
if time: start1 = tm.time()
yval = np.array([y.values for y in ydata]).T
yerr = np.std(yval,axis=0)
cvinv = np.diag(yerr**(-2))
nboot = ydata[0].nboot
args = [(chifunc,p0,fitfnc,x1,x2,yval[iboot,:],cvinv,bounds) for iboot in range(nboot)]
p = Pool(2) #Use two processors for the calculation
result = np.array(p.map(minimizer0comb,args)).T #Use the pool to map the arguments to the minimiser function.
if np.average(result[0])>np.average(result[1]):
result = np.array([ result[1], result[0], result[3], result[2], result[5], result[4]])
print('sorting')
parBS=[] #Save resulting parameters as Bootstrap objects
for i in range(len(p0)):
parBS.append(BootStrap(nboot,68))
parBS[i].values = result[i][:]
parBS[i].Stats()
if time:
print('BootFitcomb3 time: \t', tm.time()-start1)
return result, parBS
def BootFitclass2(fitfnc,p0,x,ydata,bounds=None,time=False):
if time: start1 = tm.time()
data = np.array([y.values for y in ydata]).T
yerr = np.std(data,axis=0)
cv = np.diag(yerr**(-2))
nboot=ydata[0].nboot
result=np.zeros((len(p0),nboot))
start2=tm.time()
sorttime = 0
for iboot in range(nboot):
yboot=data[iboot,:]
res=syopt.minimize(ff.chisqfn,p0,args=(fitfnc,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'disp': False})
amplitudes = res.x[::2]
energies = res.x[1::2]
sortinglist = [x for _,x in sorted(zip(energies, np.arange(len(energies)) ))]
sortedlist = np.array([ [amplitudes[i], energies[i]] for i in sortinglist ]).flatten()
if any(sortedlist!=res.x): print("Sorted!")
result[:,iboot]=sortedlist
print('----Loop time: \t', tm.time()-start2)
parBS=[]
for i in range(len(p0)):
parBS.append(BootStrap(nboot,68))
parBS[i].values = result[i][:]
parBS[i].Stats()
if time:
end1 = tm.time()
print('BootFitclass2 time: \t', end1-start1)
return result, parBS
def feynhellratioshort(G1, G2, a=0.074, alambda=0.0001, m=1, Ep=1):
ratio=[]
for gi, gj in zip(G1, G2):
ratio.append(BootStrap(G1[0].nboot, 68))
ratio[-1] = np.abs((gi)*(gj**(-1)))
ratio[-1].Stats()
return ratio
def feynhellratio5(G0, Gl, a=0.074, alambda=0.0001, m=1, Ep=1):
ratio=[]
for i in range(len(G0[0])):
ratio.append(BootStrap(G0[0][0].nboot, 68))
ratio[-1] = np.abs( ((Gl[2][i]+Gl[4][i])*(G0[6][i]+G0[8][i])*(G0[3][i]+G0[5][i])*(Gl[7][i]+Gl[9][i])) * ((G0[2][i]+G0[4][i])*(Gl[6][i]+Gl[8][i])*(Gl[3][i]+Gl[5][i])*(G0[7][i]+G0[9][i]))**(-1) )**(1/2)
ratio[-1].Stats()
return ratio
def feynhellratio2(G1, G2, G3, G4, a=0.074, alambda=0.0001, m=1, Ep=1):
ratio=[]
for gi, gj, gk, gl in zip(G1, G2, G3, G4):
ratio.append(BootStrap(G1[0].nboot, 68))
ratio[-1] = np.abs((gi*gj)*(gk*gl)**(-1))
ratio[-1].Stats()
return ratio
def read_data(pars):
"""Read data files in pickle format with Bootstrap ensembles"""
BSdata_dir = pars.workdir + 'pandapickle/' + pars.momfold[
pars.momentum][:7] + '/data_' + str(pars.nboot) + '/'
qval = np.array2string(pars.qval[pars.momentum], separator='')[1:-1]
bsfile = BSdata_dir + 'TwoptBS_q' + qval + '.pkl'
bsfile1 = BSdata_dir + 'TwoptBS_q' + qval + '_quark1_' + pars.lmbstring + '.pkl'
bsfile2 = BSdata_dir + 'TwoptBS_q' + qval + '_quark2_' + pars.lmbstring + '.pkl'
with open(bsfile, 'rb') as fileout:
nucleon = pickle.load(fileout)
with open(bsfile1, 'rb') as fileout:
nucleon_q1 = pickle.load(fileout)
with open(bsfile2, 'rb') as fileout:
nucleon_q2 = pickle.load(fileout)
nucleons_raw = [nucleon, nucleon_q1, nucleon_q2]
nucleons = [[], [], []]
for num in range(len(nucleons_raw[0])):
for type, nu in enumerate(nucleons):
nu.append([])
for t in range(len(nucleons_raw[type][num])):
nu[num].append(
BootStrap(len(nucleons_raw[type][num][t]),
pars.confidence))
nu[num][-1].values = nucleons_raw[type][num][t]
nu[num][-1].Stats()
return nucleons
def ReadEvxpt(file, par):
FF = []
f = open(file)
for line in f:
strpln = line.rstrip()
if len(strpln) > 0:
if strpln[0] == "+" and strpln[1] == "F" and strpln[
2] == "I" and strpln[5] == "0":
tmp = f.readline()
tmp = f.readline()
tmp = f.readline()
tmp = f.readline()
tmp = f.readline()
tmp = f.readline()
tmp = f.readline()
tmp = f.readline().split()
boots = int(tmp[3])
tmp = f.readline()
FF.append(BootStrap(boots, 68))
for iff in range(par + 1):
tmp = f.readline().split()
if par == iff:
FF[-1].Avg = float(tmp[2])
FF[-1].Std = float(tmp[3])
# if iff==(nff-1):
# baddata=append(baddata,float(tmp[2]))
tmp = f.readline().split()
while tmp[0] != "+NUmbers=" + str(boots):
tmp = f.readline().split()
if tmp[0] == "+NUmbers=" + str(boots):
for iboot in range(boots):
tmp = f.readline().split()
FF[-1].values[iboot] = float(tmp[2 * par + 4])
f.close()
return FF
def EnergyFit(tdata,nucleon,initialg,bounds,btbounds,evalfnc,pars,plot=True,cov=True,niter=400,stepsize=500,T=7000,name="test"):
"""Fit to the data using the combined sinks fit and plot the effective mass with the energy fit to the bootstraps"""
normdata = np.array([ normcorr(np.array(nucleon[sink]), nucleon[sink][tdata[sink][0]].Avg) for sink in range(3) ])
ydata0 = np.array([ normdata[i][tdata[i]] for i in range(3) ])
ydata = np.array([ *ydata0[0], *ydata0[1], *ydata0[2] ])
fitparam,redchisq=minimize_comb2(evalfnc, tdata[0], tdata[1], tdata[2], ydata, p0=initialg, cov=cov, pinv=False,bounds=bounds,niter=niter,stepsize=stepsize,T=T)
print(f"{fitparam=}")
print(f"{redchisq=}")
energies=np.sort(np.abs(fitparam[:2]))
print(f"{energies=}")
fitbt = BootFittComb(evalfnc,tdata[0],tdata[1],tdata[2],ydata,p0=fitparam,cov=cov,bounds=btbounds)
energiessort = np.sort(np.abs(np.array([fitbt[i][:] for i in range(2)])), axis=1)
energieserr = np.array([i.std(axis=0, ddof=1) for i in energiessort])
energiesval = np.array([np.average(i, axis=0) for i in energiessort])
fitavg = np.array([*energiesval, *[np.average(fitbt[i,:]) for i in range(2,8)] ])
print(f"{energiesval=}")
print(f"{fitavg=}")
#TODO: Import into BS elements
E0 = BootStrap(len(energiessort[0]),68)
E0.values = energiessort[0]
E0.Stats()
E1 = BootStrap(len(energiessort[1]),68)
E1.values = energiessort[1]
E1.Stats()
if plot:
pypl.figure("energycombfit", figsize=(16,9))
time = np.arange(0,64)
efftime = time+0.5
momfold = ['p+0+0+0/q+0+0+0/', 'p+1+0+0/q+0+0+0/', 'p+1+1+1/q+0+0+0/', 'p+2+1+0/q+0+0+0/', 'p+2+2+0/q+0+0+0/']
snkfold = ['ptsnk/', 'smsnk30/', 'smsnk60/']
colors = ['b', 'r', 'y']
markers=['s','o','^','*', 'v', '>', '<']
for sink in range(3):
yeffavg = np.array([y.Avg for y in effectivemass(nucleon[sink])])
yefferr = np.array([y.Std for y in effectivemass(nucleon[sink])])
pypl.errorbar(efftime[:pars.xlim]+sink/12, yeffavg[:pars.xlim], yefferr[:pars.xlim], fmt='.', capsize=4, elinewidth=1, color=colors[sink], marker=markers[sink], markerfacecolor='none', label='effective energy of the correlator ' + snkfold[sink][:-1] + ' ' + momfold[pars.momentum][:7])
fitBS = np.array([ effmass(evalfnc(tdata[sink],[fitbt[sink*2+2,nbo],fitbt[0,nbo],fitbt[sink*2+3,nbo],fitbt[1,nbo]])) for nbo in range(len(fitbt[0][:])) ])
fitBSavg = np.average(fitBS,axis=0)
fitBSstd = fitBS.std(axis=0, ddof=1)
fitBSlower = fitBSavg - fitBSstd
fitBShigher = fitBSavg + fitBSstd
pypl.plot(tdata[sink][:-1]+0.5,effmass(evalfnc(tdata[sink], [fitparam[sink*2+2],fitparam[0],fitparam[sink*2+3],fitparam[1]])), linestyle='-', color='k', label=pars.fit+' fit effmass fullcov'+str(sink))
pypl.plot(tdata[sink][:-1]+0.5,fitBSavg, linestyle='-', color=colors[sink], label=pars.fit+' fit effmass '+str(sink))
pypl.fill_between(tdata[sink][:-1]+0.5, fitBSlower, fitBShigher, color=colors[sink], alpha=0.3, linewidth=0)
pypl.legend(fontsize='small')
pypl.xlabel(r'$t/a$',labelpad=14,fontsize=18)
pypl.ylabel(r'$G_{eff}$',labelpad=5,fontsize=18)
pypl.title(r'Effective energy correlator')
pypl.grid(True, alpha=0.6)
pypl.ylim(0,1.8)
pypl.subplots_adjust(bottom=0.17)
pypl.savefig('energy_effcorr_combfit_'+ name + momfold[pars.momentum][:7] + '_' + pars.fit + '.pdf') #, bbox
pypl.close()
return energies,E0,E1
def BootFitclass3(fitfnc,p0,x,ydata,bounds=None,time=False,fullcov=False):
"""
Fit to every bootstrap ensemble and use multiprocessing to split up the task over two processors
p0: initial guess for the parameters
x: array of x values to fit over
ydata: array/list of BootStrap objects
"""
if time: start1 = tm.time() #Start counting
nboot=ydata[0].nboot
data = np.array([y.values for y in ydata]).T
yerr = np.std(data,axis=0)
cv = Invcovmat(np.array([y.values for y in ydata]),fullcov=fullcov,pinv=False)
#Fit to the data average to get a chi-squared value for this
dataavg = np.array([y.Avg for y in ydata]).T
# resavg=syopt.minimize(ff.chisqfn,p0,args=(fitfnc,x,dataavg,cv),method='L-BFGS-B',bounds=bounds,options={'disp': False})
niter=100
resavg = syopt.basinhopping(ff.chisqfn,p0,niter=niter,stepsize=8,T=150,minimizer_kwargs={'args':(fitfnc,x,dataavg,cv),'method':'L-BFGS-B','bounds':bounds}, disp=False)
redchisq1=resavg.fun/(len(data[0,:])-len(p0))
p0 = resavg.x
args = [(ff.chisqfn,p0,fitfnc,x,data[iboot,:],cv,bounds) for iboot in range(nboot)]
p = Pool(2) #Use two processors for the calculation
result = np.array(p.map(minimizer0,args)).T #Use the pool to map the arguments to the minimiser function.
# minimized = p.map(minimizer0,args) #Use the pool to map the arguments to the minimizer function.
# result = np.array([i.x for i in minimized]).T
# redchisq=np.array([i.fun for i in minimized])/(len(data[0,:])-len(p0))
# print(f"{np.average(redchisq)=}")
# print(f"{np.median(redchisq)=}")
# resultvals= p.map(minimizer0,args) #Use the pool to map the arguments to the minimizer function.
# result = np.array([i[0] for i in resultvals]).T
# redchisq=np.array([i[1] for i in resultvals])/(len(data[0,:])-len(p0))
# print(f"{resultvals=}")
# print(f"{result=}")
# print(f"{redchisq=}")
# result = np.array(p.map(minimizer0,args)).T #Use the pool to map the arguments to the minimizer function.
# redchisq=1.0
# This checks whether the energies are sorted from small to large for multiple exponential functions
for i, pars in enumerate(result.T):
if len(pars)>=4:
if pars[1]>pars[3]: #This really only checks for 2 exponential functions
#print("Not sorted")
temp = sortmompar(pars)
for j in range(len(temp)):
result[j][i]=temp[j]
parBS=[] #Save resulting parameters as Bootstrap objects
for i in range(len(p0)):
parBS.append(BootStrap(nboot,68))
parBS[i].values = result[i][:]
parBS[i].Stats()
if time: print('BootFitclass3 time: \t', tm.time()-start1) #Stop counting and print time
return result, parBS, redchisq1
def effectivemass(G, a=0.074,factor=1.):
effmass =[]
for time in range(len(G)-1):
effmass.append(BootStrap(G[0].nboot, 68))
effmass[-1] = G[time]*(G[time+1]**(-1))
effmass[-1].Avg = factor*np.log(np.abs(effmass[-1].Avg))#/a
effmass[-1].values = factor*np.log(np.abs(effmass[-1].values))#/a
effmass[-1].Stats()
return effmass
def Bootratiofit3(fitfnc,fitfncratio,p0,p1,x,xr,ydata,yratio,bounds=None,bounds2=None,time=False):
"""Fitting the correlator first and then the ratio with two energy shifts. This function will return all parameters as Bootstrap objects"""
if time: start1 = tm.time() #Start counting
data = np.array([y.values for y in ydata])
data_err = bstd(data)
cv = np.diag(data_err**(-2))
nboot = np.shape(data)[1]
result = np.zeros((fitfnc.npar,nboot))
data_ratio = np.array([y.values for y in yratio])
data_err_ratio = bstd(data_ratio)
cv_ratio = np.diag(data_err_ratio**(-2))
resultratio = np.zeros((fitfncratio.npar,nboot))
for iboot in range(nboot):
#Fit the unperturbed 2-point function to get amplitudes and energies, and set the variables for the ratio fit
yboot=data[:,iboot]
res = syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'disp': False})
sortres = sortmompar(res.x)
result[:,iboot]=sortres.copy()
fitfncratio.q = sortres.copy()
#Fit the ratio of 2-point functions to get the shift in the amplitudes and energies
ybootr=data_ratio[:,iboot]
res2 = syopt.minimize(ff.chisqfn,p1,args=(fitfncratio.eval,xr,ybootr,cv_ratio),method='L-BFGS-B',bounds=bounds2,options={'disp': False})
resultratio[:,iboot] = res2.x.copy()
parBS=[] #Save resulting parameters as Bootstrap objects
parBS_ratio=[]
for i in range(len(p0)):
parBS.append(BootStrap(nboot,68))
parBS[i].values = result[i][:]
parBS[i].Stats()
for i in range(len(p1)):
parBS_ratio.append(BootStrap(nboot,68))
parBS_ratio[i].values = resultratio[i][:]
parBS_ratio[i].Stats()
if time: print('Bootratiofit3 time: \t', tm.time()-start1) #Stop counting and print time
return parBS, parBS_ratio
def makeratio(nclns, opnum):
"""Construct the ratio of correlators"""
ratiou = stats.feynhellratio(nclns[1][0], nclns[0][1], nclns[0][0],
nclns[1][1])
ratiod = stats.feynhellratio(nclns[2][0], nclns[0][1], nclns[0][0],
nclns[2][1])
# ratiou = stats.feynhellratioshort(nclns[1][0], nclns[0][0])
# ratiod = stats.feynhellratioshort(nclns[2][0], nclns[0][0])
ratios = [ratiou, ratiod]
# Take the average of the (pos. parity, trev=0) and (neg parity, trev=1) two-point functions to get an energy value
unpert_2p = []
for i in range(len(nclns[0][0])): #64
unpert_2p.append(BootStrap(nclns[0][0][i].nboot, 68))
unpert_2p[-1] = (nclns[0][0][i] + nclns[0][1][i]) * 0.5
unpert_2p[-1].Stats()
return ratios, unpert_2p
def Bootratiofit4(fitfncratio,p0,xr,yratio,energyBS,bounds=None,time=False,fullcov=False):
"""Fitting the correlator first and then the ratio with two energy shifts. This function will return all parameters as Bootstrap objects"""
if time: start1 = tm.time() #Start counting
nboot = yratio[0].nboot
data_ratio = np.array([y.values for y in yratio])
data_err_ratio = bstd(data_ratio)
# cv_ratio = np.diag(data_err_ratio**(-2))
cv_ratio = Invcovmat(data_ratio,fullcov=fullcov)
cv_ratio_diag = Invcovmat(data_ratio,fullcov=False)
resultratio = np.zeros((fitfncratio.npar,nboot))
#INFO: Fit to the average of the ratio data to get a chi-square value
fitfncratio.q = [i.Avg for i in energyBS] #Set the energyfit parameters
ydata=np.average(data_ratio,axis=1)
niter=50
res = syopt.basinhopping(ff.chisqfn,p0,niter=niter,stepsize=8,T=150,minimizer_kwargs={'args':(fitfncratio.eval,xr,ydata,cv_ratio),'method':'L-BFGS-B','bounds':bounds}, disp=False)
#res = syopt.minimize(ff.chisqfn,p0,args=(fitfncratio.eval,xr,ydata,cv_ratio),method='L-BFGS-B',bounds=bounds,options={'disp': False})
redchisq = res.fun/(len(ydata) - len(p0))
for iboot in range(nboot):
#Set the energyfit parameters
fitfncratio.q = [i.values[iboot] for i in energyBS]
#Fit the ratio of 2-point functions to get the shift in the amplitudes and energies
ybootr=data_ratio[:,iboot]
# res2 = syopt.minimize(ff.chisqfn,p0,args=(fitfncratio.eval,xr,ybootr,cv_ratio),method='L-BFGS-B',bounds=bounds,options={'disp': False})
# THIS NOW USES THE RESULT OF THE FIT TO THE AVG AS INITAL GUESS.
res2 = syopt.minimize(ff.chisqfn,res.x,args=(fitfncratio.eval,xr,ybootr,cv_ratio),method='L-BFGS-B',bounds=bounds,options={'disp': False})
resultratio[:,iboot] = res2.x.copy()
parBS_ratio=[] #Save resulting parameters as Bootstrap objects
for i in range(len(p0)):
parBS_ratio.append(BootStrap(nboot,68))
parBS_ratio[i].values = resultratio[i][:]
parBS_ratio[i].Stats()
if time: print('Bootratiofit4 time: \t', tm.time()-start1) #Stop counting and print time
return parBS_ratio, redchisq
def BootFitclass(fitfnc, p0,x,ydata,bounds=None):
data = np.array([y.values for y in ydata])
yerr = bstd(data)
cv = np.diag(yerr**(-2))
nboot=np.shape(data)[1]
result=np.zeros((fitfnc.npar,nboot))
for iboot in range(nboot):
yboot=data[:,iboot]
#res=syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'gtol': 1e-7, 'disp': False})
res=syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='L-BFGS-B',bounds=bounds,options={'disp': False})
#res=syopt.minimize(ff.chisqfn,p0,args=(fitfnc.eval,x,yboot,cv),method='BFGS',options={'gtol': 1e-7, 'disp': False})
result[:,iboot]=res.x
energies = np.array([result[2*i+1][:] for i in range(int(fitfnc.npar/2))])
if fitfnc.label==r"TwoexpRatio2":
energies = np.array(result[-2:][:])
energiessort = np.sort(energies, axis=0)
if np.any(energies != energiessort):
print("Energies Sorted")
BSen=[]
for i in range(len(energiessort)):
BSen.append(BootStrap(len(energiessort[0]),68))
BSen[i].values = energiessort[i]
BSen[i].Stats()
return result, BSen
